From 48ff90adfec5e69dcf3fe69c754fc2e2a9788c1d Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 17 Jun 2022 17:11:04 +0200 Subject: [PATCH 1/9] Add script for adding dates and update schema Closes #1967 --- util/add_dates.py | 69 ++++++++++++++++++++++++++++++++ util/schema/registry_schema.json | 6 +++ 2 files changed, 75 insertions(+) create mode 100644 util/add_dates.py diff --git a/util/add_dates.py b/util/add_dates.py new file mode 100644 index 000000000..3daaed01f --- /dev/null +++ b/util/add_dates.py @@ -0,0 +1,69 @@ +"""Add date added annotations to all ontologies.""" + +import datetime +import itertools as itt +import os +import pathlib + +import pystow +from dateutil.parser import parse + +HERE = pathlib.Path(__file__).parent.resolve() +ONTOLOGY_DIRECTORY = HERE.parent.joinpath("ontology").resolve() + +DATA_PATH = pystow.join("obo", name="commits.txt") + + +def main(): + """Add date added annotations to all ontologies.""" + if not DATA_PATH.is_file(): + command = f'git log --format="format:%ci" --name-only --diff-filter=A > {str(DATA_PATH)}' + print("running command:", command) + os.system(command) + + with DATA_PATH.open() as file: + lines = [line.strip() for line in file] + + ontology_to_time = {} + for flag, sublines in itt.groupby(lines, key=lambda line: not line.strip()): + if flag: + continue + time = parse(next(sublines)) + ontologies = [ + subline.removeprefix("ontology/").removesuffix(".md") + for subline in sublines + if subline.startswith("ontology/") and subline.endswith(".md") + ] + if not ontologies: + continue + for ontology in ontologies: + ontology_to_time[ontology] = time + + for ontology, time in ontology_to_time.items(): + path = ONTOLOGY_DIRECTORY.joinpath(ontology).with_suffix(".md") + if not path.is_file(): + print("File no longer exists:", path) + continue + update_markdown(path, time) + + +def update_markdown(path: pathlib.Path, date: datetime.datetime) -> None: + """Update the given markdown file.""" + with path.open() as file: + lines = [line.rstrip("\n") for line in file] + + assert lines[0] == "---" + idx = min(i for i, line in enumerate(lines[1:], start=1) if line == "---") + + with path.open("w") as file: + print("---", file=file) + for line in lines[1:idx]: + print(line, file=file) + print("added:", date.strftime("%Y-%m-%d"), file=file) + print("---", file=file) + for line in lines[idx + 1 :]: + print(line, file=file) + + +if __name__ == "__main__": + main() diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json index bbb220c5e..03c64c177 100644 --- a/util/schema/registry_schema.json +++ b/util/schema/registry_schema.json @@ -18,6 +18,11 @@ "activity_status": "${data} is not one of ${schema}." } }, + "added": { + "level": "error", + "format": "date", + "description": "The date when the ontology was added to the OBO Foundry git repository, in the YYYY-MM-DD format" + }, "browsers": { "level": "info", "description": "'browsers' is an informative field. It specifies the URL of a website in which the ontology can be browsed. OntoBee is included by default.", @@ -479,6 +484,7 @@ }, "required": [ "activity_status", + "added", "contact", "description", "homepage", From e52c7ad25b8883ac87e4e76a3fbe029ea36bbb5b Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 17 Jun 2022 17:15:22 +0200 Subject: [PATCH 2/9] Make script idempotent --- util/add_dates.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/util/add_dates.py b/util/add_dates.py index 3daaed01f..a215176c4 100644 --- a/util/add_dates.py +++ b/util/add_dates.py @@ -52,6 +52,10 @@ def update_markdown(path: pathlib.Path, date: datetime.datetime) -> None: with path.open() as file: lines = [line.rstrip("\n") for line in file] + if any(line.startswith("added:") for line in lines): + # No need to add duplicates + return + assert lines[0] == "---" idx = min(i for i, line in enumerate(lines[1:], start=1) if line == "---") From 8197f969fd1a7994f31450c0451ba5d24946ba2b Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 17 Jun 2022 17:20:50 +0200 Subject: [PATCH 3/9] Add all ontologies Note, the script failed to add a few that I had to go and do manually: ERROR AISM added: 'added' is a required property ERROR APOLLO_SV added: 'added' is a required property ERROR EPIO added: 'added' is a required property ERROR FIDEO added: 'added' is a required property ERROR NCIT added: 'added' is a required property ERROR OMO added: 'added' is a required property ERROR OOSTT added: 'added' is a required property ERROR XLMOD added: 'added' is a required property --- ontology/aao.md | 1 + ontology/adw.md | 1 + ontology/aeo.md | 1 + ontology/aero.md | 1 + ontology/agro.md | 1 + ontology/aism.md | 1 + ontology/amphx.md | 1 + ontology/apo.md | 1 + ontology/apollo_sv.md | 1 + ontology/aro.md | 1 + ontology/ato.md | 1 + ontology/bcgo.md | 1 + ontology/bco.md | 1 + ontology/bfo.md | 1 + ontology/bila.md | 1 + ontology/bootstrep.md | 1 + ontology/bspo.md | 1 + ontology/bto.md | 1 + ontology/caro.md | 1 + ontology/cdao.md | 1 + ontology/cdno.md | 1 + ontology/ceph.md | 1 + ontology/chebi.md | 1 + ontology/cheminf.md | 1 + ontology/chiro.md | 1 + ontology/chmo.md | 1 + ontology/cido.md | 1 + ontology/cio.md | 1 + ontology/cl.md | 1 + ontology/clao.md | 1 + ontology/clo.md | 1 + ontology/clyh.md | 1 + ontology/cmf.md | 1 + ontology/cmo.md | 1 + ontology/cob.md | 1 + ontology/colao.md | 1 + ontology/cro.md | 1 + ontology/cteno.md | 1 + ontology/cto.md | 1 + ontology/cvdo.md | 1 + ontology/dc_cl.md | 1 + ontology/ddanat.md | 1 + ontology/ddpheno.md | 1 + ontology/dideo.md | 1 + ontology/dinto.md | 1 + ontology/disdriv.md | 1 + ontology/doid.md | 1 + ontology/dpo.md | 1 + ontology/dron.md | 1 + ontology/duo.md | 1 + ontology/ecao.md | 1 + ontology/eco.md | 1 + ontology/ecocore.md | 1 + ontology/ecto.md | 1 + ontology/ehda.md | 1 + ontology/ehdaa.md | 1 + ontology/ehdaa2.md | 1 + ontology/emap.md | 1 + ontology/emapa.md | 1 + ontology/envo.md | 1 + ontology/eo.md | 1 + ontology/epio.md | 1 + ontology/epo.md | 1 + ontology/ero.md | 1 + ontology/eupath.md | 1 + ontology/ev.md | 1 + ontology/exo.md | 1 + ontology/fao.md | 1 + ontology/fbbi.md | 1 + ontology/fbbt.md | 1 + ontology/fbcv.md | 1 + ontology/fbdv.md | 1 + ontology/fbsp.md | 1 + ontology/fideo.md | 1 + ontology/fix.md | 1 + ontology/flopo.md | 1 + ontology/flu.md | 1 + ontology/fma.md | 1 + ontology/fobi.md | 1 + ontology/foodon.md | 1 + ontology/fovt.md | 1 + ontology/fypo.md | 1 + ontology/gaz.md | 1 + ontology/gecko.md | 1 + ontology/genepio.md | 1 + ontology/geno.md | 1 + ontology/geo.md | 1 + ontology/gno.md | 1 + ontology/go.md | 1 + ontology/gro.md | 1 + ontology/gsso.md | 1 + ontology/habronattus.md | 1 + ontology/hancestro.md | 1 + ontology/hao.md | 1 + ontology/hom.md | 1 + ontology/hp.md | 1 + ontology/hsapdv.md | 1 + ontology/hso.md | 1 + ontology/htn.md | 1 + ontology/iao.md | 1 + ontology/iceo.md | 1 + ontology/ico.md | 1 + ontology/ido.md | 1 + ontology/idomal.md | 1 + ontology/iev.md | 1 + ontology/imr.md | 1 + ontology/ino.md | 1 + ontology/ipr.md | 1 + ontology/kisao.md | 1 + ontology/labo.md | 1 + ontology/lepao.md | 1 + ontology/lipro.md | 1 + ontology/loggerhead.md | 1 + ontology/ma.md | 1 + ontology/mamo.md | 1 + ontology/mao.md | 1 + ontology/mat.md | 1 + ontology/maxo.md | 1 + ontology/mco.md | 1 + ontology/mf.md | 1 + ontology/mfmo.md | 1 + ontology/mfo.md | 1 + ontology/mfoem.md | 1 + ontology/mfomd.md | 1 + ontology/mi.md | 1 + ontology/miapa.md | 1 + ontology/micro.md | 1 + ontology/mirnao.md | 1 + ontology/miro.md | 1 + ontology/mmo.md | 1 + ontology/mmusdv.md | 1 + ontology/mo.md | 1 + ontology/mod.md | 1 + ontology/mondo.md | 1 + ontology/mop.md | 1 + ontology/mp.md | 1 + ontology/mpath.md | 1 + ontology/mpio.md | 1 + ontology/mro.md | 1 + ontology/ms.md | 1 + ontology/nbo.md | 1 + ontology/ncbitaxon.md | 1 + ontology/ncit.md | 1 + ontology/ncro.md | 1 + ontology/nif_cell.md | 1 + ontology/nif_dysfunction.md | 1 + ontology/nif_grossanatomy.md | 1 + ontology/nmr.md | 1 + ontology/nomen.md | 1 + ontology/oae.md | 1 + ontology/oarcs.md | 1 + ontology/oba.md | 1 + ontology/obcs.md | 1 + ontology/obi.md | 1 + ontology/obib.md | 1 + ontology/obo_rel.md | 1 + ontology/ogg.md | 1 + ontology/ogi.md | 1 + ontology/ogms.md | 1 + ontology/ogsf.md | 1 + ontology/ohd.md | 1 + ontology/ohmi.md | 1 + ontology/ohpi.md | 1 + ontology/olatdv.md | 1 + ontology/omiabis.md | 1 + ontology/omit.md | 1 + ontology/omo.md | 1 + ontology/omp.md | 1 + ontology/omrse.md | 1 + ontology/one.md | 1 + ontology/ons.md | 1 + ontology/ontoavida.md | 1 + ontology/ontoneo.md | 1 + ontology/oostt.md | 1 + ontology/opl.md | 1 + ontology/opmi.md | 1 + ontology/ornaseq.md | 1 + ontology/ovae.md | 1 + ontology/pao.md | 1 + ontology/pato.md | 1 + ontology/pcl.md | 1 + ontology/pco.md | 1 + ontology/pd_st.md | 1 + ontology/pdro.md | 1 + ontology/pdumdv.md | 1 + ontology/peco.md | 1 + ontology/pgdso.md | 1 + ontology/phipo.md | 1 + ontology/plana.md | 1 + ontology/planp.md | 1 + ontology/plo.md | 1 + ontology/po.md | 1 + ontology/poro.md | 1 + ontology/ppo.md | 1 + ontology/pr.md | 1 + ontology/propreo.md | 1 + ontology/psdo.md | 1 + ontology/pso.md | 1 + ontology/pw.md | 1 + ontology/rbo.md | 1 + ontology/resid.md | 1 + ontology/rex.md | 1 + ontology/rnao.md | 1 + ontology/ro.md | 1 + ontology/rs.md | 1 + ontology/rxno.md | 1 + ontology/sao.md | 1 + ontology/sbo.md | 1 + ontology/scdo.md | 1 + ontology/sep.md | 1 + ontology/sepio.md | 1 + ontology/sibo.md | 1 + ontology/so.md | 1 + ontology/sopharm.md | 1 + ontology/spd.md | 1 + ontology/stato.md | 1 + ontology/swo.md | 1 + ontology/symp.md | 1 + ontology/tads.md | 1 + ontology/tahe.md | 1 + ontology/tahh.md | 1 + ontology/tao.md | 1 + ontology/taxrank.md | 1 + ontology/tgma.md | 1 + ontology/to.md | 1 + ontology/trans.md | 1 + ontology/tto.md | 1 + ontology/txpo.md | 1 + ontology/uberon.md | 1 + ontology/uo.md | 1 + ontology/upa.md | 1 + ontology/upheno.md | 1 + ontology/vario.md | 1 + ontology/vhog.md | 1 + ontology/vo.md | 1 + ontology/vsao.md | 1 + ontology/vt.md | 1 + ontology/vto.md | 1 + ontology/wbbt.md | 1 + ontology/wbls.md | 1 + ontology/wbphenotype.md | 1 + ontology/xao.md | 1 + ontology/xco.md | 1 + ontology/xlmod.md | 1 + ontology/xpo.md | 1 + ontology/ypo.md | 1 + ontology/zea.md | 1 + ontology/zeco.md | 1 + ontology/zfa.md | 1 + ontology/zfs.md | 1 + ontology/zp.md | 1 + registry/ontologies.yml | 251 +++++++++++++++++++++++++++++++++++ tests/test_integrity.py | 18 ++- util/add_dates.py | 2 +- 254 files changed, 518 insertions(+), 4 deletions(-) diff --git a/ontology/aao.md b/ontology/aao.md index a66bd2b17..1dc780845 100644 --- a/ontology/aao.md +++ b/ontology/aao.md @@ -12,6 +12,7 @@ homepage: http://github.com/seger/aao is_obsolete: true replaced_by: uberon activity_status: inactive +added: 2015-08-21 --- A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. diff --git a/ontology/adw.md b/ontology/adw.md index 0bff2f5c8..1f206e89d 100644 --- a/ontology/adw.md +++ b/ontology/adw.md @@ -8,6 +8,7 @@ contact: homepage: http://www.animaldiversity.org is_obsolete: true activity_status: inactive +added: 2015-08-21 --- An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities. diff --git a/ontology/aeo.md b/ontology/aeo.md index 7d05dd86e..1a3aab8b1 100644 --- a/ontology/aeo.md +++ b/ontology/aeo.md @@ -22,6 +22,7 @@ build: activity_status: inactive repository: https://github.com/obophenotype/human-developmental-anatomy-ontology preferredPrefix: AEO +added: 2015-07-28 --- The AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 160 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The ~100 new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type. This site is to be used for posting details of the ontologies and updates diff --git a/ontology/aero.md b/ontology/aero.md index c50f4418a..82a09cf62 100644 --- a/ontology/aero.md +++ b/ontology/aero.md @@ -19,6 +19,7 @@ build: source_url: http://purl.obolibrary.org/obo/aero.owl method: owl2obo activity_status: inactive +added: 2015-07-28 --- The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events. diff --git a/ontology/agro.md b/ontology/agro.md index ccf777561..51ddd880e 100644 --- a/ontology/agro.md +++ b/ontology/agro.md @@ -53,6 +53,7 @@ dependencies: - id: uo - id: xco preferredPrefix: AGRO +added: 2016-06-04 --- AgrO, the Agronomy Ontology, describes agronomic practices, techniques, and variables used in agronomic experiments. AgrO is being built using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, PATO, IAO, and CHEBI. Further, AgrO powers AgroFIMS, the Agronomy Fieldbook and Information Management System modeled on a CGIAR Breeding Management System to capture agronomic data. diff --git a/ontology/aism.md b/ontology/aism.md index 4d4f454f8..8423dadfa 100644 --- a/ontology/aism.md +++ b/ontology/aism.md @@ -32,6 +32,7 @@ license: activity_status: active repository: https://github.com/insect-morphology/aism preferredPrefix: AISM +added: 2021-05-06 --- The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology. diff --git a/ontology/amphx.md b/ontology/amphx.md index b9bfd0275..34b2bfa73 100644 --- a/ontology/amphx.md +++ b/ontology/amphx.md @@ -26,6 +26,7 @@ license: activity_status: active repository: https://github.com/EBISPOT/amphx_ontology preferredPrefix: AMPHX +added: 2020-04-21 --- The Amphioxus Development and Anatomy Ontology (AMPHX) is to describe the anatomy and development of Amphioxus, also known as lancelet, member of the invertebrate subphylum Cephalochordata and the phylum Chordata. This ontology is intended to be used for description of gene expression in amphioxus (e.g. Insitus, RNA-seq). The ontology was created in the context of the European project CORBEL (https://www.corbel-project.eu/home.html), and used in the database MARIMBA (http://marimba.obs-vlfr.fr/home). diff --git a/ontology/apo.md b/ontology/apo.md index ba3a9c707..55f86b835 100644 --- a/ontology/apo.md +++ b/ontology/apo.md @@ -29,6 +29,7 @@ preferredPrefix: APO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/20157474 title: "New mutant phenotype data curation system in the Saccharomyces Genome Database" +added: 2015-07-28 --- A structured controlled vocabulary for the phenotypes of Ascomycete fungi diff --git a/ontology/apollo_sv.md b/ontology/apollo_sv.md index 7357a4c65..57d479063 100644 --- a/ontology/apollo_sv.md +++ b/ontology/apollo_sv.md @@ -22,6 +22,7 @@ preferredPrefix: APOLLO_SV publications: - id: https://doi.org/10.1186/s13326-016-0092-y title: "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation" +added: 2019-04-04 --- #Apollo Structured Vocabulary diff --git a/ontology/aro.md b/ontology/aro.md index 37e390f32..ba67ef17f 100644 --- a/ontology/aro.md +++ b/ontology/aro.md @@ -23,6 +23,7 @@ activity_status: active repository: https://github.com/arpcard/aro preferredPrefix: ARO domain: microbiology +added: 2017-11-15 --- The Antibiotic Resistance Ontology diff --git a/ontology/ato.md b/ontology/ato.md index c28927fab..a761f8ef0 100644 --- a/ontology/ato.md +++ b/ontology/ato.md @@ -11,6 +11,7 @@ taxon: homepage: http://www.amphibanat.org is_obsolete: true activity_status: inactive +added: 2015-08-21 --- A taxonomy of Amphibia diff --git a/ontology/bcgo.md b/ontology/bcgo.md index 5159a2217..63f6ec715 100644 --- a/ontology/bcgo.md +++ b/ontology/bcgo.md @@ -19,6 +19,7 @@ license: is_obsolete: true activity_status: inactive repository: https://github.com/obi-bcgo/bcgo +added: 2015-07-28 --- The Beta Cell Genomics Ontology (BCGO) is an application ontology built for the beta cell genomics studies aiming to support database annotation, complicated semantic queries, and automated cell type classification. diff --git a/ontology/bco.md b/ontology/bco.md index 8c3c5e5ac..810572152 100644 --- a/ontology/bco.md +++ b/ontology/bco.md @@ -22,6 +22,7 @@ tracker: https://github.com/BiodiversityOntologies/bco/issues activity_status: active repository: https://github.com/BiodiversityOntologies/bco preferredPrefix: BCO +added: 2015-07-29 --- The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework. The goal of the BCO is to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. diff --git a/ontology/bfo.md b/ontology/bfo.md index b9d76d81b..d8b0d588d 100644 --- a/ontology/bfo.md +++ b/ontology/bfo.md @@ -37,6 +37,7 @@ usages: activity_status: active repository: https://github.com/BFO-ontology/BFO preferredPrefix: BFO +added: 2015-07-28 --- BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the special sciences domains. BFO is the upper level ontology upon which OBO Foundry ontologies are built. diff --git a/ontology/bila.md b/ontology/bila.md index 65b6eff48..b60e8d9f4 100644 --- a/ontology/bila.md +++ b/ontology/bila.md @@ -19,4 +19,5 @@ build: is_obsolete: true replaced_by: uberon activity_status: inactive +added: 2015-07-28 --- diff --git a/ontology/bootstrep.md b/ontology/bootstrep.md index 04a3531ee..cd2f5a619 100644 --- a/ontology/bootstrep.md +++ b/ontology/bootstrep.md @@ -9,6 +9,7 @@ homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html is_obsolete: true replaced_by: molecular_function activity_status: inactive +added: 2015-08-21 --- The BOOTStrep Ontology is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of). diff --git a/ontology/bspo.md b/ontology/bspo.md index 56d700904..0892ff92f 100644 --- a/ontology/bspo.md +++ b/ontology/bspo.md @@ -29,6 +29,7 @@ publications: activity_status: active repository: https://github.com/obophenotype/biological-spatial-ontology preferredPrefix: BSPO +added: 2015-07-28 --- An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. diff --git a/ontology/bto.md b/ontology/bto.md index 50fdbd3f8..e1f4f1534 100644 --- a/ontology/bto.md +++ b/ontology/bto.md @@ -29,6 +29,7 @@ build: activity_status: active repository: https://github.com/BRENDA-Enzymes/BTO preferredPrefix: BTO +added: 2015-07-28 --- A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. diff --git a/ontology/caro.md b/ontology/caro.md index 7f09a884d..eef08d917 100644 --- a/ontology/caro.md +++ b/ontology/caro.md @@ -23,6 +23,7 @@ tracker: https://github.com/obophenotype/caro/issues activity_status: active repository: https://github.com/obophenotype/caro preferredPrefix: CARO +added: 2015-07-28 --- The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO will be described in Anatomy Ontologies for Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and Richard Baldock (Editors) diff --git a/ontology/cdao.md b/ontology/cdao.md index 694bf1f66..b06ee189d 100644 --- a/ontology/cdao.md +++ b/ontology/cdao.md @@ -25,6 +25,7 @@ activity_status: active repository: https://github.com/evoinfo/cdao preferredPrefix: CDAO domain: organisms +added: 2015-07-28 --- A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science diff --git a/ontology/cdno.md b/ontology/cdno.md index 6f628a7de..8bd78a5d6 100644 --- a/ontology/cdno.md +++ b/ontology/cdno.md @@ -35,6 +35,7 @@ publications: activity_status: active repository: https://github.com/Southern-Cross-Plant-Science/cdno preferredPrefix: CDNO +added: 2021-02-08 --- The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. diff --git a/ontology/ceph.md b/ontology/ceph.md index 59475380a..2c08c956f 100644 --- a/ontology/ceph.md +++ b/ontology/ceph.md @@ -32,6 +32,7 @@ license: label: CC BY 3.0 activity_status: inactive repository: https://github.com/obophenotype/cephalopod-ontology +added: 2015-08-21 --- Welcome to the Cephalopod Ontology diff --git a/ontology/chebi.md b/ontology/chebi.md index 09b3bfdbb..bb078a9df 100644 --- a/ontology/chebi.md +++ b/ontology/chebi.md @@ -54,6 +54,7 @@ usages: activity_status: active repository: https://github.com/ebi-chebi/ChEBI preferredPrefix: CHEBI +added: 2015-07-28 --- A freely available dictionary of molecular entities focused on ‘small’ chemical compounds. diff --git a/ontology/cheminf.md b/ontology/cheminf.md index 53d9fcc52..0a91d73c0 100644 --- a/ontology/cheminf.md +++ b/ontology/cheminf.md @@ -26,6 +26,7 @@ build: activity_status: active repository: https://github.com/semanticchemistry/semanticchemistry preferredPrefix: CHEMINF +added: 2015-07-28 --- Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. diff --git a/ontology/chiro.md b/ontology/chiro.md index ab8b4aa7b..dc79ec4b6 100644 --- a/ontology/chiro.md +++ b/ontology/chiro.md @@ -41,4 +41,5 @@ license: activity_status: active repository: https://github.com/obophenotype/chiro preferredPrefix: CHIRO +added: 2019-09-26 --- diff --git a/ontology/chmo.md b/ontology/chmo.md index 64646b3d6..23937ea8b 100644 --- a/ontology/chmo.md +++ b/ontology/chmo.md @@ -20,6 +20,7 @@ tracker: https://github.com/rsc-ontologies/rsc-cmo/issues activity_status: active repository: https://github.com/rsc-ontologies/rsc-cmo preferredPrefix: CHMO +added: 2015-07-28 --- CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). diff --git a/ontology/cido.md b/ontology/cido.md index 769cb6ed1..9d5bf5440 100644 --- a/ontology/cido.md +++ b/ontology/cido.md @@ -20,6 +20,7 @@ activity_status: active repository: https://github.com/cido-ontology/cido preferredPrefix: CIDO domain: health +added: 2020-03-12 --- The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. Its development follows the OBO Foundry Principles. diff --git a/ontology/cio.md b/ontology/cio.md index e5fc1a45c..69d86d9e9 100644 --- a/ontology/cio.md +++ b/ontology/cio.md @@ -20,6 +20,7 @@ activity_status: active repository: https://github.com/BgeeDB/confidence-information-ontology preferredPrefix: CIO domain: information +added: 2016-05-17 --- The Confidence Information Ontology (CIO) is an ontology to capture confidence information about annotations. diff --git a/ontology/cl.md b/ontology/cl.md index dfd2b95d5..902157755 100644 --- a/ontology/cl.md +++ b/ontology/cl.md @@ -117,6 +117,7 @@ usages: activity_status: active repository: https://github.com/obophenotype/cell-ontology preferredPrefix: CL +added: 2015-07-28 --- ![logo](/images/CL-logo.jpg) diff --git a/ontology/clao.md b/ontology/clao.md index e9b0df51a..44c95843f 100644 --- a/ontology/clao.md +++ b/ontology/clao.md @@ -26,6 +26,7 @@ license: activity_status: active repository: https://github.com/luis-gonzalez-m/Collembola preferredPrefix: CLAO +added: 2020-10-08 --- CLAO includes 1201 classes related mainly with anatomical systems, sclerites, and chaetotaxy. This ontology should increase the anatomical knowledge in Arthropoda and interoperability with other anatomical ontologies as HAO. diff --git a/ontology/clo.md b/ontology/clo.md index 4fa599324..c96518d69 100644 --- a/ontology/clo.md +++ b/ontology/clo.md @@ -27,6 +27,7 @@ activity_status: active repository: https://github.com/CLO-Ontology/CLO preferredPrefix: CLO domain: anatomy and development +added: 2015-07-28 --- # Summary diff --git a/ontology/clyh.md b/ontology/clyh.md index 0c2e5d02d..acd82683c 100644 --- a/ontology/clyh.md +++ b/ontology/clyh.md @@ -28,6 +28,7 @@ license: activity_status: active repository: https://github.com/EBISPOT/clyh_ontology preferredPrefix: CLYH +added: 2020-05-06 --- The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle. This species is a member of the phylum Cnidaria and belongs to the hydrozoan clade Leptothecata. Its life cycle comprises three stages: a planula larva, a benthic polyp colony, and a sexually-reproducing jellyfish (medusa). diff --git a/ontology/cmf.md b/ontology/cmf.md index 13a59218a..e468634d0 100644 --- a/ontology/cmf.md +++ b/ontology/cmf.md @@ -9,6 +9,7 @@ contact: homepage: https://code.google.com/p/craniomaxillofacial-ontology/ activity_status: inactive is_obsolete: true +added: 2015-08-21 --- Ontology for oral & maxillofacial surgical procedures. diff --git a/ontology/cmo.md b/ontology/cmo.md index 2961de9c2..fd9a4224f 100644 --- a/ontology/cmo.md +++ b/ontology/cmo.md @@ -36,6 +36,7 @@ activity_status: active repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology preferredPrefix: CMO depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif +added: 2015-07-28 --- The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs. diff --git a/ontology/cob.md b/ontology/cob.md index e32a6c272..07a555d08 100644 --- a/ontology/cob.md +++ b/ontology/cob.md @@ -31,6 +31,7 @@ title: Core Ontology for Biology and Biomedicine activity_status: active repository: https://github.com/OBOFoundry/COB preferredPrefix: COB +added: 2020-04-15 --- The Core Ontology for Biology and Biomedicine (COB) brings together key terms from a wide range of OBO projects into a single, small ontology. The goal is to improve interoperabilty and reuse across the OBO community through better coordination of key terms. diff --git a/ontology/colao.md b/ontology/colao.md index 5be3aac63..41ec5851d 100644 --- a/ontology/colao.md +++ b/ontology/colao.md @@ -30,4 +30,5 @@ license: activity_status: active repository: https://github.com/insect-morphology/colao preferredPrefix: COLAO +added: 2021-12-14 --- diff --git a/ontology/cro.md b/ontology/cro.md index cf993082a..3fbf7ca94 100644 --- a/ontology/cro.md +++ b/ontology/cro.md @@ -26,6 +26,7 @@ products: activity_status: active repository: https://github.com/data2health/contributor-role-ontology preferredPrefix: CRO +added: 2017-07-20 --- The Contributor Role Ontology expands the CASRAI Contributor Roles Taxonomy (CRediT), which is a high-level classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. diff --git a/ontology/cteno.md b/ontology/cteno.md index 00c24a780..7d84600de 100644 --- a/ontology/cteno.md +++ b/ontology/cteno.md @@ -33,6 +33,7 @@ license: activity_status: active repository: https://github.com/obophenotype/ctenophore-ontology preferredPrefix: CTENO +added: 2015-07-29 --- An anatomical and developmental ontology for ctenophores (Comb Jellies). diff --git a/ontology/cto.md b/ontology/cto.md index debd702a1..cf0c10ec9 100644 --- a/ontology/cto.md +++ b/ontology/cto.md @@ -19,6 +19,7 @@ activity_status: active repository: https://github.com/ClinicalTrialOntology/CTO preferredPrefix: CTO domain: health +added: 2020-07-08 --- The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. diff --git a/ontology/cvdo.md b/ontology/cvdo.md index 44cdbaf84..863ed1cc0 100644 --- a/ontology/cvdo.md +++ b/ontology/cvdo.md @@ -25,6 +25,7 @@ tracker: https://github.com/OpenLHS/CVDO/issues activity_status: active repository: https://github.com/OpenLHS/CVDO preferredPrefix: CVDO +added: 2015-07-28 --- CVDO is an ontology based on the OGMS model of disease, designed to describe entities related to cardiovascular diseases (including the diseases themselves, the underlying disorders, and the related pathological processes). It is being developed at Sherbrooke University (Canada) and the INSERM research institute (Institut National de la Santé et de la Recherche Médicale). diff --git a/ontology/dc_cl.md b/ontology/dc_cl.md index 913184cff..89a24f3bc 100644 --- a/ontology/dc_cl.md +++ b/ontology/dc_cl.md @@ -13,6 +13,7 @@ homepage: http://www.dukeontologygroup.org/Projects.html is_obsolete: true replaced_by: cl activity_status: inactive +added: 2015-08-21 --- Representation of types of dendritic cell. Note that the domain of this ontology is wholly subsumed by the domain of the Cell ontology (CL). diff --git a/ontology/ddanat.md b/ontology/ddanat.md index 6cb320631..ae4c85243 100644 --- a/ontology/ddanat.md +++ b/ontology/ddanat.md @@ -31,6 +31,7 @@ preferredPrefix: DDANAT publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18366659 title: "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum" +added: 2015-07-28 --- A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum. diff --git a/ontology/ddpheno.md b/ontology/ddpheno.md index e047a3b78..acdd43611 100644 --- a/ontology/ddpheno.md +++ b/ontology/ddpheno.md @@ -31,4 +31,5 @@ preferredPrefix: DDPHENO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31840793 title: "dictyBase and the Dicty Stock Center (version 2.0) - a progress report" +added: 2015-08-21 --- diff --git a/ontology/dideo.md b/ontology/dideo.md index 506aabb1e..a473e2fc5 100644 --- a/ontology/dideo.md +++ b/ontology/dideo.md @@ -19,6 +19,7 @@ activity_status: active repository: https://github.com/DIDEO/DIDEO preferredPrefix: DIDEO domain: chemistry and biochemistry +added: 2015-08-21 --- DIDEO is created as part of an NIH-funded project aiming towards developing a new knowledge base for potential drug drug interaction information. In DIDEO we represent PDDIs as information content entities and we aim to also provide the evidence for those entities using nano- and micro publication approaches. diff --git a/ontology/dinto.md b/ontology/dinto.md index 853d18b27..3a48279a7 100644 --- a/ontology/dinto.md +++ b/ontology/dinto.md @@ -20,6 +20,7 @@ publications: activity_status: inactive is_obsolete: true repository: https://github.com/labda/DINTO +added: 2015-08-21 --- DINTO is an ontology that describes and categorizes drug-drug interactions (DDIs) - a significant risk group for adverse effects associated with pharmaceutical treatment - as well as all the possible mechanisms that can lead to them (including both pharmacodynamic and pharmacokinetic DDI mechanisms). diff --git a/ontology/disdriv.md b/ontology/disdriv.md index 6fd580396..30f9154f8 100644 --- a/ontology/disdriv.md +++ b/ontology/disdriv.md @@ -38,4 +38,5 @@ usages: activity_status: active repository: https://github.com/DiseaseOntology/DiseaseDriversOntology preferredPrefix: DISDRIV +added: 2021-11-05 --- diff --git a/ontology/doid.md b/ontology/doid.md index de449ca51..a53e5aa5d 100644 --- a/ontology/doid.md +++ b/ontology/doid.md @@ -68,6 +68,7 @@ activity_status: active repository: https://github.com/DiseaseOntology/HumanDiseaseOntology preferredPrefix: DOID depicted_by: http://www.disease-ontology.org/media/images/DO_logo.jpg +added: 2015-07-28 --- Creating a comprehensive classification of human diseases organized by etiology. diff --git a/ontology/dpo.md b/ontology/dpo.md index 8a581f975..1d4dfca89 100644 --- a/ontology/dpo.md +++ b/ontology/dpo.md @@ -41,6 +41,7 @@ usages: description: "alleles and constructs annotated to pupal lethal in FlyBase" activity_status: active repository: https://github.com/FlyBase/drosophila-phenotype-ontology +added: 2015-07-28 --- An ontology of commonly encountered and/or high level Drosophila phenotypes. It has significant formalisation - utilising terms from GO, CL, PATO and the Drosophila anatomy ontology. It has been used by FlyBase for > 159000 annotations of phenotype. diff --git a/ontology/dron.md b/ontology/dron.md index 1886d483f..783530880 100644 --- a/ontology/dron.md +++ b/ontology/dron.md @@ -25,6 +25,7 @@ preferredPrefix: DRON publications: - id: https://doi.org/10.1186/s13326-017-0121-5 title: "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request" +added: 2015-07-28 --- We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). diff --git a/ontology/duo.md b/ontology/duo.md index 8f16a70c7..2bbfa0b1a 100644 --- a/ontology/duo.md +++ b/ontology/duo.md @@ -29,6 +29,7 @@ activity_status: active repository: https://github.com/EBISPOT/DUO preferredPrefix: DUO domain: information +added: 2017-01-24 --- DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. diff --git a/ontology/ecao.md b/ontology/ecao.md index eaf17dc5b..2b55fdfd1 100644 --- a/ontology/ecao.md +++ b/ontology/ecao.md @@ -28,6 +28,7 @@ license: activity_status: active repository: https://github.com/echinoderm-ontology/ecao_ontology preferredPrefix: ECAO +added: 2020-05-06 --- This ontology is intended to be used for the description and curation of information related to gene regulatory processes in echinoderms (e.g., expression patterns of endogenous genes and reporter DNA constructs, phenotypic effects of gene perturbations, etc.). diff --git a/ontology/eco.md b/ontology/eco.md index 599d1ded0..c644d2519 100644 --- a/ontology/eco.md +++ b/ontology/eco.md @@ -52,6 +52,7 @@ activity_status: active repository: https://github.com/evidenceontology/evidenceontology preferredPrefix: ECO depicted_by: https://avatars1.githubusercontent.com/u/12802432 +added: 2015-07-28 --- The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about things (such as scientific conclusions, gene annotations, or other statements of fact) that result from scientific research. diff --git a/ontology/ecocore.md b/ontology/ecocore.md index 9f763724a..66e6e1ba2 100644 --- a/ontology/ecocore.md +++ b/ontology/ecocore.md @@ -41,6 +41,7 @@ license: activity_status: active repository: https://github.com/EcologicalSemantics/ecocore preferredPrefix: ECOCORE +added: 2017-08-17 --- This ontology aims to provide core semantics for ecological entities, such as ecological functions (for predators, prey, etc), food webs, and ecological interactions. The ontology, closely interoperates with existing OBO ontologies such as the Environment Ontology, the Population and Community Ontology (PCO), the Relations Ontology (RO), the Gene Ontology (for biological processes etc), the Phenotype and Quality Ontology (PATO), the Plant Ontology (PO), and many others. Ecocore is under active development. diff --git a/ontology/ecto.md b/ontology/ecto.md index 88029acde..d9d5865b2 100644 --- a/ontology/ecto.md +++ b/ontology/ecto.md @@ -52,4 +52,5 @@ activity_status: active repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology preferredPrefix: ECTO depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png +added: 2019-09-24 --- diff --git a/ontology/ehda.md b/ontology/ehda.md index 617976c3c..0816a8693 100644 --- a/ontology/ehda.md +++ b/ontology/ehda.md @@ -12,6 +12,7 @@ homepage: http://genex.hgu.mrc.ac.uk/ is_obsolete: true replaced_by: ehdaa2 activity_status: inactive +added: 2015-08-21 --- A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once. diff --git a/ontology/ehdaa.md b/ontology/ehdaa.md index 1e023c769..9b135eef6 100644 --- a/ontology/ehdaa.md +++ b/ontology/ehdaa.md @@ -12,6 +12,7 @@ homepage: is_obsolete: true replaced_by: ehdaa2 activity_status: inactive +added: 2015-08-21 --- A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release. diff --git a/ontology/ehdaa2.md b/ontology/ehdaa2.md index 3f2a6651f..d9873a6a4 100644 --- a/ontology/ehdaa2.md +++ b/ontology/ehdaa2.md @@ -32,6 +32,7 @@ dependencies: - id: cl activity_status: inactive repository: https://github.com/obophenotype/human-developmental-anatomy-ontology +added: 2015-07-28 --- A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release. diff --git a/ontology/emap.md b/ontology/emap.md index 09a8cccee..7615e6e74 100644 --- a/ontology/emap.md +++ b/ontology/emap.md @@ -24,6 +24,7 @@ build: is_obsolete: true replaced_by: emapa activity_status: inactive +added: 2015-07-28 --- ## BACKGROUND diff --git a/ontology/emapa.md b/ontology/emapa.md index 321e9b07f..c843f6c4f 100644 --- a/ontology/emapa.md +++ b/ontology/emapa.md @@ -31,6 +31,7 @@ usages: activity_status: active repository: https://github.com/obophenotype/mouse-anatomy-ontology preferredPrefix: EMAPA +added: 2015-08-21 --- ## BACKGROUND diff --git a/ontology/envo.md b/ontology/envo.md index 3edb649ea..3b590c017 100644 --- a/ontology/envo.md +++ b/ontology/envo.md @@ -86,6 +86,7 @@ activity_status: active repository: https://github.com/EnvironmentOntology/envo preferredPrefix: ENVO depicted_by: /logos/envo.png +added: 2015-07-28 --- EnvO is a community ontology for the concise, controlled description of environments. diff --git a/ontology/eo.md b/ontology/eo.md index 91552cf01..69f006f9d 100644 --- a/ontology/eo.md +++ b/ontology/eo.md @@ -40,6 +40,7 @@ usages: activity_status: inactive repository: https://github.com/Planteome/plant-environment-ontology depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG +added: 2015-07-29 --- A structured, controlled vocabulary for the representation of plant environmental conditions. diff --git a/ontology/epio.md b/ontology/epio.md index a513accf9..c1b0c5b70 100644 --- a/ontology/epio.md +++ b/ontology/epio.md @@ -25,6 +25,7 @@ homepage: https://github.com/SCAI-BIO/EpilepsyOntology repository: https://github.com/SCAI-BIO/EpilepsyOntology activity_status: active preferredPrefix: EPIO +added: 2021-12-16 --- EPIO is a community Ontology maintained by Fraunhofer SCAI. diff --git a/ontology/epo.md b/ontology/epo.md index c3dcf1413..152c73519 100644 --- a/ontology/epo.md +++ b/ontology/epo.md @@ -12,6 +12,7 @@ build: method: owl2obo is_obsolete: true activity_status: inactive +added: 2015-07-29 --- The Epidemiology Ontology is an ontology designed to support the semantic annotation of epidemiology resources. It is being developed under the EU-funded EPIWORK project, a multidisciplinary research effort which aims at increasing the amount of epidemiological data available, improving disease surveillance systems, and promoting the collaboration among epidemiological researchers. The EO is integrated into NERO (Network of Epidemiology Related Ontologies), a collection of existing ontologies that supports the semantic annotation of epidemiology resources contained in the Epidemic Marketplace (EM), a platform for sharing resources and knowledge within the Epidemiology community. NERO currently includes thirteen external ontologies (the majority are OBO or OBO candidate ontologies) which already provide a high coverage of most epidemiology related areas. As such, the EPO focuses on neglected/highly specific areas of epidemiology and will articulate with other OBO ontologies as needed. diff --git a/ontology/ero.md b/ontology/ero.md index e06990043..0778db8cb 100644 --- a/ontology/ero.md +++ b/ontology/ero.md @@ -21,6 +21,7 @@ build: method: owl2obo activity_status: inactive is_obsolete: true +added: 2015-07-28 --- ERO models research resources such instruments. protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/). diff --git a/ontology/eupath.md b/ontology/eupath.md index 4dbf234cb..d7d8fe1c7 100644 --- a/ontology/eupath.md +++ b/ontology/eupath.md @@ -35,6 +35,7 @@ usages: activity_status: active repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology preferredPrefix: EUPATH +added: 2018-01-02 --- The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available. diff --git a/ontology/ev.md b/ontology/ev.md index 40ce86ad4..5594c73d3 100644 --- a/ontology/ev.md +++ b/ontology/ev.md @@ -8,6 +8,7 @@ contact: homepage: http://www.evocontology.org/ is_obsolete: true activity_status: inactive +added: 2015-08-21 --- Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment. diff --git a/ontology/exo.md b/ontology/exo.md index 068b0bc14..c145ae18a 100644 --- a/ontology/exo.md +++ b/ontology/exo.md @@ -20,6 +20,7 @@ products: title: Exposure ontology activity_status: active repository: https://github.com/CTDbase/exposure-ontology +added: 2015-07-28 --- Significant progress has been made over the last several years in collecting and improving access to genomic, toxicology, and health data to promote understanding about environmental influences on human health. The resulting information resources, however, lack extensive and reliable exposure data, which are required to translate molecular insights, elucidate environmental contributions to diseases, and assess human health risks at the individual and population levels. We report our development of an Exposure Ontology, ExO, designed to address this information gap by facilitating centralization and integration of exposure data to inform understanding of environmental health. Like other widely used ontologies, ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics diff --git a/ontology/fao.md b/ontology/fao.md index ea5de62a8..6db184fd0 100644 --- a/ontology/fao.md +++ b/ontology/fao.md @@ -28,6 +28,7 @@ build: activity_status: active repository: https://github.com/obophenotype/fungal-anatomy-ontology preferredPrefix: FAO +added: 2015-07-28 --- ![FAO image](http://www.yeastgenome.org/images/fao.color.png) diff --git a/ontology/fbbi.md b/ontology/fbbi.md index a5bba4728..a3c089480 100644 --- a/ontology/fbbi.md +++ b/ontology/fbbi.md @@ -24,6 +24,7 @@ build: method: obo2owl activity_status: active repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology +added: 2015-07-28 --- A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. diff --git a/ontology/fbbt.md b/ontology/fbbt.md index c4f14f1f8..fb28fb6c6 100644 --- a/ontology/fbbt.md +++ b/ontology/fbbt.md @@ -64,6 +64,7 @@ usages: - url: "http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBbt:00005106" description: "alleles, constructs and insertions annotated to neuron in FlyBase" activity_status: active +added: 2015-07-28 --- An ontology representing the gross anatomy of Drosophila melanogaster. diff --git a/ontology/fbcv.md b/ontology/fbcv.md index ab389c2ca..213fbfec4 100644 --- a/ontology/fbcv.md +++ b/ontology/fbcv.md @@ -36,6 +36,7 @@ usages: activity_status: active repository: https://github.com/FlyBase/flybase-controlled-vocabulary publications: [] +added: 2015-08-06 --- A structured controlled vocabulary used for various aspects of annotation by FlyBase. It includes the Drosophila Phenotype Ontology (dpo) which is also released separately. diff --git a/ontology/fbdv.md b/ontology/fbdv.md index 9c1710505..bf977c1df 100644 --- a/ontology/fbdv.md +++ b/ontology/fbdv.md @@ -35,6 +35,7 @@ browsers: url: http://flybase.org/.bin/cvreport.html?cvterm=FBdv:00007008 activity_status: active publications: [] +added: 2015-07-29 --- A structured controlled vocabulary of the development of Drosophila melanogaster. diff --git a/ontology/fbsp.md b/ontology/fbsp.md index 5269a3dd3..57b447620 100644 --- a/ontology/fbsp.md +++ b/ontology/fbsp.md @@ -23,6 +23,7 @@ build: insert_ontology_id: true is_obsolete: true activity_status: inactive +added: 2015-07-28 --- The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. diff --git a/ontology/fideo.md b/ontology/fideo.md index c484bf468..494a45fb2 100644 --- a/ontology/fideo.md +++ b/ontology/fideo.md @@ -19,6 +19,7 @@ tracker: https://github.com/getbordea/fideo/issues activity_status: active repository: https://github.com/getbordea/fideo preferredPrefix: FIDEO +added: 2020-07-29 --- FIDEO represents food-drug interactions automatically extracted from scientific literature. diff --git a/ontology/fix.md b/ontology/fix.md index e327f2047..b3ef02eb7 100644 --- a/ontology/fix.md +++ b/ontology/fix.md @@ -17,4 +17,5 @@ products: - id: fix.obo title: Physico-chemical methods and properties activity_status: orphaned +added: 2015-07-29 --- diff --git a/ontology/flopo.md b/ontology/flopo.md index feb7b1a2b..65a29c65e 100644 --- a/ontology/flopo.md +++ b/ontology/flopo.md @@ -28,4 +28,5 @@ preferredPrefix: FLOPO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27842607 title: "The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants" +added: 2015-12-16 --- diff --git a/ontology/flu.md b/ontology/flu.md index ce6168036..e8832d215 100644 --- a/ontology/flu.md +++ b/ontology/flu.md @@ -16,4 +16,5 @@ build: tracker: http://purl.obolibrary.org/obo/flu/tracker is_obsolete: true activity_status: inactive +added: 2015-07-29 --- diff --git a/ontology/fma.md b/ontology/fma.md index 6f9eefcc5..ac3b61347 100644 --- a/ontology/fma.md +++ b/ontology/fma.md @@ -32,6 +32,7 @@ tracker: https://bitbucket.org/uwsig/fma/issues repository: https://bitbucket.org/uwsig/fma activity_status: inactive preferredPrefix: FMA +added: 2015-07-28 --- Obo format translation of the FMA, omitting all relationships other than is_a, part_of and has_part. Future versions of fma_obo will include more relationships diff --git a/ontology/fobi.md b/ontology/fobi.md index b6785e727..5db4d0009 100644 --- a/ontology/fobi.md +++ b/ontology/fobi.md @@ -29,6 +29,7 @@ homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology activity_status: active repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology preferredPrefix: FOBI +added: 2019-12-04 --- FOBI (Food-Biomarker Ontology) is composed of two interconnected sub-ontologies. One is a ”Food Ontology” consisting of raw foods and multi-ingredient foods while the second is a ”Biomarker Ontology” containing food intake biomarkers classified by their chemical classes. These two sub-ontologies are conceptually independent but interconnected by different properties. diff --git a/ontology/foodon.md b/ontology/foodon.md index 6431a41ba..77ccaf44b 100644 --- a/ontology/foodon.md +++ b/ontology/foodon.md @@ -38,6 +38,7 @@ preferredPrefix: FOODON publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31304272 title: "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration" +added: 2016-07-25 --- A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and food webs as well as human-centric categorization and handling of food. diff --git a/ontology/fovt.md b/ontology/fovt.md index cc08aaa37..1e9d394b2 100644 --- a/ontology/fovt.md +++ b/ontology/fovt.md @@ -45,6 +45,7 @@ license: activity_status: active repository: https://github.com/futres/fovt preferredPrefix: FOVT +added: 2020-05-06 --- The FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheets to triples, using the [Ontology Data Pipeline](https://github.com/biocodellc/ontology-data-pipeline) from Biocode LLC. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA). diff --git a/ontology/fypo.md b/ontology/fypo.md index 674a76bdb..31c7ee3aa 100644 --- a/ontology/fypo.md +++ b/ontology/fypo.md @@ -37,6 +37,7 @@ usages: activity_status: active repository: https://github.com/pombase/fypo preferredPrefix: FYPO +added: 2015-07-29 --- FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the new online fission yeast resource (www.pombase.org). Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions. diff --git a/ontology/gaz.md b/ontology/gaz.md index 138fad0da..5e2287b59 100644 --- a/ontology/gaz.md +++ b/ontology/gaz.md @@ -23,4 +23,5 @@ license: label: CC0 1.0 activity_status: inactive repository: https://github.com/EnvironmentOntology/gaz +added: 2015-07-28 --- diff --git a/ontology/gecko.md b/ontology/gecko.md index f49096aa2..7348d1cf3 100644 --- a/ontology/gecko.md +++ b/ontology/gecko.md @@ -24,6 +24,7 @@ usages: activity_status: active repository: https://github.com/IHCC-cohorts/GECKO preferredPrefix: GECKO +added: 2020-08-11 --- Genomics Cohorts Knowledge Ontology (GECKO) is an ontology to represent genomics cohort attributes. The GECKO is maintained by the [CINECA project]( https://www.cineca-project.eu), and standardises attributes commonly used for genomics cohort description as well as individual-level data items. A series of tools is being developed to enable automated generation of harmonised data files based on a JSON schema mapping file. For more information please contact [CINECA](mailto:info@cineca-project.eu). diff --git a/ontology/genepio.md b/ontology/genepio.md index 6dc14b3b1..15b407431 100644 --- a/ontology/genepio.md +++ b/ontology/genepio.md @@ -27,6 +27,7 @@ tracker: https://github.com/GenEpiO/genepio/issues/ activity_status: active repository: https://github.com/GenEpiO/genepio preferredPrefix: GENEPIO +added: 2016-07-25 --- Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. We envision various subdomains including genomic laboratory testing, specimen and isolate metadata, and epidemiological case investigations. diff --git a/ontology/geno.md b/ontology/geno.md index 300bd010e..f0234b17f 100644 --- a/ontology/geno.md +++ b/ontology/geno.md @@ -28,6 +28,7 @@ products: activity_status: active repository: https://github.com/monarch-initiative/GENO-ontology preferredPrefix: GENO +added: 2017-01-05 --- GENO is an OWL2 ontology that represents the levels of genetic variation specified in genotypes, to support genotype-to-phenotype (G2P) data aggregation and analysis across diverse research communities and sources. The core of the ontology is a graph decomposing a genotype into smaller components of variation, from a complete genotype specifying sequence variation across an entire genome, down to specific allelic variants and sequence alterations. Structuring genotype instance data according to this model supports a primary use case of GENO to enable integrated analysis of G2P data where phenotype annotations are made at different levels of granularity in this genotype partonomy. GENO also enables description of various attributes of genotypes and genetic variants. These attributes include zygosity, genomic position, expression, dominance, and functional dependencies or consequences of a given variant. diff --git a/ontology/geo.md b/ontology/geo.md index 695a34d2d..2cf1e3601 100644 --- a/ontology/geo.md +++ b/ontology/geo.md @@ -19,6 +19,7 @@ tracker: https://github.com/ufbmi/geographical-entity-ontology/issues activity_status: active repository: https://github.com/ufbmi/geographical-entity-ontology preferredPrefix: GEO +added: 2015-07-28 --- An ontology of geographical entities implemented in Web Ontology Language 2 (OWL2) and based on Basic Formal Ontology (BFO). The developers aim to adhere to the OBO Foundry principles. diff --git a/ontology/gno.md b/ontology/gno.md index 14065ceb9..306eb2113 100644 --- a/ontology/gno.md +++ b/ontology/gno.md @@ -53,4 +53,5 @@ usages: activity_status: active repository: https://github.com/glygen-glycan-data/GNOme preferredPrefix: GNO +added: 2019-08-15 --- diff --git a/ontology/go.md b/ontology/go.md index b05477961..d290a3d46 100644 --- a/ontology/go.md +++ b/ontology/go.md @@ -136,6 +136,7 @@ publications: title: "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium" - id: https://www.ncbi.nlm.nih.gov/pubmed/33290552 title: "The Gene Ontology resource: enriching a GOld mine" +added: 2015-07-28 --- The goal of the GeneOntology (GO) project is to provide a uniformway to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data diff --git a/ontology/gro.md b/ontology/gro.md index cc986d7be..e7f3b08cd 100644 --- a/ontology/gro.md +++ b/ontology/gro.md @@ -8,6 +8,7 @@ contact: homepage: http://www.gramene.org/plant_ontology/ is_obsolete: true activity_status: inactive +added: 2015-08-21 --- A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the Plant Ontology. diff --git a/ontology/gsso.md b/ontology/gsso.md index a25654021..08b769c66 100644 --- a/ontology/gsso.md +++ b/ontology/gsso.md @@ -25,6 +25,7 @@ license: activity_status: active repository: https://github.com/Superraptor/GSSO preferredPrefix: GSSO +added: 2020-10-01 --- GSSO on BioPortal: https://bioportal.bioontology.org/ontologies/GSSO diff --git a/ontology/habronattus.md b/ontology/habronattus.md index 2f874c4ca..84733961a 100644 --- a/ontology/habronattus.md +++ b/ontology/habronattus.md @@ -9,6 +9,7 @@ contact: homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html is_obsolete: true activity_status: inactive +added: 2015-08-21 --- A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for courtship behavior of the spider Habronattus californicus. diff --git a/ontology/hancestro.md b/ontology/hancestro.md index 56a68da7e..6547af719 100644 --- a/ontology/hancestro.md +++ b/ontology/hancestro.md @@ -45,6 +45,7 @@ usages: activity_status: active repository: https://github.com/EBISPOT/ancestro preferredPrefix: HANCESTRO +added: 2018-07-13 --- # Summary diff --git a/ontology/hao.md b/ontology/hao.md index e3cdba1aa..36c8a855c 100644 --- a/ontology/hao.md +++ b/ontology/hao.md @@ -30,6 +30,7 @@ preferredPrefix: HAO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21209921 title: "A gross anatomy ontology for hymenoptera" +added: 2015-07-28 --- A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) diff --git a/ontology/hom.md b/ontology/hom.md index 710124f2e..f131cf91a 100644 --- a/ontology/hom.md +++ b/ontology/hom.md @@ -24,6 +24,7 @@ activity_status: active repository: https://github.com/BgeeDB/homology-ontology preferredPrefix: HOM domain: anatomy and development +added: 2015-07-28 --- This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. The ontology can be cited as: diff --git a/ontology/hp.md b/ontology/hp.md index 935d47e20..f69f443b9 100644 --- a/ontology/hp.md +++ b/ontology/hp.md @@ -57,6 +57,7 @@ activity_status: active repository: https://github.com/obophenotype/human-phenotype-ontology preferredPrefix: HP depicted_by: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png +added: 2015-07-28 --- An ontology is a computational representation of a domain of knowledge based upon a controlled, standardized vocabulary for describing entities and the semantic relationships between them. diff --git a/ontology/hsapdv.md b/ontology/hsapdv.md index f2b9583d1..02a97bbe5 100644 --- a/ontology/hsapdv.md +++ b/ontology/hsapdv.md @@ -25,6 +25,7 @@ products: activity_status: active repository: https://github.com/obophenotype/developmental-stage-ontologies domain: anatomy and development +added: 2015-08-21 --- HumanEmbryogenesis diff --git a/ontology/hso.md b/ontology/hso.md index fcbd8ec41..9947f926b 100644 --- a/ontology/hso.md +++ b/ontology/hso.md @@ -27,6 +27,7 @@ tracker: https://github.com/SVA-SE/HSO/issues/ activity_status: active repository: https://github.com/SVA-SE/HSO preferredPrefix: HSO +added: 2020-11-28 --- The Health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. "Surveillance" is defined as any activity that collects information which is analysed to inform disease control (https://www.fp7-risksur.eu/terminology/glossary). A typical example of a One-Health surveillance activity, in this context, is the investigation of foodborne zoonotic outbreaks. diff --git a/ontology/htn.md b/ontology/htn.md index 8a78f1f63..8818d5e36 100644 --- a/ontology/htn.md +++ b/ontology/htn.md @@ -20,6 +20,7 @@ activity_status: active repository: https://github.com/aellenhicks/htn_owl preferredPrefix: HTN domain: health +added: 2019-06-05 --- The Hypertension Ontology is a realism-based reference ontology for semantically managing clinical data about hypertension. Definitions of hypertension and elevated blood pressure are highly sensitive to context. Thresholds may vary according to population, guidelines, or clinical context. Variations in the clinical interpretation of blood pressure pose challenges to using blood pressure data for cohort identification, semantic data integration across data sets, and semantically enriching clinical data for clinical decision support applications. The Hypertension Ontology provides a framework for connecting clinical data to context-sensitive definitions of elevated blood pressure and hypertension. diff --git a/ontology/iao.md b/ontology/iao.md index ee465620e..0f601b418 100644 --- a/ontology/iao.md +++ b/ontology/iao.md @@ -38,6 +38,7 @@ usages: activity_status: active repository: https://github.com/information-artifact-ontology/IAO preferredPrefix: IAO +added: 2015-07-28 --- The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. diff --git a/ontology/iceo.md b/ontology/iceo.md index b1717d5cf..645b0db97 100644 --- a/ontology/iceo.md +++ b/ontology/iceo.md @@ -19,6 +19,7 @@ activity_status: active repository: https://github.com/ontoice/ICEO preferredPrefix: ICEO domain: microbiology +added: 2019-09-02 --- # ICEO: Integrative and Conjugative Element Ontology diff --git a/ontology/ico.md b/ontology/ico.md index d7fb7c0c5..91d344bb0 100644 --- a/ontology/ico.md +++ b/ontology/ico.md @@ -24,6 +24,7 @@ usages: activity_status: active repository: https://github.com/ICO-ontology/ICO preferredPrefix: ICO +added: 2015-08-21 --- # Summary diff --git a/ontology/ido.md b/ontology/ido.md index 74975ea1a..dbb3336f9 100644 --- a/ontology/ido.md +++ b/ontology/ido.md @@ -25,4 +25,5 @@ tracker: https://github.com/infectious-disease-ontology/infectious-disease-ontol activity_status: active repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology preferredPrefix: IDO +added: 2015-07-28 --- diff --git a/ontology/idomal.md b/ontology/idomal.md index 4b2639ece..80d9c0691 100644 --- a/ontology/idomal.md +++ b/ontology/idomal.md @@ -16,6 +16,7 @@ products: title: Malaria Ontology activity_status: inactive repository: https://github.com/VEuPathDB-ontology/IDOMAL +added: 2015-07-28 --- An application ontology to cover all aspects of malaria (clinical, epidemiological, biological, etc) as well as the intervention attempts to control it. diff --git a/ontology/iev.md b/ontology/iev.md index 7419e1ea1..ac1dbf12c 100644 --- a/ontology/iev.md +++ b/ontology/iev.md @@ -9,6 +9,7 @@ build: method: obo2owl insert_ontology_id: true activity_status: inactive +added: 2015-08-21 --- A structured controlled vocabulary of pathway centric biological processes. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate biological processes, pathways, sub-pathways in the INOH pathway data.
INOH is part of the BioPAX working group. diff --git a/ontology/imr.md b/ontology/imr.md index b704d8aa4..92375cf73 100644 --- a/ontology/imr.md +++ b/ontology/imr.md @@ -12,6 +12,7 @@ build: method: obo2owl insert_ontology_id: true activity_status: inactive +added: 2015-08-21 --- A structured controlled vocabulary of concrete protein names and generic (abstract) protein names. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate protein names, protein family names, generic/concrete protein names in the INOH pathway data.
INOH is part of the BioPAX working group. diff --git a/ontology/ino.md b/ontology/ino.md index 9c51a0ec6..b58bf3fdd 100644 --- a/ontology/ino.md +++ b/ontology/ino.md @@ -19,6 +19,7 @@ activity_status: active repository: https://github.com/INO-ontology/ino preferredPrefix: INO domain: biological systems +added: 2018-03-10 --- # Summary diff --git a/ontology/ipr.md b/ontology/ipr.md index 22a33c15a..a40e4f253 100644 --- a/ontology/ipr.md +++ b/ontology/ipr.md @@ -8,6 +8,7 @@ contact: homepage: http://www.ebi.ac.uk/interpro/index.html is_obsolete: true activity_status: inactive +added: 2015-08-21 --- A database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. diff --git a/ontology/kisao.md b/ontology/kisao.md index 224e4202e..94fc89a0f 100644 --- a/ontology/kisao.md +++ b/ontology/kisao.md @@ -71,6 +71,7 @@ publications: funded_by: - "NIH P41EB023912" - "NIH R35GM119771" +added: 2015-07-28 --- The Kinetic Simulation Algorithm Ontology (KiSAO) describes algorithms for simulating models in biology, their parameters, and their outputs. diff --git a/ontology/labo.md b/ontology/labo.md index b9311071c..95a067d85 100644 --- a/ontology/labo.md +++ b/ontology/labo.md @@ -39,6 +39,7 @@ license: activity_status: active repository: https://github.com/OpenLHS/LABO preferredPrefix: LABO +added: 2019-08-29 --- LABO is an ontology of informational entities describing laboratory tests prescriptions and reporting documents. LABO is a component of a core ontological model, along with the ontology of drug prescriptions PDRO, that aims to enable interoperability between various clinical data sources in the context of a Learning Health System. diff --git a/ontology/lepao.md b/ontology/lepao.md index 4af6a5d76..9d3c76b5b 100644 --- a/ontology/lepao.md +++ b/ontology/lepao.md @@ -30,4 +30,5 @@ license: activity_status: active repository: https://github.com/insect-morphology/lepao preferredPrefix: LEPAO +added: 2021-12-14 --- diff --git a/ontology/lipro.md b/ontology/lipro.md index 16506b1e1..3a35a73fb 100644 --- a/ontology/lipro.md +++ b/ontology/lipro.md @@ -15,6 +15,7 @@ build: method: owl2obo is_obsolete: true activity_status: inactive +added: 2015-07-29 --- Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. The ontology describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. diff --git a/ontology/loggerhead.md b/ontology/loggerhead.md index 2ac98aa3f..11019eec0 100644 --- a/ontology/loggerhead.md +++ b/ontology/loggerhead.md @@ -9,6 +9,7 @@ contact: homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html is_obsolete: true activity_status: inactive +added: 2015-08-21 --- A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for Loggerhead sea turtle (Caretta caretta) nesting behavior, based on the published ethogram of Hailman and Elowson. diff --git a/ontology/ma.md b/ontology/ma.md index 4d0f455df..daa652f42 100644 --- a/ontology/ma.md +++ b/ontology/ma.md @@ -33,6 +33,7 @@ usages: activity_status: active repository: https://github.com/obophenotype/mouse-anatomy-ontology preferredPrefix: MA +added: 2015-07-29 --- A structured controlled vocabulary of the adult anatomy of the mouse (Mus). diff --git a/ontology/mamo.md b/ontology/mamo.md index d7585dbba..06d41a3e4 100644 --- a/ontology/mamo.md +++ b/ontology/mamo.md @@ -22,6 +22,7 @@ license: activity_status: active preferredPrefix: MAMO domain: simulation +added: 2015-07-28 --- The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. diff --git a/ontology/mao.md b/ontology/mao.md index 2ddd19738..ae433712f 100644 --- a/ontology/mao.md +++ b/ontology/mao.md @@ -8,6 +8,7 @@ contact: homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html is_obsolete: true activity_status: inactive +added: 2015-08-21 --- An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment. diff --git a/ontology/mat.md b/ontology/mat.md index 784468a44..de7c47e5e 100644 --- a/ontology/mat.md +++ b/ontology/mat.md @@ -8,6 +8,7 @@ contact: homepage: is_obsolete: true activity_status: inactive +added: 2015-08-21 --- Minimal set of terms for anatomy diff --git a/ontology/maxo.md b/ontology/maxo.md index ea78b175c..a309843aa 100644 --- a/ontology/maxo.md +++ b/ontology/maxo.md @@ -48,6 +48,7 @@ activity_status: active repository: https://github.com/monarch-initiative/MAxO preferredPrefix: MAXO depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png +added: 2020-02-12 --- The Medical Action Ontology (MAxO) provides a structured vocabulary for medical procedures, interventions, therapies, and treatments for disease with an emphasis on rare disease (RD). It is often difficult to find relevant clinical literature about strategies to manage RD patients. Responding to this need, MAxO provides a vocabulary to annotate diseases and phenotypes with recommended treatments and interventions. diff --git a/ontology/mco.md b/ontology/mco.md index 2daf89633..3d49a8d10 100644 --- a/ontology/mco.md +++ b/ontology/mco.md @@ -44,6 +44,7 @@ license: activity_status: active repository: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology preferredPrefix: MCO +added: 2019-02-15 --- Enter a detailed description of your ontology here diff --git a/ontology/mf.md b/ontology/mf.md index 033e3e11d..94ca35193 100644 --- a/ontology/mf.md +++ b/ontology/mf.md @@ -22,6 +22,7 @@ license: activity_status: active repository: https://github.com/jannahastings/mental-functioning-ontology preferredPrefix: MF +added: 2015-07-28 --- The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning, founded on the Basic Formal Ontology (BFO) and related to the Ontology for General Medical Science (OGMS). diff --git a/ontology/mfmo.md b/ontology/mfmo.md index 88ab3f878..3fda612fe 100644 --- a/ontology/mfmo.md +++ b/ontology/mfmo.md @@ -24,6 +24,7 @@ products: - id: mfmo.owl activity_status: active preferredPrefix: MFMO +added: 2015-08-11 --- ADD DESCRIPTION HERE diff --git a/ontology/mfo.md b/ontology/mfo.md index 4536dcf7f..8b0eb42ec 100644 --- a/ontology/mfo.md +++ b/ontology/mfo.md @@ -15,6 +15,7 @@ title: Medaka fish anatomy and development is_obsolete: true replaced_by: olatdv activity_status: inactive +added: 2015-07-28 --- A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. diff --git a/ontology/mfoem.md b/ontology/mfoem.md index 5950530e1..8c6cbc2f2 100644 --- a/ontology/mfoem.md +++ b/ontology/mfoem.md @@ -22,6 +22,7 @@ license: activity_status: active repository: https://github.com/jannahastings/emotion-ontology preferredPrefix: MFOEM +added: 2015-07-28 --- An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings, designed to support interdisciplinary research by providing unified annotations. diff --git a/ontology/mfomd.md b/ontology/mfomd.md index 09187c44b..11cab6394 100644 --- a/ontology/mfomd.md +++ b/ontology/mfomd.md @@ -19,6 +19,7 @@ license: activity_status: active repository: https://github.com/jannahastings/mental-functioning-ontology preferredPrefix: MFOMD +added: 2015-08-21 --- An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable. diff --git a/ontology/mi.md b/ontology/mi.md index 2dffaedcf..06992db8a 100644 --- a/ontology/mi.md +++ b/ontology/mi.md @@ -25,6 +25,7 @@ build: activity_status: active repository: https://github.com/HUPO-PSI/psi-mi-CV preferredPrefix: MI +added: 2015-07-28 --- A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative. diff --git a/ontology/miapa.md b/ontology/miapa.md index c96e756e0..14a26a5ba 100644 --- a/ontology/miapa.md +++ b/ontology/miapa.md @@ -21,6 +21,7 @@ mailing_list: http://groups.google.com/group/miapa-discuss activity_status: active preferredPrefix: MIAPA domain: information +added: 2015-07-28 --- The MIAPA ontology is an application ontology to formalize annotation of phylogenetic data according to the emerging Minimum Information About a Phylogenetic Analysis (MIAPA) metadata reporting standard. Please see [Leebens-Mack _et al._ (2006)](https://doi.org/10.1089/omi.2006.10.231) for the initial introduction of MIAPA. diff --git a/ontology/micro.md b/ontology/micro.md index f7e7218a2..106562491 100644 --- a/ontology/micro.md +++ b/ontology/micro.md @@ -19,6 +19,7 @@ products: activity_status: active repository: https://github.com/carrineblank/MicrO preferredPrefix: MICRO +added: 2015-10-20 --- Includes terms and term synonyms extracted from > 1500 prokaryotic taxonomic descriptions, collected from a large number of taxonomic descriptions from Archaea, Cyanobacteria, Bacteroidetes, Firmicutes, and Mollicutes. diff --git a/ontology/mirnao.md b/ontology/mirnao.md index dde37f18c..d5b86d0d7 100644 --- a/ontology/mirnao.md +++ b/ontology/mirnao.md @@ -14,6 +14,7 @@ products: title: microRNA Ontology is_obsolete: true activity_status: inactive +added: 2015-07-28 --- microRNA Ontology (miRNAO) is an application ontology and it has been developed in order to drive miRNA databases. diff --git a/ontology/miro.md b/ontology/miro.md index dfe754f81..cb5ecdc1b 100644 --- a/ontology/miro.md +++ b/ontology/miro.md @@ -15,6 +15,7 @@ taxon: title: Mosquito insecticide resistance activity_status: inactive repository: https://github.com/VEuPathDB-ontology/MIRO +added: 2015-07-28 --- Application ontology for entities related to insecticide resistance in mosquitos diff --git a/ontology/mmo.md b/ontology/mmo.md index 8eda7a6b4..f260072e4 100644 --- a/ontology/mmo.md +++ b/ontology/mmo.md @@ -35,6 +35,7 @@ browsers: activity_status: active repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology preferredPrefix: MMO +added: 2015-07-28 --- The Measurement Method Ontology is designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms. diff --git a/ontology/mmusdv.md b/ontology/mmusdv.md index fa31f4ba9..c4ebdfe23 100644 --- a/ontology/mmusdv.md +++ b/ontology/mmusdv.md @@ -24,6 +24,7 @@ products: activity_status: active repository: https://github.com/obophenotype/developmental-stage-ontologies domain: anatomy and development +added: 2015-08-21 --- MmusDv was developed by the Bgee group with assistance from the core Uberon developers and the Mouse anatomy ontology developers. diff --git a/ontology/mo.md b/ontology/mo.md index 4a52215e4..2cd2515d0 100644 --- a/ontology/mo.md +++ b/ontology/mo.md @@ -15,6 +15,7 @@ title: Microarray experimental conditions is_obsolete: true replaced_by: obi activity_status: inactive +added: 2015-07-28 --- Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. diff --git a/ontology/mod.md b/ontology/mod.md index 1d72c1746..5a29d8cd0 100644 --- a/ontology/mod.md +++ b/ontology/mod.md @@ -33,6 +33,7 @@ build: activity_status: active repository: https://github.com/HUPO-PSI/psi-mod-CV preferredPrefix: MOD +added: 2015-07-28 --- PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified. diff --git a/ontology/mondo.md b/ontology/mondo.md index 53df3a1b0..be1bebc57 100644 --- a/ontology/mondo.md +++ b/ontology/mondo.md @@ -84,6 +84,7 @@ usages: activity_status: active repository: https://github.com/monarch-initiative/mondo preferredPrefix: MONDO +added: 2016-07-12 --- The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. Original versions of Mondo were constructed entirely automatically and used the IDs of source databases and ontologies. Later, additional manually curated cross-ontology axioms were added, and a native Mondo ID system was used to avoid confusion with source databases. diff --git a/ontology/mop.md b/ontology/mop.md index e3167fa81..194e76e43 100644 --- a/ontology/mop.md +++ b/ontology/mop.md @@ -24,4 +24,5 @@ activity_status: active repository: https://github.com/rsc-ontologies/rxno preferredPrefix: MOP domain: chemistry and biochemistry +added: 2015-08-17 --- diff --git a/ontology/mp.md b/ontology/mp.md index e30bb66b4..f477d4405 100644 --- a/ontology/mp.md +++ b/ontology/mp.md @@ -75,6 +75,7 @@ mailing_list: https://groups.google.com/forum/#!forum/phenotype-ontologies-edito activity_status: active repository: https://github.com/mgijax/mammalian-phenotype-ontology preferredPrefix: MP +added: 2015-07-28 --- The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data. diff --git a/ontology/mpath.md b/ontology/mpath.md index 33e77614c..844b4cf71 100644 --- a/ontology/mpath.md +++ b/ontology/mpath.md @@ -26,6 +26,7 @@ build: activity_status: active repository: https://github.com/PaulNSchofield/mpath preferredPrefix: MPATH +added: 2015-07-28 --- A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes diff --git a/ontology/mpio.md b/ontology/mpio.md index b8a3045e9..12f387b63 100644 --- a/ontology/mpio.md +++ b/ontology/mpio.md @@ -19,6 +19,7 @@ license: activity_status: active repository: https://github.com/MPIO-Developers/MPIO preferredPrefix: MPIO +added: 2017-11-02 --- MPIO (Minimum PDDI Information Ontology) is an OWL representation of minimum information regarding potential drug-drug interaction information. It is based on and meant to be use in alignment with DIDEO or DINTO. diff --git a/ontology/mro.md b/ontology/mro.md index 3af04e8e2..06403772b 100644 --- a/ontology/mro.md +++ b/ontology/mro.md @@ -31,6 +31,7 @@ usages: activity_status: active repository: https://github.com/IEDB/MRO preferredPrefix: MRO +added: 2015-09-17 --- The MHC Restriction Ontology (MRO) is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. diff --git a/ontology/ms.md b/ontology/ms.md index 36e1c8e20..90ff88fb2 100644 --- a/ontology/ms.md +++ b/ontology/ms.md @@ -35,6 +35,7 @@ build: activity_status: active repository: https://github.com/HUPO-PSI/psi-ms-CV preferredPrefix: MS +added: 2015-07-28 --- A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. Developed by the HUPO Proteomics Standards Initiative (PSI). diff --git a/ontology/nbo.md b/ontology/nbo.md index c2e03bcd2..814b6e158 100644 --- a/ontology/nbo.md +++ b/ontology/nbo.md @@ -31,4 +31,5 @@ preferredPrefix: NBO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24177753 title: "Analyzing gene expression data in mice with the Neuro Behavior Ontology" +added: 2015-07-28 --- diff --git a/ontology/ncbitaxon.md b/ontology/ncbitaxon.md index 82f3fe851..bbd54d918 100644 --- a/ontology/ncbitaxon.md +++ b/ontology/ncbitaxon.md @@ -46,6 +46,7 @@ license: label: CC0 1.0 activity_status: active repository: https://github.com/obophenotype/ncbitaxon +added: 2015-07-28 --- The NCBITaxon ontology is an automatic translation of the [NCBI taxonomy database](http://www.ncbi.nlm.nih.gov/taxonomy) into obo/owl. diff --git a/ontology/ncit.md b/ontology/ncit.md index d63aac031..2407ce8af 100644 --- a/ontology/ncit.md +++ b/ontology/ncit.md @@ -32,6 +32,7 @@ activity_status: active repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition preferredPrefix: NCIT domain: health +added: 2016-04-01 --- The NCI Thesaurus is a reference terminology that includes broad diff --git a/ontology/ncro.md b/ontology/ncro.md index 65170262e..b2e2e1df0 100644 --- a/ontology/ncro.md +++ b/ontology/ncro.md @@ -27,6 +27,7 @@ build: activity_status: active repository: https://github.com/OmniSearch/ncro preferredPrefix: NCRO +added: 2015-11-18 --- The NCRO is a reference ontology in the non-coding RNA (ncRNA) field, diff --git a/ontology/nif_cell.md b/ontology/nif_cell.md index 6f1e89ab3..00cbe8403 100644 --- a/ontology/nif_cell.md +++ b/ontology/nif_cell.md @@ -10,6 +10,7 @@ homepage: http://neuinfo.org/ is_obsolete: true replaced_by: cl activity_status: inactive +added: 2015-08-21 --- Cell types from NIFSTD diff --git a/ontology/nif_dysfunction.md b/ontology/nif_dysfunction.md index b87d86294..a92a52756 100644 --- a/ontology/nif_dysfunction.md +++ b/ontology/nif_dysfunction.md @@ -9,6 +9,7 @@ homepage: http://neuinfo.org/ is_obsolete: true replaced_by: doid activity_status: inactive +added: 2015-08-21 --- This ontology contains the former BIRNLex-Disease, version 1.3.2. diff --git a/ontology/nif_grossanatomy.md b/ontology/nif_grossanatomy.md index 7e2e61b87..7ee51cd9e 100644 --- a/ontology/nif_grossanatomy.md +++ b/ontology/nif_grossanatomy.md @@ -9,6 +9,7 @@ homepage: http://neuinfo.org/ is_obsolete: true replaced_by: uberon activity_status: inactive +added: 2015-08-21 --- NIF-GrossAnatomy: anatomical entities of relevance to neuroscience. Contains most classes from BIRNLex-Anatomy diff --git a/ontology/nmr.md b/ontology/nmr.md index 30eac2a84..acf8aa999 100644 --- a/ontology/nmr.md +++ b/ontology/nmr.md @@ -16,6 +16,7 @@ build: method: owl2obo is_obsolete: true activity_status: inactive +added: 2015-07-28 --- Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation. diff --git a/ontology/nomen.md b/ontology/nomen.md index 4b6f457b8..2f264c88e 100644 --- a/ontology/nomen.md +++ b/ontology/nomen.md @@ -39,6 +39,7 @@ canonical: nomen.owl activity_status: active repository: https://github.com/SpeciesFileGroup/nomen preferredPrefix: NOMEN +added: 2019-01-11 --- NOMEN is a nomenclatural ontology for biological names (not concepts). See the NOMEN homepage for more info. diff --git a/ontology/oae.md b/ontology/oae.md index aff61f839..e444dd669 100644 --- a/ontology/oae.md +++ b/ontology/oae.md @@ -24,6 +24,7 @@ license: activity_status: active repository: https://github.com/OAE-ontology/OAE preferredPrefix: OAE +added: 2015-07-28 --- The Ontology of Adverse Events (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. diff --git a/ontology/oarcs.md b/ontology/oarcs.md index c377ccea2..e8d9a19b2 100644 --- a/ontology/oarcs.md +++ b/ontology/oarcs.md @@ -19,6 +19,7 @@ products: - id: oarcs.owl activity_status: active preferredPrefix: OARCS +added: 2017-02-10 --- OArCS is an ontology describing the Arthropod ciruclatory system. diff --git a/ontology/oba.md b/ontology/oba.md index a6c78354f..4371a03ac 100644 --- a/ontology/oba.md +++ b/ontology/oba.md @@ -30,6 +30,7 @@ build: activity_status: active repository: https://github.com/obophenotype/bio-attribute-ontology preferredPrefix: OBA +added: 2015-07-28 --- A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with diff --git a/ontology/obcs.md b/ontology/obcs.md index c516a913e..c7560eb13 100644 --- a/ontology/obcs.md +++ b/ontology/obcs.md @@ -22,6 +22,7 @@ license: activity_status: active repository: https://github.com/obcs/obcs preferredPrefix: OBCS +added: 2015-07-31 --- The Ontology of Biological and Clinical Statistics (OBCS) is a biomedical ontology in the domain of biological and clinical statistics. OBCS is primarily targeted for statistical term representation in the fields in biological, biomedical, and clinical domains. diff --git a/ontology/obi.md b/ontology/obi.md index c4d587e7c..72de4de30 100644 --- a/ontology/obi.md +++ b/ontology/obi.md @@ -75,6 +75,7 @@ usages: description: A specific OBI term used to autocomplete in NIF search OBI:0100026 'organism' activity_status: active preferredPrefix: OBI +added: 2015-07-28 --- The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of life-science and clinical investigations. diff --git a/ontology/obib.md b/ontology/obib.md index e61724da5..1a3d2a8ce 100644 --- a/ontology/obib.md +++ b/ontology/obib.md @@ -33,6 +33,7 @@ license: activity_status: active repository: https://github.com/biobanking/biobanking preferredPrefix: OBIB +added: 2015-08-17 --- The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. diff --git a/ontology/obo_rel.md b/ontology/obo_rel.md index e0bcc9b14..ea27c4726 100644 --- a/ontology/obo_rel.md +++ b/ontology/obo_rel.md @@ -10,6 +10,7 @@ homepage: http://www.obofoundry.org/ro is_obsolete: true replaced_by: ro activity_status: inactive +added: 2015-08-21 --- Defines core relations used in all OBO ontologies. Importand note: this ontology is now deprecated - use RO instead diff --git a/ontology/ogg.md b/ontology/ogg.md index 98a37a0df..bca54c0d8 100644 --- a/ontology/ogg.md +++ b/ontology/ogg.md @@ -19,6 +19,7 @@ license: activity_status: active preferredPrefix: OGG domain: biological systems +added: 2015-07-29 --- # Summary diff --git a/ontology/ogi.md b/ontology/ogi.md index 6baf5564b..570a76ce2 100644 --- a/ontology/ogi.md +++ b/ontology/ogi.md @@ -8,6 +8,7 @@ products: title: Ontology for genetic interval tracker: https://code.google.com/p/ontology-for-genetic-interval/issues/list activity_status: orphaned +added: 2015-07-28 --- Using BFO as its framwork, OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is "the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure. diff --git a/ontology/ogms.md b/ontology/ogms.md index fcde4a5c7..ece008121 100644 --- a/ontology/ogms.md +++ b/ontology/ogms.md @@ -25,6 +25,7 @@ depicted_by: https://avatars2.githubusercontent.com/u/12973154?s=200&v=4 activity_status: active repository: https://github.com/OGMS/ogms preferredPrefix: OGMS +added: 2015-07-29 --- The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. See http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf diff --git a/ontology/ogsf.md b/ontology/ogsf.md index 6cdb2fa78..04226203b 100644 --- a/ontology/ogsf.md +++ b/ontology/ogsf.md @@ -19,6 +19,7 @@ activity_status: active repository: https://github.com/linikujp/OGSF preferredPrefix: OGSF domain: investigations +added: 2015-07-28 --- Ontology for Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO2.0's framwork. The ontology is under the domain of genetic epidemiology. diff --git a/ontology/ohd.md b/ontology/ohd.md index aa48f7296..fdcd6e66a 100644 --- a/ontology/ohd.md +++ b/ontology/ohd.md @@ -24,6 +24,7 @@ tracker: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/issu repository: https://github.com/oral-health-and-disease-ontologies/ohd-ontology activity_status: active preferredPrefix: OHD +added: 2016-12-01 --- The Oral Health and Disease Ontology is intended as a BFO and OBO diff --git a/ontology/ohmi.md b/ontology/ohmi.md index d65fcc175..468cf54a0 100644 --- a/ontology/ohmi.md +++ b/ontology/ohmi.md @@ -20,6 +20,7 @@ activity_status: active repository: https://github.com/ohmi-ontology/ohmi preferredPrefix: OHMI domain: organisms +added: 2017-04-21 --- The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions. diff --git a/ontology/ohpi.md b/ontology/ohpi.md index 4bdcf2b78..df088b30e 100644 --- a/ontology/ohpi.md +++ b/ontology/ohpi.md @@ -20,6 +20,7 @@ activity_status: active repository: https://github.com/OHPI/ohpi preferredPrefix: OHPI domain: biological systems +added: 2019-07-22 --- # OHPI: Ontology of Host-Pathogen Interactions diff --git a/ontology/olatdv.md b/ontology/olatdv.md index a8c6f8c2d..cf413584a 100644 --- a/ontology/olatdv.md +++ b/ontology/olatdv.md @@ -24,4 +24,5 @@ license: activity_status: active repository: https://github.com/obophenotype/developmental-stage-ontologies domain: anatomy and development +added: 2015-08-21 --- diff --git a/ontology/omiabis.md b/ontology/omiabis.md index 8710eb866..a126ee96d 100644 --- a/ontology/omiabis.md +++ b/ontology/omiabis.md @@ -18,6 +18,7 @@ license: is_obsolete: true activity_status: inactive repository: https://github.com/OMIABIS/omiabis-dev +added: 2016-02-05 --- OMIABIS has been merged into OBIB (http://www.obofoundry.org/ontology/obib.html). diff --git a/ontology/omit.md b/ontology/omit.md index 495cba12c..9e3cf21ba 100644 --- a/ontology/omit.md +++ b/ontology/omit.md @@ -21,6 +21,7 @@ activity_status: active repository: https://github.com/OmniSearch/omit preferredPrefix: OMIT domain: chemistry and biochemistry +added: 2015-07-29 --- The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). OMIT has reused and extended a set of well-established concepts from existing bio-ontologies, e.g., Gene Ontology, Sequence Ontology, Protein Ontology, NCBI Organism Taxonomy, Human Disease Ontology, Foundational Model of Anatomy, and so forth. diff --git a/ontology/omo.md b/ontology/omo.md index 3e12b25e8..ca8121284 100644 --- a/ontology/omo.md +++ b/ontology/omo.md @@ -25,4 +25,5 @@ usages: activity_status: active repository: https://github.com/information-artifact-ontology/ontology-metadata preferredPrefix: OMO +added: 2020-05-02 --- diff --git a/ontology/omp.md b/ontology/omp.md index 458736874..519cb397b 100644 --- a/ontology/omp.md +++ b/ontology/omp.md @@ -23,6 +23,7 @@ tracker: https://github.com/microbialphenotypes/OMP-ontology/issues activity_status: active repository: https://github.com/microbialphenotypes/OMP-ontology preferredPrefix: OMP +added: 2015-08-21 --- OMP is a community ontology for annotating microbial phenotypes. diff --git a/ontology/omrse.md b/ontology/omrse.md index cd7ecd0f5..196348eae 100644 --- a/ontology/omrse.md +++ b/ontology/omrse.md @@ -31,6 +31,7 @@ publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27406187 title: "The ontology of medically related social entities: recent developments" +added: 2015-07-28 --- This ontology covers the domain of social entities that are related to health care, such as demographic information (social entities for recording gender (but not sex) and marital status, for example) and the roles of various individuals and organizations (patient, hospital,etc.) diff --git a/ontology/one.md b/ontology/one.md index 93bdf5674..633b21d9d 100644 --- a/ontology/one.md +++ b/ontology/one.md @@ -29,6 +29,7 @@ tracker: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies/issue activity_status: active repository: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies preferredPrefix: ONE +added: 2020-11-17 --- Nutritional epidemiology is a specific research area. The generic ontologies for food science, nutrition science or medical science failed to cover the specific characteristics of nutritional epidemiologic studies. As a result, we developed the ontology for nutritional epidemiology (ONE) in order to describe nutritional epidemiologic studies accurately. diff --git a/ontology/ons.md b/ontology/ons.md index d9dbffcd4..d1ea77b1d 100644 --- a/ontology/ons.md +++ b/ontology/ons.md @@ -36,6 +36,7 @@ tracker: https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues activity_status: active repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies preferredPrefix: ONS +added: 2020-05-28 --- ONS was developed under the ENPADASI European project, to assist the standardized description of (human) nutritional studies. As such, it includes and covers classes and relations that are commonly encountered while conducting, storing, harmonizing, integrating, describing and querying for nutritional studies. ONS main objective and long-term goal, is to represent a comprehensive resource for the description of concepts in the broader human nutrition domain, representing a solid and extensible formal ontology framework, where integration of new information can be easily achieved by the addition of extra modules. diff --git a/ontology/ontoavida.md b/ontology/ontoavida.md index d621bc054..939e1ef14 100644 --- a/ontology/ontoavida.md +++ b/ontology/ontoavida.md @@ -29,4 +29,5 @@ license: activity_status: active repository: https://gitlab.com/fortunalab/ontoavida preferredPrefix: ONTOAVIDA +added: 2021-12-01 --- diff --git a/ontology/ontoneo.md b/ontology/ontoneo.md index ed2d6165a..30e32086f 100644 --- a/ontology/ontoneo.md +++ b/ontology/ontoneo.md @@ -28,6 +28,7 @@ browsers: activity_status: active repository: https://github.com/ontoneo-project/Ontoneo preferredPrefix: ONTONEO +added: 2016-11-22 --- The OntONeo suite is a collection of open ontologies available about Obstetric and Neonatal domain, currently designed to be composed by three complementary sub-ontologies covering several data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. diff --git a/ontology/oostt.md b/ontology/oostt.md index 74c08cdbf..8d9f76e1e 100644 --- a/ontology/oostt.md +++ b/ontology/oostt.md @@ -19,6 +19,7 @@ license: activity_status: active repository: https://github.com/OOSTT/OOSTT preferredPrefix: OOSTT +added: 2016-04-04 --- The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2). It is developed collaboratively by domain and ontology experts in the NIH-funded CAFE (Comparative Assessment Framework for Environments of trauma care) project (1R01GM111324-01A1). It will be used as the ontology backbone of a graphical user interface comparing graphical representations of organizational structures. diff --git a/ontology/opl.md b/ontology/opl.md index db8f89bc5..769bd954b 100644 --- a/ontology/opl.md +++ b/ontology/opl.md @@ -30,6 +30,7 @@ usages: activity_status: active repository: https://github.com/OPL-ontology/OPL preferredPrefix: OPL +added: 2015-07-28 --- The Ontology for Parasite LifeCycle (OPL) is designed to serve as a reference ontology for parasite life cycle stages. It models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location diff --git a/ontology/opmi.md b/ontology/opmi.md index 161144216..676e01811 100644 --- a/ontology/opmi.md +++ b/ontology/opmi.md @@ -20,6 +20,7 @@ activity_status: active repository: https://github.com/OPMI/opmi preferredPrefix: OPMI domain: investigations +added: 2018-08-30 --- The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions. diff --git a/ontology/ornaseq.md b/ontology/ornaseq.md index 0f78649f8..371aa7e9e 100644 --- a/ontology/ornaseq.md +++ b/ontology/ornaseq.md @@ -19,6 +19,7 @@ license: activity_status: active repository: https://github.com/safisher/ornaseq preferredPrefix: ORNASEQ +added: 2019-06-20 --- This is an application ontology used to annotate next-generation sequencing experiments performed on RNA (RNAseq). It uses terms from BFO, CHEBI, CL, GENEPIO, GO, IAO, NCBITaxon, NCIT, OBI, OBIws, OGMS, OMIABIS, SO, TAXRANK, and UBERON as well as EFO. diff --git a/ontology/ovae.md b/ontology/ovae.md index c8cd5aab6..df5650e1d 100644 --- a/ontology/ovae.md +++ b/ontology/ovae.md @@ -19,6 +19,7 @@ activity_status: active repository: https://github.com/OVAE-Ontology/ovae preferredPrefix: OVAE domain: health +added: 2015-07-28 --- # Summary diff --git a/ontology/pao.md b/ontology/pao.md index 10e86abb7..c35017d42 100644 --- a/ontology/pao.md +++ b/ontology/pao.md @@ -13,6 +13,7 @@ taxon: homepage: http://www.plantontology.org is_obsolete: true activity_status: inactive +added: 2015-08-21 --- REPLACED BY: PO. A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization. Note that this has been subsumed into the PO diff --git a/ontology/pato.md b/ontology/pato.md index 74977d6ab..fda3c8b7c 100644 --- a/ontology/pato.md +++ b/ontology/pato.md @@ -52,6 +52,7 @@ publications: title: "The anatomy of phenotype ontologies: principles, properties and applications" - id: https://www.ncbi.nlm.nih.gov/pubmed/15642100 title: "Using ontologies to describe mouse phenotypes" +added: 2015-07-28 --- Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested. diff --git a/ontology/pcl.md b/ontology/pcl.md index caa0af374..202822ff2 100644 --- a/ontology/pcl.md +++ b/ontology/pcl.md @@ -43,4 +43,5 @@ license: activity_status: active repository: https://github.com/obophenotype/provisional_cell_ontology preferredPrefix: PCL +added: 2022-01-25 --- diff --git a/ontology/pco.md b/ontology/pco.md index 5ff03a631..bfd482767 100644 --- a/ontology/pco.md +++ b/ontology/pco.md @@ -38,6 +38,7 @@ license: activity_status: active repository: https://github.com/PopulationAndCommunityOntology/pco preferredPrefix: PCO +added: 2015-07-28 --- The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. diff --git a/ontology/pd_st.md b/ontology/pd_st.md index 287709d30..7ea4556a7 100644 --- a/ontology/pd_st.md +++ b/ontology/pd_st.md @@ -12,4 +12,5 @@ homepage: http://4dx.embl.de/platy is_obsolete: true replaced_by: pdumdv activity_status: inactive +added: 2015-08-21 --- diff --git a/ontology/pdro.md b/ontology/pdro.md index 2606fca63..6b415082e 100644 --- a/ontology/pdro.md +++ b/ontology/pdro.md @@ -27,6 +27,7 @@ tracker: https://github.com/OpenLHS/PDRO/issues activity_status: active repository: https://github.com/OpenLHS/PDRO preferredPrefix: PDRO +added: 2016-11-11 --- PDRO is a realist ontology that aims to represent the domain of drug prescriptions. Such an ontology is currently missing in the OBOFoundry and is highly relevant to the domains of existing ontologies like DRON, OMRSE and OAE. PDRO's central focus is the structure of a drug prescription, which is represented as a mereology of informational entities. Our current use cases are (1) refining this structure (e.g., adding closure axioms, cardinality, datatype bindings, etc) for prospectively standardizing local electronic prescriptions and (2) annotating prescription data of differing EHRs for detecting inappropriate prescriptions using a central semantic framework. Future ontological work will include aligning PDRO more closely with the Document Acts Ontology. diff --git a/ontology/pdumdv.md b/ontology/pdumdv.md index 7fe1e1c5d..8058627e7 100644 --- a/ontology/pdumdv.md +++ b/ontology/pdumdv.md @@ -24,4 +24,5 @@ license: activity_status: active repository: https://github.com/obophenotype/developmental-stage-ontologies domain: anatomy and development +added: 2015-08-21 --- diff --git a/ontology/peco.md b/ontology/peco.md index 267e56a99..10a624f06 100644 --- a/ontology/peco.md +++ b/ontology/peco.md @@ -27,6 +27,7 @@ activity_status: active repository: https://github.com/Planteome/plant-experimental-conditions-ontology preferredPrefix: PECO depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG +added: 2017-06-05 --- A structured, controlled vocabulary for the representation of plant experimental conditions. diff --git a/ontology/pgdso.md b/ontology/pgdso.md index 100a3a8a1..682755ff3 100644 --- a/ontology/pgdso.md +++ b/ontology/pgdso.md @@ -11,6 +11,7 @@ taxon: homepage: http://www.plantontology.org is_obsolete: true activity_status: inactive +added: 2015-08-21 --- REPLACED BY: PO. A controlled vocabulary of growth and developmental stages in various plants. Note that this has been subsumed into the PO diff --git a/ontology/phipo.md b/ontology/phipo.md index cb4d69a4e..8b79d9457 100644 --- a/ontology/phipo.md +++ b/ontology/phipo.md @@ -32,6 +32,7 @@ preferredPrefix: PHIPO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/34788826 title: "PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions" +added: 2018-08-15 --- PHIPO is being developed to support the comprehensive and detailed representation of phenotypes in PHI-base, the multi-species Pathogen-Host Interactions database available online at . PHIPO is pre-composed and logically defined. diff --git a/ontology/plana.md b/ontology/plana.md index 7f1c465bd..76ee9ef11 100644 --- a/ontology/plana.md +++ b/ontology/plana.md @@ -39,6 +39,7 @@ license: activity_status: active repository: https://github.com/obophenotype/planaria-ontology preferredPrefix: PLANA +added: 2017-02-07 --- Anatomy ontology for planaria and terms specific to the developmental stages of the planarian __Schmidtea mediterranea__ diff --git a/ontology/planp.md b/ontology/planp.md index 06bf5bc8f..19ed7f1e9 100644 --- a/ontology/planp.md +++ b/ontology/planp.md @@ -32,6 +32,7 @@ license: activity_status: active repository: https://github.com/obophenotype/planarian-phenotype-ontology preferredPrefix: PLANP +added: 2018-11-19 --- Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. Many of the phenotypes were seen durning RNAi experiments. diff --git a/ontology/plo.md b/ontology/plo.md index 08a511899..5cbd1103b 100644 --- a/ontology/plo.md +++ b/ontology/plo.md @@ -8,6 +8,7 @@ contact: homepage: http://www.sanger.ac.uk/Users/mb4/PLO/ is_obsolete: true activity_status: inactive +added: 2015-08-21 --- A structured controlled vocabulary for the life cycle of the malaria parasite Plasmodium. diff --git a/ontology/po.md b/ontology/po.md index ca0e53030..48d4c26f2 100644 --- a/ontology/po.md +++ b/ontology/po.md @@ -70,6 +70,7 @@ activity_status: active repository: https://github.com/Planteome/plant-ontology preferredPrefix: PO depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG +added: 2015-07-28 --- The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants. diff --git a/ontology/poro.md b/ontology/poro.md index 8991d718d..7292d997e 100644 --- a/ontology/poro.md +++ b/ontology/poro.md @@ -38,6 +38,7 @@ tracker: https://github.com/obophenotype/porifera-ontology/issues activity_status: active repository: https://github.com/obophenotype/porifera-ontology preferredPrefix: PORO +added: 2015-07-28 --- An ontology covering the anatomy of Porifera (sponges) diff --git a/ontology/ppo.md b/ontology/ppo.md index 90d165ef7..82f7c712b 100644 --- a/ontology/ppo.md +++ b/ontology/ppo.md @@ -25,6 +25,7 @@ taxon: activity_status: active repository: https://github.com/PlantPhenoOntology/PPO preferredPrefix: PPO +added: 2016-12-30 --- Plant phenology — the timing of plant life-cycle events, such as flowering or leafing-out — has cascading effects on multiple levels of biological organization, from individuals to ecosystems, and is crucial for understanding the links between climate and biological communities. Plant phenology data are collected and used by many different types of researchers, from plant breeders to ecosystem ecologists. Today, thanks to data digitization and aggregation initiatives, phenology monitoring networks, and the efforts of citizen scientists, more phenologically relevant data is available than ever before. Unfortunately, combining these data in large-scale analyses remains prohibitively difficult, mostly because the individuals and organizations producing the data are using non-standardized terminologies and metrics during data collection and processing. Lack of standardization remains particularly problematic for historical datasets, which are crucial for time-based analyses. diff --git a/ontology/pr.md b/ontology/pr.md index 5dd8e09c2..060e0c96c 100644 --- a/ontology/pr.md +++ b/ontology/pr.md @@ -58,6 +58,7 @@ usages: activity_status: active repository: https://github.com/PROconsortium/PRoteinOntology preferredPrefix: PR +added: 2015-07-28 --- The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. diff --git a/ontology/propreo.md b/ontology/propreo.md index f9558c378..70c91c9c3 100644 --- a/ontology/propreo.md +++ b/ontology/propreo.md @@ -8,6 +8,7 @@ contact: homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/ is_obsolete: true activity_status: inactive +added: 2015-08-21 --- A comprehensive proteomics data and process provenance ontology. diff --git a/ontology/psdo.md b/ontology/psdo.md index 5d5246bf2..30a6c8b89 100644 --- a/ontology/psdo.md +++ b/ontology/psdo.md @@ -30,6 +30,7 @@ license: activity_status: active repository: https://github.com/Display-Lab/psdo preferredPrefix: PSDO +added: 2019-04-04 --- The Performance Summary Display Ontology (PSDO) is a lightweight application ontology used to diff --git a/ontology/pso.md b/ontology/pso.md index 2b2087a20..61ae90c9b 100644 --- a/ontology/pso.md +++ b/ontology/pso.md @@ -35,6 +35,7 @@ license: activity_status: active repository: https://github.com/Planteome/plant-stress-ontology preferredPrefix: PSO +added: 2020-05-14 --- Enter a detailed description of your ontology here diff --git a/ontology/pw.md b/ontology/pw.md index 874102716..d6cea3199 100644 --- a/ontology/pw.md +++ b/ontology/pw.md @@ -36,6 +36,7 @@ activity_status: active repository: https://github.com/rat-genome-database/PW-Pathway-Ontology preferredPrefix: PW depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif +added: 2015-07-28 --- The Pathway Ontology is a controlled vocabulary for pathways that provides standard terms for the annotation of gene products. The Pathway Ontology is under development at Rat Genome Database. diff --git a/ontology/rbo.md b/ontology/rbo.md index 1f1a537ae..06bd4a9c0 100644 --- a/ontology/rbo.md +++ b/ontology/rbo.md @@ -48,6 +48,7 @@ license: activity_status: active repository: https://github.com/Radiobiology-Informatics-Consortium/RBO preferredPrefix: RBO +added: 2021-01-28 --- The effects of all kinds of radiation on biological systems is the subject of much research, both on earth and in space environments. This ontology is designed to support the needs of these investigators, particularly for organizing, describing and archiving data from experiments and observations examining these effects. diff --git a/ontology/resid.md b/ontology/resid.md index 1d1373324..8700a8638 100644 --- a/ontology/resid.md +++ b/ontology/resid.md @@ -12,6 +12,7 @@ homepage: http://www.ebi.ac.uk/RESID/ title: Protein covalent bond is_obsolete: true activity_status: inactive +added: 2015-07-28 --- For the description of covalent bonds in proteins. diff --git a/ontology/rex.md b/ontology/rex.md index 4ef092547..2b173d285 100644 --- a/ontology/rex.md +++ b/ontology/rex.md @@ -10,6 +10,7 @@ build: insert_ontology_id: true method: obo2owl activity_status: orphaned +added: 2015-07-28 --- REX is an ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. REX includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX. diff --git a/ontology/rnao.md b/ontology/rnao.md index f006781e2..7feb2bf55 100644 --- a/ontology/rnao.md +++ b/ontology/rnao.md @@ -28,4 +28,5 @@ build: tracker: https://github.com/BGSU-RNA/rnao/issues activity_status: inactive repository: https://github.com/BGSU-RNA/rnao +added: 2015-07-28 --- diff --git a/ontology/ro.md b/ontology/ro.md index ac51d29fc..54d802f11 100644 --- a/ontology/ro.md +++ b/ontology/ro.md @@ -66,6 +66,7 @@ usages: activity_status: active repository: https://github.com/oborel/obo-relations preferredPrefix: RO +added: 2015-07-28 --- ![logo](/images/ro_logo.png) diff --git a/ontology/rs.md b/ontology/rs.md index 962da7e62..b46cc3832 100644 --- a/ontology/rs.md +++ b/ontology/rs.md @@ -35,6 +35,7 @@ repository: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology preferredPrefix: RS depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif domain: organisms +added: 2015-07-28 --- Ontology of rat strains diff --git a/ontology/rxno.md b/ontology/rxno.md index b3c7b2241..e706a0d6d 100644 --- a/ontology/rxno.md +++ b/ontology/rxno.md @@ -24,6 +24,7 @@ activity_status: active repository: https://github.com/rsc-ontologies/rxno preferredPrefix: RXNO domain: chemistry and biochemistry +added: 2015-08-17 --- RXNO, the name reaction ontology, connects organic name reactions such as the Diels-Alder cyclization and the Cannizzaro reaction to their roles in an organic synthesis and to processes in MOP. diff --git a/ontology/sao.md b/ontology/sao.md index c701d0975..66d0a2a18 100644 --- a/ontology/sao.md +++ b/ontology/sao.md @@ -12,6 +12,7 @@ homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html is_obsolete: true replaced_by: go activity_status: inactive +added: 2015-08-21 --- We have developed the Subcellular Anatomy Ontology for the Nervous System (SAO) to provide a formal ontology to describe structures from the dimensional range known as the “mesoscale,” encompassing cellular and subcellular structure, supracellular domains, and macromolecules. The SAO describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil (Fong et al., submitted). Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their approporiate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration. diff --git a/ontology/sbo.md b/ontology/sbo.md index 33636fdaf..7db0f3a68 100644 --- a/ontology/sbo.md +++ b/ontology/sbo.md @@ -23,6 +23,7 @@ license: label: Artistic License 2.0 activity_status: active preferredPrefix: SBO +added: 2015-07-28 --- The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of six orthogonal vocabularies defining: the roles of reaction participants (eg. "substrate"), quantitative parameters (eg. "Michaelis constant"), a precise classification of mathematical expressions that describe the system (eg. "mass action rate law"), the modeling framework used (eg. "logical framework"), and a branch each to describe entity (eg. "macromolecule") and interaction (eg. "process") types. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. More information about SBO can be found from the project FAQ, at http://www.ebi.ac.uk/sbo/ SBO is a project of the BioModels.net effort and is developed through community collaboration diff --git a/ontology/scdo.md b/ontology/scdo.md index 9f015cc7e..41edc85cb 100644 --- a/ontology/scdo.md +++ b/ontology/scdo.md @@ -65,6 +65,7 @@ dependencies: - id: vo - id: vt preferredPrefix: SCDO +added: 2021-04-16 --- The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to: 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD, 3) links to other ontologies and bodies of work such as DO, PhenX, MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM. Once complete, we anticipate that the ontology will: 1) be the most comprehensive collection of knowledge on SCD, 2) facilitate exploration of new scientific questions and ideas, 3) facilitate seamless data sharing and collaborations including meta-analysis within the SCD community, 4) support the building of databasing and clinical informatics in SCD. diff --git a/ontology/sep.md b/ontology/sep.md index 658955e75..a275eec36 100644 --- a/ontology/sep.md +++ b/ontology/sep.md @@ -19,6 +19,7 @@ build: insert_ontology_id: true activity_status: inactive is_obsolete: true +added: 2015-07-28 --- A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative. diff --git a/ontology/sepio.md b/ontology/sepio.md index 2de7d0d83..b6ac1d549 100644 --- a/ontology/sepio.md +++ b/ontology/sepio.md @@ -28,6 +28,7 @@ activity_status: active repository: https://github.com/monarch-initiative/SEPIO-ontology preferredPrefix: SEPIO depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/SEPIO-LOGOS/sepio_logo_black-banner.png +added: 2017-06-30 --- The Scientific Evidence and Provenance Information Ontology (SEPIO) was developed to support description of evidence and provenance information for scientific claims. The core model represents the relationships between claims, their evidence lines, the information items that comprise these lines of evidence, and the methods, tools, and agents involved in the creation of these entities. Use cases driving SEPIO development include integration of scientific claims and their associated evidence/provenance metadata, and support for the discovery, analysis, and evaluation of claims based on this metadata. diff --git a/ontology/sibo.md b/ontology/sibo.md index 74be89383..b24a85ced 100644 --- a/ontology/sibo.md +++ b/ontology/sibo.md @@ -25,6 +25,7 @@ build: activity_status: orphaned repository: https://github.com/obophenotype/sibo preferredPrefix: SIBO +added: 2015-07-29 --- The Social Insect Behavior Ontology (SIBO), created by Chris Smith of the BDGP/SFSU. It was been adopted by Chris Mungall, but I am currently looking to hand it over or to merge it into the NBO diff --git a/ontology/so.md b/ontology/so.md index f8b5682ec..e43282dea 100644 --- a/ontology/so.md +++ b/ontology/so.md @@ -42,6 +42,7 @@ depicted_by: http://sequenceontology.org/img/so_icon.png activity_status: active repository: https://github.com/The-Sequence-Ontology/SO-Ontologies preferredPrefix: SO +added: 2015-07-28 --- SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. SO is also part of the Open Biomedical Ontologies library. Our aim is to develop an ontology suitable for describing the features of biological sequences. For questions, please send mail to the SO developers mailing list. For new term suggestions, please use the [Term Tracker](https://github.com/The-Sequence-Ontology/SO-Ontologies/issues). diff --git a/ontology/sopharm.md b/ontology/sopharm.md index 7f3aa9d8c..5abd0d13f 100644 --- a/ontology/sopharm.md +++ b/ontology/sopharm.md @@ -11,6 +11,7 @@ taxon: homepage: http://www.loria.fr/~coulet/sopharm2.0_description.php is_obsolete: true activity_status: inactive +added: 2015-08-21 --- SO-Pharm is a formal ontology that represent domain knowledge in pharmacogenomics. To achieve this goal SO-Pharm articulates ontologies from sub domains of phamacogenomics (i.e. genotype, phenotype, drug, trial representations). SO-Pharm enables to support knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. diff --git a/ontology/spd.md b/ontology/spd.md index ef1be3a37..b83a5a823 100644 --- a/ontology/spd.md +++ b/ontology/spd.md @@ -29,6 +29,7 @@ preferredPrefix: SPD publications: - id: https://doi.org/10.3390/d11100202 title: "The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data" +added: 2015-07-28 --- An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). diff --git a/ontology/stato.md b/ontology/stato.md index 72820626e..42d1c3f30 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -23,6 +23,7 @@ tracker: https://github.com/ISA-tools/stato/issues activity_status: active repository: https://github.com/ISA-tools/stato preferredPrefix: STATO +added: 2015-08-17 --- The STATistics Ontology (STATO) project started in early 2012, as part of the requirement of the community-driven ISA Commons to represent the results of data analysis. STATO is a standalone project since Nov 2012. STATO is driven and funded by several ISA-based projects and their user community, but also by collaborations with data publication platforms. STATO is applicable to, but not limited, the broad life, natural and biomedical science domain with documented applications for factorial design, association studies, differential expression, hit selection and meta-analysis. STATO has been developed to interoperate with other OBO Foundry ontologies, hence relies on the Basics Formal Ontology (BFO) as a top level ontology and uses the Ontology for Biomedical Investigations (OBI) as mid-level ontology. diff --git a/ontology/swo.md b/ontology/swo.md index 6b5f11df3..674c2b144 100644 --- a/ontology/swo.md +++ b/ontology/swo.md @@ -27,4 +27,5 @@ build: activity_status: active repository: https://github.com/allysonlister/swo preferredPrefix: SWO +added: 2015-07-28 --- diff --git a/ontology/symp.md b/ontology/symp.md index 3ba012396..3289327d1 100644 --- a/ontology/symp.md +++ b/ontology/symp.md @@ -40,6 +40,7 @@ usages: activity_status: active repository: https://github.com/DiseaseOntology/SymptomOntology preferredPrefix: SYMP +added: 2015-07-28 --- The symptom ontology was designed around the guiding concept of a symptom being: "A perceived change in function, sensation or appearance reported by a patient indicative of a disease". Understanding the close relationship of Signs and Symptoms, where Signs are the objective observation of an illness, the Symptom Ontology will work to broaden it's scope to capture and document in a more robust manor these two sets of terms. Understanding that at times, the same term may be both a Sign and a Symptom. diff --git a/ontology/tads.md b/ontology/tads.md index 3d4385229..df4c9baea 100644 --- a/ontology/tads.md +++ b/ontology/tads.md @@ -19,6 +19,7 @@ taxon: title: Tick Anatomy Ontology activity_status: inactive repository: https://github.com/VEuPathDB-ontology/TADS +added: 2015-07-28 --- The anatomy of the Tick, Families: Ixodidae, Argassidae diff --git a/ontology/tahe.md b/ontology/tahe.md index 8ff299642..7bc4b3cbe 100644 --- a/ontology/tahe.md +++ b/ontology/tahe.md @@ -11,4 +11,5 @@ taxon: homepage: is_obsolete: true activity_status: inactive +added: 2015-08-21 --- diff --git a/ontology/tahh.md b/ontology/tahh.md index dc3f75ea7..b75f4d6d0 100644 --- a/ontology/tahh.md +++ b/ontology/tahh.md @@ -11,4 +11,5 @@ taxon: homepage: is_obsolete: true activity_status: inactive +added: 2015-08-21 --- diff --git a/ontology/tao.md b/ontology/tao.md index 2ffd42b17..995787851 100644 --- a/ontology/tao.md +++ b/ontology/tao.md @@ -26,6 +26,7 @@ publications: is_obsolete: true replaced_by: uberon activity_status: inactive +added: 2015-07-28 --- Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa. diff --git a/ontology/taxrank.md b/ontology/taxrank.md index 7e2ffa151..ef205f340 100644 --- a/ontology/taxrank.md +++ b/ontology/taxrank.md @@ -32,6 +32,7 @@ license: activity_status: active repository: https://github.com/phenoscape/taxrank preferredPrefix: TAXRANK +added: 2015-07-28 --- A vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Cross references to appearances of each term in each source are provided. Consistent with its intended use as a vocabulary of labels, there is no relation specifying an ordering of the rank terms. diff --git a/ontology/tgma.md b/ontology/tgma.md index 0dbd25bd6..70aebd8b2 100644 --- a/ontology/tgma.md +++ b/ontology/tgma.md @@ -19,6 +19,7 @@ taxon: title: Mosquito gross anatomy ontology activity_status: inactive repository: https://github.com/VEuPathDB-ontology/TGMA +added: 2015-07-28 --- A structured controlled vocabulary of the anatomy of mosquitoes. diff --git a/ontology/to.md b/ontology/to.md index d967417a1..f761c001b 100644 --- a/ontology/to.md +++ b/ontology/to.md @@ -52,6 +52,7 @@ activity_status: active repository: https://github.com/Planteome/plant-trait-ontology preferredPrefix: TO depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG +added: 2015-07-28 --- A controlled vocabulary of describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant. diff --git a/ontology/trans.md b/ontology/trans.md index b27ff3a21..3875d75d5 100644 --- a/ontology/trans.md +++ b/ontology/trans.md @@ -37,6 +37,7 @@ usages: activity_status: active repository: https://github.com/DiseaseOntology/PathogenTransmissionOntology preferredPrefix: TRANS +added: 2015-07-28 --- The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. diff --git a/ontology/tto.md b/ontology/tto.md index ef2cefc8b..9e2087875 100644 --- a/ontology/tto.md +++ b/ontology/tto.md @@ -28,6 +28,7 @@ tracker: https://github.com/phenoscape/teleost-taxonomy-ontology/issues activity_status: active repository: https://github.com/phenoscape/teleost-taxonomy-ontology preferredPrefix: TTO +added: 2015-07-28 --- The Teleost taxonomy ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. Taxonomy ontologies can also be valuable in annotating legacy data, where authors make phenotype or ecological assertions (e.g., host-parasite associations) that refer to groups that are reorganized or no longer recognized. The taxonomy ontology serves as the source of taxa for our project's use for identifying evolutionary changes that match the phenotype of a zebrafish mutant. diff --git a/ontology/txpo.md b/ontology/txpo.md index 49122ae03..7402e8c96 100644 --- a/ontology/txpo.md +++ b/ontology/txpo.md @@ -33,6 +33,7 @@ preferredPrefix: TXPO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/32883995 title: "Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management" +added: 2019-09-26 --- Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. diff --git a/ontology/uberon.md b/ontology/uberon.md index 20d46aa47..194154a4b 100644 --- a/ontology/uberon.md +++ b/ontology/uberon.md @@ -176,6 +176,7 @@ products: - ehdaa2 activity_status: active preferredPrefix: UBERON +added: 2015-07-28 --- Uberon is an integrated cross-species ontology covering anatomical structures in animals. See the Uberon website for more info, or read the Caenorhabditis elegans. diff --git a/ontology/wbls.md b/ontology/wbls.md index 9e61efbed..430174d7d 100644 --- a/ontology/wbls.md +++ b/ontology/wbls.md @@ -42,6 +42,7 @@ usages: title: "WormBase: a modern Model Organism Information Resource" activity_status: active repository: https://github.com/obophenotype/c-elegans-development-ontology +added: 2015-07-28 --- A structured controlled vocabulary of the development of Caenorhabditis elegans. diff --git a/ontology/wbphenotype.md b/ontology/wbphenotype.md index c949c3335..e026fca1d 100644 --- a/ontology/wbphenotype.md +++ b/ontology/wbphenotype.md @@ -50,6 +50,7 @@ usages: title: "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species " activity_status: active repository: https://github.com/obophenotype/c-elegans-phenotype-ontology +added: 2015-07-28 --- A structured controlled vocabulary of Caenorhabditis elegans phenotypes diff --git a/ontology/xao.md b/ontology/xao.md index 16e289cae..6b3e9b4ba 100644 --- a/ontology/xao.md +++ b/ontology/xao.md @@ -41,6 +41,7 @@ license: activity_status: active repository: https://github.com/xenopus-anatomy/xao preferredPrefix: XAO +added: 2015-07-28 --- The Xenopus Anatomy Ontology represents and standardizes the anatomy and development of the African frogs Xenopus laevis and tropicalis. It supports the annotation of gene expression data in Xenbase and is designed to facilitate cross-taxa comparisons. diff --git a/ontology/xco.md b/ontology/xco.md index 814fd8c5b..2dd998ef7 100644 --- a/ontology/xco.md +++ b/ontology/xco.md @@ -36,6 +36,7 @@ activity_status: active repository: https://github.com/rat-genome-database/XCO-experimental-condition-ontology preferredPrefix: XCO depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif +added: 2015-07-29 --- Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. diff --git a/ontology/xlmod.md b/ontology/xlmod.md index c72791888..cb6feed5c 100644 --- a/ontology/xlmod.md +++ b/ontology/xlmod.md @@ -25,6 +25,7 @@ license: activity_status: active repository: https://github.com/HUPO-PSI/xlmod-CV preferredPrefix: XLMOD +added: 2019-04-18 --- A structured controlled vocabulary for cross-linker reagents used in cross-linking mass spectrometry experiments. Developed by the HUPO Proteomics Standards Initiative (PSI). diff --git a/ontology/xpo.md b/ontology/xpo.md index ab28185df..da43f84f4 100644 --- a/ontology/xpo.md +++ b/ontology/xpo.md @@ -42,6 +42,7 @@ license: activity_status: active repository: https://github.com/obophenotype/xenopus-phenotype-ontology preferredPrefix: XPO +added: 2018-11-30 --- The Xenopus Phenotype Ontology represents and standardizes phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. It supports the annotation of phenotypes in Xenbase and is designed to integrate Xenopus data with genotype, phenotype, and disease data across species. diff --git a/ontology/ypo.md b/ontology/ypo.md index bad83c9ca..8ca20a3e7 100644 --- a/ontology/ypo.md +++ b/ontology/ypo.md @@ -13,6 +13,7 @@ homepage: http://www.yeastgenome.org/ is_obsolete: true replaced_by: apo activity_status: inactive +added: 2015-08-21 --- A structured controlled vocabulary for the phenotypes of budding yeast. diff --git a/ontology/zea.md b/ontology/zea.md index a509d5fbf..ee1e55d9c 100644 --- a/ontology/zea.md +++ b/ontology/zea.md @@ -12,6 +12,7 @@ taxon: homepage: http://www.maizemap.org/ is_obsolete: true activity_status: inactive +added: 2015-08-21 --- A structured controlled vocabulary for the anatomy of Zea mays. diff --git a/ontology/zeco.md b/ontology/zeco.md index e8a30286b..7cc03be98 100644 --- a/ontology/zeco.md +++ b/ontology/zeco.md @@ -27,6 +27,7 @@ tracker: https://github.com/ybradford/zebrafish-experimental-conditions-ontology activity_status: active repository: https://github.com/ybradford/zebrafish-experimental-conditions-ontology preferredPrefix: ZECO +added: 2016-07-28 --- This ontology is designed to represent the experimental conditions diff --git a/ontology/zfa.md b/ontology/zfa.md index 668382f97..bb82bdf52 100644 --- a/ontology/zfa.md +++ b/ontology/zfa.md @@ -40,6 +40,7 @@ usages: activity_status: active repository: https://github.com/cerivs/zebrafish-anatomical-ontology preferredPrefix: ZFA +added: 2015-07-28 --- A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). diff --git a/ontology/zfs.md b/ontology/zfs.md index 5b6f2af4b..6f092ae16 100644 --- a/ontology/zfs.md +++ b/ontology/zfs.md @@ -29,6 +29,7 @@ build: activity_status: active repository: https://github.com/cerivs/zebrafish-anatomical-ontology preferredPrefix: ZFS +added: 2015-07-29 --- An ontology of developmental stages of the Zebrafish (Danio rerio). Note that ZFA includes the leaf nodes of this ontology diff --git a/ontology/zp.md b/ontology/zp.md index cad5c93b5..9b59ec755 100644 --- a/ontology/zp.md +++ b/ontology/zp.md @@ -45,4 +45,5 @@ usages: activity_status: active repository: https://github.com/obophenotype/zebrafish-phenotype-ontology preferredPrefix: ZP +added: 2019-01-02 --- diff --git a/registry/ontologies.yml b/registry/ontologies.yml index ed20c02e6..605ddfaa8 100644 --- a/registry/ontologies.yml +++ b/registry/ontologies.yml @@ -1,5 +1,6 @@ ontologies: - activity_status: active + added: 2015-07-28 browsers: - label: BioPortal title: BioPortal Browser @@ -42,6 +43,7 @@ ontologies: type: owl_import user: http://obofoundry.org - activity_status: active + added: 2015-07-28 browsers: - label: CHEBI title: EBI CHEBI Browser @@ -106,6 +108,7 @@ ontologies: url: http://zfin.org/action/expression/experiment?id=ZDB-EXP-190627-10 user: http://zfin.org - activity_status: active + added: 2015-07-28 browsers: - label: DO title: DO Browser @@ -182,6 +185,7 @@ ontologies: url: https://www.iedb.org user: https://www.iedb.org - activity_status: active + added: 2015-07-28 browsers: - label: AmiGO title: Gene Ontology AmiGO 2 Browser @@ -345,6 +349,7 @@ ontologies: type: mapping user: https://www.rhea-db.org - activity_status: active + added: 2015-07-28 browsers: - label: BioPortal title: BioPortal Browser @@ -441,6 +446,7 @@ ontologies: url: https://neuinfo.org/data/search?q=organism&l=organism#all user: http://www.neuinfo.org - activity_status: active + added: 2015-07-28 browsers: - label: BioPortal title: BioPortal Ontology Browser @@ -502,6 +508,7 @@ ontologies: type: annotation user: https://hpo.jax.org/app/ - activity_status: active + added: 2015-07-28 browsers: - label: Planteome title: Planteome browser @@ -582,6 +589,7 @@ ontologies: url: http://archive.gramene.org/db/ontology/search?id=PO:0025034 user: http://gramene.org/ - activity_status: active + added: 2015-07-28 browsers: - label: BioPortal title: BioPortal Browser @@ -648,6 +656,7 @@ ontologies: url: http://purl.obolibrary.org/obo/CL_0001201 user: http://www.obofoundry.org/ontology/cl.html - activity_status: active + added: 2015-07-28 build: infallible: 0 method: obo2owl @@ -696,6 +705,7 @@ ontologies: url: http://www.xenbase.org/anatomy/showanatomy.do?method=displayAnatomySummary&anatomyId=463 user: http://www.xenbase.org - activity_status: active + added: 2015-07-28 build: infallible: 1 method: obo2owl @@ -744,6 +754,7 @@ ontologies: url: http://zfin.org/ZFA:0000029 user: http://zfin.org - activity_status: active + added: 2016-06-04 build: checkout: git clone https://github.com/AgriculturalSemantics/agro.git path: . @@ -805,6 +816,7 @@ ontologies: and datasets for use in quantitative analyses. user: https://gardian.bigdata.cgiar.org/ - activity_status: active + added: 2021-05-06 build: checkout: git clone https://github.com/insect-morphology/aism path: . @@ -846,6 +858,7 @@ ontologies: title: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) tracker: https://github.com/insect-morphology/aism/issues - activity_status: active + added: 2020-04-21 build: checkout: git clone https://github.com/EBISPOT/amphx_ontology.git path: . @@ -878,6 +891,7 @@ ontologies: title: The Amphioxus Development and Anatomy Ontology tracker: https://github.com/EBISPOT/amphx_ontology/issues - activity_status: active + added: 2015-07-28 build: method: obo2owl source_url: https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo @@ -913,6 +927,7 @@ ontologies: title: Ascomycete phenotype ontology tracker: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues - activity_status: active + added: 2019-04-04 contact: email: hoganwr@ufl.edu github: hoganwr @@ -941,6 +956,7 @@ ontologies: title: Apollo Structured Vocabulary tracker: https://github.com/ApolloDev/apollo-sv/issues - activity_status: active + added: 2017-11-15 contact: email: mcarthua@mcmaster.ca github: agmcarthur @@ -969,6 +985,7 @@ ontologies: title: Antibiotic Resistance Ontology tracker: https://github.com/arpcard/aro/issues - activity_status: active + added: 2015-07-29 contact: email: rlwalls2008@gmail.com github: ramonawalls @@ -997,6 +1014,7 @@ ontologies: title: Biological Collections Ontology tracker: https://github.com/BiodiversityOntologies/bco/issues - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/biological-spatial-ontology.git infallible: 1 @@ -1033,6 +1051,7 @@ ontologies: title: Biological Spatial Ontology tracker: https://github.com/obophenotype/biological-spatial-ontology/issues - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/BRENDA-Enzymes/BTO.git path: . @@ -1070,6 +1089,7 @@ ontologies: title: BRENDA tissue / enzyme source tracker: https://github.com/BRENDA-Enzymes/BTO/issues - activity_status: active + added: 2015-07-28 build: method: obo2owl notes: moving to owl soon @@ -1098,6 +1118,7 @@ ontologies: title: Common Anatomy Reference Ontology tracker: https://github.com/obophenotype/caro/issues - activity_status: active + added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/cdao.owl @@ -1128,6 +1149,7 @@ ontologies: title: Comparative Data Analysis Ontology tracker: https://github.com/evoinfo/cdao/issues - activity_status: active + added: 2021-02-08 build: checkout: git clone https://github.com/Southern-Cross-Plant-Science/cdno.git path: . @@ -1170,6 +1192,7 @@ ontologies: title: Compositional Dietary Nutrition Ontology tracker: https://github.com/Southern-Cross-Plant-Science/cdno/issues - activity_status: active + added: 2015-07-28 build: method: owl2obo source_url: https://raw.githubusercontent.com/semanticchemistry/semanticchemistry/master/ontology/cheminf.owl @@ -1202,6 +1225,7 @@ ontologies: title: Chemical Information Ontology tracker: https://github.com/semanticchemistry/semanticchemistry/issues - activity_status: active + added: 2019-09-26 build: checkout: git clone https://github.com/obophenotype/chiro.git path: . @@ -1252,6 +1276,7 @@ ontologies: title: CHEBI Integrated Role Ontology tracker: https://github.com/obophenotype/chiro/issues - activity_status: active + added: 2015-07-28 contact: email: batchelorc@rsc.org github: batchelorc @@ -1276,6 +1301,7 @@ ontologies: title: Chemical Methods Ontology tracker: https://github.com/rsc-ontologies/rsc-cmo/issues - activity_status: active + added: 2020-03-12 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -1303,6 +1329,7 @@ ontologies: title: Coronavirus Infectious Disease Ontology tracker: https://github.com/cido-ontology/cido/issues - activity_status: active + added: 2016-05-17 contact: email: frederic.bastian@unil.ch github: fbastian @@ -1328,6 +1355,7 @@ ontologies: title: Confidence Information Ontology tracker: https://github.com/BgeeDB/confidence-information-ontology - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/cell-ontology.git email_cc: cl_edit@googlegroups.com @@ -1483,6 +1511,7 @@ ontologies: type: annotation user: http://fantom5-collaboration.gsc.riken.jp/ - activity_status: active + added: 2020-10-08 build: checkout: git clone https://github.com/luis-gonzalez-m/Collembola.git path: . @@ -1515,6 +1544,7 @@ ontologies: title: Collembola Anatomy Ontology tracker: https://github.com/luis-gonzalez-m/Collembola/issues - activity_status: active + added: 2015-07-28 contact: email: siiraa@umich.edu github: siiraa @@ -1547,6 +1577,7 @@ ontologies: title: Cell Line Ontology tracker: https://github.com/CLO-Ontology/CLO/issues - activity_status: active + added: 2020-05-06 build: checkout: git clone https://github.com/EBISPOT/clyh_ontology.git path: . @@ -1581,6 +1612,7 @@ ontologies: title: Clytia hemisphaerica Development and Anatomy Ontology tracker: https://github.com/EBISPOT/clyh_ontology/issues - activity_status: active + added: 2015-07-28 browsers: - label: RGD title: RGD Ontology Browser @@ -1624,6 +1656,7 @@ ontologies: title: Clinical measurement ontology tracker: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues - activity_status: active + added: 2020-04-15 contact: email: bpeters@lji.org github: bpeters42 @@ -1664,6 +1697,7 @@ ontologies: title: Core Ontology for Biology and Biomedicine tracker: https://github.com/OBOFoundry/COB/issues - activity_status: active + added: 2021-12-14 contact: email: entiminae@gmail.com github: JCGiron @@ -1702,6 +1736,7 @@ ontologies: title: Coleoptera Anatomy Ontology (COLAO) tracker: https://github.com/insect-morphology/colao/issues - activity_status: active + added: 2017-07-20 build: checkout: git clone https://github.com/data2health/contributor-role-ontology.git path: src/ontology @@ -1735,6 +1770,7 @@ ontologies: title: Contributor Role Ontology tracker: https://github.com/data2health/contributor-role-ontology/issues - activity_status: active + added: 2015-07-29 build: checkout: git clone https://github.com/obophenotype/ctenophore-ontology.git method: vcs @@ -1772,6 +1808,7 @@ ontologies: title: Ctenophore Ontology tracker: https://github.com/obophenotype/ctenophore-ontology/issues - activity_status: active + added: 2020-07-08 contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil @@ -1799,6 +1836,7 @@ ontologies: title: 'CTO: Core Ontology of Clinical Trials' tracker: https://github.com/ClinicalTrialOntology/CTO/issues - activity_status: active + added: 2015-07-28 build: method: owl2obo publications: @@ -1828,6 +1866,7 @@ ontologies: title: Cardiovascular Disease Ontology tracker: https://github.com/OpenLHS/CVDO/issues - activity_status: active + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -1866,6 +1905,7 @@ ontologies: tracker: https://github.com/dictyBase/migration-data/issues twitter: dictybase - activity_status: active + added: 2015-08-21 build: checkout: git clone https://github.com/obophenotype/dicty-phenotype-ontology.git path: . @@ -1903,6 +1943,7 @@ ontologies: tracker: https://github.com/obophenotype/dicty-phenotype-ontology/issues twitter: dictybase - activity_status: active + added: 2015-08-21 contact: email: mbrochhausen@gmail.com github: mbrochhausen @@ -1927,6 +1968,7 @@ ontologies: title: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology tracker: https://github.com/DIDEO/DIDEO/issues - activity_status: active + added: 2021-11-05 browsers: - label: DO title: DO Browser @@ -1970,6 +2012,7 @@ ontologies: url: https://www.disease-ontology.org/?id=DOID:0050665 user: https://www.disease-ontology.org - activity_status: active + added: 2015-07-28 browsers: - label: FB title: FlyBase Browser @@ -2017,6 +2060,7 @@ ontologies: url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0002030 user: http://flybase.org - activity_status: active + added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/dron.owl @@ -2049,6 +2093,7 @@ ontologies: title: The Drug Ontology tracker: https://github.com/ufbmi/dron/issues - activity_status: active + added: 2017-01-24 build: checkout: git clone https://github.com/EBISPOT/duo.git path: . @@ -2082,6 +2127,7 @@ ontologies: title: Data Use Ontology tracker: https://github.com/EBISPOT/DUO/issues - activity_status: active + added: 2020-05-06 build: checkout: git clone https://github.com/echinoderm-ontology/ecao_ontology.git path: . @@ -2116,6 +2162,7 @@ ontologies: title: The Echinoderm Anatomy and Development Ontology tracker: https://github.com/echinoderm-ontology/ecao_ontology/issues - activity_status: active + added: 2015-07-28 build: infallible: 1 method: obo2owl @@ -2180,6 +2227,7 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active + added: 2017-08-17 build: checkout: git clone https://github.com/EcologicalSemantics/ecocore.git path: . @@ -2227,6 +2275,7 @@ ontologies: title: An ontology of core ecological entities tracker: https://github.com/EcologicalSemantics/ecocore/issues - activity_status: active + added: 2019-09-24 build: checkout: git clone https://github.com/EnvironmentOntology/environmental-exposure-ontology.git path: . @@ -2302,6 +2351,7 @@ ontologies: title: Environmental conditions, treatments and exposures ontology tracker: https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues - activity_status: active + added: 2015-08-21 build: method: obo2owl notes: new url soon @@ -2339,6 +2389,7 @@ ontologies: seeAlso: https://www.biosharing.org/biodbcore-000659 user: http://www.informatics.jax.org/expression.shtml - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/EnvironmentOntology/envo.git email_cc: cjmungall@lbl.gov @@ -2441,6 +2492,7 @@ ontologies: url: https://www.planetmicrobe.org/project/#/samples/200 user: https://www.planetmicrobe.org/project/ - activity_status: active + added: 2021-12-16 contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil @@ -2472,6 +2524,7 @@ ontologies: title: Epilepsy Ontology tracker: https://github.com/SCAI-BIO/EpilepsyOntology/issues - activity_status: active + added: 2018-01-02 contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 @@ -2515,6 +2568,7 @@ ontologies: type: annotation and query user: https://microbiomedb.org - activity_status: active + added: 2015-07-28 contact: email: annethessen@gmail.com github: diatomsRcool @@ -2541,6 +2595,7 @@ ontologies: title: Exposure ontology tracker: https://github.com/CTDbase/exposure-ontology/issues - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/fungal-anatomy-ontology.git infallible: 1 @@ -2574,6 +2629,7 @@ ontologies: title: Fungal gross anatomy tracker: https://github.com/obophenotype/fungal-anatomy-ontology/issues - activity_status: active + added: 2015-07-28 build: method: obo2owl source_url: https://raw.githubusercontent.com/dosumis/fbbi/master/src/ontology/fbbi.obo @@ -2603,6 +2659,7 @@ ontologies: title: Biological Imaging Methods Ontology tracker: https://github.com/CRBS/Biological_Imaging_Methods_Ontology/issues - activity_status: active + added: 2015-07-28 browsers: - label: FB title: FlyBase Browser @@ -2676,6 +2733,7 @@ ontologies: url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBbt:00005106 user: http://flybase.org - activity_status: active + added: 2015-08-06 browsers: - label: FB title: FlyBase Browser @@ -2719,6 +2777,7 @@ ontologies: url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0000391 user: http://flybase.org - activity_status: active + added: 2015-07-29 browsers: - label: FB title: FlyBase Browser @@ -2763,6 +2822,7 @@ ontologies: title: Drosophila development tracker: http://purl.obolibrary.org/obo/fbdv/tracker - activity_status: active + added: 2020-07-29 contact: email: georgeta.bordea@u-bordeaux.fr github: getbordea @@ -2786,6 +2846,7 @@ ontologies: title: Food Interactions with Drugs Evidence Ontology tracker: https://github.com/getbordea/fideo/issues - activity_status: active + added: 2015-12-16 build: method: owl2obo source_url: https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl @@ -2819,6 +2880,7 @@ ontologies: title: Flora Phenotype Ontology tracker: https://github.com/flora-phenotype-ontology/flopoontology/issues - activity_status: active + added: 2019-12-04 contact: email: polcaes@gmail.com github: pcastellanoescuder @@ -2855,6 +2917,7 @@ ontologies: title: Food-Biomarker Ontology tracker: https://github.com/pcastellanoescuder/FoodBiomarkerOntology/issues - activity_status: active + added: 2016-07-25 contact: email: damion_dooley@sfu.ca github: ddooley @@ -2905,6 +2968,7 @@ ontologies: title: Food Ontology tracker: https://github.com/FoodOntology/foodon/issues/ - activity_status: active + added: 2020-05-06 build: checkout: git clone https://github.com/futres/fovt.git path: . @@ -2960,6 +3024,7 @@ ontologies: title: FuTRES Ontology of Vertebrate Traits tracker: https://github.com/futres/fovt/issues - activity_status: active + added: 2015-07-29 build: infallible: 1 method: obo2owl @@ -3002,6 +3067,7 @@ ontologies: url: https://www.pombase.org/term/FYPO:0000059 user: https://www.pombase.org - activity_status: active + added: 2020-08-11 contact: email: rbca.jackson@gmail.com github: beckyjackson @@ -3031,6 +3097,7 @@ ontologies: IHCC cohort browser user: https://ihccglobal.org/ - activity_status: active + added: 2016-07-25 contact: email: damion_dooley@sfu.ca github: ddooley @@ -3063,6 +3130,7 @@ ontologies: title: Genomic Epidemiology Ontology tracker: https://github.com/GenEpiO/genepio/issues/ - activity_status: active + added: 2017-01-05 build: checkout: git clone https://github.com/monarch-initiative/GENO-ontology.git path: src/ontology @@ -3094,6 +3162,7 @@ ontologies: title: Genotype Ontology tracker: https://github.com/monarch-initiative/GENO-ontology/issues - activity_status: active + added: 2015-07-28 contact: email: hoganwr@gmail.com github: hoganwr @@ -3117,6 +3186,7 @@ ontologies: title: Geographical Entity Ontology tracker: https://github.com/ufbmi/geographical-entity-ontology/issues - activity_status: active + added: 2019-08-15 browsers: - label: Structure Browser title: GNOme Glycan Structure Browser @@ -3182,6 +3252,7 @@ ontologies: url: http://purl.obolibrary.org/obo/CHEBI_167503 user: https://www.ebi.ac.uk/chebi/init.do - activity_status: active + added: 2018-07-13 contact: email: danielle.welter@uni.lu github: daniwelter @@ -3246,6 +3317,7 @@ ontologies: url: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false user: http://foodon.org - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/hymao/hao.git system: git @@ -3283,6 +3355,7 @@ ontologies: title: Hymenoptera Anatomy Ontology tracker: https://github.com/hymao/hao/issues - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/BgeeDB/homology-ontology.git method: vcs @@ -3312,6 +3385,7 @@ ontologies: title: Homology Ontology tracker: https://github.com/BgeeDB/homology-ontology/issues - activity_status: active + added: 2015-08-21 build: infallible: 1 method: obo2owl @@ -3342,6 +3416,7 @@ ontologies: title: Human Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active + added: 2020-11-28 contact: email: fernanda.dorea@sva.se github: nandadorea @@ -3376,6 +3451,7 @@ ontologies: title: Health Surveillance Ontology tracker: https://github.com/SVA-SE/HSO/issues/ - activity_status: active + added: 2019-06-05 contact: email: aellenhicks@gmail.com github: aellenhicks @@ -3401,6 +3477,7 @@ ontologies: title: Hypertension Ontology tracker: https://github.com/aellenhicks/htn_owl/issues - activity_status: active + added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/iao.owl @@ -3447,6 +3524,7 @@ ontologies: type: owl_import user: http://obofoundry.org - activity_status: active + added: 2019-09-02 contact: email: liumeng94@sjtu.edu.cn github: Lemon-Liu @@ -3471,6 +3549,7 @@ ontologies: title: Integrative and Conjugative Element Ontology tracker: https://github.com/ontoice/ICEO/issues - activity_status: active + added: 2015-08-21 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -3500,6 +3579,7 @@ ontologies: that has over 20 institutes involved. user: http://kpmp.org - activity_status: active + added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/ido.owl @@ -3532,6 +3612,7 @@ ontologies: title: Infectious Disease Ontology tracker: https://github.com/infectious-disease-ontology/infectious-disease-ontology/issues - activity_status: active + added: 2018-03-10 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -3555,6 +3636,7 @@ ontologies: title: Interaction Network Ontology tracker: https://github.com/INO-ontology/ino/issues - activity_status: active + added: 2019-08-29 contact: email: paul.fabry@usherbrooke.ca github: pfabry @@ -3600,6 +3682,7 @@ ontologies: type: database architecture user: https://griis.ca/ - activity_status: active + added: 2021-12-14 contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m @@ -3638,6 +3721,7 @@ ontologies: title: Lepidoptera Anatomy Ontology tracker: https://github.com/insect-morphology/lepao/issues - activity_status: active + added: 2015-07-29 build: infallible: 1 insert_ontology_id: true @@ -3677,6 +3761,7 @@ ontologies: seeAlso: https://www.biosharing.org/biodbcore-000659 user: http://www.informatics.jax.org/expression.shtml - activity_status: active + added: 2020-02-12 build: checkout: git clone https://github.com/monarch-initiative/MAxO.git path: . @@ -3733,6 +3818,7 @@ ontologies: title: Medical Action Ontology tracker: https://github.com/monarch-initiative/MAxO/issues - activity_status: active + added: 2019-02-15 build: checkout: git clone https://github.com/microbial-conditions-ontology/microbial-conditions-ontology.git path: . @@ -3782,6 +3868,7 @@ ontologies: title: Microbial Conditions Ontology tracker: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology/issues - activity_status: active + added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/mf.owl @@ -3809,6 +3896,7 @@ ontologies: title: Mental Functioning Ontology tracker: https://github.com/jannahastings/mental-functioning-ontology/issues - activity_status: active + added: 2015-08-11 contact: email: druzinsk@uic.edu github: RDruzinsky @@ -3839,6 +3927,7 @@ ontologies: title: Mammalian Feeding Muscle Ontology tracker: https://github.com/RDruzinsky/feedontology/issues - activity_status: active + added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/mfoem.owl @@ -3866,6 +3955,7 @@ ontologies: title: Emotion Ontology tracker: https://github.com/jannahastings/emotion-ontology/issues - activity_status: active + added: 2015-08-21 contact: email: janna.hastings@gmail.com github: jannahastings @@ -3890,6 +3980,7 @@ ontologies: title: Mental Disease Ontology tracker: https://github.com/jannahastings/mental-functioning-ontology/issues - activity_status: active + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -3921,6 +4012,7 @@ ontologies: title: Molecular Interactions Controlled Vocabulary tracker: https://github.com/HUPO-PSI/psi-mi-CV/issues - activity_status: active + added: 2015-07-28 contact: email: hilmar.lapp@duke.edu github: hlapp @@ -3946,6 +4038,7 @@ ontologies: title: MIAPA Ontology tracker: https://github.com/evoinfo/miapa/issues - activity_status: active + added: 2015-10-20 contact: email: carrine.blank@umontana.edu github: carrineblank @@ -3969,6 +4062,7 @@ ontologies: title: Ontology of Prokaryotic Phenotypic and Metabolic Characters tracker: https://github.com/carrineblank/MicrO/issues - activity_status: active + added: 2015-07-28 browsers: - label: RGD title: RGD Ontology Browser @@ -4011,6 +4105,7 @@ ontologies: title: Measurement method ontology tracker: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues - activity_status: active + added: 2015-08-21 build: method: obo2owl source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/mmusdv/mmusdv.obo @@ -4040,6 +4135,7 @@ ontologies: title: Mouse Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -4080,6 +4176,7 @@ ontologies: title: Protein modification tracker: https://github.com/HUPO-PSI/psi-mod-CV/issues - activity_status: active + added: 2016-07-12 browsers: - label: Monarch title: Monarch Initiative Disease Browser @@ -4182,6 +4279,7 @@ ontologies: type: annotation user: https://www.humancellatlas.org/ - activity_status: active + added: 2015-08-17 build: method: owl2obo source_url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.owl @@ -4210,6 +4308,7 @@ ontologies: title: Molecular Process Ontology tracker: https://github.com/rsc-ontologies/rxno/issues - activity_status: active + added: 2015-07-28 browsers: - label: MGI title: MGI MP Browser @@ -4302,6 +4401,7 @@ ontologies: url: https://www.mousephenotype.org/data/phenotypes/MP:0013522 user: https://www.mousephenotype.org/ - activity_status: active + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -4333,6 +4433,7 @@ ontologies: title: Mouse pathology ontology tracker: https://github.com/PaulNSchofield/mpath/issues - activity_status: active + added: 2017-11-02 contact: email: mbrochhausen@uams.edu github: mbrochhausen @@ -4357,6 +4458,7 @@ ontologies: title: Minimum PDDI Information Ontology tracker: https://github.com/MPIO-Developers/MPIO/issues - activity_status: active + added: 2015-09-17 contact: email: bpeters@lji.org github: bpeters42 @@ -4393,6 +4495,7 @@ ontologies: type: annotation user: https://www.iedb.org/ - activity_status: active + added: 2015-07-28 build: method: obo2owl source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo @@ -4435,6 +4538,7 @@ ontologies: title: Mass spectrometry ontology tracker: https://github.com/HUPO-PSI/psi-ms-CV/issues - activity_status: active + added: 2015-07-28 browsers: - label: BioPortal title: BioPortal Ontology Browser @@ -4470,6 +4574,7 @@ ontologies: title: Neuro Behavior Ontology tracker: https://github.com/obo-behavior/behavior-ontology/issues - activity_status: active + added: 2015-07-28 browsers: - label: NCBI title: NCBI Taxonomy Browser @@ -4524,6 +4629,7 @@ ontologies: tracker: https://github.com/obophenotype/ncbitaxon/issues wasDerivedFrom: ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat - activity_status: active + added: 2016-04-01 contact: email: haendel@ohsu.edu github: mellybelly @@ -4572,6 +4678,7 @@ ontologies: title: NCI Thesaurus OBO Edition tracker: https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues - activity_status: active + added: 2015-11-18 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl @@ -4600,6 +4707,7 @@ ontologies: title: Non-Coding RNA Ontology tracker: https://github.com/OmniSearch/ncro/issues - activity_status: active + added: 2019-01-11 build: checkout: git clone https://github.com/SpeciesFileGroup/nomen.git system: git @@ -4645,6 +4753,7 @@ ontologies: type: application user: https://taxonworks.org - activity_status: active + added: 2015-07-28 build: method: owl2obo source_url: https://raw.githubusercontent.com/OAE-ontology/OAE/master/src/oae_merged.owl @@ -4673,6 +4782,7 @@ ontologies: title: Ontology of Adverse Events tracker: https://github.com/OAE-ontology/OAE/issues - activity_status: active + added: 2017-02-10 contact: email: mjyoder@illinois.edu github: mjy @@ -4696,6 +4806,7 @@ ontologies: title: Ontology of Arthropod Circulatory Systems tracker: https://github.com/aszool/oarcs/issues - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/bio-attribute-ontology.git method: vcs @@ -4733,6 +4844,7 @@ ontologies: title: Ontology of Biological Attributes tracker: https://github.com/obophenotype/bio-attribute-ontology/issues - activity_status: active + added: 2015-07-31 contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 @@ -4759,6 +4871,7 @@ ontologies: title: Ontology of Biological and Clinical Statistics tracker: https://github.com/obcs/obcs/issues - activity_status: active + added: 2015-08-17 contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 @@ -4803,6 +4916,7 @@ ontologies: to biospecimen collection, processing, and storage, also known as biobanking. user: https://biospecimens.cancer.gov/resources/vocabularies.asp - activity_status: active + added: 2015-07-29 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -4826,6 +4940,7 @@ ontologies: title: The Ontology of Genes and Genomes tracker: https://bitbucket.org/hegroup/ogg/issues/ - activity_status: active + added: 2015-07-29 contact: email: baeverma@jcvi.org github: BAevermann @@ -4856,6 +4971,7 @@ ontologies: title: Ontology for General Medical Science tracker: https://github.com/OGMS/ogms/issues - activity_status: active + added: 2015-07-28 contact: email: linikujp@gmail.com github: linikujp @@ -4880,6 +4996,7 @@ ontologies: title: Ontology of Genetic Susceptibility Factor tracker: https://github.com/linikujp/OGSF/issues - activity_status: active + added: 2016-12-01 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/ohd.owl @@ -4910,6 +5027,7 @@ ontologies: title: Oral Health and Disease Ontology tracker: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/issues - activity_status: active + added: 2017-04-21 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -4937,6 +5055,7 @@ ontologies: title: Ontology of Host-Microbiome Interactions tracker: https://github.com/ohmi-ontology/ohmi/issues - activity_status: active + added: 2019-07-22 contact: email: edong@umich.edu github: e4ong1031 @@ -4964,6 +5083,7 @@ ontologies: title: Ontology of Host Pathogen Interactions tracker: https://github.com/OHPI/ohpi/issues - activity_status: active + added: 2015-08-21 build: method: obo2owl source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/olatdv/olatdv.obo @@ -4993,6 +5113,7 @@ ontologies: title: Medaka Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active + added: 2015-07-29 contact: email: huang@southalabama.edu github: Huang-OMIT @@ -5019,6 +5140,7 @@ ontologies: title: Ontology for MIRNA Target tracker: https://github.com/OmniSearch/omit/issues - activity_status: active + added: 2020-05-02 contact: email: cjmungall@lbl.gov github: cmungall @@ -5050,6 +5172,7 @@ ontologies: type: owl_import user: http://obofoundry.org - activity_status: active + added: 2015-08-21 build: method: obo2owl source_url: https://raw.githubusercontent.com/microbialphenotypes/OMP-ontology-files/master/omp.obo @@ -5078,6 +5201,7 @@ ontologies: title: Ontology of Microbial Phenotypes tracker: https://github.com/microbialphenotypes/OMP-ontology/issues - activity_status: active + added: 2015-07-28 build: method: owl2obo source_url: https://github.com/ufbmi/OMRSE @@ -5114,6 +5238,7 @@ ontologies: title: Ontology of Medically Related Social Entities tracker: https://github.com/ufbmi/OMRSE/issues - activity_status: active + added: 2020-11-17 contact: email: chenyangnutrition@gmail.com github: cyang0128 @@ -5148,6 +5273,7 @@ ontologies: title: Ontology for Nutritional Epidemiology tracker: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies/issues - activity_status: active + added: 2020-05-28 contact: email: francesco.vitali@ibba.cnr.it github: FrancescoVit @@ -5190,6 +5316,7 @@ ontologies: title: Ontology for Nutritional Studies tracker: https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues - activity_status: active + added: 2021-12-01 contact: email: fortuna@ebd.csic.es github: miguelfortuna @@ -5227,6 +5354,7 @@ ontologies: title: 'OntoAvida: ontology for Avida digital evolution platform' tracker: https://gitlab.com/fortunalab/ontoavida/-/issues - activity_status: active + added: 2016-11-22 browsers: - label: BioPortal title: BioPortal Browser @@ -5261,6 +5389,7 @@ ontologies: title: Obstetric and Neonatal Ontology tracker: https://github.com/ontoneo-project/Ontoneo/issues - activity_status: active + added: 2016-04-04 contact: email: mbrochhausen@gmail.com github: mbrochhausen @@ -5285,6 +5414,7 @@ ontologies: title: Ontology of Organizational Structures of Trauma centers and Trauma systems tracker: https://github.com/OOSTT/OOSTT/issues - activity_status: active + added: 2015-07-28 contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 @@ -5320,6 +5450,7 @@ ontologies: type: annotation and query user: https://www.genedb.org - activity_status: active + added: 2018-08-30 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -5346,6 +5477,7 @@ ontologies: title: Ontology of Precision Medicine and Investigation tracker: https://github.com/OPMI/opmi/issues - activity_status: active + added: 2019-06-20 contact: email: safisher@upenn.edu github: safisher @@ -5370,6 +5502,7 @@ ontologies: title: Ontology of RNA Sequencing tracker: https://github.com/safisher/ornaseq/issues - activity_status: active + added: 2015-07-28 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -5393,6 +5526,7 @@ ontologies: title: Ontology of Vaccine Adverse Events tracker: https://github.com/OVAE-Ontology/ovae/issues - activity_status: active + added: 2022-01-25 contact: email: davidos@ebi.ac.uk github: dosumis @@ -5453,6 +5587,7 @@ ontologies: title: Provisional Cell Ontology tracker: https://github.com/obophenotype/provisional_cell_ontology/issues - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/PopulationAndCommunityOntology/pco.git path: . @@ -5496,6 +5631,7 @@ ontologies: title: Population and Community Ontology tracker: https://github.com/PopulationAndCommunityOntology/pco/issues - activity_status: active + added: 2016-11-11 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/pdro.owl @@ -5528,6 +5664,7 @@ ontologies: title: The Prescription of Drugs Ontology tracker: https://github.com/OpenLHS/PDRO/issues - activity_status: active + added: 2015-08-21 build: method: obo2owl source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/pdumdv/pdumdv.obo @@ -5557,6 +5694,7 @@ ontologies: title: Platynereis Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active + added: 2017-06-05 contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp @@ -5591,6 +5729,7 @@ ontologies: title: Plant Experimental Conditions Ontology tracker: https://github.com/Planteome/plant-experimental-conditions-ontology/issues - activity_status: active + added: 2018-08-15 build: checkout: git clone https://github.com/PHI-base/phipo.git path: . @@ -5630,6 +5769,7 @@ ontologies: title: Pathogen Host Interaction Phenotype Ontology tracker: https://github.com/PHI-base/phipo/issues - activity_status: active + added: 2017-02-07 build: checkout: git clone https://github.com/obophenotype/planaria-ontology.git path: . @@ -5678,6 +5818,7 @@ ontologies: url: https://planosphere.stowers.org/ontology/PLANA_0000034 user: https://planosphere.stowers.org/ - activity_status: active + added: 2018-11-19 build: checkout: git clone https://github.com/obophenotype/planarian-phenotype-ontology.git path: . @@ -5716,6 +5857,7 @@ ontologies: title: Planarian Phenotype Ontology tracker: https://github.com/obophenotype/planarian-phenotype-ontology/issues - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/porifera-ontology.git infallible: 1 @@ -5760,6 +5902,7 @@ ontologies: title: Porifera Ontology tracker: https://github.com/obophenotype/porifera-ontology/issues - activity_status: active + added: 2016-12-30 contact: email: rlwalls2008@gmail.com github: ramonawalls @@ -5790,6 +5933,7 @@ ontologies: title: Plant Phenology Ontology tracker: https://github.com/PlantPhenoOntology/PPO/issues - activity_status: active + added: 2019-04-04 build: checkout: https://github.com/Display-Lab/psdo.git path: . @@ -5824,6 +5968,7 @@ ontologies: title: Performance Summary Display Ontology tracker: https://github.com/Display-Lab/psdo/issues - activity_status: active + added: 2020-05-14 build: checkout: git clone https://github.com/Planteome/plant-stress-ontology.git path: . @@ -5866,6 +6011,7 @@ ontologies: title: Plant Stress Ontology tracker: https://github.com/Planteome/plant-stress-ontology/issues - activity_status: active + added: 2015-07-28 browsers: - label: RGD title: RGD Ontology Browser @@ -5907,6 +6053,7 @@ ontologies: title: Pathway ontology tracker: https://github.com/rat-genome-database/PW-Pathway-Ontology/issues - activity_status: active + added: 2021-01-28 build: checkout: git clone https://github.com/Radiobiology-Informatics-Consortium/RBO.git path: . @@ -5964,6 +6111,7 @@ ontologies: title: Radiation Biology Ontology tracker: https://github.com/Radiobiology-Informatics-Consortium/RBO/issues - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/oborel/obo-relations.git infallible: 1 @@ -6044,6 +6192,7 @@ ontologies: type: annotation user: http://geneontology.org - activity_status: active + added: 2015-07-28 browsers: - label: RGD title: RGD Ontology Browser @@ -6085,6 +6234,7 @@ ontologies: title: Rat Strain Ontology tracker: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology/issues - activity_status: active + added: 2015-08-17 build: method: owl2obo source_url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/rxno.owl @@ -6114,6 +6264,7 @@ ontologies: title: Name Reaction Ontology tracker: https://github.com/rsc-ontologies/rxno/issues - activity_status: active + added: 2017-06-30 build: checkout: git clone https://github.com/monarch-initiative/SEPIO-ontology.git path: src/ontology @@ -6147,6 +6298,7 @@ ontologies: title: Scientific Evidence and Provenance Information Ontology tracker: https://github.com/monarch-initiative/SEPIO-ontology/issues - activity_status: active + added: 2015-07-28 build: method: obo2owl notes: SWITCH @@ -6199,6 +6351,7 @@ ontologies: title: Sequence types and features ontology tracker: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues - activity_status: active + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -6235,6 +6388,7 @@ ontologies: title: Spider Ontology tracker: https://github.com/obophenotype/spider-ontology/issues - activity_status: active + added: 2015-08-17 contact: email: alejandra.gonzalez.beltran@gmail.com github: agbeltran @@ -6268,6 +6422,7 @@ ontologies: title: The Statistical Methods Ontology tracker: https://github.com/ISA-tools/stato/issues - activity_status: active + added: 2015-07-28 build: method: owl2obo source_url: https://raw.githubusercontent.com/allysonlister/swo/master/release/swo_inferred.owl @@ -6303,6 +6458,7 @@ ontologies: title: Software ontology tracker: https://github.com/allysonlister/swo/issues - activity_status: active + added: 2015-07-28 build: infallible: 1 method: obo2owl @@ -6351,6 +6507,7 @@ ontologies: url: http://www.disease-ontology.org/?id=DOID:0060164 user: http://www.disease-ontology.org - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/phenoscape/taxrank.git path: . @@ -6389,6 +6546,7 @@ ontologies: title: Taxonomic rank vocabulary tracker: https://github.com/phenoscape/taxrank/issues - activity_status: active + added: 2015-07-28 browsers: - label: Planteome title: Planteome browser @@ -6448,6 +6606,7 @@ ontologies: url: http://archive.gramene.org/db/ontology/search?id=TO:0000286 user: http://gramene.org/ - activity_status: active + added: 2015-07-28 build: infallible: 1 method: obo2owl @@ -6493,6 +6652,7 @@ ontologies: url: http://www.disease-ontology.org/?id=DOID:12365 user: http://www.disease-ontology.org - activity_status: active + added: 2015-07-28 contact: email: balhoff@renci.org github: balhoff @@ -6526,6 +6686,7 @@ ontologies: title: Teleost taxonomy ontology tracker: https://github.com/phenoscape/teleost-taxonomy-ontology/issues - activity_status: active + added: 2019-09-26 browsers: - label: BioPortal title: BioPortal Browser @@ -6564,6 +6725,7 @@ ontologies: title: Toxic Process Ontology tracker: https://github.com/txpo-ontology/TXPO/issues - activity_status: active + added: 2015-07-28 browsers: - label: RGD title: Gene Ontology AmiGO 2 Browser @@ -6772,6 +6934,7 @@ ontologies: user: https://www.ebi.ac.uk/chembl/ wikidata_template: https://en.wikipedia.org/wiki/Template:Uberon - activity_status: active + added: 2015-07-29 build: method: obo2owl source_url: https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo @@ -6804,6 +6967,7 @@ ontologies: title: Units of measurement ontology tracker: https://github.com/bio-ontology-research-group/unit-ontology/issues - activity_status: active + added: 2015-08-21 build: method: archive path: archive/ontology @@ -6871,6 +7035,7 @@ ontologies: type: analysis user: https://monarchinitiative.org/ - activity_status: active + added: 2015-07-29 build: source_url: https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl contact: @@ -6903,6 +7068,7 @@ ontologies: title: Vaccine Ontology tracker: https://github.com/vaccineontology/VO/issues - activity_status: active + added: 2015-08-21 build: checkout: svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt method: vcs @@ -6951,6 +7117,7 @@ ontologies: url: https://phenome.jax.org/ontologies/VT:0002224 user: https://phenome.jax.org/ontologies/navigate/VT:0000001 - activity_status: active + added: 2015-07-28 contact: email: balhoff@renci.org github: balhoff @@ -6983,6 +7150,7 @@ ontologies: - description: Phenoscape uses VTO to annotate systematics data user: http://phenoscape.org - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git path: . @@ -7030,6 +7198,7 @@ ontologies: type: annotation user: https://www.wormbase.org/ - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/c-elegans-development-ontology.git path: . @@ -7079,6 +7248,7 @@ ontologies: type: annotation user: https://www.wormbase.org/ - activity_status: active + added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git path: . @@ -7141,6 +7311,7 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active + added: 2015-07-29 browsers: - label: RGD title: RGD Ontology Browser @@ -7184,6 +7355,7 @@ ontologies: title: Experimental condition ontology tracker: https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues - activity_status: active + added: 2019-04-18 contact: email: lutz.fischer@tu-berlin.de github: lutzfischer @@ -7215,6 +7387,7 @@ ontologies: title: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary tracker: https://github.com/HUPO-PSI/xlmod-CV/issues - activity_status: active + added: 2018-11-30 build: checkout: git clone https://github.com/obophenotype/xenopus-phenotype-ontology.git path: . @@ -7264,6 +7437,7 @@ ontologies: title: Xenopus Phenotype Ontology tracker: https://github.com/obophenotype/xenopus-phenotype-ontology/issues - activity_status: active + added: 2016-07-28 build: method: obo2owl source_url: https://raw.githubusercontent.com/ybradford/zebrafish-experimental-conditions-ontology/master/zeco.obo @@ -7298,6 +7472,7 @@ ontologies: title: Zebrafish Experimental Conditions Ontology tracker: https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues - activity_status: active + added: 2015-07-29 build: infallible: 1 method: obo2owl @@ -7332,6 +7507,7 @@ ontologies: title: Zebrafish developmental stages ontology tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues - activity_status: active + added: 2019-01-02 build: checkout: git clone https://github.com/obophenotype/zebrafish-phenotype-ontology.git path: . @@ -7386,6 +7562,7 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active + added: 2020-10-01 build: checkout: git clone https://github.com/Superraptor/GSSO.git path: . @@ -7418,6 +7595,7 @@ ontologies: title: Gender, Sex, and Sexual Orientation (GSSO) ontology tracker: https://github.com/Superraptor/GSSO/issues - activity_status: active + added: 2015-07-28 browsers: - label: HPO title: JAX HPO Browser @@ -7483,6 +7661,7 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active + added: 2015-07-28 browsers: - label: OLS title: Ontology Lookup Service @@ -7560,6 +7739,7 @@ ontologies: type: annotation user: https://biosimulators.org/ - activity_status: active + added: 2015-07-28 build: method: owl2obo source_url: https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl @@ -7587,6 +7767,7 @@ ontologies: title: Mathematical modeling ontology tracker: http://sourceforge.net/p/mamo-ontology/tickets/ - activity_status: active + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -7614,6 +7795,7 @@ ontologies: title: Systems Biology Ontology tracker: https://github.com/EBI-BioModels/SBO/issues - activity_status: active + added: 2021-04-16 build: checkout: git clone https://github.com/scdodev/scdo-ontology.git path: . @@ -7687,6 +7869,7 @@ ontologies: title: Sickle Cell Disease Ontology tracker: https://github.com/scdodev/scdo-ontology/issues - activity_status: orphaned + added: 2015-07-29 build: infallible: 1 insert_ontology_id: true @@ -7708,6 +7891,7 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/fix.obo title: Physico-chemical methods and properties - activity_status: orphaned + added: 2015-07-28 description: An ontology that formalizes the genomic element by defining an upper class genetic interval homepage: https://code.google.com/p/ontology-for-genetic-interval/ @@ -7720,6 +7904,7 @@ ontologies: title: Ontology for genetic interval tracker: https://code.google.com/p/ontology-for-genetic-interval/issues/list - activity_status: orphaned + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -7734,6 +7919,7 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/rex.owl title: Physico-chemical process - activity_status: orphaned + added: 2015-07-29 build: checkout: git clone https://github.com/obophenotype/sibo.git method: vcs @@ -7764,6 +7950,7 @@ ontologies: title: Social Insect Behavior Ontology tracker: https://github.com/obophenotype/sibo/issues - activity_status: orphaned + added: 2015-07-28 build: method: obo2owl source_url: http://variationontology.org/vario_download/vario.obo @@ -7784,6 +7971,7 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/vario.obo title: Variation Ontology - activity_status: inactive + added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git method: vcs @@ -7811,6 +7999,7 @@ ontologies: title: Anatomical Entity Ontology tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues - activity_status: inactive + added: 2015-08-21 build: checkout: git clone https://github.com/obophenotype/cephalopod-ontology.git method: vcs @@ -7848,6 +8037,7 @@ ontologies: title: Cephalopod Ontology tracker: https://github.com/obophenotype/cephalopod-ontology/issues - activity_status: inactive + added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git method: vcs @@ -7887,6 +8077,7 @@ ontologies: title: Human developmental anatomy, abstract tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues - activity_status: inactive + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -7924,6 +8115,7 @@ ontologies: title: Foundational Model of Anatomy Ontology (subset) tracker: https://bitbucket.org/uwsig/fma/issues - activity_status: inactive + added: 2015-07-28 build: method: archive path: archive @@ -7952,6 +8144,7 @@ ontologies: title: Gazetteer tracker: https://github.com/EnvironmentOntology/gaz/issues - activity_status: inactive + added: 2015-07-28 contact: email: topalis@imbb.forth.gr label: Pantelis Topalis @@ -7974,6 +8167,7 @@ ontologies: repository: https://github.com/VEuPathDB-ontology/IDOMAL title: Malaria Ontology - activity_status: inactive + added: 2015-07-28 contact: email: louis@imbb.forth.gr label: Christos (Kitsos) Louis @@ -7994,6 +8188,7 @@ ontologies: label: Anopheles title: Mosquito insecticide resistance - activity_status: inactive + added: 2015-07-28 browsers: - label: RNAO title: RNA Ontology jOWL Browser @@ -8028,6 +8223,7 @@ ontologies: title: RNA ontology tracker: https://github.com/BGSU-RNA/rnao/issues - activity_status: inactive + added: 2015-07-28 contact: email: dsonensh@odu.edu label: Daniel Sonenshine @@ -8052,6 +8248,7 @@ ontologies: label: Ixodidae title: Tick Anatomy Ontology - activity_status: inactive + added: 2015-07-28 contact: email: topalis@imbb.forth.gr label: Pantelis Topalis @@ -8076,6 +8273,7 @@ ontologies: label: Anopheles title: Mosquito gross anatomy ontology - activity_status: inactive + added: 2018-12-12 build: checkout: git clone https://github.com/geneontology/unipathway.git path: . @@ -8116,6 +8314,7 @@ ontologies: title: Unipathway tracker: https://github.com/geneontology/unipathway/issues - activity_status: inactive + added: 2015-08-21 contact: email: david.c.blackburn@gmail.com label: David Blackburn @@ -8129,6 +8328,7 @@ ontologies: label: Amphibia title: Amphibian gross anatomy - activity_status: inactive + added: 2015-08-21 contact: email: adw_geeks@umich.edu label: Animal Diversity Web technical staff @@ -8138,6 +8338,7 @@ ontologies: layout: ontology_detail title: Animal natural history and life history - activity_status: inactive + added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/aero.owl @@ -8162,6 +8363,7 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/aero.owl title: Adverse Event Reporting Ontology - activity_status: inactive + added: 2015-08-21 contact: email: david.c.blackburn@gmail.com label: David Blackburn @@ -8174,6 +8376,7 @@ ontologies: label: Amphibia title: Amphibian taxonomy - activity_status: inactive + added: 2015-07-28 contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 @@ -8196,6 +8399,7 @@ ontologies: title: Beta Cell Genomics Ontology tracker: https://github.com/obi-bcgo/bcgo/issues - activity_status: inactive + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -8217,6 +8421,7 @@ ontologies: label: Bilateria title: Bilateria anatomy - activity_status: inactive + added: 2015-08-21 contact: email: vlee@ebi.ac.uk label: Vivian Lee @@ -8227,6 +8432,7 @@ ontologies: replaced_by: molecular_function title: Gene Regulation Ontology - activity_status: inactive + added: 2015-08-21 contact: email: engelsta@ohsu.edu label: Mark Engelstad @@ -8237,6 +8443,7 @@ ontologies: layout: ontology_detail title: CranioMaxilloFacial ontology - activity_status: inactive + added: 2015-08-21 contact: email: Lindsay.Cowell@utsouthwestern.edu label: Lindsay Cowell @@ -8251,6 +8458,7 @@ ontologies: label: null title: Dendritic cell - activity_status: inactive + added: 2015-08-21 contact: email: maria.herrero@kcl.ac.uk label: Maria Herrero @@ -8275,6 +8483,7 @@ ontologies: title: The Drug-Drug Interactions Ontology tracker: https://github.com/labda/DINTO/issues - activity_status: inactive + added: 2015-08-21 contact: email: J.Bard@ed.ac.uk label: Jonathan Bard @@ -8288,6 +8497,7 @@ ontologies: label: Homo sapiens title: Human developmental anatomy, timed version - activity_status: inactive + added: 2015-08-21 contact: email: J.Bard@ed.ac.uk label: Jonathan Bard @@ -8301,6 +8511,7 @@ ontologies: label: Homo sapiens title: Human developmental anatomy, abstract version - activity_status: inactive + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -8328,6 +8539,7 @@ ontologies: label: Mus title: Mouse gross anatomy and development, timed - activity_status: inactive + added: 2015-07-29 build: method: obo2owl source_url: https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl @@ -8373,6 +8585,7 @@ ontologies: url: http://archive.gramene.org/db/ontology/search?id=EO:0007174 user: http://gramene.org/ - activity_status: inactive + added: 2015-07-29 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/epo.owl @@ -8388,6 +8601,7 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/epo.owl title: Epidemiology Ontology - activity_status: inactive + added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/ero.owl @@ -8413,6 +8627,7 @@ ontologies: - resources title: eagle-i resource ontology - activity_status: inactive + added: 2015-08-21 contact: email: evoc@sanbi.ac.za label: eVOC mailing list @@ -8422,6 +8637,7 @@ ontologies: layout: ontology_detail title: eVOC (Expressed Sequence Annotation for Humans) - activity_status: inactive + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -8448,6 +8664,7 @@ ontologies: label: Drosophila title: Fly taxonomy - activity_status: inactive + added: 2015-07-29 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/flu.owl @@ -8466,6 +8683,7 @@ ontologies: title: Influenza Ontology tracker: http://purl.obolibrary.org/obo/flu/tracker - activity_status: inactive + added: 2015-08-21 contact: email: po-discuss@plantontology.org label: Plant Ontology Administrators @@ -8475,6 +8693,7 @@ ontologies: layout: ontology_detail title: Cereal Plant Gross Anatomy - activity_status: inactive + added: 2015-08-21 contact: email: peteremidford@yahoo.com label: Peter Midford @@ -8485,6 +8704,7 @@ ontologies: layout: ontology_detail title: Habronattus courtship - activity_status: inactive + added: 2015-08-21 build: insert_ontology_id: true method: obo2owl @@ -8495,6 +8715,7 @@ ontologies: layout: ontology_detail title: Event (INOH pathway ontology) - activity_status: inactive + added: 2015-08-21 build: insert_ontology_id: true method: obo2owl @@ -8508,6 +8729,7 @@ ontologies: layout: ontology_detail title: Molecule role (INOH Protein name/family name ontology) - activity_status: inactive + added: 2015-08-21 contact: email: interhelp@ebi.ac.uk label: InterPro Help @@ -8517,6 +8739,7 @@ ontologies: layout: ontology_detail title: Protein Domains - activity_status: inactive + added: 2015-07-29 build: method: owl2obo source_url: http://www.lipidprofiles.com/LipidOntology @@ -8533,6 +8756,7 @@ ontologies: - lipids title: Lipid Ontology - activity_status: inactive + added: 2015-08-21 contact: email: peteremidford@yahoo.com label: Peter Midford @@ -8543,6 +8767,7 @@ ontologies: layout: ontology_detail title: Loggerhead nesting - activity_status: inactive + added: 2015-08-21 contact: email: julie@igbmc.u-strasbg.fr label: Julie Thompson @@ -8552,6 +8777,7 @@ ontologies: layout: ontology_detail title: Multiple alignment - activity_status: inactive + added: 2015-08-21 contact: email: j.bard@ed.ac.uk label: Jonathan Bard @@ -8561,6 +8787,7 @@ ontologies: layout: ontology_detail title: Minimal anatomical terminology - activity_status: inactive + added: 2015-07-28 contact: email: Thorsten.Henrich@embl-heidelberg.de label: Thorsten Henrich @@ -8579,6 +8806,7 @@ ontologies: label: Oryzias title: Medaka fish anatomy and development - activity_status: inactive + added: 2015-07-28 contact: email: topalis@imbb.forth.gr label: Pantelis Topalis @@ -8596,6 +8824,7 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/mirnao.owl title: microRNA Ontology - activity_status: inactive + added: 2015-07-28 contact: email: stoeckrt@pcbi.upenn.edu label: Chris Stoeckert @@ -8614,6 +8843,7 @@ ontologies: replaced_by: obi title: Microarray experimental conditions - activity_status: inactive + added: 2015-08-21 contact: email: smtifahim@gmail.com label: Fahim Imam @@ -8625,6 +8855,7 @@ ontologies: replaced_by: cl title: NIF Cell - activity_status: inactive + added: 2015-08-21 contact: email: smtifahim@gmail.com label: Fahim Imam @@ -8635,6 +8866,7 @@ ontologies: replaced_by: doid title: NIF Dysfunction - activity_status: inactive + added: 2015-08-21 contact: email: smtifahim@gmail.com label: Fahim Imam @@ -8645,6 +8877,7 @@ ontologies: replaced_by: uberon title: NIF Gross Anatomy - activity_status: inactive + added: 2015-07-28 build: method: owl2obo source_url: https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl @@ -8664,6 +8897,7 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/nmr.owl title: NMR-instrument specific component of metabolomics investigations - activity_status: inactive + added: 2015-08-21 contact: email: cjmungall@lbl.gov label: Chris Mungall @@ -8675,6 +8909,7 @@ ontologies: replaced_by: ro title: OBO relationship types (legacy) - activity_status: inactive + added: 2016-02-05 contact: email: mbrochhausen@gmail.com label: Mathias Brochhausen @@ -8697,6 +8932,7 @@ ontologies: title: Ontologized MIABIS tracker: https://github.com/OMIABIS/omiabis-dev/issues - activity_status: inactive + added: 2015-08-21 contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp @@ -8711,6 +8947,7 @@ ontologies: label: Viridiplantae title: Plant Anatomy Ontology - activity_status: inactive + added: 2015-08-21 contact: email: henrich@embl.de label: Thorsten Heinrich @@ -8724,6 +8961,7 @@ ontologies: label: Platynereis title: Platynereis stage ontology - activity_status: inactive + added: 2015-08-21 contact: email: po-discuss@plantontology.org label: Plant Ontology Administrators @@ -8736,6 +8974,7 @@ ontologies: label: Viridiplantae title: Plant Growth and Development Stage - activity_status: inactive + added: 2015-08-21 contact: email: mb4@sanger.ac.uk label: Matt Berriman @@ -8745,6 +8984,7 @@ ontologies: layout: ontology_detail title: Plasmodium life cycle - activity_status: inactive + added: 2015-08-21 contact: email: satya30@uga.edu label: Satya S. Sahoo @@ -8754,6 +8994,7 @@ ontologies: layout: ontology_detail title: Proteomics data and process provenance - activity_status: inactive + added: 2015-07-28 contact: email: john.garavelli@ebi.ac.uk label: John Garavelli @@ -8767,6 +9008,7 @@ ontologies: - proteins title: Protein covalent bond - activity_status: inactive + added: 2015-08-21 contact: email: slarson@ncmir.ucsd.edu label: Stephen Larson @@ -8780,6 +9022,7 @@ ontologies: label: Homo sapiens title: Subcellular anatomy ontology - activity_status: inactive + added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -8802,6 +9045,7 @@ ontologies: - provenance title: Sample processing and separation techniques - activity_status: inactive + added: 2015-08-21 contact: email: Adrien.Coulet@loria.fr label: Adrien Coulet @@ -8814,6 +9058,7 @@ ontologies: label: Homo sapiens title: Suggested Ontology for Pharmacogenomics - activity_status: inactive + added: 2015-08-21 contact: email: pierre.sprumont@unifr.ch label: Pierre Sprumont @@ -8826,6 +9071,7 @@ ontologies: label: Homo sapiens title: Terminology of Anatomy of Human Embryology - activity_status: inactive + added: 2015-08-21 contact: email: pierre.sprumont@unifr.ch label: Pierre Sprumont @@ -8838,6 +9084,7 @@ ontologies: label: Homo sapiens title: Terminology of Anatomy of Human Histology - activity_status: inactive + added: 2015-07-28 build: method: obo2owl source_url: http://purl.obolibrary.org/obo/tao.obo @@ -8869,6 +9116,7 @@ ontologies: label: Teleostei title: Teleost Anatomy Ontology - activity_status: inactive + added: 2015-07-28 depicted_by: http://bgee.org/img/logo/bgee13_logo.png id: vhog is_obsolete: true @@ -8879,6 +9127,7 @@ ontologies: replaced_by: uberon title: Vertebrate Homologous Ontology Group Ontology - activity_status: inactive + added: 2015-07-28 build: method: obo2owl source_url: http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo @@ -8902,6 +9151,7 @@ ontologies: label: Vertebrata title: Vertebrate Skeletal Anatomy Ontology- - activity_status: inactive + added: 2015-08-21 contact: email: cherry@genome.stanford.edu label: Mike Cherry @@ -8916,6 +9166,7 @@ ontologies: label: Saccharomyces cerevisiae title: Yeast phenotypes - activity_status: inactive + added: 2015-08-21 contact: email: Leszek@missouri.edu label: Leszek Vincent diff --git a/tests/test_integrity.py b/tests/test_integrity.py index e579db9ab..aa93ef26e 100644 --- a/tests/test_integrity.py +++ b/tests/test_integrity.py @@ -20,6 +20,7 @@ DOI_PREFIX = "https://doi.org/" CHEMRXIV_DOI_PREFIX = "https://doi.org/10.26434/chemrxiv" + def get_data(): """Get ontology data.""" ontologies = {} @@ -83,8 +84,14 @@ def test_publications(self): for i, usage in enumerate(data.get("usages", [])): for j, publication in enumerate(usage.get("publications", [])): - self.assertIn("user", usage, msg=f"Malformed usage missing a user in {ontology}") - with self.subTest(ontology=ontology, user=usage["user"], id=publication["id"]): + self.assertIn( + "user", + usage, + msg=f"Malformed usage missing a user in {ontology}", + ) + with self.subTest( + ontology=ontology, user=usage["user"], id=publication["id"] + ): self.assert_valid_publication_id( publication, msg=f"{ontology} usage {i} publication {j} has unexpected identifier: {publication['id']}", @@ -127,7 +134,12 @@ def assert_valid_publication_id(self, publication, msg=None): ) # Make sure that the unversioned DOI is used - if is_arxiv or is_biorxiv or is_medrxiv or identifier.startswith(CHEMRXIV_DOI_PREFIX): + if ( + is_arxiv + or is_biorxiv + or is_medrxiv + or identifier.startswith(CHEMRXIV_DOI_PREFIX) + ): for v in range(1, 100): self.assertFalse( identifier.endswith(f".v{v}"), msg="Please use an unversioned DOI" diff --git a/util/add_dates.py b/util/add_dates.py index a215176c4..17610289f 100644 --- a/util/add_dates.py +++ b/util/add_dates.py @@ -42,7 +42,7 @@ def main(): for ontology, time in ontology_to_time.items(): path = ONTOLOGY_DIRECTORY.joinpath(ontology).with_suffix(".md") if not path.is_file(): - print("File no longer exists:", path) + print(f"File no longer exists: {path} added on {time}") continue update_markdown(path, time) From c033c86b8c16f0ab3f3c6b16ffe1e51690fa1927 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 17 Jun 2022 17:26:36 +0200 Subject: [PATCH 4/9] Update registry_schema.json --- util/schema/registry_schema.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json index 03c64c177..4744fac7b 100644 --- a/util/schema/registry_schema.json +++ b/util/schema/registry_schema.json @@ -20,7 +20,8 @@ }, "added": { "level": "error", - "format": "date", + "type": "string", + "regex": "^\\d{4}-\\d{2}-\\d{2}$", "description": "The date when the ontology was added to the OBO Foundry git repository, in the YYYY-MM-DD format" }, "browsers": { From 63cdd1293606248e62e1cea755168aae2e2a34eb Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 17 Jun 2022 17:30:33 +0200 Subject: [PATCH 5/9] Update registry_schema.json --- util/schema/registry_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json index 4744fac7b..e689a7985 100644 --- a/util/schema/registry_schema.json +++ b/util/schema/registry_schema.json @@ -20,7 +20,7 @@ }, "added": { "level": "error", - "type": "string", + "format": "date", "regex": "^\\d{4}-\\d{2}-\\d{2}$", "description": "The date when the ontology was added to the OBO Foundry git repository, in the YYYY-MM-DD format" }, From bedcdcf175c337dbf75285729a43f9a4c047ca7f Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 22 Jun 2022 10:48:07 +0200 Subject: [PATCH 6/9] Update ontologies.yml --- registry/ontologies.yml | 350 ++++++++++------------------------------ 1 file changed, 84 insertions(+), 266 deletions(-) diff --git a/registry/ontologies.yml b/registry/ontologies.yml index 605ddfaa8..9ccdc9edc 100644 --- a/registry/ontologies.yml +++ b/registry/ontologies.yml @@ -1,6 +1,5 @@ ontologies: - activity_status: active - added: 2015-07-28 browsers: - label: BioPortal title: BioPortal Browser @@ -43,7 +42,6 @@ ontologies: type: owl_import user: http://obofoundry.org - activity_status: active - added: 2015-07-28 browsers: - label: CHEBI title: EBI CHEBI Browser @@ -108,7 +106,6 @@ ontologies: url: http://zfin.org/action/expression/experiment?id=ZDB-EXP-190627-10 user: http://zfin.org - activity_status: active - added: 2015-07-28 browsers: - label: DO title: DO Browser @@ -185,7 +182,6 @@ ontologies: url: https://www.iedb.org user: https://www.iedb.org - activity_status: active - added: 2015-07-28 browsers: - label: AmiGO title: Gene Ontology AmiGO 2 Browser @@ -349,7 +345,6 @@ ontologies: type: mapping user: https://www.rhea-db.org - activity_status: active - added: 2015-07-28 browsers: - label: BioPortal title: BioPortal Browser @@ -446,7 +441,6 @@ ontologies: url: https://neuinfo.org/data/search?q=organism&l=organism#all user: http://www.neuinfo.org - activity_status: active - added: 2015-07-28 browsers: - label: BioPortal title: BioPortal Ontology Browser @@ -508,7 +502,6 @@ ontologies: type: annotation user: https://hpo.jax.org/app/ - activity_status: active - added: 2015-07-28 browsers: - label: Planteome title: Planteome browser @@ -589,7 +582,6 @@ ontologies: url: http://archive.gramene.org/db/ontology/search?id=PO:0025034 user: http://gramene.org/ - activity_status: active - added: 2015-07-28 browsers: - label: BioPortal title: BioPortal Browser @@ -656,7 +648,6 @@ ontologies: url: http://purl.obolibrary.org/obo/CL_0001201 user: http://www.obofoundry.org/ontology/cl.html - activity_status: active - added: 2015-07-28 build: infallible: 0 method: obo2owl @@ -705,7 +696,6 @@ ontologies: url: http://www.xenbase.org/anatomy/showanatomy.do?method=displayAnatomySummary&anatomyId=463 user: http://www.xenbase.org - activity_status: active - added: 2015-07-28 build: infallible: 1 method: obo2owl @@ -754,7 +744,35 @@ ontologies: url: http://zfin.org/ZFA:0000029 user: http://zfin.org - activity_status: active - added: 2016-06-04 + contact: + email: alpha.tom.kodamullil@scai.fraunhofer.de + github: akodamullil + label: Alpha Tom Kodamullil + orcid: 0000-0001-9896-3531 + dependencies: + - id: bfo + description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses + varieties of concepts related to Alzheimer'S Disease, structured by upper level + Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities + that demonstrate the network of the understanding on Alzheimer's disease and can + be readily applied for text mining. + domain: health + homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO + id: ado + layout: ontology_detail + license: + label: CC BY 4.0 + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png + url: https://creativecommons.org/licenses/by/4.0/ + ontology_purl: http://purl.obolibrary.org/obo/ado.owl + preferredPrefix: ADO + products: + - id: ado.owl + ontology_purl: http://purl.obolibrary.org/obo/ado.owl + repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO + title: Alzheimer's Disease Ontology + tracker: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues +- activity_status: active build: checkout: git clone https://github.com/AgriculturalSemantics/agro.git path: . @@ -816,7 +834,6 @@ ontologies: and datasets for use in quantitative analyses. user: https://gardian.bigdata.cgiar.org/ - activity_status: active - added: 2021-05-06 build: checkout: git clone https://github.com/insect-morphology/aism path: . @@ -858,7 +875,6 @@ ontologies: title: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) tracker: https://github.com/insect-morphology/aism/issues - activity_status: active - added: 2020-04-21 build: checkout: git clone https://github.com/EBISPOT/amphx_ontology.git path: . @@ -891,7 +907,6 @@ ontologies: title: The Amphioxus Development and Anatomy Ontology tracker: https://github.com/EBISPOT/amphx_ontology/issues - activity_status: active - added: 2015-07-28 build: method: obo2owl source_url: https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo @@ -927,7 +942,6 @@ ontologies: title: Ascomycete phenotype ontology tracker: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues - activity_status: active - added: 2019-04-04 contact: email: hoganwr@ufl.edu github: hoganwr @@ -956,7 +970,6 @@ ontologies: title: Apollo Structured Vocabulary tracker: https://github.com/ApolloDev/apollo-sv/issues - activity_status: active - added: 2017-11-15 contact: email: mcarthua@mcmaster.ca github: agmcarthur @@ -985,7 +998,6 @@ ontologies: title: Antibiotic Resistance Ontology tracker: https://github.com/arpcard/aro/issues - activity_status: active - added: 2015-07-29 contact: email: rlwalls2008@gmail.com github: ramonawalls @@ -1014,7 +1026,6 @@ ontologies: title: Biological Collections Ontology tracker: https://github.com/BiodiversityOntologies/bco/issues - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/biological-spatial-ontology.git infallible: 1 @@ -1051,7 +1062,6 @@ ontologies: title: Biological Spatial Ontology tracker: https://github.com/obophenotype/biological-spatial-ontology/issues - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/BRENDA-Enzymes/BTO.git path: . @@ -1089,7 +1099,6 @@ ontologies: title: BRENDA tissue / enzyme source tracker: https://github.com/BRENDA-Enzymes/BTO/issues - activity_status: active - added: 2015-07-28 build: method: obo2owl notes: moving to owl soon @@ -1118,7 +1127,6 @@ ontologies: title: Common Anatomy Reference Ontology tracker: https://github.com/obophenotype/caro/issues - activity_status: active - added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/cdao.owl @@ -1149,7 +1157,6 @@ ontologies: title: Comparative Data Analysis Ontology tracker: https://github.com/evoinfo/cdao/issues - activity_status: active - added: 2021-02-08 build: checkout: git clone https://github.com/Southern-Cross-Plant-Science/cdno.git path: . @@ -1192,7 +1199,6 @@ ontologies: title: Compositional Dietary Nutrition Ontology tracker: https://github.com/Southern-Cross-Plant-Science/cdno/issues - activity_status: active - added: 2015-07-28 build: method: owl2obo source_url: https://raw.githubusercontent.com/semanticchemistry/semanticchemistry/master/ontology/cheminf.owl @@ -1225,7 +1231,6 @@ ontologies: title: Chemical Information Ontology tracker: https://github.com/semanticchemistry/semanticchemistry/issues - activity_status: active - added: 2019-09-26 build: checkout: git clone https://github.com/obophenotype/chiro.git path: . @@ -1276,7 +1281,6 @@ ontologies: title: CHEBI Integrated Role Ontology tracker: https://github.com/obophenotype/chiro/issues - activity_status: active - added: 2015-07-28 contact: email: batchelorc@rsc.org github: batchelorc @@ -1301,7 +1305,6 @@ ontologies: title: Chemical Methods Ontology tracker: https://github.com/rsc-ontologies/rsc-cmo/issues - activity_status: active - added: 2020-03-12 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -1329,7 +1332,6 @@ ontologies: title: Coronavirus Infectious Disease Ontology tracker: https://github.com/cido-ontology/cido/issues - activity_status: active - added: 2016-05-17 contact: email: frederic.bastian@unil.ch github: fbastian @@ -1355,7 +1357,6 @@ ontologies: title: Confidence Information Ontology tracker: https://github.com/BgeeDB/confidence-information-ontology - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/cell-ontology.git email_cc: cl_edit@googlegroups.com @@ -1511,7 +1512,6 @@ ontologies: type: annotation user: http://fantom5-collaboration.gsc.riken.jp/ - activity_status: active - added: 2020-10-08 build: checkout: git clone https://github.com/luis-gonzalez-m/Collembola.git path: . @@ -1544,7 +1544,6 @@ ontologies: title: Collembola Anatomy Ontology tracker: https://github.com/luis-gonzalez-m/Collembola/issues - activity_status: active - added: 2015-07-28 contact: email: siiraa@umich.edu github: siiraa @@ -1577,7 +1576,6 @@ ontologies: title: Cell Line Ontology tracker: https://github.com/CLO-Ontology/CLO/issues - activity_status: active - added: 2020-05-06 build: checkout: git clone https://github.com/EBISPOT/clyh_ontology.git path: . @@ -1612,7 +1610,6 @@ ontologies: title: Clytia hemisphaerica Development and Anatomy Ontology tracker: https://github.com/EBISPOT/clyh_ontology/issues - activity_status: active - added: 2015-07-28 browsers: - label: RGD title: RGD Ontology Browser @@ -1656,7 +1653,6 @@ ontologies: title: Clinical measurement ontology tracker: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues - activity_status: active - added: 2020-04-15 contact: email: bpeters@lji.org github: bpeters42 @@ -1697,7 +1693,6 @@ ontologies: title: Core Ontology for Biology and Biomedicine tracker: https://github.com/OBOFoundry/COB/issues - activity_status: active - added: 2021-12-14 contact: email: entiminae@gmail.com github: JCGiron @@ -1736,7 +1731,6 @@ ontologies: title: Coleoptera Anatomy Ontology (COLAO) tracker: https://github.com/insect-morphology/colao/issues - activity_status: active - added: 2017-07-20 build: checkout: git clone https://github.com/data2health/contributor-role-ontology.git path: src/ontology @@ -1770,7 +1764,6 @@ ontologies: title: Contributor Role Ontology tracker: https://github.com/data2health/contributor-role-ontology/issues - activity_status: active - added: 2015-07-29 build: checkout: git clone https://github.com/obophenotype/ctenophore-ontology.git method: vcs @@ -1808,7 +1801,6 @@ ontologies: title: Ctenophore Ontology tracker: https://github.com/obophenotype/ctenophore-ontology/issues - activity_status: active - added: 2020-07-08 contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil @@ -1836,7 +1828,6 @@ ontologies: title: 'CTO: Core Ontology of Clinical Trials' tracker: https://github.com/ClinicalTrialOntology/CTO/issues - activity_status: active - added: 2015-07-28 build: method: owl2obo publications: @@ -1866,7 +1857,6 @@ ontologies: title: Cardiovascular Disease Ontology tracker: https://github.com/OpenLHS/CVDO/issues - activity_status: active - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -1905,7 +1895,6 @@ ontologies: tracker: https://github.com/dictyBase/migration-data/issues twitter: dictybase - activity_status: active - added: 2015-08-21 build: checkout: git clone https://github.com/obophenotype/dicty-phenotype-ontology.git path: . @@ -1943,7 +1932,6 @@ ontologies: tracker: https://github.com/obophenotype/dicty-phenotype-ontology/issues twitter: dictybase - activity_status: active - added: 2015-08-21 contact: email: mbrochhausen@gmail.com github: mbrochhausen @@ -1968,7 +1956,6 @@ ontologies: title: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology tracker: https://github.com/DIDEO/DIDEO/issues - activity_status: active - added: 2021-11-05 browsers: - label: DO title: DO Browser @@ -2012,7 +1999,6 @@ ontologies: url: https://www.disease-ontology.org/?id=DOID:0050665 user: https://www.disease-ontology.org - activity_status: active - added: 2015-07-28 browsers: - label: FB title: FlyBase Browser @@ -2060,7 +2046,6 @@ ontologies: url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0002030 user: http://flybase.org - activity_status: active - added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/dron.owl @@ -2093,7 +2078,6 @@ ontologies: title: The Drug Ontology tracker: https://github.com/ufbmi/dron/issues - activity_status: active - added: 2017-01-24 build: checkout: git clone https://github.com/EBISPOT/duo.git path: . @@ -2127,7 +2111,6 @@ ontologies: title: Data Use Ontology tracker: https://github.com/EBISPOT/DUO/issues - activity_status: active - added: 2020-05-06 build: checkout: git clone https://github.com/echinoderm-ontology/ecao_ontology.git path: . @@ -2162,7 +2145,6 @@ ontologies: title: The Echinoderm Anatomy and Development Ontology tracker: https://github.com/echinoderm-ontology/ecao_ontology/issues - activity_status: active - added: 2015-07-28 build: infallible: 1 method: obo2owl @@ -2227,7 +2209,6 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active - added: 2017-08-17 build: checkout: git clone https://github.com/EcologicalSemantics/ecocore.git path: . @@ -2275,7 +2256,6 @@ ontologies: title: An ontology of core ecological entities tracker: https://github.com/EcologicalSemantics/ecocore/issues - activity_status: active - added: 2019-09-24 build: checkout: git clone https://github.com/EnvironmentOntology/environmental-exposure-ontology.git path: . @@ -2351,7 +2331,6 @@ ontologies: title: Environmental conditions, treatments and exposures ontology tracker: https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues - activity_status: active - added: 2015-08-21 build: method: obo2owl notes: new url soon @@ -2389,7 +2368,6 @@ ontologies: seeAlso: https://www.biosharing.org/biodbcore-000659 user: http://www.informatics.jax.org/expression.shtml - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/EnvironmentOntology/envo.git email_cc: cjmungall@lbl.gov @@ -2492,7 +2470,6 @@ ontologies: url: https://www.planetmicrobe.org/project/#/samples/200 user: https://www.planetmicrobe.org/project/ - activity_status: active - added: 2021-12-16 contact: email: alpha.tom.kodamullil@scai.fraunhofer.de github: akodamullil @@ -2524,7 +2501,6 @@ ontologies: title: Epilepsy Ontology tracker: https://github.com/SCAI-BIO/EpilepsyOntology/issues - activity_status: active - added: 2018-01-02 contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 @@ -2568,7 +2544,6 @@ ontologies: type: annotation and query user: https://microbiomedb.org - activity_status: active - added: 2015-07-28 contact: email: annethessen@gmail.com github: diatomsRcool @@ -2595,7 +2570,6 @@ ontologies: title: Exposure ontology tracker: https://github.com/CTDbase/exposure-ontology/issues - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/fungal-anatomy-ontology.git infallible: 1 @@ -2629,7 +2603,6 @@ ontologies: title: Fungal gross anatomy tracker: https://github.com/obophenotype/fungal-anatomy-ontology/issues - activity_status: active - added: 2015-07-28 build: method: obo2owl source_url: https://raw.githubusercontent.com/dosumis/fbbi/master/src/ontology/fbbi.obo @@ -2659,7 +2632,6 @@ ontologies: title: Biological Imaging Methods Ontology tracker: https://github.com/CRBS/Biological_Imaging_Methods_Ontology/issues - activity_status: active - added: 2015-07-28 browsers: - label: FB title: FlyBase Browser @@ -2733,7 +2705,6 @@ ontologies: url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBbt:00005106 user: http://flybase.org - activity_status: active - added: 2015-08-06 browsers: - label: FB title: FlyBase Browser @@ -2777,7 +2748,6 @@ ontologies: url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBcv:0000391 user: http://flybase.org - activity_status: active - added: 2015-07-29 browsers: - label: FB title: FlyBase Browser @@ -2822,7 +2792,6 @@ ontologies: title: Drosophila development tracker: http://purl.obolibrary.org/obo/fbdv/tracker - activity_status: active - added: 2020-07-29 contact: email: georgeta.bordea@u-bordeaux.fr github: getbordea @@ -2846,7 +2815,6 @@ ontologies: title: Food Interactions with Drugs Evidence Ontology tracker: https://github.com/getbordea/fideo/issues - activity_status: active - added: 2015-12-16 build: method: owl2obo source_url: https://github.com/flora-phenotype-ontology/flopoontology/raw/master/ontology/flopo.owl @@ -2880,7 +2848,6 @@ ontologies: title: Flora Phenotype Ontology tracker: https://github.com/flora-phenotype-ontology/flopoontology/issues - activity_status: active - added: 2019-12-04 contact: email: polcaes@gmail.com github: pcastellanoescuder @@ -2917,7 +2884,6 @@ ontologies: title: Food-Biomarker Ontology tracker: https://github.com/pcastellanoescuder/FoodBiomarkerOntology/issues - activity_status: active - added: 2016-07-25 contact: email: damion_dooley@sfu.ca github: ddooley @@ -2968,7 +2934,6 @@ ontologies: title: Food Ontology tracker: https://github.com/FoodOntology/foodon/issues/ - activity_status: active - added: 2020-05-06 build: checkout: git clone https://github.com/futres/fovt.git path: . @@ -3024,7 +2989,6 @@ ontologies: title: FuTRES Ontology of Vertebrate Traits tracker: https://github.com/futres/fovt/issues - activity_status: active - added: 2015-07-29 build: infallible: 1 method: obo2owl @@ -3067,7 +3031,6 @@ ontologies: url: https://www.pombase.org/term/FYPO:0000059 user: https://www.pombase.org - activity_status: active - added: 2020-08-11 contact: email: rbca.jackson@gmail.com github: beckyjackson @@ -3097,7 +3060,6 @@ ontologies: IHCC cohort browser user: https://ihccglobal.org/ - activity_status: active - added: 2016-07-25 contact: email: damion_dooley@sfu.ca github: ddooley @@ -3130,7 +3092,6 @@ ontologies: title: Genomic Epidemiology Ontology tracker: https://github.com/GenEpiO/genepio/issues/ - activity_status: active - added: 2017-01-05 build: checkout: git clone https://github.com/monarch-initiative/GENO-ontology.git path: src/ontology @@ -3147,9 +3108,9 @@ ontologies: id: geno layout: ontology_detail license: - label: CC BY-SA 2.0 - logo: https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png - url: https://creativecommons.org/licenses/by-sa/2.0/ + label: CC BY 4.0 + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png + url: https://creativecommons.org/licenses/by/4.0/ ontology_purl: http://purl.obolibrary.org/obo/geno.owl preferredPrefix: GENO products: @@ -3162,7 +3123,6 @@ ontologies: title: Genotype Ontology tracker: https://github.com/monarch-initiative/GENO-ontology/issues - activity_status: active - added: 2015-07-28 contact: email: hoganwr@gmail.com github: hoganwr @@ -3186,7 +3146,6 @@ ontologies: title: Geographical Entity Ontology tracker: https://github.com/ufbmi/geographical-entity-ontology/issues - activity_status: active - added: 2019-08-15 browsers: - label: Structure Browser title: GNOme Glycan Structure Browser @@ -3230,6 +3189,9 @@ ontologies: from OWL) id: gno.json ontology_purl: http://purl.obolibrary.org/obo/gno.json + publications: + - id: https://doi.org/10.5281/zenodo.6678278 + title: GNOme - Glycan Naming and Subsumption Ontology repository: https://github.com/glygen-glycan-data/GNOme tags: - glycan structure @@ -3252,7 +3214,6 @@ ontologies: url: http://purl.obolibrary.org/obo/CHEBI_167503 user: https://www.ebi.ac.uk/chebi/init.do - activity_status: active - added: 2018-07-13 contact: email: danielle.welter@uni.lu github: daniwelter @@ -3317,7 +3278,6 @@ ontologies: url: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHANCESTRO_0004&viewMode=All&siblings=false user: http://foodon.org - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/hymao/hao.git system: git @@ -3355,7 +3315,6 @@ ontologies: title: Hymenoptera Anatomy Ontology tracker: https://github.com/hymao/hao/issues - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/BgeeDB/homology-ontology.git method: vcs @@ -3385,7 +3344,6 @@ ontologies: title: Homology Ontology tracker: https://github.com/BgeeDB/homology-ontology/issues - activity_status: active - added: 2015-08-21 build: infallible: 1 method: obo2owl @@ -3416,7 +3374,6 @@ ontologies: title: Human Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active - added: 2020-11-28 contact: email: fernanda.dorea@sva.se github: nandadorea @@ -3451,7 +3408,6 @@ ontologies: title: Health Surveillance Ontology tracker: https://github.com/SVA-SE/HSO/issues/ - activity_status: active - added: 2019-06-05 contact: email: aellenhicks@gmail.com github: aellenhicks @@ -3477,7 +3433,6 @@ ontologies: title: Hypertension Ontology tracker: https://github.com/aellenhicks/htn_owl/issues - activity_status: active - added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/iao.owl @@ -3524,7 +3479,6 @@ ontologies: type: owl_import user: http://obofoundry.org - activity_status: active - added: 2019-09-02 contact: email: liumeng94@sjtu.edu.cn github: Lemon-Liu @@ -3549,7 +3503,6 @@ ontologies: title: Integrative and Conjugative Element Ontology tracker: https://github.com/ontoice/ICEO/issues - activity_status: active - added: 2015-08-21 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -3579,7 +3532,6 @@ ontologies: that has over 20 institutes involved. user: http://kpmp.org - activity_status: active - added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/ido.owl @@ -3612,7 +3564,6 @@ ontologies: title: Infectious Disease Ontology tracker: https://github.com/infectious-disease-ontology/infectious-disease-ontology/issues - activity_status: active - added: 2018-03-10 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -3636,7 +3587,6 @@ ontologies: title: Interaction Network Ontology tracker: https://github.com/INO-ontology/ino/issues - activity_status: active - added: 2019-08-29 contact: email: paul.fabry@usherbrooke.ca github: pfabry @@ -3682,7 +3632,6 @@ ontologies: type: database architecture user: https://griis.ca/ - activity_status: active - added: 2021-12-14 contact: email: lagonzalezmo@unal.edu.co github: luis-gonzalez-m @@ -3721,7 +3670,6 @@ ontologies: title: Lepidoptera Anatomy Ontology tracker: https://github.com/insect-morphology/lepao/issues - activity_status: active - added: 2015-07-29 build: infallible: 1 insert_ontology_id: true @@ -3761,7 +3709,6 @@ ontologies: seeAlso: https://www.biosharing.org/biodbcore-000659 user: http://www.informatics.jax.org/expression.shtml - activity_status: active - added: 2020-02-12 build: checkout: git clone https://github.com/monarch-initiative/MAxO.git path: . @@ -3818,7 +3765,6 @@ ontologies: title: Medical Action Ontology tracker: https://github.com/monarch-initiative/MAxO/issues - activity_status: active - added: 2019-02-15 build: checkout: git clone https://github.com/microbial-conditions-ontology/microbial-conditions-ontology.git path: . @@ -3868,7 +3814,6 @@ ontologies: title: Microbial Conditions Ontology tracker: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology/issues - activity_status: active - added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/mf.owl @@ -3896,7 +3841,6 @@ ontologies: title: Mental Functioning Ontology tracker: https://github.com/jannahastings/mental-functioning-ontology/issues - activity_status: active - added: 2015-08-11 contact: email: druzinsk@uic.edu github: RDruzinsky @@ -3927,7 +3871,6 @@ ontologies: title: Mammalian Feeding Muscle Ontology tracker: https://github.com/RDruzinsky/feedontology/issues - activity_status: active - added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/mfoem.owl @@ -3955,7 +3898,6 @@ ontologies: title: Emotion Ontology tracker: https://github.com/jannahastings/emotion-ontology/issues - activity_status: active - added: 2015-08-21 contact: email: janna.hastings@gmail.com github: jannahastings @@ -3980,7 +3922,6 @@ ontologies: title: Mental Disease Ontology tracker: https://github.com/jannahastings/mental-functioning-ontology/issues - activity_status: active - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -4012,7 +3953,6 @@ ontologies: title: Molecular Interactions Controlled Vocabulary tracker: https://github.com/HUPO-PSI/psi-mi-CV/issues - activity_status: active - added: 2015-07-28 contact: email: hilmar.lapp@duke.edu github: hlapp @@ -4038,7 +3978,6 @@ ontologies: title: MIAPA Ontology tracker: https://github.com/evoinfo/miapa/issues - activity_status: active - added: 2015-10-20 contact: email: carrine.blank@umontana.edu github: carrineblank @@ -4062,7 +4001,6 @@ ontologies: title: Ontology of Prokaryotic Phenotypic and Metabolic Characters tracker: https://github.com/carrineblank/MicrO/issues - activity_status: active - added: 2015-07-28 browsers: - label: RGD title: RGD Ontology Browser @@ -4105,7 +4043,6 @@ ontologies: title: Measurement method ontology tracker: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/issues - activity_status: active - added: 2015-08-21 build: method: obo2owl source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/mmusdv/mmusdv.obo @@ -4135,7 +4072,6 @@ ontologies: title: Mouse Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -4176,7 +4112,6 @@ ontologies: title: Protein modification tracker: https://github.com/HUPO-PSI/psi-mod-CV/issues - activity_status: active - added: 2016-07-12 browsers: - label: Monarch title: Monarch Initiative Disease Browser @@ -4279,7 +4214,6 @@ ontologies: type: annotation user: https://www.humancellatlas.org/ - activity_status: active - added: 2015-08-17 build: method: owl2obo source_url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.owl @@ -4308,7 +4242,6 @@ ontologies: title: Molecular Process Ontology tracker: https://github.com/rsc-ontologies/rxno/issues - activity_status: active - added: 2015-07-28 browsers: - label: MGI title: MGI MP Browser @@ -4401,7 +4334,6 @@ ontologies: url: https://www.mousephenotype.org/data/phenotypes/MP:0013522 user: https://www.mousephenotype.org/ - activity_status: active - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -4433,7 +4365,6 @@ ontologies: title: Mouse pathology ontology tracker: https://github.com/PaulNSchofield/mpath/issues - activity_status: active - added: 2017-11-02 contact: email: mbrochhausen@uams.edu github: mbrochhausen @@ -4458,7 +4389,6 @@ ontologies: title: Minimum PDDI Information Ontology tracker: https://github.com/MPIO-Developers/MPIO/issues - activity_status: active - added: 2015-09-17 contact: email: bpeters@lji.org github: bpeters42 @@ -4495,7 +4425,6 @@ ontologies: type: annotation user: https://www.iedb.org/ - activity_status: active - added: 2015-07-28 build: method: obo2owl source_url: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo @@ -4538,7 +4467,6 @@ ontologies: title: Mass spectrometry ontology tracker: https://github.com/HUPO-PSI/psi-ms-CV/issues - activity_status: active - added: 2015-07-28 browsers: - label: BioPortal title: BioPortal Ontology Browser @@ -4574,7 +4502,6 @@ ontologies: title: Neuro Behavior Ontology tracker: https://github.com/obo-behavior/behavior-ontology/issues - activity_status: active - added: 2015-07-28 browsers: - label: NCBI title: NCBI Taxonomy Browser @@ -4629,7 +4556,6 @@ ontologies: tracker: https://github.com/obophenotype/ncbitaxon/issues wasDerivedFrom: ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat - activity_status: active - added: 2016-04-01 contact: email: haendel@ohsu.edu github: mellybelly @@ -4678,7 +4604,6 @@ ontologies: title: NCI Thesaurus OBO Edition tracker: https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues - activity_status: active - added: 2015-11-18 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl @@ -4707,7 +4632,6 @@ ontologies: title: Non-Coding RNA Ontology tracker: https://github.com/OmniSearch/ncro/issues - activity_status: active - added: 2019-01-11 build: checkout: git clone https://github.com/SpeciesFileGroup/nomen.git system: git @@ -4753,7 +4677,6 @@ ontologies: type: application user: https://taxonworks.org - activity_status: active - added: 2015-07-28 build: method: owl2obo source_url: https://raw.githubusercontent.com/OAE-ontology/OAE/master/src/oae_merged.owl @@ -4782,7 +4705,6 @@ ontologies: title: Ontology of Adverse Events tracker: https://github.com/OAE-ontology/OAE/issues - activity_status: active - added: 2017-02-10 contact: email: mjyoder@illinois.edu github: mjy @@ -4806,7 +4728,6 @@ ontologies: title: Ontology of Arthropod Circulatory Systems tracker: https://github.com/aszool/oarcs/issues - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/bio-attribute-ontology.git method: vcs @@ -4844,7 +4765,6 @@ ontologies: title: Ontology of Biological Attributes tracker: https://github.com/obophenotype/bio-attribute-ontology/issues - activity_status: active - added: 2015-07-31 contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 @@ -4871,7 +4791,6 @@ ontologies: title: Ontology of Biological and Clinical Statistics tracker: https://github.com/obcs/obcs/issues - activity_status: active - added: 2015-08-17 contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 @@ -4916,7 +4835,6 @@ ontologies: to biospecimen collection, processing, and storage, also known as biobanking. user: https://biospecimens.cancer.gov/resources/vocabularies.asp - activity_status: active - added: 2015-07-29 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -4940,7 +4858,6 @@ ontologies: title: The Ontology of Genes and Genomes tracker: https://bitbucket.org/hegroup/ogg/issues/ - activity_status: active - added: 2015-07-29 contact: email: baeverma@jcvi.org github: BAevermann @@ -4971,7 +4888,6 @@ ontologies: title: Ontology for General Medical Science tracker: https://github.com/OGMS/ogms/issues - activity_status: active - added: 2015-07-28 contact: email: linikujp@gmail.com github: linikujp @@ -4996,7 +4912,6 @@ ontologies: title: Ontology of Genetic Susceptibility Factor tracker: https://github.com/linikujp/OGSF/issues - activity_status: active - added: 2016-12-01 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/ohd.owl @@ -5027,7 +4942,6 @@ ontologies: title: Oral Health and Disease Ontology tracker: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/issues - activity_status: active - added: 2017-04-21 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -5055,7 +4969,6 @@ ontologies: title: Ontology of Host-Microbiome Interactions tracker: https://github.com/ohmi-ontology/ohmi/issues - activity_status: active - added: 2019-07-22 contact: email: edong@umich.edu github: e4ong1031 @@ -5083,7 +4996,6 @@ ontologies: title: Ontology of Host Pathogen Interactions tracker: https://github.com/OHPI/ohpi/issues - activity_status: active - added: 2015-08-21 build: method: obo2owl source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/olatdv/olatdv.obo @@ -5113,7 +5025,6 @@ ontologies: title: Medaka Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active - added: 2015-07-29 contact: email: huang@southalabama.edu github: Huang-OMIT @@ -5140,7 +5051,6 @@ ontologies: title: Ontology for MIRNA Target tracker: https://github.com/OmniSearch/omit/issues - activity_status: active - added: 2020-05-02 contact: email: cjmungall@lbl.gov github: cmungall @@ -5172,7 +5082,6 @@ ontologies: type: owl_import user: http://obofoundry.org - activity_status: active - added: 2015-08-21 build: method: obo2owl source_url: https://raw.githubusercontent.com/microbialphenotypes/OMP-ontology-files/master/omp.obo @@ -5201,7 +5110,6 @@ ontologies: title: Ontology of Microbial Phenotypes tracker: https://github.com/microbialphenotypes/OMP-ontology/issues - activity_status: active - added: 2015-07-28 build: method: owl2obo source_url: https://github.com/ufbmi/OMRSE @@ -5238,7 +5146,6 @@ ontologies: title: Ontology of Medically Related Social Entities tracker: https://github.com/ufbmi/OMRSE/issues - activity_status: active - added: 2020-11-17 contact: email: chenyangnutrition@gmail.com github: cyang0128 @@ -5273,7 +5180,6 @@ ontologies: title: Ontology for Nutritional Epidemiology tracker: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies/issues - activity_status: active - added: 2020-05-28 contact: email: francesco.vitali@ibba.cnr.it github: FrancescoVit @@ -5316,7 +5222,6 @@ ontologies: title: Ontology for Nutritional Studies tracker: https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues - activity_status: active - added: 2021-12-01 contact: email: fortuna@ebd.csic.es github: miguelfortuna @@ -5354,7 +5259,6 @@ ontologies: title: 'OntoAvida: ontology for Avida digital evolution platform' tracker: https://gitlab.com/fortunalab/ontoavida/-/issues - activity_status: active - added: 2016-11-22 browsers: - label: BioPortal title: BioPortal Browser @@ -5389,7 +5293,6 @@ ontologies: title: Obstetric and Neonatal Ontology tracker: https://github.com/ontoneo-project/Ontoneo/issues - activity_status: active - added: 2016-04-04 contact: email: mbrochhausen@gmail.com github: mbrochhausen @@ -5414,7 +5317,6 @@ ontologies: title: Ontology of Organizational Structures of Trauma centers and Trauma systems tracker: https://github.com/OOSTT/OOSTT/issues - activity_status: active - added: 2015-07-28 contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 @@ -5450,7 +5352,6 @@ ontologies: type: annotation and query user: https://www.genedb.org - activity_status: active - added: 2018-08-30 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -5477,7 +5378,6 @@ ontologies: title: Ontology of Precision Medicine and Investigation tracker: https://github.com/OPMI/opmi/issues - activity_status: active - added: 2019-06-20 contact: email: safisher@upenn.edu github: safisher @@ -5502,7 +5402,6 @@ ontologies: title: Ontology of RNA Sequencing tracker: https://github.com/safisher/ornaseq/issues - activity_status: active - added: 2015-07-28 contact: email: yongqunh@med.umich.edu github: yongqunh @@ -5526,7 +5425,6 @@ ontologies: title: Ontology of Vaccine Adverse Events tracker: https://github.com/OVAE-Ontology/ovae/issues - activity_status: active - added: 2022-01-25 contact: email: davidos@ebi.ac.uk github: dosumis @@ -5587,7 +5485,6 @@ ontologies: title: Provisional Cell Ontology tracker: https://github.com/obophenotype/provisional_cell_ontology/issues - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/PopulationAndCommunityOntology/pco.git path: . @@ -5631,7 +5528,6 @@ ontologies: title: Population and Community Ontology tracker: https://github.com/PopulationAndCommunityOntology/pco/issues - activity_status: active - added: 2016-11-11 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/pdro.owl @@ -5664,7 +5560,6 @@ ontologies: title: The Prescription of Drugs Ontology tracker: https://github.com/OpenLHS/PDRO/issues - activity_status: active - added: 2015-08-21 build: method: obo2owl source_url: https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/pdumdv/pdumdv.obo @@ -5694,7 +5589,6 @@ ontologies: title: Platynereis Developmental Stages tracker: https://github.com/obophenotype/developmental-stage-ontologies/issues - activity_status: active - added: 2017-06-05 contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp @@ -5729,7 +5623,6 @@ ontologies: title: Plant Experimental Conditions Ontology tracker: https://github.com/Planteome/plant-experimental-conditions-ontology/issues - activity_status: active - added: 2018-08-15 build: checkout: git clone https://github.com/PHI-base/phipo.git path: . @@ -5769,7 +5662,6 @@ ontologies: title: Pathogen Host Interaction Phenotype Ontology tracker: https://github.com/PHI-base/phipo/issues - activity_status: active - added: 2017-02-07 build: checkout: git clone https://github.com/obophenotype/planaria-ontology.git path: . @@ -5818,7 +5710,6 @@ ontologies: url: https://planosphere.stowers.org/ontology/PLANA_0000034 user: https://planosphere.stowers.org/ - activity_status: active - added: 2018-11-19 build: checkout: git clone https://github.com/obophenotype/planarian-phenotype-ontology.git path: . @@ -5857,7 +5748,6 @@ ontologies: title: Planarian Phenotype Ontology tracker: https://github.com/obophenotype/planarian-phenotype-ontology/issues - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/porifera-ontology.git infallible: 1 @@ -5902,7 +5792,6 @@ ontologies: title: Porifera Ontology tracker: https://github.com/obophenotype/porifera-ontology/issues - activity_status: active - added: 2016-12-30 contact: email: rlwalls2008@gmail.com github: ramonawalls @@ -5933,7 +5822,37 @@ ontologies: title: Plant Phenology Ontology tracker: https://github.com/PlantPhenoOntology/PPO/issues - activity_status: active - added: 2019-04-04 + contact: + email: wes_schafer@merck.com + github: schaferw + label: Wes Schafer + orcid: 0000-0002-8786-1756 + dependencies: + - id: ro + - id: obi + - id: chebi + - id: pato + - id: cheminf + - id: sbo + description: PROCO covers process chemistry, the chemical field concerned with scaling + up laboratory syntheses to commercially viable processes. + domain: chemistry and biochemistry + homepage: https://github.com/proco-ontology/PROCO + id: proco + layout: ontology_detail + license: + label: CC BY 4.0 + logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png + url: https://creativecommons.org/licenses/by/4.0/ + ontology_purl: http://purl.obolibrary.org/obo/proco.owl + preferredPrefix: PROCO + products: + - id: proco.owl + ontology_purl: http://purl.obolibrary.org/obo/proco.owl + repository: https://github.com/proco-ontology/PROCO + title: Process Chemistry Ontology + tracker: https://github.com/proco-ontology/PROCO/issues +- activity_status: active build: checkout: https://github.com/Display-Lab/psdo.git path: . @@ -5968,7 +5887,6 @@ ontologies: title: Performance Summary Display Ontology tracker: https://github.com/Display-Lab/psdo/issues - activity_status: active - added: 2020-05-14 build: checkout: git clone https://github.com/Planteome/plant-stress-ontology.git path: . @@ -6011,7 +5929,6 @@ ontologies: title: Plant Stress Ontology tracker: https://github.com/Planteome/plant-stress-ontology/issues - activity_status: active - added: 2015-07-28 browsers: - label: RGD title: RGD Ontology Browser @@ -6053,7 +5970,6 @@ ontologies: title: Pathway ontology tracker: https://github.com/rat-genome-database/PW-Pathway-Ontology/issues - activity_status: active - added: 2021-01-28 build: checkout: git clone https://github.com/Radiobiology-Informatics-Consortium/RBO.git path: . @@ -6111,7 +6027,6 @@ ontologies: title: Radiation Biology Ontology tracker: https://github.com/Radiobiology-Informatics-Consortium/RBO/issues - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/oborel/obo-relations.git infallible: 1 @@ -6192,7 +6107,6 @@ ontologies: type: annotation user: http://geneontology.org - activity_status: active - added: 2015-07-28 browsers: - label: RGD title: RGD Ontology Browser @@ -6234,7 +6148,6 @@ ontologies: title: Rat Strain Ontology tracker: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology/issues - activity_status: active - added: 2015-08-17 build: method: owl2obo source_url: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/rxno.owl @@ -6264,7 +6177,6 @@ ontologies: title: Name Reaction Ontology tracker: https://github.com/rsc-ontologies/rxno/issues - activity_status: active - added: 2017-06-30 build: checkout: git clone https://github.com/monarch-initiative/SEPIO-ontology.git path: src/ontology @@ -6298,7 +6210,6 @@ ontologies: title: Scientific Evidence and Provenance Information Ontology tracker: https://github.com/monarch-initiative/SEPIO-ontology/issues - activity_status: active - added: 2015-07-28 build: method: obo2owl notes: SWITCH @@ -6351,7 +6262,6 @@ ontologies: title: Sequence types and features ontology tracker: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues - activity_status: active - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -6388,7 +6298,6 @@ ontologies: title: Spider Ontology tracker: https://github.com/obophenotype/spider-ontology/issues - activity_status: active - added: 2015-08-17 contact: email: alejandra.gonzalez.beltran@gmail.com github: agbeltran @@ -6422,7 +6331,6 @@ ontologies: title: The Statistical Methods Ontology tracker: https://github.com/ISA-tools/stato/issues - activity_status: active - added: 2015-07-28 build: method: owl2obo source_url: https://raw.githubusercontent.com/allysonlister/swo/master/release/swo_inferred.owl @@ -6458,7 +6366,6 @@ ontologies: title: Software ontology tracker: https://github.com/allysonlister/swo/issues - activity_status: active - added: 2015-07-28 build: infallible: 1 method: obo2owl @@ -6507,7 +6414,6 @@ ontologies: url: http://www.disease-ontology.org/?id=DOID:0060164 user: http://www.disease-ontology.org - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/phenoscape/taxrank.git path: . @@ -6546,7 +6452,6 @@ ontologies: title: Taxonomic rank vocabulary tracker: https://github.com/phenoscape/taxrank/issues - activity_status: active - added: 2015-07-28 browsers: - label: Planteome title: Planteome browser @@ -6606,7 +6511,6 @@ ontologies: url: http://archive.gramene.org/db/ontology/search?id=TO:0000286 user: http://gramene.org/ - activity_status: active - added: 2015-07-28 build: infallible: 1 method: obo2owl @@ -6652,7 +6556,6 @@ ontologies: url: http://www.disease-ontology.org/?id=DOID:12365 user: http://www.disease-ontology.org - activity_status: active - added: 2015-07-28 contact: email: balhoff@renci.org github: balhoff @@ -6686,7 +6589,6 @@ ontologies: title: Teleost taxonomy ontology tracker: https://github.com/phenoscape/teleost-taxonomy-ontology/issues - activity_status: active - added: 2019-09-26 browsers: - label: BioPortal title: BioPortal Browser @@ -6725,7 +6627,6 @@ ontologies: title: Toxic Process Ontology tracker: https://github.com/txpo-ontology/TXPO/issues - activity_status: active - added: 2015-07-28 browsers: - label: RGD title: Gene Ontology AmiGO 2 Browser @@ -6934,7 +6835,6 @@ ontologies: user: https://www.ebi.ac.uk/chembl/ wikidata_template: https://en.wikipedia.org/wiki/Template:Uberon - activity_status: active - added: 2015-07-29 build: method: obo2owl source_url: https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo @@ -6967,7 +6867,6 @@ ontologies: title: Units of measurement ontology tracker: https://github.com/bio-ontology-research-group/unit-ontology/issues - activity_status: active - added: 2015-08-21 build: method: archive path: archive/ontology @@ -7035,7 +6934,6 @@ ontologies: type: analysis user: https://monarchinitiative.org/ - activity_status: active - added: 2015-07-29 build: source_url: https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl contact: @@ -7068,7 +6966,6 @@ ontologies: title: Vaccine Ontology tracker: https://github.com/vaccineontology/VO/issues - activity_status: active - added: 2015-08-21 build: checkout: svn co http://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/vt method: vcs @@ -7117,7 +7014,6 @@ ontologies: url: https://phenome.jax.org/ontologies/VT:0002224 user: https://phenome.jax.org/ontologies/navigate/VT:0000001 - activity_status: active - added: 2015-07-28 contact: email: balhoff@renci.org github: balhoff @@ -7150,7 +7046,6 @@ ontologies: - description: Phenoscape uses VTO to annotate systematics data user: http://phenoscape.org - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/c-elegans-gross-anatomy-ontology.git path: . @@ -7198,7 +7093,6 @@ ontologies: type: annotation user: https://www.wormbase.org/ - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/c-elegans-development-ontology.git path: . @@ -7248,7 +7142,6 @@ ontologies: type: annotation user: https://www.wormbase.org/ - activity_status: active - added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/c-elegans-phenotype-ontology.git path: . @@ -7311,7 +7204,6 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active - added: 2015-07-29 browsers: - label: RGD title: RGD Ontology Browser @@ -7355,7 +7247,6 @@ ontologies: title: Experimental condition ontology tracker: https://github.com/rat-genome-database/XCO-experimental-condition-ontology/issues - activity_status: active - added: 2019-04-18 contact: email: lutz.fischer@tu-berlin.de github: lutzfischer @@ -7387,7 +7278,6 @@ ontologies: title: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary tracker: https://github.com/HUPO-PSI/xlmod-CV/issues - activity_status: active - added: 2018-11-30 build: checkout: git clone https://github.com/obophenotype/xenopus-phenotype-ontology.git path: . @@ -7437,7 +7327,6 @@ ontologies: title: Xenopus Phenotype Ontology tracker: https://github.com/obophenotype/xenopus-phenotype-ontology/issues - activity_status: active - added: 2016-07-28 build: method: obo2owl source_url: https://raw.githubusercontent.com/ybradford/zebrafish-experimental-conditions-ontology/master/zeco.obo @@ -7472,7 +7361,6 @@ ontologies: title: Zebrafish Experimental Conditions Ontology tracker: https://github.com/ybradford/zebrafish-experimental-conditions-ontology/issues - activity_status: active - added: 2015-07-29 build: infallible: 1 method: obo2owl @@ -7507,7 +7395,6 @@ ontologies: title: Zebrafish developmental stages ontology tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues - activity_status: active - added: 2019-01-02 build: checkout: git clone https://github.com/obophenotype/zebrafish-phenotype-ontology.git path: . @@ -7562,7 +7449,6 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active - added: 2020-10-01 build: checkout: git clone https://github.com/Superraptor/GSSO.git path: . @@ -7595,7 +7481,6 @@ ontologies: title: Gender, Sex, and Sexual Orientation (GSSO) ontology tracker: https://github.com/Superraptor/GSSO/issues - activity_status: active - added: 2015-07-28 browsers: - label: HPO title: JAX HPO Browser @@ -7661,7 +7546,6 @@ ontologies: type: annotation user: https://monarchinitiative.org/ - activity_status: active - added: 2015-07-28 browsers: - label: OLS title: Ontology Lookup Service @@ -7739,7 +7623,6 @@ ontologies: type: annotation user: https://biosimulators.org/ - activity_status: active - added: 2015-07-28 build: method: owl2obo source_url: https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl @@ -7767,7 +7650,6 @@ ontologies: title: Mathematical modeling ontology tracker: http://sourceforge.net/p/mamo-ontology/tickets/ - activity_status: active - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -7795,7 +7677,6 @@ ontologies: title: Systems Biology Ontology tracker: https://github.com/EBI-BioModels/SBO/issues - activity_status: active - added: 2021-04-16 build: checkout: git clone https://github.com/scdodev/scdo-ontology.git path: . @@ -7869,7 +7750,6 @@ ontologies: title: Sickle Cell Disease Ontology tracker: https://github.com/scdodev/scdo-ontology/issues - activity_status: orphaned - added: 2015-07-29 build: infallible: 1 insert_ontology_id: true @@ -7891,20 +7771,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/fix.obo title: Physico-chemical methods and properties - activity_status: orphaned - added: 2015-07-28 - description: An ontology that formalizes the genomic element by defining an upper - class genetic interval - homepage: https://code.google.com/p/ontology-for-genetic-interval/ - id: ogi - layout: ontology_detail - ontology_purl: http://purl.obolibrary.org/obo/ogi.owl - products: - - id: ogi.owl - ontology_purl: http://purl.obolibrary.org/obo/ogi.owl - title: Ontology for genetic interval - tracker: https://code.google.com/p/ontology-for-genetic-interval/issues/list -- activity_status: orphaned - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -7919,7 +7785,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/rex.owl title: Physico-chemical process - activity_status: orphaned - added: 2015-07-29 build: checkout: git clone https://github.com/obophenotype/sibo.git method: vcs @@ -7950,7 +7815,6 @@ ontologies: title: Social Insect Behavior Ontology tracker: https://github.com/obophenotype/sibo/issues - activity_status: orphaned - added: 2015-07-28 build: method: obo2owl source_url: http://variationontology.org/vario_download/vario.obo @@ -7971,7 +7835,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/vario.obo title: Variation Ontology - activity_status: inactive - added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git method: vcs @@ -7999,7 +7862,6 @@ ontologies: title: Anatomical Entity Ontology tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues - activity_status: inactive - added: 2015-08-21 build: checkout: git clone https://github.com/obophenotype/cephalopod-ontology.git method: vcs @@ -8037,7 +7899,6 @@ ontologies: title: Cephalopod Ontology tracker: https://github.com/obophenotype/cephalopod-ontology/issues - activity_status: inactive - added: 2015-07-28 build: checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git method: vcs @@ -8077,7 +7938,6 @@ ontologies: title: Human developmental anatomy, abstract tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues - activity_status: inactive - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -8115,7 +7975,6 @@ ontologies: title: Foundational Model of Anatomy Ontology (subset) tracker: https://bitbucket.org/uwsig/fma/issues - activity_status: inactive - added: 2015-07-28 build: method: archive path: archive @@ -8144,7 +8003,6 @@ ontologies: title: Gazetteer tracker: https://github.com/EnvironmentOntology/gaz/issues - activity_status: inactive - added: 2015-07-28 contact: email: topalis@imbb.forth.gr label: Pantelis Topalis @@ -8167,7 +8025,6 @@ ontologies: repository: https://github.com/VEuPathDB-ontology/IDOMAL title: Malaria Ontology - activity_status: inactive - added: 2015-07-28 contact: email: louis@imbb.forth.gr label: Christos (Kitsos) Louis @@ -8188,7 +8045,6 @@ ontologies: label: Anopheles title: Mosquito insecticide resistance - activity_status: inactive - added: 2015-07-28 browsers: - label: RNAO title: RNA Ontology jOWL Browser @@ -8223,7 +8079,6 @@ ontologies: title: RNA ontology tracker: https://github.com/BGSU-RNA/rnao/issues - activity_status: inactive - added: 2015-07-28 contact: email: dsonensh@odu.edu label: Daniel Sonenshine @@ -8248,7 +8103,6 @@ ontologies: label: Ixodidae title: Tick Anatomy Ontology - activity_status: inactive - added: 2015-07-28 contact: email: topalis@imbb.forth.gr label: Pantelis Topalis @@ -8273,7 +8127,6 @@ ontologies: label: Anopheles title: Mosquito gross anatomy ontology - activity_status: inactive - added: 2018-12-12 build: checkout: git clone https://github.com/geneontology/unipathway.git path: . @@ -8314,7 +8167,6 @@ ontologies: title: Unipathway tracker: https://github.com/geneontology/unipathway/issues - activity_status: inactive - added: 2015-08-21 contact: email: david.c.blackburn@gmail.com label: David Blackburn @@ -8328,7 +8180,6 @@ ontologies: label: Amphibia title: Amphibian gross anatomy - activity_status: inactive - added: 2015-08-21 contact: email: adw_geeks@umich.edu label: Animal Diversity Web technical staff @@ -8338,7 +8189,6 @@ ontologies: layout: ontology_detail title: Animal natural history and life history - activity_status: inactive - added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/aero.owl @@ -8363,7 +8213,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/aero.owl title: Adverse Event Reporting Ontology - activity_status: inactive - added: 2015-08-21 contact: email: david.c.blackburn@gmail.com label: David Blackburn @@ -8376,7 +8225,6 @@ ontologies: label: Amphibia title: Amphibian taxonomy - activity_status: inactive - added: 2015-07-28 contact: email: jiezheng@pennmedicine.upenn.edu github: zhengj2007 @@ -8399,7 +8247,6 @@ ontologies: title: Beta Cell Genomics Ontology tracker: https://github.com/obi-bcgo/bcgo/issues - activity_status: inactive - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -8421,7 +8268,6 @@ ontologies: label: Bilateria title: Bilateria anatomy - activity_status: inactive - added: 2015-08-21 contact: email: vlee@ebi.ac.uk label: Vivian Lee @@ -8432,7 +8278,6 @@ ontologies: replaced_by: molecular_function title: Gene Regulation Ontology - activity_status: inactive - added: 2015-08-21 contact: email: engelsta@ohsu.edu label: Mark Engelstad @@ -8443,7 +8288,6 @@ ontologies: layout: ontology_detail title: CranioMaxilloFacial ontology - activity_status: inactive - added: 2015-08-21 contact: email: Lindsay.Cowell@utsouthwestern.edu label: Lindsay Cowell @@ -8458,7 +8302,6 @@ ontologies: label: null title: Dendritic cell - activity_status: inactive - added: 2015-08-21 contact: email: maria.herrero@kcl.ac.uk label: Maria Herrero @@ -8483,7 +8326,6 @@ ontologies: title: The Drug-Drug Interactions Ontology tracker: https://github.com/labda/DINTO/issues - activity_status: inactive - added: 2015-08-21 contact: email: J.Bard@ed.ac.uk label: Jonathan Bard @@ -8497,7 +8339,6 @@ ontologies: label: Homo sapiens title: Human developmental anatomy, timed version - activity_status: inactive - added: 2015-08-21 contact: email: J.Bard@ed.ac.uk label: Jonathan Bard @@ -8511,7 +8352,6 @@ ontologies: label: Homo sapiens title: Human developmental anatomy, abstract version - activity_status: inactive - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -8539,7 +8379,6 @@ ontologies: label: Mus title: Mouse gross anatomy and development, timed - activity_status: inactive - added: 2015-07-29 build: method: obo2owl source_url: https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl @@ -8585,7 +8424,6 @@ ontologies: url: http://archive.gramene.org/db/ontology/search?id=EO:0007174 user: http://gramene.org/ - activity_status: inactive - added: 2015-07-29 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/epo.owl @@ -8601,7 +8439,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/epo.owl title: Epidemiology Ontology - activity_status: inactive - added: 2015-07-28 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/ero.owl @@ -8627,7 +8464,6 @@ ontologies: - resources title: eagle-i resource ontology - activity_status: inactive - added: 2015-08-21 contact: email: evoc@sanbi.ac.za label: eVOC mailing list @@ -8637,7 +8473,6 @@ ontologies: layout: ontology_detail title: eVOC (Expressed Sequence Annotation for Humans) - activity_status: inactive - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -8664,7 +8499,6 @@ ontologies: label: Drosophila title: Fly taxonomy - activity_status: inactive - added: 2015-07-29 build: method: owl2obo source_url: http://purl.obolibrary.org/obo/flu.owl @@ -8683,7 +8517,6 @@ ontologies: title: Influenza Ontology tracker: http://purl.obolibrary.org/obo/flu/tracker - activity_status: inactive - added: 2015-08-21 contact: email: po-discuss@plantontology.org label: Plant Ontology Administrators @@ -8693,7 +8526,6 @@ ontologies: layout: ontology_detail title: Cereal Plant Gross Anatomy - activity_status: inactive - added: 2015-08-21 contact: email: peteremidford@yahoo.com label: Peter Midford @@ -8704,7 +8536,6 @@ ontologies: layout: ontology_detail title: Habronattus courtship - activity_status: inactive - added: 2015-08-21 build: insert_ontology_id: true method: obo2owl @@ -8715,7 +8546,6 @@ ontologies: layout: ontology_detail title: Event (INOH pathway ontology) - activity_status: inactive - added: 2015-08-21 build: insert_ontology_id: true method: obo2owl @@ -8729,7 +8559,6 @@ ontologies: layout: ontology_detail title: Molecule role (INOH Protein name/family name ontology) - activity_status: inactive - added: 2015-08-21 contact: email: interhelp@ebi.ac.uk label: InterPro Help @@ -8739,7 +8568,6 @@ ontologies: layout: ontology_detail title: Protein Domains - activity_status: inactive - added: 2015-07-29 build: method: owl2obo source_url: http://www.lipidprofiles.com/LipidOntology @@ -8756,7 +8584,6 @@ ontologies: - lipids title: Lipid Ontology - activity_status: inactive - added: 2015-08-21 contact: email: peteremidford@yahoo.com label: Peter Midford @@ -8767,7 +8594,6 @@ ontologies: layout: ontology_detail title: Loggerhead nesting - activity_status: inactive - added: 2015-08-21 contact: email: julie@igbmc.u-strasbg.fr label: Julie Thompson @@ -8777,7 +8603,6 @@ ontologies: layout: ontology_detail title: Multiple alignment - activity_status: inactive - added: 2015-08-21 contact: email: j.bard@ed.ac.uk label: Jonathan Bard @@ -8787,7 +8612,6 @@ ontologies: layout: ontology_detail title: Minimal anatomical terminology - activity_status: inactive - added: 2015-07-28 contact: email: Thorsten.Henrich@embl-heidelberg.de label: Thorsten Henrich @@ -8806,7 +8630,6 @@ ontologies: label: Oryzias title: Medaka fish anatomy and development - activity_status: inactive - added: 2015-07-28 contact: email: topalis@imbb.forth.gr label: Pantelis Topalis @@ -8824,7 +8647,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/mirnao.owl title: microRNA Ontology - activity_status: inactive - added: 2015-07-28 contact: email: stoeckrt@pcbi.upenn.edu label: Chris Stoeckert @@ -8843,7 +8665,6 @@ ontologies: replaced_by: obi title: Microarray experimental conditions - activity_status: inactive - added: 2015-08-21 contact: email: smtifahim@gmail.com label: Fahim Imam @@ -8855,7 +8676,6 @@ ontologies: replaced_by: cl title: NIF Cell - activity_status: inactive - added: 2015-08-21 contact: email: smtifahim@gmail.com label: Fahim Imam @@ -8866,7 +8686,6 @@ ontologies: replaced_by: doid title: NIF Dysfunction - activity_status: inactive - added: 2015-08-21 contact: email: smtifahim@gmail.com label: Fahim Imam @@ -8877,7 +8696,6 @@ ontologies: replaced_by: uberon title: NIF Gross Anatomy - activity_status: inactive - added: 2015-07-28 build: method: owl2obo source_url: https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl @@ -8897,7 +8715,6 @@ ontologies: ontology_purl: http://purl.obolibrary.org/obo/nmr.owl title: NMR-instrument specific component of metabolomics investigations - activity_status: inactive - added: 2015-08-21 contact: email: cjmungall@lbl.gov label: Chris Mungall @@ -8909,7 +8726,24 @@ ontologies: replaced_by: ro title: OBO relationship types (legacy) - activity_status: inactive - added: 2016-02-05 + contact: + email: linikujp@gmail.com + github: linikujp + label: Asiyah Yu Lin + orcid: 0000-0002-5379-5359 + description: An ontology that formalizes the genomic element by defining an upper + class genetic interval + homepage: https://code.google.com/p/ontology-for-genetic-interval/ + id: ogi + is_obsolete: true + layout: ontology_detail + products: + - id: ogi.owl + ontology_purl: http://purl.obolibrary.org/obo/ogi.owl + replaced_by: ogsf + title: Ontology for genetic interval + tracker: https://code.google.com/p/ontology-for-genetic-interval/issues/list +- activity_status: inactive contact: email: mbrochhausen@gmail.com label: Mathias Brochhausen @@ -8932,7 +8766,6 @@ ontologies: title: Ontologized MIABIS tracker: https://github.com/OMIABIS/omiabis-dev/issues - activity_status: inactive - added: 2015-08-21 contact: email: jaiswalp@science.oregonstate.edu github: jaiswalp @@ -8947,7 +8780,6 @@ ontologies: label: Viridiplantae title: Plant Anatomy Ontology - activity_status: inactive - added: 2015-08-21 contact: email: henrich@embl.de label: Thorsten Heinrich @@ -8961,7 +8793,6 @@ ontologies: label: Platynereis title: Platynereis stage ontology - activity_status: inactive - added: 2015-08-21 contact: email: po-discuss@plantontology.org label: Plant Ontology Administrators @@ -8974,7 +8805,6 @@ ontologies: label: Viridiplantae title: Plant Growth and Development Stage - activity_status: inactive - added: 2015-08-21 contact: email: mb4@sanger.ac.uk label: Matt Berriman @@ -8984,7 +8814,6 @@ ontologies: layout: ontology_detail title: Plasmodium life cycle - activity_status: inactive - added: 2015-08-21 contact: email: satya30@uga.edu label: Satya S. Sahoo @@ -8994,7 +8823,6 @@ ontologies: layout: ontology_detail title: Proteomics data and process provenance - activity_status: inactive - added: 2015-07-28 contact: email: john.garavelli@ebi.ac.uk label: John Garavelli @@ -9008,7 +8836,6 @@ ontologies: - proteins title: Protein covalent bond - activity_status: inactive - added: 2015-08-21 contact: email: slarson@ncmir.ucsd.edu label: Stephen Larson @@ -9022,7 +8849,6 @@ ontologies: label: Homo sapiens title: Subcellular anatomy ontology - activity_status: inactive - added: 2015-07-28 build: insert_ontology_id: true method: obo2owl @@ -9045,7 +8871,6 @@ ontologies: - provenance title: Sample processing and separation techniques - activity_status: inactive - added: 2015-08-21 contact: email: Adrien.Coulet@loria.fr label: Adrien Coulet @@ -9058,7 +8883,6 @@ ontologies: label: Homo sapiens title: Suggested Ontology for Pharmacogenomics - activity_status: inactive - added: 2015-08-21 contact: email: pierre.sprumont@unifr.ch label: Pierre Sprumont @@ -9071,7 +8895,6 @@ ontologies: label: Homo sapiens title: Terminology of Anatomy of Human Embryology - activity_status: inactive - added: 2015-08-21 contact: email: pierre.sprumont@unifr.ch label: Pierre Sprumont @@ -9084,7 +8907,6 @@ ontologies: label: Homo sapiens title: Terminology of Anatomy of Human Histology - activity_status: inactive - added: 2015-07-28 build: method: obo2owl source_url: http://purl.obolibrary.org/obo/tao.obo @@ -9116,7 +8938,6 @@ ontologies: label: Teleostei title: Teleost Anatomy Ontology - activity_status: inactive - added: 2015-07-28 depicted_by: http://bgee.org/img/logo/bgee13_logo.png id: vhog is_obsolete: true @@ -9127,7 +8948,6 @@ ontologies: replaced_by: uberon title: Vertebrate Homologous Ontology Group Ontology - activity_status: inactive - added: 2015-07-28 build: method: obo2owl source_url: http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo @@ -9151,7 +8971,6 @@ ontologies: label: Vertebrata title: Vertebrate Skeletal Anatomy Ontology- - activity_status: inactive - added: 2015-08-21 contact: email: cherry@genome.stanford.edu label: Mike Cherry @@ -9166,7 +8985,6 @@ ontologies: label: Saccharomyces cerevisiae title: Yeast phenotypes - activity_status: inactive - added: 2015-08-21 contact: email: Leszek@missouri.edu label: Leszek Vincent From 9ee81798869e23863316c805b2329ebe696dc291 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 22 Jun 2022 10:56:17 +0200 Subject: [PATCH 7/9] Update field name --- ontology/aao.md | 2 +- ontology/adw.md | 2 +- ontology/aeo.md | 2 +- ontology/aero.md | 2 +- ontology/agro.md | 2 +- ontology/aism.md | 2 +- ontology/amphx.md | 2 +- ontology/apo.md | 2 +- ontology/apollo_sv.md | 2 +- ontology/aro.md | 2 +- ontology/ato.md | 2 +- ontology/bcgo.md | 2 +- ontology/bco.md | 2 +- ontology/bfo.md | 2 +- ontology/bila.md | 2 +- ontology/bootstrep.md | 2 +- ontology/bspo.md | 2 +- ontology/bto.md | 2 +- ontology/caro.md | 2 +- ontology/cdao.md | 2 +- ontology/cdno.md | 2 +- ontology/ceph.md | 2 +- ontology/chebi.md | 2 +- ontology/cheminf.md | 2 +- ontology/chiro.md | 2 +- ontology/chmo.md | 2 +- ontology/cido.md | 2 +- ontology/cio.md | 2 +- ontology/cl.md | 2 +- ontology/clao.md | 2 +- ontology/clo.md | 2 +- ontology/clyh.md | 2 +- ontology/cmf.md | 2 +- ontology/cmo.md | 2 +- ontology/cob.md | 2 +- ontology/colao.md | 2 +- ontology/cro.md | 2 +- ontology/cteno.md | 2 +- ontology/cto.md | 2 +- ontology/cvdo.md | 2 +- ontology/dc_cl.md | 2 +- ontology/ddanat.md | 2 +- ontology/ddpheno.md | 2 +- ontology/dideo.md | 2 +- ontology/dinto.md | 2 +- ontology/disdriv.md | 2 +- ontology/doid.md | 2 +- ontology/dpo.md | 2 +- ontology/dron.md | 2 +- ontology/duo.md | 2 +- ontology/ecao.md | 2 +- ontology/eco.md | 2 +- ontology/ecocore.md | 2 +- ontology/ecto.md | 2 +- ontology/ehda.md | 2 +- ontology/ehdaa.md | 2 +- ontology/ehdaa2.md | 2 +- ontology/emap.md | 2 +- ontology/emapa.md | 2 +- ontology/envo.md | 2 +- ontology/eo.md | 2 +- ontology/epio.md | 2 +- ontology/epo.md | 2 +- ontology/ero.md | 2 +- ontology/eupath.md | 2 +- ontology/ev.md | 2 +- ontology/exo.md | 2 +- ontology/fao.md | 2 +- ontology/fbbi.md | 2 +- ontology/fbbt.md | 2 +- ontology/fbcv.md | 2 +- ontology/fbdv.md | 2 +- ontology/fbsp.md | 2 +- ontology/fideo.md | 2 +- ontology/fix.md | 2 +- ontology/flopo.md | 2 +- ontology/flu.md | 2 +- ontology/fma.md | 2 +- ontology/fobi.md | 2 +- ontology/foodon.md | 2 +- ontology/fovt.md | 2 +- ontology/fypo.md | 2 +- ontology/gaz.md | 2 +- ontology/gecko.md | 2 +- ontology/genepio.md | 2 +- ontology/geno.md | 2 +- ontology/geo.md | 2 +- ontology/gno.md | 2 +- ontology/go.md | 2 +- ontology/gro.md | 2 +- ontology/gsso.md | 2 +- ontology/habronattus.md | 2 +- ontology/hancestro.md | 2 +- ontology/hao.md | 2 +- ontology/hom.md | 2 +- ontology/hp.md | 2 +- ontology/hsapdv.md | 2 +- ontology/hso.md | 2 +- ontology/htn.md | 2 +- ontology/iao.md | 2 +- ontology/iceo.md | 2 +- ontology/ico.md | 2 +- ontology/ido.md | 2 +- ontology/idomal.md | 2 +- ontology/iev.md | 2 +- ontology/imr.md | 2 +- ontology/ino.md | 2 +- ontology/ipr.md | 2 +- ontology/kisao.md | 2 +- ontology/labo.md | 2 +- ontology/lepao.md | 2 +- ontology/lipro.md | 2 +- ontology/loggerhead.md | 2 +- ontology/ma.md | 2 +- ontology/mamo.md | 2 +- ontology/mao.md | 2 +- ontology/mat.md | 2 +- ontology/maxo.md | 2 +- ontology/mco.md | 2 +- ontology/mf.md | 2 +- ontology/mfmo.md | 2 +- ontology/mfo.md | 2 +- ontology/mfoem.md | 2 +- ontology/mfomd.md | 2 +- ontology/mi.md | 2 +- ontology/miapa.md | 2 +- ontology/micro.md | 2 +- ontology/mirnao.md | 2 +- ontology/miro.md | 2 +- ontology/mmo.md | 2 +- ontology/mmusdv.md | 2 +- ontology/mo.md | 2 +- ontology/mod.md | 2 +- ontology/mondo.md | 2 +- ontology/mop.md | 2 +- ontology/mp.md | 2 +- ontology/mpath.md | 2 +- ontology/mpio.md | 2 +- ontology/mro.md | 2 +- ontology/ms.md | 2 +- ontology/nbo.md | 2 +- ontology/ncbitaxon.md | 2 +- ontology/ncit.md | 2 +- ontology/ncro.md | 2 +- ontology/nif_cell.md | 2 +- ontology/nif_dysfunction.md | 2 +- ontology/nif_grossanatomy.md | 2 +- ontology/nmr.md | 2 +- ontology/nomen.md | 2 +- ontology/oae.md | 2 +- ontology/oarcs.md | 2 +- ontology/oba.md | 2 +- ontology/obcs.md | 2 +- ontology/obi.md | 2 +- ontology/obib.md | 2 +- ontology/obo_rel.md | 2 +- ontology/ogg.md | 2 +- ontology/ogi.md | 2 +- ontology/ogms.md | 2 +- ontology/ogsf.md | 2 +- ontology/ohd.md | 2 +- ontology/ohmi.md | 2 +- ontology/ohpi.md | 2 +- ontology/olatdv.md | 2 +- ontology/omiabis.md | 2 +- ontology/omit.md | 2 +- ontology/omo.md | 2 +- ontology/omp.md | 2 +- ontology/omrse.md | 2 +- ontology/one.md | 2 +- ontology/ons.md | 2 +- ontology/ontoavida.md | 2 +- ontology/ontoneo.md | 2 +- ontology/oostt.md | 2 +- ontology/opl.md | 2 +- ontology/opmi.md | 2 +- ontology/ornaseq.md | 2 +- ontology/ovae.md | 2 +- ontology/pao.md | 2 +- ontology/pato.md | 2 +- ontology/pcl.md | 2 +- ontology/pco.md | 2 +- ontology/pd_st.md | 2 +- ontology/pdro.md | 2 +- ontology/pdumdv.md | 2 +- ontology/peco.md | 2 +- ontology/pgdso.md | 2 +- ontology/phipo.md | 2 +- ontology/plana.md | 2 +- ontology/planp.md | 2 +- ontology/plo.md | 2 +- ontology/po.md | 2 +- ontology/poro.md | 2 +- ontology/ppo.md | 2 +- ontology/pr.md | 2 +- ontology/propreo.md | 2 +- ontology/psdo.md | 2 +- ontology/pso.md | 2 +- ontology/pw.md | 2 +- ontology/rbo.md | 2 +- ontology/resid.md | 2 +- ontology/rex.md | 2 +- ontology/rnao.md | 2 +- ontology/ro.md | 2 +- ontology/rs.md | 2 +- ontology/rxno.md | 2 +- ontology/sao.md | 2 +- ontology/sbo.md | 2 +- ontology/scdo.md | 2 +- ontology/sep.md | 2 +- ontology/sepio.md | 2 +- ontology/sibo.md | 2 +- ontology/so.md | 2 +- ontology/sopharm.md | 2 +- ontology/spd.md | 2 +- ontology/stato.md | 2 +- ontology/swo.md | 2 +- ontology/symp.md | 2 +- ontology/tads.md | 2 +- ontology/tahe.md | 2 +- ontology/tahh.md | 2 +- ontology/tao.md | 2 +- ontology/taxrank.md | 2 +- ontology/tgma.md | 2 +- ontology/to.md | 2 +- ontology/trans.md | 2 +- ontology/tto.md | 2 +- ontology/txpo.md | 2 +- ontology/uberon.md | 2 +- ontology/uo.md | 2 +- ontology/upa.md | 2 +- ontology/upheno.md | 2 +- ontology/vario.md | 2 +- ontology/vhog.md | 2 +- ontology/vo.md | 2 +- ontology/vsao.md | 2 +- ontology/vt.md | 2 +- ontology/vto.md | 2 +- ontology/wbbt.md | 2 +- ontology/wbls.md | 2 +- ontology/wbphenotype.md | 2 +- ontology/xao.md | 2 +- ontology/xco.md | 2 +- ontology/xlmod.md | 2 +- ontology/xpo.md | 2 +- ontology/ypo.md | 2 +- ontology/zea.md | 2 +- ontology/zeco.md | 2 +- ontology/zfa.md | 2 +- ontology/zfs.md | 2 +- ontology/zp.md | 2 +- util/bulk_field_rename.py | 37 ++++++++++++++++++++++++++++++++ util/schema/registry_schema.json | 6 +++--- 253 files changed, 291 insertions(+), 254 deletions(-) create mode 100644 util/bulk_field_rename.py diff --git a/ontology/aao.md b/ontology/aao.md index 1dc780845..f325ef779 100644 --- a/ontology/aao.md +++ b/ontology/aao.md @@ -12,7 +12,7 @@ homepage: http://github.com/seger/aao is_obsolete: true replaced_by: uberon activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. diff --git a/ontology/adw.md b/ontology/adw.md index 1f206e89d..c2fc01df9 100644 --- a/ontology/adw.md +++ b/ontology/adw.md @@ -8,7 +8,7 @@ contact: homepage: http://www.animaldiversity.org is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities. diff --git a/ontology/aeo.md b/ontology/aeo.md index 1a3aab8b1..8b3833be0 100644 --- a/ontology/aeo.md +++ b/ontology/aeo.md @@ -22,7 +22,7 @@ build: activity_status: inactive repository: https://github.com/obophenotype/human-developmental-anatomy-ontology preferredPrefix: AEO -added: 2015-07-28 +github_date_added: 2015-07-28 --- The AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 160 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The ~100 new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type. This site is to be used for posting details of the ontologies and updates diff --git a/ontology/aero.md b/ontology/aero.md index 82a09cf62..c9b1900e1 100644 --- a/ontology/aero.md +++ b/ontology/aero.md @@ -19,7 +19,7 @@ build: source_url: http://purl.obolibrary.org/obo/aero.owl method: owl2obo activity_status: inactive -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events. diff --git a/ontology/agro.md b/ontology/agro.md index 51ddd880e..f0e8e1c56 100644 --- a/ontology/agro.md +++ b/ontology/agro.md @@ -53,7 +53,7 @@ dependencies: - id: uo - id: xco preferredPrefix: AGRO -added: 2016-06-04 +github_date_added: 2016-06-04 --- AgrO, the Agronomy Ontology, describes agronomic practices, techniques, and variables used in agronomic experiments. AgrO is being built using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, PATO, IAO, and CHEBI. Further, AgrO powers AgroFIMS, the Agronomy Fieldbook and Information Management System modeled on a CGIAR Breeding Management System to capture agronomic data. diff --git a/ontology/aism.md b/ontology/aism.md index 8423dadfa..e778c7750 100644 --- a/ontology/aism.md +++ b/ontology/aism.md @@ -32,7 +32,7 @@ license: activity_status: active repository: https://github.com/insect-morphology/aism preferredPrefix: AISM -added: 2021-05-06 +github_date_added: 2021-05-06 --- The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology. diff --git a/ontology/amphx.md b/ontology/amphx.md index 34b2bfa73..1df4f32b9 100644 --- a/ontology/amphx.md +++ b/ontology/amphx.md @@ -26,7 +26,7 @@ license: activity_status: active repository: https://github.com/EBISPOT/amphx_ontology preferredPrefix: AMPHX -added: 2020-04-21 +github_date_added: 2020-04-21 --- The Amphioxus Development and Anatomy Ontology (AMPHX) is to describe the anatomy and development of Amphioxus, also known as lancelet, member of the invertebrate subphylum Cephalochordata and the phylum Chordata. This ontology is intended to be used for description of gene expression in amphioxus (e.g. Insitus, RNA-seq). The ontology was created in the context of the European project CORBEL (https://www.corbel-project.eu/home.html), and used in the database MARIMBA (http://marimba.obs-vlfr.fr/home). diff --git a/ontology/apo.md b/ontology/apo.md index 55f86b835..f30e099ac 100644 --- a/ontology/apo.md +++ b/ontology/apo.md @@ -29,7 +29,7 @@ preferredPrefix: APO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/20157474 title: "New mutant phenotype data curation system in the Saccharomyces Genome Database" -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary for the phenotypes of Ascomycete fungi diff --git a/ontology/apollo_sv.md b/ontology/apollo_sv.md index 57d479063..c46119922 100644 --- a/ontology/apollo_sv.md +++ b/ontology/apollo_sv.md @@ -22,7 +22,7 @@ preferredPrefix: APOLLO_SV publications: - id: https://doi.org/10.1186/s13326-016-0092-y title: "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation" -added: 2019-04-04 +github_date_added: 2019-04-04 --- #Apollo Structured Vocabulary diff --git a/ontology/aro.md b/ontology/aro.md index ba67ef17f..34406e570 100644 --- a/ontology/aro.md +++ b/ontology/aro.md @@ -23,7 +23,7 @@ activity_status: active repository: https://github.com/arpcard/aro preferredPrefix: ARO domain: microbiology -added: 2017-11-15 +github_date_added: 2017-11-15 --- The Antibiotic Resistance Ontology diff --git a/ontology/ato.md b/ontology/ato.md index a761f8ef0..7a262a426 100644 --- a/ontology/ato.md +++ b/ontology/ato.md @@ -11,7 +11,7 @@ taxon: homepage: http://www.amphibanat.org is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A taxonomy of Amphibia diff --git a/ontology/bcgo.md b/ontology/bcgo.md index 63f6ec715..c64e3e730 100644 --- a/ontology/bcgo.md +++ b/ontology/bcgo.md @@ -19,7 +19,7 @@ license: is_obsolete: true activity_status: inactive repository: https://github.com/obi-bcgo/bcgo -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Beta Cell Genomics Ontology (BCGO) is an application ontology built for the beta cell genomics studies aiming to support database annotation, complicated semantic queries, and automated cell type classification. diff --git a/ontology/bco.md b/ontology/bco.md index 810572152..fa71dcf79 100644 --- a/ontology/bco.md +++ b/ontology/bco.md @@ -22,7 +22,7 @@ tracker: https://github.com/BiodiversityOntologies/bco/issues activity_status: active repository: https://github.com/BiodiversityOntologies/bco preferredPrefix: BCO -added: 2015-07-29 +github_date_added: 2015-07-29 --- The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework. The goal of the BCO is to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. diff --git a/ontology/bfo.md b/ontology/bfo.md index d8b0d588d..cb59243e5 100644 --- a/ontology/bfo.md +++ b/ontology/bfo.md @@ -37,7 +37,7 @@ usages: activity_status: active repository: https://github.com/BFO-ontology/BFO preferredPrefix: BFO -added: 2015-07-28 +github_date_added: 2015-07-28 --- BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the special sciences domains. BFO is the upper level ontology upon which OBO Foundry ontologies are built. diff --git a/ontology/bila.md b/ontology/bila.md index b60e8d9f4..e6ef733c4 100644 --- a/ontology/bila.md +++ b/ontology/bila.md @@ -19,5 +19,5 @@ build: is_obsolete: true replaced_by: uberon activity_status: inactive -added: 2015-07-28 +github_date_added: 2015-07-28 --- diff --git a/ontology/bootstrep.md b/ontology/bootstrep.md index cd2f5a619..648d23eb2 100644 --- a/ontology/bootstrep.md +++ b/ontology/bootstrep.md @@ -9,7 +9,7 @@ homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html is_obsolete: true replaced_by: molecular_function activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- The BOOTStrep Ontology is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of). diff --git a/ontology/bspo.md b/ontology/bspo.md index 0892ff92f..3fc6f025b 100644 --- a/ontology/bspo.md +++ b/ontology/bspo.md @@ -29,7 +29,7 @@ publications: activity_status: active repository: https://github.com/obophenotype/biological-spatial-ontology preferredPrefix: BSPO -added: 2015-07-28 +github_date_added: 2015-07-28 --- An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. diff --git a/ontology/bto.md b/ontology/bto.md index e1f4f1534..3f9f28e48 100644 --- a/ontology/bto.md +++ b/ontology/bto.md @@ -29,7 +29,7 @@ build: activity_status: active repository: https://github.com/BRENDA-Enzymes/BTO preferredPrefix: BTO -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. diff --git a/ontology/caro.md b/ontology/caro.md index eef08d917..82ce17d2a 100644 --- a/ontology/caro.md +++ b/ontology/caro.md @@ -23,7 +23,7 @@ tracker: https://github.com/obophenotype/caro/issues activity_status: active repository: https://github.com/obophenotype/caro preferredPrefix: CARO -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO will be described in Anatomy Ontologies for Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and Richard Baldock (Editors) diff --git a/ontology/cdao.md b/ontology/cdao.md index b06ee189d..e23dafb14 100644 --- a/ontology/cdao.md +++ b/ontology/cdao.md @@ -25,7 +25,7 @@ activity_status: active repository: https://github.com/evoinfo/cdao preferredPrefix: CDAO domain: organisms -added: 2015-07-28 +github_date_added: 2015-07-28 --- A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science diff --git a/ontology/cdno.md b/ontology/cdno.md index 8bd78a5d6..64b9c1c25 100644 --- a/ontology/cdno.md +++ b/ontology/cdno.md @@ -35,7 +35,7 @@ publications: activity_status: active repository: https://github.com/Southern-Cross-Plant-Science/cdno preferredPrefix: CDNO -added: 2021-02-08 +github_date_added: 2021-02-08 --- The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. diff --git a/ontology/ceph.md b/ontology/ceph.md index 2c08c956f..c4ecf6b1f 100644 --- a/ontology/ceph.md +++ b/ontology/ceph.md @@ -32,7 +32,7 @@ license: label: CC BY 3.0 activity_status: inactive repository: https://github.com/obophenotype/cephalopod-ontology -added: 2015-08-21 +github_date_added: 2015-08-21 --- Welcome to the Cephalopod Ontology diff --git a/ontology/chebi.md b/ontology/chebi.md index bb078a9df..780ffcc94 100644 --- a/ontology/chebi.md +++ b/ontology/chebi.md @@ -54,7 +54,7 @@ usages: activity_status: active repository: https://github.com/ebi-chebi/ChEBI preferredPrefix: CHEBI -added: 2015-07-28 +github_date_added: 2015-07-28 --- A freely available dictionary of molecular entities focused on ‘small’ chemical compounds. diff --git a/ontology/cheminf.md b/ontology/cheminf.md index 0a91d73c0..89660d15f 100644 --- a/ontology/cheminf.md +++ b/ontology/cheminf.md @@ -26,7 +26,7 @@ build: activity_status: active repository: https://github.com/semanticchemistry/semanticchemistry preferredPrefix: CHEMINF -added: 2015-07-28 +github_date_added: 2015-07-28 --- Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. diff --git a/ontology/chiro.md b/ontology/chiro.md index dc79ec4b6..199039038 100644 --- a/ontology/chiro.md +++ b/ontology/chiro.md @@ -41,5 +41,5 @@ license: activity_status: active repository: https://github.com/obophenotype/chiro preferredPrefix: CHIRO -added: 2019-09-26 +github_date_added: 2019-09-26 --- diff --git a/ontology/chmo.md b/ontology/chmo.md index 23937ea8b..66cdf8776 100644 --- a/ontology/chmo.md +++ b/ontology/chmo.md @@ -20,7 +20,7 @@ tracker: https://github.com/rsc-ontologies/rsc-cmo/issues activity_status: active repository: https://github.com/rsc-ontologies/rsc-cmo preferredPrefix: CHMO -added: 2015-07-28 +github_date_added: 2015-07-28 --- CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). diff --git a/ontology/cido.md b/ontology/cido.md index 9d5bf5440..be4b2dc43 100644 --- a/ontology/cido.md +++ b/ontology/cido.md @@ -20,7 +20,7 @@ activity_status: active repository: https://github.com/cido-ontology/cido preferredPrefix: CIDO domain: health -added: 2020-03-12 +github_date_added: 2020-03-12 --- The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. Its development follows the OBO Foundry Principles. diff --git a/ontology/cio.md b/ontology/cio.md index 69d86d9e9..810ab6e37 100644 --- a/ontology/cio.md +++ b/ontology/cio.md @@ -20,7 +20,7 @@ activity_status: active repository: https://github.com/BgeeDB/confidence-information-ontology preferredPrefix: CIO domain: information -added: 2016-05-17 +github_date_added: 2016-05-17 --- The Confidence Information Ontology (CIO) is an ontology to capture confidence information about annotations. diff --git a/ontology/cl.md b/ontology/cl.md index 902157755..70da012ed 100644 --- a/ontology/cl.md +++ b/ontology/cl.md @@ -117,7 +117,7 @@ usages: activity_status: active repository: https://github.com/obophenotype/cell-ontology preferredPrefix: CL -added: 2015-07-28 +github_date_added: 2015-07-28 --- ![logo](/images/CL-logo.jpg) diff --git a/ontology/clao.md b/ontology/clao.md index 44c95843f..9a9e603f7 100644 --- a/ontology/clao.md +++ b/ontology/clao.md @@ -26,7 +26,7 @@ license: activity_status: active repository: https://github.com/luis-gonzalez-m/Collembola preferredPrefix: CLAO -added: 2020-10-08 +github_date_added: 2020-10-08 --- CLAO includes 1201 classes related mainly with anatomical systems, sclerites, and chaetotaxy. This ontology should increase the anatomical knowledge in Arthropoda and interoperability with other anatomical ontologies as HAO. diff --git a/ontology/clo.md b/ontology/clo.md index c96518d69..393a77b72 100644 --- a/ontology/clo.md +++ b/ontology/clo.md @@ -27,7 +27,7 @@ activity_status: active repository: https://github.com/CLO-Ontology/CLO preferredPrefix: CLO domain: anatomy and development -added: 2015-07-28 +github_date_added: 2015-07-28 --- # Summary diff --git a/ontology/clyh.md b/ontology/clyh.md index acd82683c..12286fbf5 100644 --- a/ontology/clyh.md +++ b/ontology/clyh.md @@ -28,7 +28,7 @@ license: activity_status: active repository: https://github.com/EBISPOT/clyh_ontology preferredPrefix: CLYH -added: 2020-05-06 +github_date_added: 2020-05-06 --- The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle. This species is a member of the phylum Cnidaria and belongs to the hydrozoan clade Leptothecata. Its life cycle comprises three stages: a planula larva, a benthic polyp colony, and a sexually-reproducing jellyfish (medusa). diff --git a/ontology/cmf.md b/ontology/cmf.md index e468634d0..4042aac2d 100644 --- a/ontology/cmf.md +++ b/ontology/cmf.md @@ -9,7 +9,7 @@ contact: homepage: https://code.google.com/p/craniomaxillofacial-ontology/ activity_status: inactive is_obsolete: true -added: 2015-08-21 +github_date_added: 2015-08-21 --- Ontology for oral & maxillofacial surgical procedures. diff --git a/ontology/cmo.md b/ontology/cmo.md index fd9a4224f..5407640b0 100644 --- a/ontology/cmo.md +++ b/ontology/cmo.md @@ -36,7 +36,7 @@ activity_status: active repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology preferredPrefix: CMO depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs. diff --git a/ontology/cob.md b/ontology/cob.md index 07a555d08..659281741 100644 --- a/ontology/cob.md +++ b/ontology/cob.md @@ -31,7 +31,7 @@ title: Core Ontology for Biology and Biomedicine activity_status: active repository: https://github.com/OBOFoundry/COB preferredPrefix: COB -added: 2020-04-15 +github_date_added: 2020-04-15 --- The Core Ontology for Biology and Biomedicine (COB) brings together key terms from a wide range of OBO projects into a single, small ontology. The goal is to improve interoperabilty and reuse across the OBO community through better coordination of key terms. diff --git a/ontology/colao.md b/ontology/colao.md index 41ec5851d..c6c5c8f3a 100644 --- a/ontology/colao.md +++ b/ontology/colao.md @@ -30,5 +30,5 @@ license: activity_status: active repository: https://github.com/insect-morphology/colao preferredPrefix: COLAO -added: 2021-12-14 +github_date_added: 2021-12-14 --- diff --git a/ontology/cro.md b/ontology/cro.md index 3fbf7ca94..6e0bdf4c3 100644 --- a/ontology/cro.md +++ b/ontology/cro.md @@ -26,7 +26,7 @@ products: activity_status: active repository: https://github.com/data2health/contributor-role-ontology preferredPrefix: CRO -added: 2017-07-20 +github_date_added: 2017-07-20 --- The Contributor Role Ontology expands the CASRAI Contributor Roles Taxonomy (CRediT), which is a high-level classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. diff --git a/ontology/cteno.md b/ontology/cteno.md index 7d84600de..9d32ffedc 100644 --- a/ontology/cteno.md +++ b/ontology/cteno.md @@ -33,7 +33,7 @@ license: activity_status: active repository: https://github.com/obophenotype/ctenophore-ontology preferredPrefix: CTENO -added: 2015-07-29 +github_date_added: 2015-07-29 --- An anatomical and developmental ontology for ctenophores (Comb Jellies). diff --git a/ontology/cto.md b/ontology/cto.md index cf0c10ec9..5b757ce93 100644 --- a/ontology/cto.md +++ b/ontology/cto.md @@ -19,7 +19,7 @@ activity_status: active repository: https://github.com/ClinicalTrialOntology/CTO preferredPrefix: CTO domain: health -added: 2020-07-08 +github_date_added: 2020-07-08 --- The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. diff --git a/ontology/cvdo.md b/ontology/cvdo.md index 863ed1cc0..af78b5bb1 100644 --- a/ontology/cvdo.md +++ b/ontology/cvdo.md @@ -25,7 +25,7 @@ tracker: https://github.com/OpenLHS/CVDO/issues activity_status: active repository: https://github.com/OpenLHS/CVDO preferredPrefix: CVDO -added: 2015-07-28 +github_date_added: 2015-07-28 --- CVDO is an ontology based on the OGMS model of disease, designed to describe entities related to cardiovascular diseases (including the diseases themselves, the underlying disorders, and the related pathological processes). It is being developed at Sherbrooke University (Canada) and the INSERM research institute (Institut National de la Santé et de la Recherche Médicale). diff --git a/ontology/dc_cl.md b/ontology/dc_cl.md index 89a24f3bc..132ffa315 100644 --- a/ontology/dc_cl.md +++ b/ontology/dc_cl.md @@ -13,7 +13,7 @@ homepage: http://www.dukeontologygroup.org/Projects.html is_obsolete: true replaced_by: cl activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- Representation of types of dendritic cell. Note that the domain of this ontology is wholly subsumed by the domain of the Cell ontology (CL). diff --git a/ontology/ddanat.md b/ontology/ddanat.md index ae4c85243..81cad2d65 100644 --- a/ontology/ddanat.md +++ b/ontology/ddanat.md @@ -31,7 +31,7 @@ preferredPrefix: DDANAT publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/18366659 title: "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum" -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum. diff --git a/ontology/ddpheno.md b/ontology/ddpheno.md index acdd43611..4525122bf 100644 --- a/ontology/ddpheno.md +++ b/ontology/ddpheno.md @@ -31,5 +31,5 @@ preferredPrefix: DDPHENO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31840793 title: "dictyBase and the Dicty Stock Center (version 2.0) - a progress report" -added: 2015-08-21 +github_date_added: 2015-08-21 --- diff --git a/ontology/dideo.md b/ontology/dideo.md index a473e2fc5..fc2b34acb 100644 --- a/ontology/dideo.md +++ b/ontology/dideo.md @@ -19,7 +19,7 @@ activity_status: active repository: https://github.com/DIDEO/DIDEO preferredPrefix: DIDEO domain: chemistry and biochemistry -added: 2015-08-21 +github_date_added: 2015-08-21 --- DIDEO is created as part of an NIH-funded project aiming towards developing a new knowledge base for potential drug drug interaction information. In DIDEO we represent PDDIs as information content entities and we aim to also provide the evidence for those entities using nano- and micro publication approaches. diff --git a/ontology/dinto.md b/ontology/dinto.md index 3a48279a7..3c123b78c 100644 --- a/ontology/dinto.md +++ b/ontology/dinto.md @@ -20,7 +20,7 @@ publications: activity_status: inactive is_obsolete: true repository: https://github.com/labda/DINTO -added: 2015-08-21 +github_date_added: 2015-08-21 --- DINTO is an ontology that describes and categorizes drug-drug interactions (DDIs) - a significant risk group for adverse effects associated with pharmaceutical treatment - as well as all the possible mechanisms that can lead to them (including both pharmacodynamic and pharmacokinetic DDI mechanisms). diff --git a/ontology/disdriv.md b/ontology/disdriv.md index 30f9154f8..83e87a576 100644 --- a/ontology/disdriv.md +++ b/ontology/disdriv.md @@ -38,5 +38,5 @@ usages: activity_status: active repository: https://github.com/DiseaseOntology/DiseaseDriversOntology preferredPrefix: DISDRIV -added: 2021-11-05 +github_date_added: 2021-11-05 --- diff --git a/ontology/doid.md b/ontology/doid.md index a53e5aa5d..1491c2b10 100644 --- a/ontology/doid.md +++ b/ontology/doid.md @@ -68,7 +68,7 @@ activity_status: active repository: https://github.com/DiseaseOntology/HumanDiseaseOntology preferredPrefix: DOID depicted_by: http://www.disease-ontology.org/media/images/DO_logo.jpg -added: 2015-07-28 +github_date_added: 2015-07-28 --- Creating a comprehensive classification of human diseases organized by etiology. diff --git a/ontology/dpo.md b/ontology/dpo.md index 1d4dfca89..5ed329702 100644 --- a/ontology/dpo.md +++ b/ontology/dpo.md @@ -41,7 +41,7 @@ usages: description: "alleles and constructs annotated to pupal lethal in FlyBase" activity_status: active repository: https://github.com/FlyBase/drosophila-phenotype-ontology -added: 2015-07-28 +github_date_added: 2015-07-28 --- An ontology of commonly encountered and/or high level Drosophila phenotypes. It has significant formalisation - utilising terms from GO, CL, PATO and the Drosophila anatomy ontology. It has been used by FlyBase for > 159000 annotations of phenotype. diff --git a/ontology/dron.md b/ontology/dron.md index 783530880..8d7b4786d 100644 --- a/ontology/dron.md +++ b/ontology/dron.md @@ -25,7 +25,7 @@ preferredPrefix: DRON publications: - id: https://doi.org/10.1186/s13326-017-0121-5 title: "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request" -added: 2015-07-28 +github_date_added: 2015-07-28 --- We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). diff --git a/ontology/duo.md b/ontology/duo.md index 2bbfa0b1a..846a463f4 100644 --- a/ontology/duo.md +++ b/ontology/duo.md @@ -29,7 +29,7 @@ activity_status: active repository: https://github.com/EBISPOT/DUO preferredPrefix: DUO domain: information -added: 2017-01-24 +github_date_added: 2017-01-24 --- DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. diff --git a/ontology/ecao.md b/ontology/ecao.md index 2b55fdfd1..4cd7d5d53 100644 --- a/ontology/ecao.md +++ b/ontology/ecao.md @@ -28,7 +28,7 @@ license: activity_status: active repository: https://github.com/echinoderm-ontology/ecao_ontology preferredPrefix: ECAO -added: 2020-05-06 +github_date_added: 2020-05-06 --- This ontology is intended to be used for the description and curation of information related to gene regulatory processes in echinoderms (e.g., expression patterns of endogenous genes and reporter DNA constructs, phenotypic effects of gene perturbations, etc.). diff --git a/ontology/eco.md b/ontology/eco.md index c644d2519..736bf8ed7 100644 --- a/ontology/eco.md +++ b/ontology/eco.md @@ -52,7 +52,7 @@ activity_status: active repository: https://github.com/evidenceontology/evidenceontology preferredPrefix: ECO depicted_by: https://avatars1.githubusercontent.com/u/12802432 -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about things (such as scientific conclusions, gene annotations, or other statements of fact) that result from scientific research. diff --git a/ontology/ecocore.md b/ontology/ecocore.md index 66e6e1ba2..2be5ad2cf 100644 --- a/ontology/ecocore.md +++ b/ontology/ecocore.md @@ -41,7 +41,7 @@ license: activity_status: active repository: https://github.com/EcologicalSemantics/ecocore preferredPrefix: ECOCORE -added: 2017-08-17 +github_date_added: 2017-08-17 --- This ontology aims to provide core semantics for ecological entities, such as ecological functions (for predators, prey, etc), food webs, and ecological interactions. The ontology, closely interoperates with existing OBO ontologies such as the Environment Ontology, the Population and Community Ontology (PCO), the Relations Ontology (RO), the Gene Ontology (for biological processes etc), the Phenotype and Quality Ontology (PATO), the Plant Ontology (PO), and many others. Ecocore is under active development. diff --git a/ontology/ecto.md b/ontology/ecto.md index d9d5865b2..809b6993d 100644 --- a/ontology/ecto.md +++ b/ontology/ecto.md @@ -52,5 +52,5 @@ activity_status: active repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology preferredPrefix: ECTO depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png -added: 2019-09-24 +github_date_added: 2019-09-24 --- diff --git a/ontology/ehda.md b/ontology/ehda.md index 0816a8693..f46a352e8 100644 --- a/ontology/ehda.md +++ b/ontology/ehda.md @@ -12,7 +12,7 @@ homepage: http://genex.hgu.mrc.ac.uk/ is_obsolete: true replaced_by: ehdaa2 activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once. diff --git a/ontology/ehdaa.md b/ontology/ehdaa.md index 9b135eef6..227e18a48 100644 --- a/ontology/ehdaa.md +++ b/ontology/ehdaa.md @@ -12,7 +12,7 @@ homepage: is_obsolete: true replaced_by: ehdaa2 activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release. diff --git a/ontology/ehdaa2.md b/ontology/ehdaa2.md index d9873a6a4..c683ae614 100644 --- a/ontology/ehdaa2.md +++ b/ontology/ehdaa2.md @@ -32,7 +32,7 @@ dependencies: - id: cl activity_status: inactive repository: https://github.com/obophenotype/human-developmental-anatomy-ontology -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release. diff --git a/ontology/emap.md b/ontology/emap.md index 7615e6e74..a584585d7 100644 --- a/ontology/emap.md +++ b/ontology/emap.md @@ -24,7 +24,7 @@ build: is_obsolete: true replaced_by: emapa activity_status: inactive -added: 2015-07-28 +github_date_added: 2015-07-28 --- ## BACKGROUND diff --git a/ontology/emapa.md b/ontology/emapa.md index c843f6c4f..99cac9a8a 100644 --- a/ontology/emapa.md +++ b/ontology/emapa.md @@ -31,7 +31,7 @@ usages: activity_status: active repository: https://github.com/obophenotype/mouse-anatomy-ontology preferredPrefix: EMAPA -added: 2015-08-21 +github_date_added: 2015-08-21 --- ## BACKGROUND diff --git a/ontology/envo.md b/ontology/envo.md index 3b590c017..f3761f8b9 100644 --- a/ontology/envo.md +++ b/ontology/envo.md @@ -86,7 +86,7 @@ activity_status: active repository: https://github.com/EnvironmentOntology/envo preferredPrefix: ENVO depicted_by: /logos/envo.png -added: 2015-07-28 +github_date_added: 2015-07-28 --- EnvO is a community ontology for the concise, controlled description of environments. diff --git a/ontology/eo.md b/ontology/eo.md index 69f006f9d..15cd56934 100644 --- a/ontology/eo.md +++ b/ontology/eo.md @@ -40,7 +40,7 @@ usages: activity_status: inactive repository: https://github.com/Planteome/plant-environment-ontology depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG -added: 2015-07-29 +github_date_added: 2015-07-29 --- A structured, controlled vocabulary for the representation of plant environmental conditions. diff --git a/ontology/epio.md b/ontology/epio.md index c1b0c5b70..5f46ec747 100644 --- a/ontology/epio.md +++ b/ontology/epio.md @@ -25,7 +25,7 @@ homepage: https://github.com/SCAI-BIO/EpilepsyOntology repository: https://github.com/SCAI-BIO/EpilepsyOntology activity_status: active preferredPrefix: EPIO -added: 2021-12-16 +github_date_added: 2021-12-16 --- EPIO is a community Ontology maintained by Fraunhofer SCAI. diff --git a/ontology/epo.md b/ontology/epo.md index 152c73519..bf636d27a 100644 --- a/ontology/epo.md +++ b/ontology/epo.md @@ -12,7 +12,7 @@ build: method: owl2obo is_obsolete: true activity_status: inactive -added: 2015-07-29 +github_date_added: 2015-07-29 --- The Epidemiology Ontology is an ontology designed to support the semantic annotation of epidemiology resources. It is being developed under the EU-funded EPIWORK project, a multidisciplinary research effort which aims at increasing the amount of epidemiological data available, improving disease surveillance systems, and promoting the collaboration among epidemiological researchers. The EO is integrated into NERO (Network of Epidemiology Related Ontologies), a collection of existing ontologies that supports the semantic annotation of epidemiology resources contained in the Epidemic Marketplace (EM), a platform for sharing resources and knowledge within the Epidemiology community. NERO currently includes thirteen external ontologies (the majority are OBO or OBO candidate ontologies) which already provide a high coverage of most epidemiology related areas. As such, the EPO focuses on neglected/highly specific areas of epidemiology and will articulate with other OBO ontologies as needed. diff --git a/ontology/ero.md b/ontology/ero.md index 0778db8cb..22f016b75 100644 --- a/ontology/ero.md +++ b/ontology/ero.md @@ -21,7 +21,7 @@ build: method: owl2obo activity_status: inactive is_obsolete: true -added: 2015-07-28 +github_date_added: 2015-07-28 --- ERO models research resources such instruments. protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/). diff --git a/ontology/eupath.md b/ontology/eupath.md index d7d8fe1c7..eab1c996c 100644 --- a/ontology/eupath.md +++ b/ontology/eupath.md @@ -35,7 +35,7 @@ usages: activity_status: active repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology preferredPrefix: EUPATH -added: 2018-01-02 +github_date_added: 2018-01-02 --- The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available. diff --git a/ontology/ev.md b/ontology/ev.md index 5594c73d3..92238ecba 100644 --- a/ontology/ev.md +++ b/ontology/ev.md @@ -8,7 +8,7 @@ contact: homepage: http://www.evocontology.org/ is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment. diff --git a/ontology/exo.md b/ontology/exo.md index c145ae18a..0a03faff5 100644 --- a/ontology/exo.md +++ b/ontology/exo.md @@ -20,7 +20,7 @@ products: title: Exposure ontology activity_status: active repository: https://github.com/CTDbase/exposure-ontology -added: 2015-07-28 +github_date_added: 2015-07-28 --- Significant progress has been made over the last several years in collecting and improving access to genomic, toxicology, and health data to promote understanding about environmental influences on human health. The resulting information resources, however, lack extensive and reliable exposure data, which are required to translate molecular insights, elucidate environmental contributions to diseases, and assess human health risks at the individual and population levels. We report our development of an Exposure Ontology, ExO, designed to address this information gap by facilitating centralization and integration of exposure data to inform understanding of environmental health. Like other widely used ontologies, ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics diff --git a/ontology/fao.md b/ontology/fao.md index 6db184fd0..86f6c9e91 100644 --- a/ontology/fao.md +++ b/ontology/fao.md @@ -28,7 +28,7 @@ build: activity_status: active repository: https://github.com/obophenotype/fungal-anatomy-ontology preferredPrefix: FAO -added: 2015-07-28 +github_date_added: 2015-07-28 --- ![FAO image](http://www.yeastgenome.org/images/fao.color.png) diff --git a/ontology/fbbi.md b/ontology/fbbi.md index a3c089480..80ca0a10c 100644 --- a/ontology/fbbi.md +++ b/ontology/fbbi.md @@ -24,7 +24,7 @@ build: method: obo2owl activity_status: active repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. diff --git a/ontology/fbbt.md b/ontology/fbbt.md index fb28fb6c6..4e8115434 100644 --- a/ontology/fbbt.md +++ b/ontology/fbbt.md @@ -64,7 +64,7 @@ usages: - url: "http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBbt:00005106" description: "alleles, constructs and insertions annotated to neuron in FlyBase" activity_status: active -added: 2015-07-28 +github_date_added: 2015-07-28 --- An ontology representing the gross anatomy of Drosophila melanogaster. diff --git a/ontology/fbcv.md b/ontology/fbcv.md index 213fbfec4..fd600db3b 100644 --- a/ontology/fbcv.md +++ b/ontology/fbcv.md @@ -36,7 +36,7 @@ usages: activity_status: active repository: https://github.com/FlyBase/flybase-controlled-vocabulary publications: [] -added: 2015-08-06 +github_date_added: 2015-08-06 --- A structured controlled vocabulary used for various aspects of annotation by FlyBase. It includes the Drosophila Phenotype Ontology (dpo) which is also released separately. diff --git a/ontology/fbdv.md b/ontology/fbdv.md index bf977c1df..5afc7ed92 100644 --- a/ontology/fbdv.md +++ b/ontology/fbdv.md @@ -35,7 +35,7 @@ browsers: url: http://flybase.org/.bin/cvreport.html?cvterm=FBdv:00007008 activity_status: active publications: [] -added: 2015-07-29 +github_date_added: 2015-07-29 --- A structured controlled vocabulary of the development of Drosophila melanogaster. diff --git a/ontology/fbsp.md b/ontology/fbsp.md index 57b447620..885019aa5 100644 --- a/ontology/fbsp.md +++ b/ontology/fbsp.md @@ -23,7 +23,7 @@ build: insert_ontology_id: true is_obsolete: true activity_status: inactive -added: 2015-07-28 +github_date_added: 2015-07-28 --- The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. diff --git a/ontology/fideo.md b/ontology/fideo.md index 494a45fb2..01b037238 100644 --- a/ontology/fideo.md +++ b/ontology/fideo.md @@ -19,7 +19,7 @@ tracker: https://github.com/getbordea/fideo/issues activity_status: active repository: https://github.com/getbordea/fideo preferredPrefix: FIDEO -added: 2020-07-29 +github_date_added: 2020-07-29 --- FIDEO represents food-drug interactions automatically extracted from scientific literature. diff --git a/ontology/fix.md b/ontology/fix.md index b3ef02eb7..e8f76b728 100644 --- a/ontology/fix.md +++ b/ontology/fix.md @@ -17,5 +17,5 @@ products: - id: fix.obo title: Physico-chemical methods and properties activity_status: orphaned -added: 2015-07-29 +github_date_added: 2015-07-29 --- diff --git a/ontology/flopo.md b/ontology/flopo.md index 65a29c65e..faf6573cc 100644 --- a/ontology/flopo.md +++ b/ontology/flopo.md @@ -28,5 +28,5 @@ preferredPrefix: FLOPO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27842607 title: "The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants" -added: 2015-12-16 +github_date_added: 2015-12-16 --- diff --git a/ontology/flu.md b/ontology/flu.md index e8832d215..6d139ca21 100644 --- a/ontology/flu.md +++ b/ontology/flu.md @@ -16,5 +16,5 @@ build: tracker: http://purl.obolibrary.org/obo/flu/tracker is_obsolete: true activity_status: inactive -added: 2015-07-29 +github_date_added: 2015-07-29 --- diff --git a/ontology/fma.md b/ontology/fma.md index ac3b61347..d88d221b6 100644 --- a/ontology/fma.md +++ b/ontology/fma.md @@ -32,7 +32,7 @@ tracker: https://bitbucket.org/uwsig/fma/issues repository: https://bitbucket.org/uwsig/fma activity_status: inactive preferredPrefix: FMA -added: 2015-07-28 +github_date_added: 2015-07-28 --- Obo format translation of the FMA, omitting all relationships other than is_a, part_of and has_part. Future versions of fma_obo will include more relationships diff --git a/ontology/fobi.md b/ontology/fobi.md index 5db4d0009..9444580f0 100644 --- a/ontology/fobi.md +++ b/ontology/fobi.md @@ -29,7 +29,7 @@ homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology activity_status: active repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology preferredPrefix: FOBI -added: 2019-12-04 +github_date_added: 2019-12-04 --- FOBI (Food-Biomarker Ontology) is composed of two interconnected sub-ontologies. One is a ”Food Ontology” consisting of raw foods and multi-ingredient foods while the second is a ”Biomarker Ontology” containing food intake biomarkers classified by their chemical classes. These two sub-ontologies are conceptually independent but interconnected by different properties. diff --git a/ontology/foodon.md b/ontology/foodon.md index 77ccaf44b..78599fbfd 100644 --- a/ontology/foodon.md +++ b/ontology/foodon.md @@ -38,7 +38,7 @@ preferredPrefix: FOODON publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/31304272 title: "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration" -added: 2016-07-25 +github_date_added: 2016-07-25 --- A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and food webs as well as human-centric categorization and handling of food. diff --git a/ontology/fovt.md b/ontology/fovt.md index 1e9d394b2..145b316f9 100644 --- a/ontology/fovt.md +++ b/ontology/fovt.md @@ -45,7 +45,7 @@ license: activity_status: active repository: https://github.com/futres/fovt preferredPrefix: FOVT -added: 2020-05-06 +github_date_added: 2020-05-06 --- The FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheets to triples, using the [Ontology Data Pipeline](https://github.com/biocodellc/ontology-data-pipeline) from Biocode LLC. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA). diff --git a/ontology/fypo.md b/ontology/fypo.md index 31c7ee3aa..504fc39db 100644 --- a/ontology/fypo.md +++ b/ontology/fypo.md @@ -37,7 +37,7 @@ usages: activity_status: active repository: https://github.com/pombase/fypo preferredPrefix: FYPO -added: 2015-07-29 +github_date_added: 2015-07-29 --- FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the new online fission yeast resource (www.pombase.org). Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions. diff --git a/ontology/gaz.md b/ontology/gaz.md index 5e2287b59..e99446228 100644 --- a/ontology/gaz.md +++ b/ontology/gaz.md @@ -23,5 +23,5 @@ license: label: CC0 1.0 activity_status: inactive repository: https://github.com/EnvironmentOntology/gaz -added: 2015-07-28 +github_date_added: 2015-07-28 --- diff --git a/ontology/gecko.md b/ontology/gecko.md index 7348d1cf3..44e5f33d5 100644 --- a/ontology/gecko.md +++ b/ontology/gecko.md @@ -24,7 +24,7 @@ usages: activity_status: active repository: https://github.com/IHCC-cohorts/GECKO preferredPrefix: GECKO -added: 2020-08-11 +github_date_added: 2020-08-11 --- Genomics Cohorts Knowledge Ontology (GECKO) is an ontology to represent genomics cohort attributes. The GECKO is maintained by the [CINECA project]( https://www.cineca-project.eu), and standardises attributes commonly used for genomics cohort description as well as individual-level data items. A series of tools is being developed to enable automated generation of harmonised data files based on a JSON schema mapping file. For more information please contact [CINECA](mailto:info@cineca-project.eu). diff --git a/ontology/genepio.md b/ontology/genepio.md index 15b407431..cae3462f6 100644 --- a/ontology/genepio.md +++ b/ontology/genepio.md @@ -27,7 +27,7 @@ tracker: https://github.com/GenEpiO/genepio/issues/ activity_status: active repository: https://github.com/GenEpiO/genepio preferredPrefix: GENEPIO -added: 2016-07-25 +github_date_added: 2016-07-25 --- Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. We envision various subdomains including genomic laboratory testing, specimen and isolate metadata, and epidemiological case investigations. diff --git a/ontology/geno.md b/ontology/geno.md index 13a64a446..c5429c89b 100644 --- a/ontology/geno.md +++ b/ontology/geno.md @@ -28,7 +28,7 @@ products: activity_status: active repository: https://github.com/monarch-initiative/GENO-ontology preferredPrefix: GENO -added: 2017-01-05 +github_date_added: 2017-01-05 --- GENO is an OWL2 ontology that represents the levels of genetic variation specified in genotypes, to support genotype-to-phenotype (G2P) data aggregation and analysis across diverse research communities and sources. The core of the ontology is a graph decomposing a genotype into smaller components of variation, from a complete genotype specifying sequence variation across an entire genome, down to specific allelic variants and sequence alterations. Structuring genotype instance data according to this model supports a primary use case of GENO to enable integrated analysis of G2P data where phenotype annotations are made at different levels of granularity in this genotype partonomy. GENO also enables description of various attributes of genotypes and genetic variants. These attributes include zygosity, genomic position, expression, dominance, and functional dependencies or consequences of a given variant. diff --git a/ontology/geo.md b/ontology/geo.md index 2cf1e3601..f5beb8ca1 100644 --- a/ontology/geo.md +++ b/ontology/geo.md @@ -19,7 +19,7 @@ tracker: https://github.com/ufbmi/geographical-entity-ontology/issues activity_status: active repository: https://github.com/ufbmi/geographical-entity-ontology preferredPrefix: GEO -added: 2015-07-28 +github_date_added: 2015-07-28 --- An ontology of geographical entities implemented in Web Ontology Language 2 (OWL2) and based on Basic Formal Ontology (BFO). The developers aim to adhere to the OBO Foundry principles. diff --git a/ontology/gno.md b/ontology/gno.md index 487e34cb0..037c6b691 100644 --- a/ontology/gno.md +++ b/ontology/gno.md @@ -56,5 +56,5 @@ usages: activity_status: active repository: https://github.com/glygen-glycan-data/GNOme preferredPrefix: GNO -added: 2019-08-15 +github_date_added: 2019-08-15 --- diff --git a/ontology/go.md b/ontology/go.md index d290a3d46..27411afa5 100644 --- a/ontology/go.md +++ b/ontology/go.md @@ -136,7 +136,7 @@ publications: title: "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium" - id: https://www.ncbi.nlm.nih.gov/pubmed/33290552 title: "The Gene Ontology resource: enriching a GOld mine" -added: 2015-07-28 +github_date_added: 2015-07-28 --- The goal of the GeneOntology (GO) project is to provide a uniformway to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data diff --git a/ontology/gro.md b/ontology/gro.md index e7f3b08cd..4a3e0c8a8 100644 --- a/ontology/gro.md +++ b/ontology/gro.md @@ -8,7 +8,7 @@ contact: homepage: http://www.gramene.org/plant_ontology/ is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the Plant Ontology. diff --git a/ontology/gsso.md b/ontology/gsso.md index 08b769c66..e5e8c7314 100644 --- a/ontology/gsso.md +++ b/ontology/gsso.md @@ -25,7 +25,7 @@ license: activity_status: active repository: https://github.com/Superraptor/GSSO preferredPrefix: GSSO -added: 2020-10-01 +github_date_added: 2020-10-01 --- GSSO on BioPortal: https://bioportal.bioontology.org/ontologies/GSSO diff --git a/ontology/habronattus.md b/ontology/habronattus.md index 84733961a..7fb714443 100644 --- a/ontology/habronattus.md +++ b/ontology/habronattus.md @@ -9,7 +9,7 @@ contact: homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for courtship behavior of the spider Habronattus californicus. diff --git a/ontology/hancestro.md b/ontology/hancestro.md index 6547af719..feff16231 100644 --- a/ontology/hancestro.md +++ b/ontology/hancestro.md @@ -45,7 +45,7 @@ usages: activity_status: active repository: https://github.com/EBISPOT/ancestro preferredPrefix: HANCESTRO -added: 2018-07-13 +github_date_added: 2018-07-13 --- # Summary diff --git a/ontology/hao.md b/ontology/hao.md index 36c8a855c..b2de64978 100644 --- a/ontology/hao.md +++ b/ontology/hao.md @@ -30,7 +30,7 @@ preferredPrefix: HAO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/21209921 title: "A gross anatomy ontology for hymenoptera" -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) diff --git a/ontology/hom.md b/ontology/hom.md index f131cf91a..ea89b0979 100644 --- a/ontology/hom.md +++ b/ontology/hom.md @@ -24,7 +24,7 @@ activity_status: active repository: https://github.com/BgeeDB/homology-ontology preferredPrefix: HOM domain: anatomy and development -added: 2015-07-28 +github_date_added: 2015-07-28 --- This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. The ontology can be cited as: diff --git a/ontology/hp.md b/ontology/hp.md index f69f443b9..45c0e024a 100644 --- a/ontology/hp.md +++ b/ontology/hp.md @@ -57,7 +57,7 @@ activity_status: active repository: https://github.com/obophenotype/human-phenotype-ontology preferredPrefix: HP depicted_by: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png -added: 2015-07-28 +github_date_added: 2015-07-28 --- An ontology is a computational representation of a domain of knowledge based upon a controlled, standardized vocabulary for describing entities and the semantic relationships between them. diff --git a/ontology/hsapdv.md b/ontology/hsapdv.md index 02a97bbe5..bf1e22b2b 100644 --- a/ontology/hsapdv.md +++ b/ontology/hsapdv.md @@ -25,7 +25,7 @@ products: activity_status: active repository: https://github.com/obophenotype/developmental-stage-ontologies domain: anatomy and development -added: 2015-08-21 +github_date_added: 2015-08-21 --- HumanEmbryogenesis diff --git a/ontology/hso.md b/ontology/hso.md index 9947f926b..6e6ca144e 100644 --- a/ontology/hso.md +++ b/ontology/hso.md @@ -27,7 +27,7 @@ tracker: https://github.com/SVA-SE/HSO/issues/ activity_status: active repository: https://github.com/SVA-SE/HSO preferredPrefix: HSO -added: 2020-11-28 +github_date_added: 2020-11-28 --- The Health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. "Surveillance" is defined as any activity that collects information which is analysed to inform disease control (https://www.fp7-risksur.eu/terminology/glossary). A typical example of a One-Health surveillance activity, in this context, is the investigation of foodborne zoonotic outbreaks. diff --git a/ontology/htn.md b/ontology/htn.md index 8818d5e36..e316aa303 100644 --- a/ontology/htn.md +++ b/ontology/htn.md @@ -20,7 +20,7 @@ activity_status: active repository: https://github.com/aellenhicks/htn_owl preferredPrefix: HTN domain: health -added: 2019-06-05 +github_date_added: 2019-06-05 --- The Hypertension Ontology is a realism-based reference ontology for semantically managing clinical data about hypertension. Definitions of hypertension and elevated blood pressure are highly sensitive to context. Thresholds may vary according to population, guidelines, or clinical context. Variations in the clinical interpretation of blood pressure pose challenges to using blood pressure data for cohort identification, semantic data integration across data sets, and semantically enriching clinical data for clinical decision support applications. The Hypertension Ontology provides a framework for connecting clinical data to context-sensitive definitions of elevated blood pressure and hypertension. diff --git a/ontology/iao.md b/ontology/iao.md index 0f601b418..7e7c043d5 100644 --- a/ontology/iao.md +++ b/ontology/iao.md @@ -38,7 +38,7 @@ usages: activity_status: active repository: https://github.com/information-artifact-ontology/IAO preferredPrefix: IAO -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. diff --git a/ontology/iceo.md b/ontology/iceo.md index 645b0db97..fc934feb1 100644 --- a/ontology/iceo.md +++ b/ontology/iceo.md @@ -19,7 +19,7 @@ activity_status: active repository: https://github.com/ontoice/ICEO preferredPrefix: ICEO domain: microbiology -added: 2019-09-02 +github_date_added: 2019-09-02 --- # ICEO: Integrative and Conjugative Element Ontology diff --git a/ontology/ico.md b/ontology/ico.md index 91d344bb0..c420aaf5e 100644 --- a/ontology/ico.md +++ b/ontology/ico.md @@ -24,7 +24,7 @@ usages: activity_status: active repository: https://github.com/ICO-ontology/ICO preferredPrefix: ICO -added: 2015-08-21 +github_date_added: 2015-08-21 --- # Summary diff --git a/ontology/ido.md b/ontology/ido.md index dbb3336f9..ad5ff9468 100644 --- a/ontology/ido.md +++ b/ontology/ido.md @@ -25,5 +25,5 @@ tracker: https://github.com/infectious-disease-ontology/infectious-disease-ontol activity_status: active repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology preferredPrefix: IDO -added: 2015-07-28 +github_date_added: 2015-07-28 --- diff --git a/ontology/idomal.md b/ontology/idomal.md index 80d9c0691..2bce948ad 100644 --- a/ontology/idomal.md +++ b/ontology/idomal.md @@ -16,7 +16,7 @@ products: title: Malaria Ontology activity_status: inactive repository: https://github.com/VEuPathDB-ontology/IDOMAL -added: 2015-07-28 +github_date_added: 2015-07-28 --- An application ontology to cover all aspects of malaria (clinical, epidemiological, biological, etc) as well as the intervention attempts to control it. diff --git a/ontology/iev.md b/ontology/iev.md index ac1dbf12c..8e8bb28d6 100644 --- a/ontology/iev.md +++ b/ontology/iev.md @@ -9,7 +9,7 @@ build: method: obo2owl insert_ontology_id: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A structured controlled vocabulary of pathway centric biological processes. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate biological processes, pathways, sub-pathways in the INOH pathway data.
INOH is part of the BioPAX working group. diff --git a/ontology/imr.md b/ontology/imr.md index 92375cf73..87dd12ef6 100644 --- a/ontology/imr.md +++ b/ontology/imr.md @@ -12,7 +12,7 @@ build: method: obo2owl insert_ontology_id: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A structured controlled vocabulary of concrete protein names and generic (abstract) protein names. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate protein names, protein family names, generic/concrete protein names in the INOH pathway data.
INOH is part of the BioPAX working group. diff --git a/ontology/ino.md b/ontology/ino.md index b58bf3fdd..fc9482f60 100644 --- a/ontology/ino.md +++ b/ontology/ino.md @@ -19,7 +19,7 @@ activity_status: active repository: https://github.com/INO-ontology/ino preferredPrefix: INO domain: biological systems -added: 2018-03-10 +github_date_added: 2018-03-10 --- # Summary diff --git a/ontology/ipr.md b/ontology/ipr.md index a40e4f253..063131e7a 100644 --- a/ontology/ipr.md +++ b/ontology/ipr.md @@ -8,7 +8,7 @@ contact: homepage: http://www.ebi.ac.uk/interpro/index.html is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. diff --git a/ontology/kisao.md b/ontology/kisao.md index 94fc89a0f..ab880962e 100644 --- a/ontology/kisao.md +++ b/ontology/kisao.md @@ -71,7 +71,7 @@ publications: funded_by: - "NIH P41EB023912" - "NIH R35GM119771" -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Kinetic Simulation Algorithm Ontology (KiSAO) describes algorithms for simulating models in biology, their parameters, and their outputs. diff --git a/ontology/labo.md b/ontology/labo.md index 95a067d85..9e7ffac9c 100644 --- a/ontology/labo.md +++ b/ontology/labo.md @@ -39,7 +39,7 @@ license: activity_status: active repository: https://github.com/OpenLHS/LABO preferredPrefix: LABO -added: 2019-08-29 +github_date_added: 2019-08-29 --- LABO is an ontology of informational entities describing laboratory tests prescriptions and reporting documents. LABO is a component of a core ontological model, along with the ontology of drug prescriptions PDRO, that aims to enable interoperability between various clinical data sources in the context of a Learning Health System. diff --git a/ontology/lepao.md b/ontology/lepao.md index 9d3c76b5b..c75d0ac62 100644 --- a/ontology/lepao.md +++ b/ontology/lepao.md @@ -30,5 +30,5 @@ license: activity_status: active repository: https://github.com/insect-morphology/lepao preferredPrefix: LEPAO -added: 2021-12-14 +github_date_added: 2021-12-14 --- diff --git a/ontology/lipro.md b/ontology/lipro.md index 3a35a73fb..7e9c4391a 100644 --- a/ontology/lipro.md +++ b/ontology/lipro.md @@ -15,7 +15,7 @@ build: method: owl2obo is_obsolete: true activity_status: inactive -added: 2015-07-29 +github_date_added: 2015-07-29 --- Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. The ontology describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. diff --git a/ontology/loggerhead.md b/ontology/loggerhead.md index 11019eec0..f46ea70de 100644 --- a/ontology/loggerhead.md +++ b/ontology/loggerhead.md @@ -9,7 +9,7 @@ contact: homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for Loggerhead sea turtle (Caretta caretta) nesting behavior, based on the published ethogram of Hailman and Elowson. diff --git a/ontology/ma.md b/ontology/ma.md index daa652f42..ec90c4103 100644 --- a/ontology/ma.md +++ b/ontology/ma.md @@ -33,7 +33,7 @@ usages: activity_status: active repository: https://github.com/obophenotype/mouse-anatomy-ontology preferredPrefix: MA -added: 2015-07-29 +github_date_added: 2015-07-29 --- A structured controlled vocabulary of the adult anatomy of the mouse (Mus). diff --git a/ontology/mamo.md b/ontology/mamo.md index 06d41a3e4..3577f1776 100644 --- a/ontology/mamo.md +++ b/ontology/mamo.md @@ -22,7 +22,7 @@ license: activity_status: active preferredPrefix: MAMO domain: simulation -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. diff --git a/ontology/mao.md b/ontology/mao.md index ae433712f..a0e53f934 100644 --- a/ontology/mao.md +++ b/ontology/mao.md @@ -8,7 +8,7 @@ contact: homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment. diff --git a/ontology/mat.md b/ontology/mat.md index de7c47e5e..9027f65c4 100644 --- a/ontology/mat.md +++ b/ontology/mat.md @@ -8,7 +8,7 @@ contact: homepage: is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- Minimal set of terms for anatomy diff --git a/ontology/maxo.md b/ontology/maxo.md index a309843aa..04714fea4 100644 --- a/ontology/maxo.md +++ b/ontology/maxo.md @@ -48,7 +48,7 @@ activity_status: active repository: https://github.com/monarch-initiative/MAxO preferredPrefix: MAXO depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png -added: 2020-02-12 +github_date_added: 2020-02-12 --- The Medical Action Ontology (MAxO) provides a structured vocabulary for medical procedures, interventions, therapies, and treatments for disease with an emphasis on rare disease (RD). It is often difficult to find relevant clinical literature about strategies to manage RD patients. Responding to this need, MAxO provides a vocabulary to annotate diseases and phenotypes with recommended treatments and interventions. diff --git a/ontology/mco.md b/ontology/mco.md index 3d49a8d10..e0a5ad7be 100644 --- a/ontology/mco.md +++ b/ontology/mco.md @@ -44,7 +44,7 @@ license: activity_status: active repository: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology preferredPrefix: MCO -added: 2019-02-15 +github_date_added: 2019-02-15 --- Enter a detailed description of your ontology here diff --git a/ontology/mf.md b/ontology/mf.md index 94ca35193..9fdc85842 100644 --- a/ontology/mf.md +++ b/ontology/mf.md @@ -22,7 +22,7 @@ license: activity_status: active repository: https://github.com/jannahastings/mental-functioning-ontology preferredPrefix: MF -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning, founded on the Basic Formal Ontology (BFO) and related to the Ontology for General Medical Science (OGMS). diff --git a/ontology/mfmo.md b/ontology/mfmo.md index 3fda612fe..7bc72483d 100644 --- a/ontology/mfmo.md +++ b/ontology/mfmo.md @@ -24,7 +24,7 @@ products: - id: mfmo.owl activity_status: active preferredPrefix: MFMO -added: 2015-08-11 +github_date_added: 2015-08-11 --- ADD DESCRIPTION HERE diff --git a/ontology/mfo.md b/ontology/mfo.md index 8b0eb42ec..eb352f10f 100644 --- a/ontology/mfo.md +++ b/ontology/mfo.md @@ -15,7 +15,7 @@ title: Medaka fish anatomy and development is_obsolete: true replaced_by: olatdv activity_status: inactive -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. diff --git a/ontology/mfoem.md b/ontology/mfoem.md index 8c6cbc2f2..d7678bb87 100644 --- a/ontology/mfoem.md +++ b/ontology/mfoem.md @@ -22,7 +22,7 @@ license: activity_status: active repository: https://github.com/jannahastings/emotion-ontology preferredPrefix: MFOEM -added: 2015-07-28 +github_date_added: 2015-07-28 --- An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings, designed to support interdisciplinary research by providing unified annotations. diff --git a/ontology/mfomd.md b/ontology/mfomd.md index 11cab6394..24223fc3e 100644 --- a/ontology/mfomd.md +++ b/ontology/mfomd.md @@ -19,7 +19,7 @@ license: activity_status: active repository: https://github.com/jannahastings/mental-functioning-ontology preferredPrefix: MFOMD -added: 2015-08-21 +github_date_added: 2015-08-21 --- An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable. diff --git a/ontology/mi.md b/ontology/mi.md index 06992db8a..f10a6ed3c 100644 --- a/ontology/mi.md +++ b/ontology/mi.md @@ -25,7 +25,7 @@ build: activity_status: active repository: https://github.com/HUPO-PSI/psi-mi-CV preferredPrefix: MI -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative. diff --git a/ontology/miapa.md b/ontology/miapa.md index 14a26a5ba..c8a2ccc4c 100644 --- a/ontology/miapa.md +++ b/ontology/miapa.md @@ -21,7 +21,7 @@ mailing_list: http://groups.google.com/group/miapa-discuss activity_status: active preferredPrefix: MIAPA domain: information -added: 2015-07-28 +github_date_added: 2015-07-28 --- The MIAPA ontology is an application ontology to formalize annotation of phylogenetic data according to the emerging Minimum Information About a Phylogenetic Analysis (MIAPA) metadata reporting standard. Please see [Leebens-Mack _et al._ (2006)](https://doi.org/10.1089/omi.2006.10.231) for the initial introduction of MIAPA. diff --git a/ontology/micro.md b/ontology/micro.md index 106562491..f376f7ec4 100644 --- a/ontology/micro.md +++ b/ontology/micro.md @@ -19,7 +19,7 @@ products: activity_status: active repository: https://github.com/carrineblank/MicrO preferredPrefix: MICRO -added: 2015-10-20 +github_date_added: 2015-10-20 --- Includes terms and term synonyms extracted from > 1500 prokaryotic taxonomic descriptions, collected from a large number of taxonomic descriptions from Archaea, Cyanobacteria, Bacteroidetes, Firmicutes, and Mollicutes. diff --git a/ontology/mirnao.md b/ontology/mirnao.md index d5b86d0d7..1bffb42a5 100644 --- a/ontology/mirnao.md +++ b/ontology/mirnao.md @@ -14,7 +14,7 @@ products: title: microRNA Ontology is_obsolete: true activity_status: inactive -added: 2015-07-28 +github_date_added: 2015-07-28 --- microRNA Ontology (miRNAO) is an application ontology and it has been developed in order to drive miRNA databases. diff --git a/ontology/miro.md b/ontology/miro.md index cb5ecdc1b..b5f2eeffe 100644 --- a/ontology/miro.md +++ b/ontology/miro.md @@ -15,7 +15,7 @@ taxon: title: Mosquito insecticide resistance activity_status: inactive repository: https://github.com/VEuPathDB-ontology/MIRO -added: 2015-07-28 +github_date_added: 2015-07-28 --- Application ontology for entities related to insecticide resistance in mosquitos diff --git a/ontology/mmo.md b/ontology/mmo.md index f260072e4..4233f106c 100644 --- a/ontology/mmo.md +++ b/ontology/mmo.md @@ -35,7 +35,7 @@ browsers: activity_status: active repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology preferredPrefix: MMO -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Measurement Method Ontology is designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms. diff --git a/ontology/mmusdv.md b/ontology/mmusdv.md index c4ebdfe23..5b8d4c1cb 100644 --- a/ontology/mmusdv.md +++ b/ontology/mmusdv.md @@ -24,7 +24,7 @@ products: activity_status: active repository: https://github.com/obophenotype/developmental-stage-ontologies domain: anatomy and development -added: 2015-08-21 +github_date_added: 2015-08-21 --- MmusDv was developed by the Bgee group with assistance from the core Uberon developers and the Mouse anatomy ontology developers. diff --git a/ontology/mo.md b/ontology/mo.md index 2cd2515d0..11dbd5a9f 100644 --- a/ontology/mo.md +++ b/ontology/mo.md @@ -15,7 +15,7 @@ title: Microarray experimental conditions is_obsolete: true replaced_by: obi activity_status: inactive -added: 2015-07-28 +github_date_added: 2015-07-28 --- Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. diff --git a/ontology/mod.md b/ontology/mod.md index 5a29d8cd0..bd3b10b3a 100644 --- a/ontology/mod.md +++ b/ontology/mod.md @@ -33,7 +33,7 @@ build: activity_status: active repository: https://github.com/HUPO-PSI/psi-mod-CV preferredPrefix: MOD -added: 2015-07-28 +github_date_added: 2015-07-28 --- PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified. diff --git a/ontology/mondo.md b/ontology/mondo.md index be1bebc57..ec99b40f0 100644 --- a/ontology/mondo.md +++ b/ontology/mondo.md @@ -84,7 +84,7 @@ usages: activity_status: active repository: https://github.com/monarch-initiative/mondo preferredPrefix: MONDO -added: 2016-07-12 +github_date_added: 2016-07-12 --- The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. Original versions of Mondo were constructed entirely automatically and used the IDs of source databases and ontologies. Later, additional manually curated cross-ontology axioms were added, and a native Mondo ID system was used to avoid confusion with source databases. diff --git a/ontology/mop.md b/ontology/mop.md index 194e76e43..28ece7568 100644 --- a/ontology/mop.md +++ b/ontology/mop.md @@ -24,5 +24,5 @@ activity_status: active repository: https://github.com/rsc-ontologies/rxno preferredPrefix: MOP domain: chemistry and biochemistry -added: 2015-08-17 +github_date_added: 2015-08-17 --- diff --git a/ontology/mp.md b/ontology/mp.md index f477d4405..8ef8ba32b 100644 --- a/ontology/mp.md +++ b/ontology/mp.md @@ -75,7 +75,7 @@ mailing_list: https://groups.google.com/forum/#!forum/phenotype-ontologies-edito activity_status: active repository: https://github.com/mgijax/mammalian-phenotype-ontology preferredPrefix: MP -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data. diff --git a/ontology/mpath.md b/ontology/mpath.md index 844b4cf71..33e58c277 100644 --- a/ontology/mpath.md +++ b/ontology/mpath.md @@ -26,7 +26,7 @@ build: activity_status: active repository: https://github.com/PaulNSchofield/mpath preferredPrefix: MPATH -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes diff --git a/ontology/mpio.md b/ontology/mpio.md index 12f387b63..eac9e362d 100644 --- a/ontology/mpio.md +++ b/ontology/mpio.md @@ -19,7 +19,7 @@ license: activity_status: active repository: https://github.com/MPIO-Developers/MPIO preferredPrefix: MPIO -added: 2017-11-02 +github_date_added: 2017-11-02 --- MPIO (Minimum PDDI Information Ontology) is an OWL representation of minimum information regarding potential drug-drug interaction information. It is based on and meant to be use in alignment with DIDEO or DINTO. diff --git a/ontology/mro.md b/ontology/mro.md index 06403772b..93ca3f7fd 100644 --- a/ontology/mro.md +++ b/ontology/mro.md @@ -31,7 +31,7 @@ usages: activity_status: active repository: https://github.com/IEDB/MRO preferredPrefix: MRO -added: 2015-09-17 +github_date_added: 2015-09-17 --- The MHC Restriction Ontology (MRO) is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. diff --git a/ontology/ms.md b/ontology/ms.md index 90ff88fb2..955b02276 100644 --- a/ontology/ms.md +++ b/ontology/ms.md @@ -35,7 +35,7 @@ build: activity_status: active repository: https://github.com/HUPO-PSI/psi-ms-CV preferredPrefix: MS -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. Developed by the HUPO Proteomics Standards Initiative (PSI). diff --git a/ontology/nbo.md b/ontology/nbo.md index 814b6e158..62a183232 100644 --- a/ontology/nbo.md +++ b/ontology/nbo.md @@ -31,5 +31,5 @@ preferredPrefix: NBO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/24177753 title: "Analyzing gene expression data in mice with the Neuro Behavior Ontology" -added: 2015-07-28 +github_date_added: 2015-07-28 --- diff --git a/ontology/ncbitaxon.md b/ontology/ncbitaxon.md index bbd54d918..27d4469a2 100644 --- a/ontology/ncbitaxon.md +++ b/ontology/ncbitaxon.md @@ -46,7 +46,7 @@ license: label: CC0 1.0 activity_status: active repository: https://github.com/obophenotype/ncbitaxon -added: 2015-07-28 +github_date_added: 2015-07-28 --- The NCBITaxon ontology is an automatic translation of the [NCBI taxonomy database](http://www.ncbi.nlm.nih.gov/taxonomy) into obo/owl. diff --git a/ontology/ncit.md b/ontology/ncit.md index 2407ce8af..1ecb02e50 100644 --- a/ontology/ncit.md +++ b/ontology/ncit.md @@ -32,7 +32,7 @@ activity_status: active repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition preferredPrefix: NCIT domain: health -added: 2016-04-01 +github_date_added: 2016-04-01 --- The NCI Thesaurus is a reference terminology that includes broad diff --git a/ontology/ncro.md b/ontology/ncro.md index b2e2e1df0..933f72212 100644 --- a/ontology/ncro.md +++ b/ontology/ncro.md @@ -27,7 +27,7 @@ build: activity_status: active repository: https://github.com/OmniSearch/ncro preferredPrefix: NCRO -added: 2015-11-18 +github_date_added: 2015-11-18 --- The NCRO is a reference ontology in the non-coding RNA (ncRNA) field, diff --git a/ontology/nif_cell.md b/ontology/nif_cell.md index 00cbe8403..b1de73ae5 100644 --- a/ontology/nif_cell.md +++ b/ontology/nif_cell.md @@ -10,7 +10,7 @@ homepage: http://neuinfo.org/ is_obsolete: true replaced_by: cl activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- Cell types from NIFSTD diff --git a/ontology/nif_dysfunction.md b/ontology/nif_dysfunction.md index a92a52756..ff9bf4ca8 100644 --- a/ontology/nif_dysfunction.md +++ b/ontology/nif_dysfunction.md @@ -9,7 +9,7 @@ homepage: http://neuinfo.org/ is_obsolete: true replaced_by: doid activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- This ontology contains the former BIRNLex-Disease, version 1.3.2. diff --git a/ontology/nif_grossanatomy.md b/ontology/nif_grossanatomy.md index 7ee51cd9e..1087cd6a2 100644 --- a/ontology/nif_grossanatomy.md +++ b/ontology/nif_grossanatomy.md @@ -9,7 +9,7 @@ homepage: http://neuinfo.org/ is_obsolete: true replaced_by: uberon activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- NIF-GrossAnatomy: anatomical entities of relevance to neuroscience. Contains most classes from BIRNLex-Anatomy diff --git a/ontology/nmr.md b/ontology/nmr.md index acf8aa999..d514bff14 100644 --- a/ontology/nmr.md +++ b/ontology/nmr.md @@ -16,7 +16,7 @@ build: method: owl2obo is_obsolete: true activity_status: inactive -added: 2015-07-28 +github_date_added: 2015-07-28 --- Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation. diff --git a/ontology/nomen.md b/ontology/nomen.md index 2f264c88e..af46fd0d7 100644 --- a/ontology/nomen.md +++ b/ontology/nomen.md @@ -39,7 +39,7 @@ canonical: nomen.owl activity_status: active repository: https://github.com/SpeciesFileGroup/nomen preferredPrefix: NOMEN -added: 2019-01-11 +github_date_added: 2019-01-11 --- NOMEN is a nomenclatural ontology for biological names (not concepts). See the NOMEN homepage for more info. diff --git a/ontology/oae.md b/ontology/oae.md index e444dd669..b787c184d 100644 --- a/ontology/oae.md +++ b/ontology/oae.md @@ -24,7 +24,7 @@ license: activity_status: active repository: https://github.com/OAE-ontology/OAE preferredPrefix: OAE -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Ontology of Adverse Events (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. diff --git a/ontology/oarcs.md b/ontology/oarcs.md index e8d9a19b2..74fa3a1c7 100644 --- a/ontology/oarcs.md +++ b/ontology/oarcs.md @@ -19,7 +19,7 @@ products: - id: oarcs.owl activity_status: active preferredPrefix: OARCS -added: 2017-02-10 +github_date_added: 2017-02-10 --- OArCS is an ontology describing the Arthropod ciruclatory system. diff --git a/ontology/oba.md b/ontology/oba.md index 4371a03ac..94c2feb3b 100644 --- a/ontology/oba.md +++ b/ontology/oba.md @@ -30,7 +30,7 @@ build: activity_status: active repository: https://github.com/obophenotype/bio-attribute-ontology preferredPrefix: OBA -added: 2015-07-28 +github_date_added: 2015-07-28 --- A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with diff --git a/ontology/obcs.md b/ontology/obcs.md index c7560eb13..688e7bdc5 100644 --- a/ontology/obcs.md +++ b/ontology/obcs.md @@ -22,7 +22,7 @@ license: activity_status: active repository: https://github.com/obcs/obcs preferredPrefix: OBCS -added: 2015-07-31 +github_date_added: 2015-07-31 --- The Ontology of Biological and Clinical Statistics (OBCS) is a biomedical ontology in the domain of biological and clinical statistics. OBCS is primarily targeted for statistical term representation in the fields in biological, biomedical, and clinical domains. diff --git a/ontology/obi.md b/ontology/obi.md index 72de4de30..ee2526cf0 100644 --- a/ontology/obi.md +++ b/ontology/obi.md @@ -75,7 +75,7 @@ usages: description: A specific OBI term used to autocomplete in NIF search OBI:0100026 'organism' activity_status: active preferredPrefix: OBI -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of life-science and clinical investigations. diff --git a/ontology/obib.md b/ontology/obib.md index 1a3d2a8ce..91d3f188e 100644 --- a/ontology/obib.md +++ b/ontology/obib.md @@ -33,7 +33,7 @@ license: activity_status: active repository: https://github.com/biobanking/biobanking preferredPrefix: OBIB -added: 2015-08-17 +github_date_added: 2015-08-17 --- The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. diff --git a/ontology/obo_rel.md b/ontology/obo_rel.md index ea27c4726..9f8c19519 100644 --- a/ontology/obo_rel.md +++ b/ontology/obo_rel.md @@ -10,7 +10,7 @@ homepage: http://www.obofoundry.org/ro is_obsolete: true replaced_by: ro activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- Defines core relations used in all OBO ontologies. Importand note: this ontology is now deprecated - use RO instead diff --git a/ontology/ogg.md b/ontology/ogg.md index bca54c0d8..65899323b 100644 --- a/ontology/ogg.md +++ b/ontology/ogg.md @@ -19,7 +19,7 @@ license: activity_status: active preferredPrefix: OGG domain: biological systems -added: 2015-07-29 +github_date_added: 2015-07-29 --- # Summary diff --git a/ontology/ogi.md b/ontology/ogi.md index 9cf1ac998..5c5934525 100644 --- a/ontology/ogi.md +++ b/ontology/ogi.md @@ -15,7 +15,7 @@ tracker: https://code.google.com/p/ontology-for-genetic-interval/issues/list activity_status: inactive is_obsolete: true replaced_by: ogsf -added: 2015-07-28 +github_date_added: 2015-07-28 --- Using BFO as its framwork, OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is "the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure. diff --git a/ontology/ogms.md b/ontology/ogms.md index ece008121..d11649cbf 100644 --- a/ontology/ogms.md +++ b/ontology/ogms.md @@ -25,7 +25,7 @@ depicted_by: https://avatars2.githubusercontent.com/u/12973154?s=200&v=4 activity_status: active repository: https://github.com/OGMS/ogms preferredPrefix: OGMS -added: 2015-07-29 +github_date_added: 2015-07-29 --- The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. See http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf diff --git a/ontology/ogsf.md b/ontology/ogsf.md index 04226203b..6d39bc642 100644 --- a/ontology/ogsf.md +++ b/ontology/ogsf.md @@ -19,7 +19,7 @@ activity_status: active repository: https://github.com/linikujp/OGSF preferredPrefix: OGSF domain: investigations -added: 2015-07-28 +github_date_added: 2015-07-28 --- Ontology for Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO2.0's framwork. The ontology is under the domain of genetic epidemiology. diff --git a/ontology/ohd.md b/ontology/ohd.md index fdcd6e66a..d7988c3c5 100644 --- a/ontology/ohd.md +++ b/ontology/ohd.md @@ -24,7 +24,7 @@ tracker: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/issu repository: https://github.com/oral-health-and-disease-ontologies/ohd-ontology activity_status: active preferredPrefix: OHD -added: 2016-12-01 +github_date_added: 2016-12-01 --- The Oral Health and Disease Ontology is intended as a BFO and OBO diff --git a/ontology/ohmi.md b/ontology/ohmi.md index 468cf54a0..3fe690171 100644 --- a/ontology/ohmi.md +++ b/ontology/ohmi.md @@ -20,7 +20,7 @@ activity_status: active repository: https://github.com/ohmi-ontology/ohmi preferredPrefix: OHMI domain: organisms -added: 2017-04-21 +github_date_added: 2017-04-21 --- The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions. diff --git a/ontology/ohpi.md b/ontology/ohpi.md index df088b30e..7bae45bba 100644 --- a/ontology/ohpi.md +++ b/ontology/ohpi.md @@ -20,7 +20,7 @@ activity_status: active repository: https://github.com/OHPI/ohpi preferredPrefix: OHPI domain: biological systems -added: 2019-07-22 +github_date_added: 2019-07-22 --- # OHPI: Ontology of Host-Pathogen Interactions diff --git a/ontology/olatdv.md b/ontology/olatdv.md index cf413584a..7657774a3 100644 --- a/ontology/olatdv.md +++ b/ontology/olatdv.md @@ -24,5 +24,5 @@ license: activity_status: active repository: https://github.com/obophenotype/developmental-stage-ontologies domain: anatomy and development -added: 2015-08-21 +github_date_added: 2015-08-21 --- diff --git a/ontology/omiabis.md b/ontology/omiabis.md index a126ee96d..fbb9ce280 100644 --- a/ontology/omiabis.md +++ b/ontology/omiabis.md @@ -18,7 +18,7 @@ license: is_obsolete: true activity_status: inactive repository: https://github.com/OMIABIS/omiabis-dev -added: 2016-02-05 +github_date_added: 2016-02-05 --- OMIABIS has been merged into OBIB (http://www.obofoundry.org/ontology/obib.html). diff --git a/ontology/omit.md b/ontology/omit.md index 9e3cf21ba..6a96ad113 100644 --- a/ontology/omit.md +++ b/ontology/omit.md @@ -21,7 +21,7 @@ activity_status: active repository: https://github.com/OmniSearch/omit preferredPrefix: OMIT domain: chemistry and biochemistry -added: 2015-07-29 +github_date_added: 2015-07-29 --- The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). OMIT has reused and extended a set of well-established concepts from existing bio-ontologies, e.g., Gene Ontology, Sequence Ontology, Protein Ontology, NCBI Organism Taxonomy, Human Disease Ontology, Foundational Model of Anatomy, and so forth. diff --git a/ontology/omo.md b/ontology/omo.md index ca8121284..45ce7be70 100644 --- a/ontology/omo.md +++ b/ontology/omo.md @@ -25,5 +25,5 @@ usages: activity_status: active repository: https://github.com/information-artifact-ontology/ontology-metadata preferredPrefix: OMO -added: 2020-05-02 +github_date_added: 2020-05-02 --- diff --git a/ontology/omp.md b/ontology/omp.md index 519cb397b..226280123 100644 --- a/ontology/omp.md +++ b/ontology/omp.md @@ -23,7 +23,7 @@ tracker: https://github.com/microbialphenotypes/OMP-ontology/issues activity_status: active repository: https://github.com/microbialphenotypes/OMP-ontology preferredPrefix: OMP -added: 2015-08-21 +github_date_added: 2015-08-21 --- OMP is a community ontology for annotating microbial phenotypes. diff --git a/ontology/omrse.md b/ontology/omrse.md index 196348eae..6601b60bb 100644 --- a/ontology/omrse.md +++ b/ontology/omrse.md @@ -31,7 +31,7 @@ publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/27406187 title: "The ontology of medically related social entities: recent developments" -added: 2015-07-28 +github_date_added: 2015-07-28 --- This ontology covers the domain of social entities that are related to health care, such as demographic information (social entities for recording gender (but not sex) and marital status, for example) and the roles of various individuals and organizations (patient, hospital,etc.) diff --git a/ontology/one.md b/ontology/one.md index 633b21d9d..49a226b30 100644 --- a/ontology/one.md +++ b/ontology/one.md @@ -29,7 +29,7 @@ tracker: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies/issue activity_status: active repository: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies preferredPrefix: ONE -added: 2020-11-17 +github_date_added: 2020-11-17 --- Nutritional epidemiology is a specific research area. The generic ontologies for food science, nutrition science or medical science failed to cover the specific characteristics of nutritional epidemiologic studies. As a result, we developed the ontology for nutritional epidemiology (ONE) in order to describe nutritional epidemiologic studies accurately. diff --git a/ontology/ons.md b/ontology/ons.md index d1ea77b1d..d5088dc17 100644 --- a/ontology/ons.md +++ b/ontology/ons.md @@ -36,7 +36,7 @@ tracker: https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues activity_status: active repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies preferredPrefix: ONS -added: 2020-05-28 +github_date_added: 2020-05-28 --- ONS was developed under the ENPADASI European project, to assist the standardized description of (human) nutritional studies. As such, it includes and covers classes and relations that are commonly encountered while conducting, storing, harmonizing, integrating, describing and querying for nutritional studies. ONS main objective and long-term goal, is to represent a comprehensive resource for the description of concepts in the broader human nutrition domain, representing a solid and extensible formal ontology framework, where integration of new information can be easily achieved by the addition of extra modules. diff --git a/ontology/ontoavida.md b/ontology/ontoavida.md index 939e1ef14..503dbab7e 100644 --- a/ontology/ontoavida.md +++ b/ontology/ontoavida.md @@ -29,5 +29,5 @@ license: activity_status: active repository: https://gitlab.com/fortunalab/ontoavida preferredPrefix: ONTOAVIDA -added: 2021-12-01 +github_date_added: 2021-12-01 --- diff --git a/ontology/ontoneo.md b/ontology/ontoneo.md index 30e32086f..da6e6f73c 100644 --- a/ontology/ontoneo.md +++ b/ontology/ontoneo.md @@ -28,7 +28,7 @@ browsers: activity_status: active repository: https://github.com/ontoneo-project/Ontoneo preferredPrefix: ONTONEO -added: 2016-11-22 +github_date_added: 2016-11-22 --- The OntONeo suite is a collection of open ontologies available about Obstetric and Neonatal domain, currently designed to be composed by three complementary sub-ontologies covering several data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. diff --git a/ontology/oostt.md b/ontology/oostt.md index 8d9f76e1e..428fd3fd0 100644 --- a/ontology/oostt.md +++ b/ontology/oostt.md @@ -19,7 +19,7 @@ license: activity_status: active repository: https://github.com/OOSTT/OOSTT preferredPrefix: OOSTT -added: 2016-04-04 +github_date_added: 2016-04-04 --- The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2). It is developed collaboratively by domain and ontology experts in the NIH-funded CAFE (Comparative Assessment Framework for Environments of trauma care) project (1R01GM111324-01A1). It will be used as the ontology backbone of a graphical user interface comparing graphical representations of organizational structures. diff --git a/ontology/opl.md b/ontology/opl.md index 769bd954b..2d12e0ef1 100644 --- a/ontology/opl.md +++ b/ontology/opl.md @@ -30,7 +30,7 @@ usages: activity_status: active repository: https://github.com/OPL-ontology/OPL preferredPrefix: OPL -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Ontology for Parasite LifeCycle (OPL) is designed to serve as a reference ontology for parasite life cycle stages. It models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location diff --git a/ontology/opmi.md b/ontology/opmi.md index 676e01811..017376733 100644 --- a/ontology/opmi.md +++ b/ontology/opmi.md @@ -20,7 +20,7 @@ activity_status: active repository: https://github.com/OPMI/opmi preferredPrefix: OPMI domain: investigations -added: 2018-08-30 +github_date_added: 2018-08-30 --- The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions. diff --git a/ontology/ornaseq.md b/ontology/ornaseq.md index 371aa7e9e..64f942b81 100644 --- a/ontology/ornaseq.md +++ b/ontology/ornaseq.md @@ -19,7 +19,7 @@ license: activity_status: active repository: https://github.com/safisher/ornaseq preferredPrefix: ORNASEQ -added: 2019-06-20 +github_date_added: 2019-06-20 --- This is an application ontology used to annotate next-generation sequencing experiments performed on RNA (RNAseq). It uses terms from BFO, CHEBI, CL, GENEPIO, GO, IAO, NCBITaxon, NCIT, OBI, OBIws, OGMS, OMIABIS, SO, TAXRANK, and UBERON as well as EFO. diff --git a/ontology/ovae.md b/ontology/ovae.md index df5650e1d..01ae7a138 100644 --- a/ontology/ovae.md +++ b/ontology/ovae.md @@ -19,7 +19,7 @@ activity_status: active repository: https://github.com/OVAE-Ontology/ovae preferredPrefix: OVAE domain: health -added: 2015-07-28 +github_date_added: 2015-07-28 --- # Summary diff --git a/ontology/pao.md b/ontology/pao.md index c35017d42..9da6f3221 100644 --- a/ontology/pao.md +++ b/ontology/pao.md @@ -13,7 +13,7 @@ taxon: homepage: http://www.plantontology.org is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- REPLACED BY: PO. A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization. Note that this has been subsumed into the PO diff --git a/ontology/pato.md b/ontology/pato.md index fda3c8b7c..11cc9ccb2 100644 --- a/ontology/pato.md +++ b/ontology/pato.md @@ -52,7 +52,7 @@ publications: title: "The anatomy of phenotype ontologies: principles, properties and applications" - id: https://www.ncbi.nlm.nih.gov/pubmed/15642100 title: "Using ontologies to describe mouse phenotypes" -added: 2015-07-28 +github_date_added: 2015-07-28 --- Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested. diff --git a/ontology/pcl.md b/ontology/pcl.md index 202822ff2..3269753e1 100644 --- a/ontology/pcl.md +++ b/ontology/pcl.md @@ -43,5 +43,5 @@ license: activity_status: active repository: https://github.com/obophenotype/provisional_cell_ontology preferredPrefix: PCL -added: 2022-01-25 +github_date_added: 2022-01-25 --- diff --git a/ontology/pco.md b/ontology/pco.md index bfd482767..7807cd241 100644 --- a/ontology/pco.md +++ b/ontology/pco.md @@ -38,7 +38,7 @@ license: activity_status: active repository: https://github.com/PopulationAndCommunityOntology/pco preferredPrefix: PCO -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. diff --git a/ontology/pd_st.md b/ontology/pd_st.md index 7ea4556a7..633066e10 100644 --- a/ontology/pd_st.md +++ b/ontology/pd_st.md @@ -12,5 +12,5 @@ homepage: http://4dx.embl.de/platy is_obsolete: true replaced_by: pdumdv activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- diff --git a/ontology/pdro.md b/ontology/pdro.md index 6b415082e..13683b922 100644 --- a/ontology/pdro.md +++ b/ontology/pdro.md @@ -27,7 +27,7 @@ tracker: https://github.com/OpenLHS/PDRO/issues activity_status: active repository: https://github.com/OpenLHS/PDRO preferredPrefix: PDRO -added: 2016-11-11 +github_date_added: 2016-11-11 --- PDRO is a realist ontology that aims to represent the domain of drug prescriptions. Such an ontology is currently missing in the OBOFoundry and is highly relevant to the domains of existing ontologies like DRON, OMRSE and OAE. PDRO's central focus is the structure of a drug prescription, which is represented as a mereology of informational entities. Our current use cases are (1) refining this structure (e.g., adding closure axioms, cardinality, datatype bindings, etc) for prospectively standardizing local electronic prescriptions and (2) annotating prescription data of differing EHRs for detecting inappropriate prescriptions using a central semantic framework. Future ontological work will include aligning PDRO more closely with the Document Acts Ontology. diff --git a/ontology/pdumdv.md b/ontology/pdumdv.md index 8058627e7..51927e122 100644 --- a/ontology/pdumdv.md +++ b/ontology/pdumdv.md @@ -24,5 +24,5 @@ license: activity_status: active repository: https://github.com/obophenotype/developmental-stage-ontologies domain: anatomy and development -added: 2015-08-21 +github_date_added: 2015-08-21 --- diff --git a/ontology/peco.md b/ontology/peco.md index 10a624f06..8b8ff1dc8 100644 --- a/ontology/peco.md +++ b/ontology/peco.md @@ -27,7 +27,7 @@ activity_status: active repository: https://github.com/Planteome/plant-experimental-conditions-ontology preferredPrefix: PECO depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG -added: 2017-06-05 +github_date_added: 2017-06-05 --- A structured, controlled vocabulary for the representation of plant experimental conditions. diff --git a/ontology/pgdso.md b/ontology/pgdso.md index 682755ff3..000b233fa 100644 --- a/ontology/pgdso.md +++ b/ontology/pgdso.md @@ -11,7 +11,7 @@ taxon: homepage: http://www.plantontology.org is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- REPLACED BY: PO. A controlled vocabulary of growth and developmental stages in various plants. Note that this has been subsumed into the PO diff --git a/ontology/phipo.md b/ontology/phipo.md index 8b79d9457..45625e1cf 100644 --- a/ontology/phipo.md +++ b/ontology/phipo.md @@ -32,7 +32,7 @@ preferredPrefix: PHIPO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/34788826 title: "PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions" -added: 2018-08-15 +github_date_added: 2018-08-15 --- PHIPO is being developed to support the comprehensive and detailed representation of phenotypes in PHI-base, the multi-species Pathogen-Host Interactions database available online at . PHIPO is pre-composed and logically defined. diff --git a/ontology/plana.md b/ontology/plana.md index 76ee9ef11..10cfa039c 100644 --- a/ontology/plana.md +++ b/ontology/plana.md @@ -39,7 +39,7 @@ license: activity_status: active repository: https://github.com/obophenotype/planaria-ontology preferredPrefix: PLANA -added: 2017-02-07 +github_date_added: 2017-02-07 --- Anatomy ontology for planaria and terms specific to the developmental stages of the planarian __Schmidtea mediterranea__ diff --git a/ontology/planp.md b/ontology/planp.md index 19ed7f1e9..972103ee4 100644 --- a/ontology/planp.md +++ b/ontology/planp.md @@ -32,7 +32,7 @@ license: activity_status: active repository: https://github.com/obophenotype/planarian-phenotype-ontology preferredPrefix: PLANP -added: 2018-11-19 +github_date_added: 2018-11-19 --- Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. Many of the phenotypes were seen durning RNAi experiments. diff --git a/ontology/plo.md b/ontology/plo.md index 5cbd1103b..98f0509ba 100644 --- a/ontology/plo.md +++ b/ontology/plo.md @@ -8,7 +8,7 @@ contact: homepage: http://www.sanger.ac.uk/Users/mb4/PLO/ is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A structured controlled vocabulary for the life cycle of the malaria parasite Plasmodium. diff --git a/ontology/po.md b/ontology/po.md index 48d4c26f2..988af01bd 100644 --- a/ontology/po.md +++ b/ontology/po.md @@ -70,7 +70,7 @@ activity_status: active repository: https://github.com/Planteome/plant-ontology preferredPrefix: PO depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants. diff --git a/ontology/poro.md b/ontology/poro.md index 7292d997e..dd9eea5eb 100644 --- a/ontology/poro.md +++ b/ontology/poro.md @@ -38,7 +38,7 @@ tracker: https://github.com/obophenotype/porifera-ontology/issues activity_status: active repository: https://github.com/obophenotype/porifera-ontology preferredPrefix: PORO -added: 2015-07-28 +github_date_added: 2015-07-28 --- An ontology covering the anatomy of Porifera (sponges) diff --git a/ontology/ppo.md b/ontology/ppo.md index 82f7c712b..383e6844f 100644 --- a/ontology/ppo.md +++ b/ontology/ppo.md @@ -25,7 +25,7 @@ taxon: activity_status: active repository: https://github.com/PlantPhenoOntology/PPO preferredPrefix: PPO -added: 2016-12-30 +github_date_added: 2016-12-30 --- Plant phenology — the timing of plant life-cycle events, such as flowering or leafing-out — has cascading effects on multiple levels of biological organization, from individuals to ecosystems, and is crucial for understanding the links between climate and biological communities. Plant phenology data are collected and used by many different types of researchers, from plant breeders to ecosystem ecologists. Today, thanks to data digitization and aggregation initiatives, phenology monitoring networks, and the efforts of citizen scientists, more phenologically relevant data is available than ever before. Unfortunately, combining these data in large-scale analyses remains prohibitively difficult, mostly because the individuals and organizations producing the data are using non-standardized terminologies and metrics during data collection and processing. Lack of standardization remains particularly problematic for historical datasets, which are crucial for time-based analyses. diff --git a/ontology/pr.md b/ontology/pr.md index 060e0c96c..761286292 100644 --- a/ontology/pr.md +++ b/ontology/pr.md @@ -58,7 +58,7 @@ usages: activity_status: active repository: https://github.com/PROconsortium/PRoteinOntology preferredPrefix: PR -added: 2015-07-28 +github_date_added: 2015-07-28 --- The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. diff --git a/ontology/propreo.md b/ontology/propreo.md index 70c91c9c3..c6d40258d 100644 --- a/ontology/propreo.md +++ b/ontology/propreo.md @@ -8,7 +8,7 @@ contact: homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/ is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A comprehensive proteomics data and process provenance ontology. diff --git a/ontology/psdo.md b/ontology/psdo.md index 30a6c8b89..2d9519146 100644 --- a/ontology/psdo.md +++ b/ontology/psdo.md @@ -30,7 +30,7 @@ license: activity_status: active repository: https://github.com/Display-Lab/psdo preferredPrefix: PSDO -added: 2019-04-04 +github_date_added: 2019-04-04 --- The Performance Summary Display Ontology (PSDO) is a lightweight application ontology used to diff --git a/ontology/pso.md b/ontology/pso.md index 61ae90c9b..fba0aee9b 100644 --- a/ontology/pso.md +++ b/ontology/pso.md @@ -35,7 +35,7 @@ license: activity_status: active repository: https://github.com/Planteome/plant-stress-ontology preferredPrefix: PSO -added: 2020-05-14 +github_date_added: 2020-05-14 --- Enter a detailed description of your ontology here diff --git a/ontology/pw.md b/ontology/pw.md index d6cea3199..d77b6c536 100644 --- a/ontology/pw.md +++ b/ontology/pw.md @@ -36,7 +36,7 @@ activity_status: active repository: https://github.com/rat-genome-database/PW-Pathway-Ontology preferredPrefix: PW depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Pathway Ontology is a controlled vocabulary for pathways that provides standard terms for the annotation of gene products. The Pathway Ontology is under development at Rat Genome Database. diff --git a/ontology/rbo.md b/ontology/rbo.md index 06bd4a9c0..ce68cf4b9 100644 --- a/ontology/rbo.md +++ b/ontology/rbo.md @@ -48,7 +48,7 @@ license: activity_status: active repository: https://github.com/Radiobiology-Informatics-Consortium/RBO preferredPrefix: RBO -added: 2021-01-28 +github_date_added: 2021-01-28 --- The effects of all kinds of radiation on biological systems is the subject of much research, both on earth and in space environments. This ontology is designed to support the needs of these investigators, particularly for organizing, describing and archiving data from experiments and observations examining these effects. diff --git a/ontology/resid.md b/ontology/resid.md index 8700a8638..05134760d 100644 --- a/ontology/resid.md +++ b/ontology/resid.md @@ -12,7 +12,7 @@ homepage: http://www.ebi.ac.uk/RESID/ title: Protein covalent bond is_obsolete: true activity_status: inactive -added: 2015-07-28 +github_date_added: 2015-07-28 --- For the description of covalent bonds in proteins. diff --git a/ontology/rex.md b/ontology/rex.md index 2b173d285..2bea8f35f 100644 --- a/ontology/rex.md +++ b/ontology/rex.md @@ -10,7 +10,7 @@ build: insert_ontology_id: true method: obo2owl activity_status: orphaned -added: 2015-07-28 +github_date_added: 2015-07-28 --- REX is an ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. REX includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX. diff --git a/ontology/rnao.md b/ontology/rnao.md index 7feb2bf55..f576df968 100644 --- a/ontology/rnao.md +++ b/ontology/rnao.md @@ -28,5 +28,5 @@ build: tracker: https://github.com/BGSU-RNA/rnao/issues activity_status: inactive repository: https://github.com/BGSU-RNA/rnao -added: 2015-07-28 +github_date_added: 2015-07-28 --- diff --git a/ontology/ro.md b/ontology/ro.md index 54d802f11..4d283d63f 100644 --- a/ontology/ro.md +++ b/ontology/ro.md @@ -66,7 +66,7 @@ usages: activity_status: active repository: https://github.com/oborel/obo-relations preferredPrefix: RO -added: 2015-07-28 +github_date_added: 2015-07-28 --- ![logo](/images/ro_logo.png) diff --git a/ontology/rs.md b/ontology/rs.md index b46cc3832..5c3cc806b 100644 --- a/ontology/rs.md +++ b/ontology/rs.md @@ -35,7 +35,7 @@ repository: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology preferredPrefix: RS depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif domain: organisms -added: 2015-07-28 +github_date_added: 2015-07-28 --- Ontology of rat strains diff --git a/ontology/rxno.md b/ontology/rxno.md index e706a0d6d..e39a769ab 100644 --- a/ontology/rxno.md +++ b/ontology/rxno.md @@ -24,7 +24,7 @@ activity_status: active repository: https://github.com/rsc-ontologies/rxno preferredPrefix: RXNO domain: chemistry and biochemistry -added: 2015-08-17 +github_date_added: 2015-08-17 --- RXNO, the name reaction ontology, connects organic name reactions such as the Diels-Alder cyclization and the Cannizzaro reaction to their roles in an organic synthesis and to processes in MOP. diff --git a/ontology/sao.md b/ontology/sao.md index 66d0a2a18..0820a28fd 100644 --- a/ontology/sao.md +++ b/ontology/sao.md @@ -12,7 +12,7 @@ homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html is_obsolete: true replaced_by: go activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- We have developed the Subcellular Anatomy Ontology for the Nervous System (SAO) to provide a formal ontology to describe structures from the dimensional range known as the “mesoscale,” encompassing cellular and subcellular structure, supracellular domains, and macromolecules. The SAO describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil (Fong et al., submitted). Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their approporiate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration. diff --git a/ontology/sbo.md b/ontology/sbo.md index 7db0f3a68..b4926416b 100644 --- a/ontology/sbo.md +++ b/ontology/sbo.md @@ -23,7 +23,7 @@ license: label: Artistic License 2.0 activity_status: active preferredPrefix: SBO -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of six orthogonal vocabularies defining: the roles of reaction participants (eg. "substrate"), quantitative parameters (eg. "Michaelis constant"), a precise classification of mathematical expressions that describe the system (eg. "mass action rate law"), the modeling framework used (eg. "logical framework"), and a branch each to describe entity (eg. "macromolecule") and interaction (eg. "process") types. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. More information about SBO can be found from the project FAQ, at http://www.ebi.ac.uk/sbo/ SBO is a project of the BioModels.net effort and is developed through community collaboration diff --git a/ontology/scdo.md b/ontology/scdo.md index 41edc85cb..6705a5a61 100644 --- a/ontology/scdo.md +++ b/ontology/scdo.md @@ -65,7 +65,7 @@ dependencies: - id: vo - id: vt preferredPrefix: SCDO -added: 2021-04-16 +github_date_added: 2021-04-16 --- The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to: 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD, 3) links to other ontologies and bodies of work such as DO, PhenX, MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM. Once complete, we anticipate that the ontology will: 1) be the most comprehensive collection of knowledge on SCD, 2) facilitate exploration of new scientific questions and ideas, 3) facilitate seamless data sharing and collaborations including meta-analysis within the SCD community, 4) support the building of databasing and clinical informatics in SCD. diff --git a/ontology/sep.md b/ontology/sep.md index a275eec36..1b36cc943 100644 --- a/ontology/sep.md +++ b/ontology/sep.md @@ -19,7 +19,7 @@ build: insert_ontology_id: true activity_status: inactive is_obsolete: true -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative. diff --git a/ontology/sepio.md b/ontology/sepio.md index b6ac1d549..c34ccd7d5 100644 --- a/ontology/sepio.md +++ b/ontology/sepio.md @@ -28,7 +28,7 @@ activity_status: active repository: https://github.com/monarch-initiative/SEPIO-ontology preferredPrefix: SEPIO depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/SEPIO-LOGOS/sepio_logo_black-banner.png -added: 2017-06-30 +github_date_added: 2017-06-30 --- The Scientific Evidence and Provenance Information Ontology (SEPIO) was developed to support description of evidence and provenance information for scientific claims. The core model represents the relationships between claims, their evidence lines, the information items that comprise these lines of evidence, and the methods, tools, and agents involved in the creation of these entities. Use cases driving SEPIO development include integration of scientific claims and their associated evidence/provenance metadata, and support for the discovery, analysis, and evaluation of claims based on this metadata. diff --git a/ontology/sibo.md b/ontology/sibo.md index b24a85ced..6ba82bdf5 100644 --- a/ontology/sibo.md +++ b/ontology/sibo.md @@ -25,7 +25,7 @@ build: activity_status: orphaned repository: https://github.com/obophenotype/sibo preferredPrefix: SIBO -added: 2015-07-29 +github_date_added: 2015-07-29 --- The Social Insect Behavior Ontology (SIBO), created by Chris Smith of the BDGP/SFSU. It was been adopted by Chris Mungall, but I am currently looking to hand it over or to merge it into the NBO diff --git a/ontology/so.md b/ontology/so.md index e43282dea..afa55d3f9 100644 --- a/ontology/so.md +++ b/ontology/so.md @@ -42,7 +42,7 @@ depicted_by: http://sequenceontology.org/img/so_icon.png activity_status: active repository: https://github.com/The-Sequence-Ontology/SO-Ontologies preferredPrefix: SO -added: 2015-07-28 +github_date_added: 2015-07-28 --- SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. SO is also part of the Open Biomedical Ontologies library. Our aim is to develop an ontology suitable for describing the features of biological sequences. For questions, please send mail to the SO developers mailing list. For new term suggestions, please use the [Term Tracker](https://github.com/The-Sequence-Ontology/SO-Ontologies/issues). diff --git a/ontology/sopharm.md b/ontology/sopharm.md index 5abd0d13f..3e79a1a2e 100644 --- a/ontology/sopharm.md +++ b/ontology/sopharm.md @@ -11,7 +11,7 @@ taxon: homepage: http://www.loria.fr/~coulet/sopharm2.0_description.php is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- SO-Pharm is a formal ontology that represent domain knowledge in pharmacogenomics. To achieve this goal SO-Pharm articulates ontologies from sub domains of phamacogenomics (i.e. genotype, phenotype, drug, trial representations). SO-Pharm enables to support knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. diff --git a/ontology/spd.md b/ontology/spd.md index b83a5a823..f0620a40f 100644 --- a/ontology/spd.md +++ b/ontology/spd.md @@ -29,7 +29,7 @@ preferredPrefix: SPD publications: - id: https://doi.org/10.3390/d11100202 title: "The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data" -added: 2015-07-28 +github_date_added: 2015-07-28 --- An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). diff --git a/ontology/stato.md b/ontology/stato.md index 42d1c3f30..a4421d887 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -23,7 +23,7 @@ tracker: https://github.com/ISA-tools/stato/issues activity_status: active repository: https://github.com/ISA-tools/stato preferredPrefix: STATO -added: 2015-08-17 +github_date_added: 2015-08-17 --- The STATistics Ontology (STATO) project started in early 2012, as part of the requirement of the community-driven ISA Commons to represent the results of data analysis. STATO is a standalone project since Nov 2012. STATO is driven and funded by several ISA-based projects and their user community, but also by collaborations with data publication platforms. STATO is applicable to, but not limited, the broad life, natural and biomedical science domain with documented applications for factorial design, association studies, differential expression, hit selection and meta-analysis. STATO has been developed to interoperate with other OBO Foundry ontologies, hence relies on the Basics Formal Ontology (BFO) as a top level ontology and uses the Ontology for Biomedical Investigations (OBI) as mid-level ontology. diff --git a/ontology/swo.md b/ontology/swo.md index 674c2b144..26da10ced 100644 --- a/ontology/swo.md +++ b/ontology/swo.md @@ -27,5 +27,5 @@ build: activity_status: active repository: https://github.com/allysonlister/swo preferredPrefix: SWO -added: 2015-07-28 +github_date_added: 2015-07-28 --- diff --git a/ontology/symp.md b/ontology/symp.md index 3289327d1..14f5f5056 100644 --- a/ontology/symp.md +++ b/ontology/symp.md @@ -40,7 +40,7 @@ usages: activity_status: active repository: https://github.com/DiseaseOntology/SymptomOntology preferredPrefix: SYMP -added: 2015-07-28 +github_date_added: 2015-07-28 --- The symptom ontology was designed around the guiding concept of a symptom being: "A perceived change in function, sensation or appearance reported by a patient indicative of a disease". Understanding the close relationship of Signs and Symptoms, where Signs are the objective observation of an illness, the Symptom Ontology will work to broaden it's scope to capture and document in a more robust manor these two sets of terms. Understanding that at times, the same term may be both a Sign and a Symptom. diff --git a/ontology/tads.md b/ontology/tads.md index df4c9baea..486fcf980 100644 --- a/ontology/tads.md +++ b/ontology/tads.md @@ -19,7 +19,7 @@ taxon: title: Tick Anatomy Ontology activity_status: inactive repository: https://github.com/VEuPathDB-ontology/TADS -added: 2015-07-28 +github_date_added: 2015-07-28 --- The anatomy of the Tick, Families: Ixodidae, Argassidae diff --git a/ontology/tahe.md b/ontology/tahe.md index 7bc4b3cbe..e502bdb66 100644 --- a/ontology/tahe.md +++ b/ontology/tahe.md @@ -11,5 +11,5 @@ taxon: homepage: is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- diff --git a/ontology/tahh.md b/ontology/tahh.md index b75f4d6d0..f91e03829 100644 --- a/ontology/tahh.md +++ b/ontology/tahh.md @@ -11,5 +11,5 @@ taxon: homepage: is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- diff --git a/ontology/tao.md b/ontology/tao.md index 995787851..b5220bc8f 100644 --- a/ontology/tao.md +++ b/ontology/tao.md @@ -26,7 +26,7 @@ publications: is_obsolete: true replaced_by: uberon activity_status: inactive -added: 2015-07-28 +github_date_added: 2015-07-28 --- Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa. diff --git a/ontology/taxrank.md b/ontology/taxrank.md index ef205f340..ada7985e2 100644 --- a/ontology/taxrank.md +++ b/ontology/taxrank.md @@ -32,7 +32,7 @@ license: activity_status: active repository: https://github.com/phenoscape/taxrank preferredPrefix: TAXRANK -added: 2015-07-28 +github_date_added: 2015-07-28 --- A vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Cross references to appearances of each term in each source are provided. Consistent with its intended use as a vocabulary of labels, there is no relation specifying an ordering of the rank terms. diff --git a/ontology/tgma.md b/ontology/tgma.md index 70aebd8b2..db977e13d 100644 --- a/ontology/tgma.md +++ b/ontology/tgma.md @@ -19,7 +19,7 @@ taxon: title: Mosquito gross anatomy ontology activity_status: inactive repository: https://github.com/VEuPathDB-ontology/TGMA -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary of the anatomy of mosquitoes. diff --git a/ontology/to.md b/ontology/to.md index f761c001b..a41949a9a 100644 --- a/ontology/to.md +++ b/ontology/to.md @@ -52,7 +52,7 @@ activity_status: active repository: https://github.com/Planteome/plant-trait-ontology preferredPrefix: TO depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG -added: 2015-07-28 +github_date_added: 2015-07-28 --- A controlled vocabulary of describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant. diff --git a/ontology/trans.md b/ontology/trans.md index 3875d75d5..c1a9bb0e6 100644 --- a/ontology/trans.md +++ b/ontology/trans.md @@ -37,7 +37,7 @@ usages: activity_status: active repository: https://github.com/DiseaseOntology/PathogenTransmissionOntology preferredPrefix: TRANS -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. diff --git a/ontology/tto.md b/ontology/tto.md index 9e2087875..86eacea20 100644 --- a/ontology/tto.md +++ b/ontology/tto.md @@ -28,7 +28,7 @@ tracker: https://github.com/phenoscape/teleost-taxonomy-ontology/issues activity_status: active repository: https://github.com/phenoscape/teleost-taxonomy-ontology preferredPrefix: TTO -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Teleost taxonomy ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. Taxonomy ontologies can also be valuable in annotating legacy data, where authors make phenotype or ecological assertions (e.g., host-parasite associations) that refer to groups that are reorganized or no longer recognized. The taxonomy ontology serves as the source of taxa for our project's use for identifying evolutionary changes that match the phenotype of a zebrafish mutant. diff --git a/ontology/txpo.md b/ontology/txpo.md index 7402e8c96..090203aeb 100644 --- a/ontology/txpo.md +++ b/ontology/txpo.md @@ -33,7 +33,7 @@ preferredPrefix: TXPO publications: - id: https://www.ncbi.nlm.nih.gov/pubmed/32883995 title: "Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management" -added: 2019-09-26 +github_date_added: 2019-09-26 --- Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. diff --git a/ontology/uberon.md b/ontology/uberon.md index 194154a4b..4ec76cf06 100644 --- a/ontology/uberon.md +++ b/ontology/uberon.md @@ -176,7 +176,7 @@ products: - ehdaa2 activity_status: active preferredPrefix: UBERON -added: 2015-07-28 +github_date_added: 2015-07-28 --- Uberon is an integrated cross-species ontology covering anatomical structures in animals. See the Uberon website for more info, or read the Caenorhabditis elegans. diff --git a/ontology/wbls.md b/ontology/wbls.md index 430174d7d..16f48b20c 100644 --- a/ontology/wbls.md +++ b/ontology/wbls.md @@ -42,7 +42,7 @@ usages: title: "WormBase: a modern Model Organism Information Resource" activity_status: active repository: https://github.com/obophenotype/c-elegans-development-ontology -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary of the development of Caenorhabditis elegans. diff --git a/ontology/wbphenotype.md b/ontology/wbphenotype.md index e026fca1d..d39d11fd4 100644 --- a/ontology/wbphenotype.md +++ b/ontology/wbphenotype.md @@ -50,7 +50,7 @@ usages: title: "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species " activity_status: active repository: https://github.com/obophenotype/c-elegans-phenotype-ontology -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary of Caenorhabditis elegans phenotypes diff --git a/ontology/xao.md b/ontology/xao.md index 6b3e9b4ba..eb2d0a156 100644 --- a/ontology/xao.md +++ b/ontology/xao.md @@ -41,7 +41,7 @@ license: activity_status: active repository: https://github.com/xenopus-anatomy/xao preferredPrefix: XAO -added: 2015-07-28 +github_date_added: 2015-07-28 --- The Xenopus Anatomy Ontology represents and standardizes the anatomy and development of the African frogs Xenopus laevis and tropicalis. It supports the annotation of gene expression data in Xenbase and is designed to facilitate cross-taxa comparisons. diff --git a/ontology/xco.md b/ontology/xco.md index 2dd998ef7..4db8b3727 100644 --- a/ontology/xco.md +++ b/ontology/xco.md @@ -36,7 +36,7 @@ activity_status: active repository: https://github.com/rat-genome-database/XCO-experimental-condition-ontology preferredPrefix: XCO depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif -added: 2015-07-29 +github_date_added: 2015-07-29 --- Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. diff --git a/ontology/xlmod.md b/ontology/xlmod.md index cb6feed5c..bf1df807d 100644 --- a/ontology/xlmod.md +++ b/ontology/xlmod.md @@ -25,7 +25,7 @@ license: activity_status: active repository: https://github.com/HUPO-PSI/xlmod-CV preferredPrefix: XLMOD -added: 2019-04-18 +github_date_added: 2019-04-18 --- A structured controlled vocabulary for cross-linker reagents used in cross-linking mass spectrometry experiments. Developed by the HUPO Proteomics Standards Initiative (PSI). diff --git a/ontology/xpo.md b/ontology/xpo.md index da43f84f4..512df0c33 100644 --- a/ontology/xpo.md +++ b/ontology/xpo.md @@ -42,7 +42,7 @@ license: activity_status: active repository: https://github.com/obophenotype/xenopus-phenotype-ontology preferredPrefix: XPO -added: 2018-11-30 +github_date_added: 2018-11-30 --- The Xenopus Phenotype Ontology represents and standardizes phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. It supports the annotation of phenotypes in Xenbase and is designed to integrate Xenopus data with genotype, phenotype, and disease data across species. diff --git a/ontology/ypo.md b/ontology/ypo.md index 8ca20a3e7..ad85ee1da 100644 --- a/ontology/ypo.md +++ b/ontology/ypo.md @@ -13,7 +13,7 @@ homepage: http://www.yeastgenome.org/ is_obsolete: true replaced_by: apo activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A structured controlled vocabulary for the phenotypes of budding yeast. diff --git a/ontology/zea.md b/ontology/zea.md index ee1e55d9c..68f99f8d8 100644 --- a/ontology/zea.md +++ b/ontology/zea.md @@ -12,7 +12,7 @@ taxon: homepage: http://www.maizemap.org/ is_obsolete: true activity_status: inactive -added: 2015-08-21 +github_date_added: 2015-08-21 --- A structured controlled vocabulary for the anatomy of Zea mays. diff --git a/ontology/zeco.md b/ontology/zeco.md index 7cc03be98..3d6c727ec 100644 --- a/ontology/zeco.md +++ b/ontology/zeco.md @@ -27,7 +27,7 @@ tracker: https://github.com/ybradford/zebrafish-experimental-conditions-ontology activity_status: active repository: https://github.com/ybradford/zebrafish-experimental-conditions-ontology preferredPrefix: ZECO -added: 2016-07-28 +github_date_added: 2016-07-28 --- This ontology is designed to represent the experimental conditions diff --git a/ontology/zfa.md b/ontology/zfa.md index bb82bdf52..91065477c 100644 --- a/ontology/zfa.md +++ b/ontology/zfa.md @@ -40,7 +40,7 @@ usages: activity_status: active repository: https://github.com/cerivs/zebrafish-anatomical-ontology preferredPrefix: ZFA -added: 2015-07-28 +github_date_added: 2015-07-28 --- A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). diff --git a/ontology/zfs.md b/ontology/zfs.md index 6f092ae16..70fd67bc8 100644 --- a/ontology/zfs.md +++ b/ontology/zfs.md @@ -29,7 +29,7 @@ build: activity_status: active repository: https://github.com/cerivs/zebrafish-anatomical-ontology preferredPrefix: ZFS -added: 2015-07-29 +github_date_added: 2015-07-29 --- An ontology of developmental stages of the Zebrafish (Danio rerio). Note that ZFA includes the leaf nodes of this ontology diff --git a/ontology/zp.md b/ontology/zp.md index 9b59ec755..39b526f9e 100644 --- a/ontology/zp.md +++ b/ontology/zp.md @@ -45,5 +45,5 @@ usages: activity_status: active repository: https://github.com/obophenotype/zebrafish-phenotype-ontology preferredPrefix: ZP -added: 2019-01-02 +github_date_added: 2019-01-02 --- diff --git a/util/bulk_field_rename.py b/util/bulk_field_rename.py new file mode 100644 index 000000000..cf9458fb3 --- /dev/null +++ b/util/bulk_field_rename.py @@ -0,0 +1,37 @@ +"""This script bulk renames a given key in all ontologies' metadata. + +Run with: ``python bulk_field_rename.py ``. + +Author: `Charles Tapley Hoyt `_. +""" + +import pathlib + +import click + +HERE = pathlib.Path(__file__).parent.resolve() +ONTOLOGY_DIRECTORY = HERE.parent.joinpath("ontology").resolve() + + +@click.command() +@click.argument("old_key") +@click.argument("new_key") +def main(old_key: str, new_key: str): + """Rename keys across all ontologies.""" + for path in ONTOLOGY_DIRECTORY.glob("*.md"): + with path.open() as file: + lines = [line.rstrip("\n") for line in file] + + with path.open("w") as file: + for line in lines: + prefix = f"{old_key}:" + if line.startswith(prefix): + line = line.removeprefix(prefix).lstrip() + line = f"{new_key}: {line}" + print(line, file=file) + else: + print(line, file=file) + + +if __name__ == "__main__": + main() diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json index e689a7985..c42e74476 100644 --- a/util/schema/registry_schema.json +++ b/util/schema/registry_schema.json @@ -18,11 +18,11 @@ "activity_status": "${data} is not one of ${schema}." } }, - "added": { + "github_date_added": { "level": "error", "format": "date", "regex": "^\\d{4}-\\d{2}-\\d{2}$", - "description": "The date when the ontology was added to the OBO Foundry git repository, in the YYYY-MM-DD format" + "description": "The date a markdown file was first committed to the OBO Foundry git repository on GitHub, in the YYYY-MM-DD format. Note that in several cases, this is not reflective of the date to which the ontology was added/accepted into the OBO Foundry. For example, because the GitHub repository was created at 2015-07-28, many ontologies accepted into the OBO Foundry at earlier dates will be listed with this date as their GitHub added date. Ontologies that were renamed also won't reflect their date added to the OBO Foundry in this field, such as PECO/EO." }, "browsers": { "level": "info", @@ -485,7 +485,7 @@ }, "required": [ "activity_status", - "added", + "github_date_added", "contact", "description", "homepage", From 7fdface2c60757ee680f63264adb35aaff980df5 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 22 Jun 2022 10:57:23 +0200 Subject: [PATCH 8/9] Add missing annotations --- ontology/ado.md | 1 + ontology/proco.md | 1 + 2 files changed, 2 insertions(+) diff --git a/ontology/ado.md b/ontology/ado.md index 2e5287e3c..16375f193 100644 --- a/ontology/ado.md +++ b/ontology/ado.md @@ -21,5 +21,6 @@ license: repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO preferredPrefix: ADO activity_status: active +github_date_added: 2022-06-21 --- diff --git a/ontology/proco.md b/ontology/proco.md index cbfd9febc..2d3e696b4 100644 --- a/ontology/proco.md +++ b/ontology/proco.md @@ -26,6 +26,7 @@ license: activity_status: active repository: https://github.com/proco-ontology/PROCO preferredPrefix: PROCO +github_date_added: 2022-06-21 --- Previously named the Ontology of Process Chemistry (OPC), the PROcess Chemistry Ontology (PROCO) is aimed to be a community-based ontology in the domain of process chemistry, which is a branch of chemistry (including pharmaceutical chemistry) that studies the development and optimization of the production processes for chemical compounds, and the scaling up of laboratory chemical reactions into commercially viable routes. Key considerations are product quality, process robustness, economics, environmental sustainability, regulatory compliance and safety. From 96a4ba9121b0141868e14b0a12aa22b626956cfc Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 15 Nov 2022 17:39:56 +0100 Subject: [PATCH 9/9] Update --- ontology/aao.md | 2 +- ontology/ado.md | 2 +- ontology/adw.md | 2 +- ontology/aeo.md | 1 + ontology/aero.md | 2 +- ontology/agro.md | 1 + ontology/amphx.md | 1 + ontology/apo.md | 1 + ontology/aro.md | 1 + ontology/ato.md | 2 +- ontology/bcgo.md | 1 + ontology/bco.md | 1 + ontology/bfo.md | 1 + ontology/bila.md | 2 +- ontology/bootstrep.md | 2 +- ontology/bspo.md | 1 + ontology/bto.md | 1 + ontology/caro.md | 1 + ontology/cdao.md | 1 + ontology/cdno.md | 1 + ontology/ceph.md | 1 + ontology/chebi.md | 1 + ontology/cheminf.md | 1 + ontology/chiro.md | 1 + ontology/chmo.md | 1 + ontology/cido.md | 1 + ontology/cio.md | 1 + ontology/cl.md | 1 + ontology/clao.md | 1 + ontology/clo.md | 1 + ontology/clyh.md | 1 + ontology/cmf.md | 1 + ontology/cmo.md | 1 + ontology/cob.md | 1 + ontology/colao.md | 1 + ontology/cro.md | 1 + ontology/cteno.md | 1 + ontology/cto.md | 1 + ontology/cvdo.md | 1 + ontology/dc_cl.md | 2 +- ontology/ddanat.md | 1 + ontology/ddpheno.md | 1 + ontology/dideo.md | 1 + ontology/dinto.md | 1 + ontology/disdriv.md | 1 + ontology/doid.md | 1 + ontology/dpo.md | 1 + ontology/dron.md | 1 + ontology/duo.md | 1 + ontology/ecao.md | 1 + ontology/eco.md | 1 + ontology/ecocore.md | 1 + ontology/ecto.md | 1 + ontology/ehda.md | 2 +- ontology/ehdaa.md | 2 +- ontology/ehdaa2.md | 1 + ontology/emap.md | 2 +- ontology/emapa.md | 1 + ontology/envo.md | 1 + ontology/eo.md | 1 + ontology/epo.md | 2 +- ontology/ero.md | 1 + ontology/eupath.md | 1 + ontology/ev.md | 2 +- ontology/exo.md | 1 + ontology/fao.md | 1 + ontology/fbbi.md | 1 + ontology/fbbt.md | 2 +- ontology/fbcv.md | 1 + ontology/fbdv.md | 1 + ontology/fbsp.md | 2 +- ontology/fix.md | 2 +- ontology/flopo.md | 1 + ontology/flu.md | 2 +- ontology/fma.md | 1 + ontology/fobi.md | 1 + ontology/foodon.md | 1 + ontology/fovt.md | 1 + ontology/fypo.md | 1 + ontology/gaz.md | 1 + ontology/gecko.md | 1 + ontology/genepio.md | 1 + ontology/geno.md | 1 + ontology/geo.md | 1 + ontology/gno.md | 1 + ontology/go.md | 1 + ontology/gro.md | 2 +- ontology/gsso.md | 1 + ontology/habronattus.md | 2 +- ontology/hancestro.md | 1 + ontology/hao.md | 1 + ontology/hom.md | 1 + ontology/hp.md | 1 + ontology/hsapdv.md | 1 + ontology/hso.md | 1 + ontology/htn.md | 1 + ontology/iao.md | 1 + ontology/iceo.md | 1 + ontology/ico.md | 1 + ontology/ido.md | 1 + ontology/idomal.md | 1 + ontology/iev.md | 2 +- ontology/imr.md | 2 +- ontology/ino.md | 1 + ontology/ipr.md | 2 +- ontology/kisao.md | 1 + ontology/labo.md | 1 + ontology/lepao.md | 1 + ontology/lipro.md | 2 +- ontology/loggerhead.md | 2 +- ontology/ma.md | 1 + ontology/mamo.md | 1 + ontology/mao.md | 2 +- ontology/mat.md | 2 +- ontology/maxo.md | 1 + ontology/mco.md | 1 + ontology/mf.md | 1 + ontology/mfmo.md | 1 + ontology/mfo.md | 2 +- ontology/mfoem.md | 1 + ontology/mfomd.md | 1 + ontology/mi.md | 1 + ontology/miapa.md | 1 + ontology/micro.md | 1 + ontology/mirnao.md | 2 +- ontology/miro.md | 1 + ontology/mmo.md | 1 + ontology/mmusdv.md | 1 + ontology/mo.md | 2 +- ontology/mod.md | 1 + ontology/mondo.md | 1 + ontology/mop.md | 1 + ontology/mp.md | 1 + ontology/mpath.md | 1 + ontology/mpio.md | 1 + ontology/mro.md | 1 + ontology/ms.md | 1 + ontology/nbo.md | 1 + ontology/ncbitaxon.md | 1 + ontology/ncro.md | 1 + ontology/nif_cell.md | 2 +- ontology/nif_dysfunction.md | 2 +- ontology/nif_grossanatomy.md | 2 +- ontology/nmr.md | 2 +- ontology/nomen.md | 1 + ontology/oae.md | 1 + ontology/oarcs.md | 1 + ontology/oba.md | 1 + ontology/obcs.md | 1 + ontology/obi.md | 1 + ontology/obib.md | 1 + ontology/obo_rel.md | 2 +- ontology/ogg.md | 1 + ontology/ogi.md | 1 + ontology/ogms.md | 1 + ontology/ogsf.md | 1 + ontology/ohd.md | 1 + ontology/ohmi.md | 1 + ontology/ohpi.md | 1 + ontology/olatdv.md | 1 + ontology/omiabis.md | 1 + ontology/omit.md | 1 + ontology/omp.md | 1 + ontology/omrse.md | 1 + ontology/one.md | 1 + ontology/ons.md | 1 + ontology/ontoavida.md | 1 + ontology/ontoneo.md | 1 + ontology/opl.md | 1 + ontology/opmi.md | 1 + ontology/ornaseq.md | 1 + ontology/ovae.md | 1 + ontology/pao.md | 2 +- ontology/pato.md | 1 + ontology/pcl.md | 1 + ontology/pco.md | 1 + ontology/pd_st.md | 2 +- ontology/pdro.md | 1 + ontology/pdumdv.md | 1 + ontology/peco.md | 1 + ontology/pgdso.md | 2 +- ontology/phipo.md | 1 + ontology/plana.md | 1 + ontology/planp.md | 1 + ontology/plo.md | 2 +- ontology/po.md | 1 + ontology/poro.md | 1 + ontology/ppo.md | 1 + ontology/pr.md | 1 + ontology/proco.md | 1 + ontology/propreo.md | 2 +- ontology/psdo.md | 1 + ontology/pso.md | 1 + ontology/pw.md | 1 + ontology/rbo.md | 1 + ontology/resid.md | 2 +- ontology/rex.md | 2 +- ontology/rnao.md | 1 + ontology/ro.md | 1 + ontology/rs.md | 1 + ontology/rxno.md | 1 + ontology/sao.md | 2 +- ontology/sbo.md | 1 + ontology/scdo.md | 1 + ontology/sep.md | 1 + ontology/sepio.md | 1 + ontology/sibo.md | 1 + ontology/so.md | 1 + ontology/sopharm.md | 2 +- ontology/spd.md | 1 + ontology/stato.md | 1 + ontology/swo.md | 1 + ontology/symp.md | 1 + ontology/tads.md | 1 + ontology/tahe.md | 2 +- ontology/tahh.md | 2 +- ontology/tao.md | 2 +- ontology/taxrank.md | 1 + ontology/tgma.md | 1 + ontology/to.md | 1 + ontology/trans.md | 1 + ontology/tto.md | 1 + ontology/txpo.md | 1 + ontology/uberon.md | 1 + ontology/uo.md | 1 + ontology/upa.md | 1 + ontology/upheno.md | 1 + ontology/vario.md | 2 +- ontology/vhog.md | 1 + ontology/vo.md | 1 + ontology/vsao.md | 2 +- ontology/vt.md | 1 + ontology/vto.md | 1 + ontology/wbbt.md | 1 + ontology/wbls.md | 1 + ontology/wbphenotype.md | 1 + ontology/xao.md | 1 + ontology/xco.md | 1 + ontology/xpo.md | 1 + ontology/ypo.md | 2 +- ontology/zea.md | 2 +- ontology/zeco.md | 1 + ontology/zfa.md | 1 + ontology/zfs.md | 1 + ontology/zp.md | 1 + util/add_dates.py | 4 ++-- 246 files changed, 247 insertions(+), 52 deletions(-) diff --git a/ontology/aao.md b/ontology/aao.md index 753905f5d..e80c7adaa 100644 --- a/ontology/aao.md +++ b/ontology/aao.md @@ -6,6 +6,7 @@ contact: email: david.c.blackburn@gmail.com label: David Blackburn domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://github.com/seger/aao is_obsolete: true replaced_by: uberon @@ -13,7 +14,6 @@ taxon: id: NCBITaxon:8292 label: Amphibia activity_status: inactive -github_date_added: 2015-08-21 --- A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. diff --git a/ontology/ado.md b/ontology/ado.md index 339aef9fe..f048d63a0 100644 --- a/ontology/ado.md +++ b/ontology/ado.md @@ -11,6 +11,7 @@ dependencies: - id: bfo description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining. domain: health +github_date_added: 2022-06-21 homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO license: label: CC BY 4.0 @@ -21,6 +22,5 @@ products: repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO tracker: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues activity_status: active -github_date_added: 2022-06-21 --- diff --git a/ontology/adw.md b/ontology/adw.md index ce5734256..b159467be 100644 --- a/ontology/adw.md +++ b/ontology/adw.md @@ -6,10 +6,10 @@ contact: email: adw_geeks@umich.edu label: Animal Diversity Web technical staff domain: organisms +github_date_added: 2015-08-21 homepage: http://www.animaldiversity.org is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities. diff --git a/ontology/aeo.md b/ontology/aeo.md index a32becad9..e27b5908d 100644 --- a/ontology/aeo.md +++ b/ontology/aeo.md @@ -12,6 +12,7 @@ contact: label: Jonathan Bard description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ license: label: CC BY 4.0 diff --git a/ontology/aero.md b/ontology/aero.md index 5bda8e76b..db92bfdee 100644 --- a/ontology/aero.md +++ b/ontology/aero.md @@ -11,6 +11,7 @@ contact: orcid: 0000-0002-9551-6370 description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events domain: health +github_date_added: 2015-07-28 homepage: http://purl.obolibrary.org/obo/aero is_obsolete: true license: @@ -19,7 +20,6 @@ license: products: - id: aero.owl activity_status: inactive -github_date_added: 2015-07-28 --- The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events. diff --git a/ontology/agro.md b/ontology/agro.md index 70213e84a..d8f0741f4 100644 --- a/ontology/agro.md +++ b/ontology/agro.md @@ -28,6 +28,7 @@ dependencies: - id: xco description: Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments domain: agriculture +github_date_added: 2016-06-04 homepage: https://github.com/AgriculturalSemantics/agro jobs: - id: https://travis-ci.org/AgriculturalSemantics/agro diff --git a/ontology/amphx.md b/ontology/amphx.md index ecd61c5a1..3892787a0 100644 --- a/ontology/amphx.md +++ b/ontology/amphx.md @@ -15,6 +15,7 @@ dependencies: - id: uberon description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). domain: anatomy and development +github_date_added: 2020-04-21 homepage: https://github.com/EBISPOT/amphx_ontology license: label: CC BY 3.0 diff --git a/ontology/apo.md b/ontology/apo.md index 247127b48..6e4bd770b 100644 --- a/ontology/apo.md +++ b/ontology/apo.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0001-5472-917X description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi domain: phenotype +github_date_added: 2015-07-28 homepage: http://www.yeastgenome.org/ license: label: CC BY 4.0 diff --git a/ontology/aro.md b/ontology/aro.md index 45153513b..46b940bcd 100644 --- a/ontology/aro.md +++ b/ontology/aro.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-1142-3063 description: Antibiotic resistance genes and mutations domain: microbiology +github_date_added: 2017-11-15 homepage: https://github.com/arpcard/aro license: label: CC BY 4.0 diff --git a/ontology/ato.md b/ontology/ato.md index 4f9a036c8..81aefef89 100644 --- a/ontology/ato.md +++ b/ontology/ato.md @@ -6,13 +6,13 @@ contact: email: david.c.blackburn@gmail.com label: David Blackburn domain: organisms +github_date_added: 2015-08-21 homepage: http://www.amphibanat.org is_obsolete: true taxon: id: NCBITaxon:8292 label: Amphibia activity_status: inactive -github_date_added: 2015-08-21 --- A taxonomy of Amphibia diff --git a/ontology/bcgo.md b/ontology/bcgo.md index 21a9dc307..af1203e7e 100644 --- a/ontology/bcgo.md +++ b/ontology/bcgo.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-2999-0103 description: An application ontology built for beta cell genomics studies. domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://github.com/obi-bcgo/bcgo in_foundry: false is_obsolete: true diff --git a/ontology/bco.md b/ontology/bco.md index d16c5d62f..5d3147139 100644 --- a/ontology/bco.md +++ b/ontology/bco.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-8815-0078 description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. domain: organisms +github_date_added: 2015-07-29 homepage: https://github.com/BiodiversityOntologies/bco in_foundry: false license: diff --git a/ontology/bfo.md b/ontology/bfo.md index 0571ad70d..89422a72a 100644 --- a/ontology/bfo.md +++ b/ontology/bfo.md @@ -14,6 +14,7 @@ contact: depicted_by: https://avatars2.githubusercontent.com/u/12972134?v=3&s=200 description: The upper level ontology upon which OBO Foundry ontologies are built. domain: upper +github_date_added: 2015-07-28 homepage: http://ifomis.org/bfo/ in_foundry_order: 1 license: diff --git a/ontology/bila.md b/ontology/bila.md index 6627f96c7..bd5a7e08d 100644 --- a/ontology/bila.md +++ b/ontology/bila.md @@ -10,6 +10,7 @@ contact: email: henrich@embl.de label: Thorsten Heinrich domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://4dx.embl.de/4DXpress is_obsolete: true products: @@ -19,5 +20,4 @@ taxon: id: NCBITaxon:33213 label: Bilateria activity_status: inactive -github_date_added: 2015-07-28 --- diff --git a/ontology/bootstrep.md b/ontology/bootstrep.md index 80e48b96a..76f2aa5c6 100644 --- a/ontology/bootstrep.md +++ b/ontology/bootstrep.md @@ -6,11 +6,11 @@ contact: email: vlee@ebi.ac.uk label: Vivian Lee domain: chemistry and biochemistry +github_date_added: 2015-08-21 homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html is_obsolete: true replaced_by: molecular_function activity_status: inactive -github_date_added: 2015-08-21 --- The BOOTStrep Ontology is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of). diff --git a/ontology/bspo.md b/ontology/bspo.md index 24b88c4fa..868fc9737 100644 --- a/ontology/bspo.md +++ b/ontology/bspo.md @@ -15,6 +15,7 @@ contact: orcid: 0000-0002-6601-2165 description: An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://github.com/obophenotype/biological-spatial-ontology license: label: CC BY 3.0 diff --git a/ontology/bto.md b/ontology/bto.md index 7acb4f83c..b7c089097 100644 --- a/ontology/bto.md +++ b/ontology/bto.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0001-9117-7909 description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://www.brenda-enzymes.org license: label: CC BY 4.0 diff --git a/ontology/caro.md b/ontology/caro.md index 7a7b84e87..34bcd4f12 100644 --- a/ontology/caro.md +++ b/ontology/caro.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0001-9114-8737 description: An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://github.com/obophenotype/caro/ license: label: CC BY 4.0 diff --git a/ontology/cdao.md b/ontology/cdao.md index eacacfe7e..05c0b3272 100644 --- a/ontology/cdao.md +++ b/ontology/cdao.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-8688-6599 description: a formalization of concepts and relations relevant to evolutionary comparative analysis domain: organisms +github_date_added: 2015-07-28 homepage: https://github.com/evoinfo/cdao license: label: CC0 1.0 diff --git a/ontology/cdno.md b/ontology/cdno.md index efc894f83..c7854596e 100644 --- a/ontology/cdno.md +++ b/ontology/cdno.md @@ -19,6 +19,7 @@ dependencies: - id: ro description: CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. domain: diet, metabolomics, and nutrition +github_date_added: 2021-02-08 homepage: https://cdno.info/ license: label: CC BY 3.0 diff --git a/ontology/ceph.md b/ontology/ceph.md index c4654bd13..552b4eaa1 100644 --- a/ontology/ceph.md +++ b/ontology/ceph.md @@ -14,6 +14,7 @@ contact: orcid: 0000-0002-6601-2165 description: An anatomical and developmental ontology for cephalopods domain: anatomy and development +github_date_added: 2015-08-21 homepage: https://github.com/obophenotype/cephalopod-ontology jobs: - id: https://travis-ci.org/obophenotype/cephalopod-ontology diff --git a/ontology/chebi.md b/ontology/chebi.md index 876bac4b1..e921c3b1f 100644 --- a/ontology/chebi.md +++ b/ontology/chebi.md @@ -18,6 +18,7 @@ contact: depicted_by: https://www.ebi.ac.uk/chebi/images/ChEBI_logo.png description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. domain: chemistry and biochemistry +github_date_added: 2015-07-28 homepage: http://www.ebi.ac.uk/chebi in_foundry_order: 1 license: diff --git a/ontology/cheminf.md b/ontology/cheminf.md index 2fdee7cec..f958ffb5e 100644 --- a/ontology/cheminf.md +++ b/ontology/cheminf.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0001-7542-0286 description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. domain: chemistry and biochemistry +github_date_added: 2015-07-28 homepage: https://github.com/semanticchemistry/semanticchemistry license: label: CC0 1.0 diff --git a/ontology/chiro.md b/ontology/chiro.md index f6a3475e1..ee3ce419a 100644 --- a/ontology/chiro.md +++ b/ontology/chiro.md @@ -21,6 +21,7 @@ dependencies: - id: uberon description: CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes. domain: chemistry and biochemistry +github_date_added: 2019-09-26 homepage: https://github.com/obophenotype/chiro jobs: - id: https://travis-ci.org/obophenotype/chiro diff --git a/ontology/chmo.md b/ontology/chmo.md index d2dd69860..c5009db5c 100644 --- a/ontology/chmo.md +++ b/ontology/chmo.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-5985-7429 description: CHMO, the chemical methods ontology, describes methods used to domain: health +github_date_added: 2015-07-28 homepage: https://github.com/rsc-ontologies/rsc-cmo license: label: CC BY 4.0 diff --git a/ontology/cido.md b/ontology/cido.md index a4491b3f4..c49844b3d 100644 --- a/ontology/cido.md +++ b/ontology/cido.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-9189-9661 description: The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically represent and standardize various aspects of coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. domain: health +github_date_added: 2020-03-12 homepage: https://github.com/cido-ontology/cido license: label: CC BY 4.0 diff --git a/ontology/cio.md b/ontology/cio.md index 877c03dc9..4c75074ce 100644 --- a/ontology/cio.md +++ b/ontology/cio.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-9415-5104 description: An ontology to capture confidence information about annotations. domain: information +github_date_added: 2016-05-17 homepage: https://github.com/BgeeDB/confidence-information-ontology license: label: CC0 1.0 diff --git a/ontology/cl.md b/ontology/cl.md index 527e007bc..4ffdf4ecd 100644 --- a/ontology/cl.md +++ b/ontology/cl.md @@ -25,6 +25,7 @@ dependencies: depicted_by: /images/CL-logo.jpg description: The Cell Ontology is a structured controlled vocabulary for cell types in animals. domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://obophenotype.github.io/cell-ontology/ integration_server: http://build.berkeleybop.org/job/build-cl/ jobs: diff --git a/ontology/clao.md b/ontology/clao.md index 2fc2479ab..6e805af88 100644 --- a/ontology/clao.md +++ b/ontology/clao.md @@ -15,6 +15,7 @@ dependencies: - id: ro description: 'CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).' domain: anatomy and development +github_date_added: 2020-10-08 homepage: https://github.com/luis-gonzalez-m/Collembola license: label: CC0 1.0 diff --git a/ontology/clo.md b/ontology/clo.md index 84620f738..f59c62ff8 100644 --- a/ontology/clo.md +++ b/ontology/clo.md @@ -14,6 +14,7 @@ dependencies: - id: uberon description: An ontology to standardize and integrate cell line information and to support computer-assisted reasoning. domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://www.clo-ontology.org license: label: CC BY 3.0 diff --git a/ontology/clyh.md b/ontology/clyh.md index 83d35165b..85d6de1f7 100644 --- a/ontology/clyh.md +++ b/ontology/clyh.md @@ -17,6 +17,7 @@ dependencies: - id: uberon description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle. domain: anatomy and development +github_date_added: 2020-05-06 homepage: https://github.com/EBISPOT/clyh_ontology license: label: CC BY 3.0 diff --git a/ontology/cmf.md b/ontology/cmf.md index 3176f8b4f..6a9f83ef0 100644 --- a/ontology/cmf.md +++ b/ontology/cmf.md @@ -7,6 +7,7 @@ contact: label: Mark Engelstad orcid: 0000-0001-5889-4463 domain: health +github_date_added: 2015-08-21 homepage: https://code.google.com/p/craniomaxillofacial-ontology/ is_obsolete: true activity_status: inactive diff --git a/ontology/cmo.md b/ontology/cmo.md index e4a006e41..4168e1bef 100644 --- a/ontology/cmo.md +++ b/ontology/cmo.md @@ -17,6 +17,7 @@ contact: depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. domain: health +github_date_added: 2015-07-28 homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html license: label: CC0 1.0 diff --git a/ontology/cob.md b/ontology/cob.md index 5a32b2302..0be345946 100644 --- a/ontology/cob.md +++ b/ontology/cob.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-8457-6693 description: COB brings together key terms from a wide range of OBO projects to improve interoperability. domain: upper +github_date_added: 2020-04-15 homepage: https://obofoundry.org/COB/ license: label: CC0 1.0 diff --git a/ontology/colao.md b/ontology/colao.md index ff7c5dbc1..10fbc9919 100644 --- a/ontology/colao.md +++ b/ontology/colao.md @@ -17,6 +17,7 @@ dependencies: - id: uberon description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone. domain: anatomy and development +github_date_added: 2021-12-14 homepage: https://github.com/insect-morphology/colao license: label: CC BY 4.0 diff --git a/ontology/cro.md b/ontology/cro.md index c991c4a73..f4dac62fc 100644 --- a/ontology/cro.md +++ b/ontology/cro.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0001-5059-4132 description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. domain: information +github_date_added: 2017-07-20 homepage: https://github.com/data2health/contributor-role-ontology license: label: CC BY 2.0 diff --git a/ontology/cteno.md b/ontology/cteno.md index 8de158577..78838157f 100644 --- a/ontology/cteno.md +++ b/ontology/cteno.md @@ -17,6 +17,7 @@ dependencies: - id: uberon description: An anatomical and developmental ontology for ctenophores (Comb Jellies) domain: anatomy and development +github_date_added: 2015-07-29 homepage: https://github.com/obophenotype/ctenophore-ontology jobs: - id: https://travis-ci.org/obophenotype/ctenophore-ontology diff --git a/ontology/cto.md b/ontology/cto.md index 50a53cf4e..48806c1c4 100644 --- a/ontology/cto.md +++ b/ontology/cto.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-9896-3531 description: The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. domain: health +github_date_added: 2020-07-08 homepage: https://github.com/ClinicalTrialOntology/CTO/ license: label: CC BY 4.0 diff --git a/ontology/cvdo.md b/ontology/cvdo.md index 29f5d1db6..ea8e69abb 100644 --- a/ontology/cvdo.md +++ b/ontology/cvdo.md @@ -15,6 +15,7 @@ contact: orcid: 0000-0002-3336-2476 description: An ontology to describe entities related to cardiovascular diseases domain: health +github_date_added: 2015-07-28 homepage: https://github.com/OpenLHS/CVDO license: label: CC BY 4.0 diff --git a/ontology/dc_cl.md b/ontology/dc_cl.md index 71aa97ec8..4fbbbb842 100644 --- a/ontology/dc_cl.md +++ b/ontology/dc_cl.md @@ -7,6 +7,7 @@ contact: label: Lindsay Cowell orcid: 0000-0003-1617-8244 domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://www.dukeontologygroup.org/Projects.html is_obsolete: true replaced_by: cl @@ -14,7 +15,6 @@ taxon: id: all label: null activity_status: inactive -github_date_added: 2015-08-21 --- Representation of types of dendritic cell. Note that the domain of this ontology is wholly subsumed by the domain of the Cell ontology (CL). diff --git a/ontology/ddanat.md b/ontology/ddanat.md index 4096810f2..74340042a 100644 --- a/ontology/ddanat.md +++ b/ontology/ddanat.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-4532-2703 description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://dictybase.org/ license: label: CC0 1.0 diff --git a/ontology/ddpheno.md b/ontology/ddpheno.md index 439d705f9..b80a130e1 100644 --- a/ontology/ddpheno.md +++ b/ontology/ddpheno.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-4532-2703 description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://dictybase.org/ license: label: CC0 1.0 diff --git a/ontology/dideo.md b/ontology/dideo.md index 5bc220d2c..27fdfabc6 100644 --- a/ontology/dideo.md +++ b/ontology/dideo.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0003-1834-3856 description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology domain: chemistry and biochemistry +github_date_added: 2015-08-21 homepage: https://github.com/DIDEO/DIDEO license: label: CC BY 4.0 diff --git a/ontology/dinto.md b/ontology/dinto.md index 7bbb47652..3282f9e7d 100644 --- a/ontology/dinto.md +++ b/ontology/dinto.md @@ -7,6 +7,7 @@ contact: label: Maria Herrero description: A formal represention for drug-drug interactions knowledge. domain: health +github_date_added: 2015-08-21 homepage: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto is_obsolete: true license: diff --git a/ontology/disdriv.md b/ontology/disdriv.md index 89e1da3eb..f915ad924 100644 --- a/ontology/disdriv.md +++ b/ontology/disdriv.md @@ -15,6 +15,7 @@ contact: orcid: 0000-0001-8910-9851 description: Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI. domain: health +github_date_added: 2021-11-05 homepage: http://www.disease-ontology.org license: label: CC0 1.0 diff --git a/ontology/doid.md b/ontology/doid.md index 77709fca0..ebfde049b 100644 --- a/ontology/doid.md +++ b/ontology/doid.md @@ -18,6 +18,7 @@ contact: depicted_by: http://www.disease-ontology.org/media/images/DO_logo.jpg description: An ontology for describing the classification of human diseases organized by etiology. domain: health +github_date_added: 2015-07-28 homepage: http://www.disease-ontology.org in_foundry_order: 1 license: diff --git a/ontology/dpo.md b/ontology/dpo.md index 58b431300..fdecd5e7e 100644 --- a/ontology/dpo.md +++ b/ontology/dpo.md @@ -17,6 +17,7 @@ contact: orcid: 0000-0002-1373-1705 description: An ontology of commonly encountered and/or high level Drosophila phenotypes. domain: phenotype +github_date_added: 2015-07-28 homepage: http://purl.obolibrary.org/obo/fbcv license: label: CC BY 4.0 diff --git a/ontology/dron.md b/ontology/dron.md index ae49da15c..47312cc24 100644 --- a/ontology/dron.md +++ b/ontology/dron.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-9881-1017 description: An ontology to support comparative effectiveness researchers studying claims data. domain: health +github_date_added: 2015-07-28 homepage: https://github.com/ufbmi/dron license: label: CC BY 3.0 diff --git a/ontology/duo.md b/ontology/duo.md index 71bf1d9b7..4b356efd6 100644 --- a/ontology/duo.md +++ b/ontology/duo.md @@ -16,6 +16,7 @@ dependencies: - id: iao description: DUO is an ontology which represent data use conditions. domain: information +github_date_added: 2017-01-24 homepage: https://github.com/EBISPOT/DUO jobs: - id: https://travis-ci.org/EBISPOT/DUO diff --git a/ontology/ecao.md b/ontology/ecao.md index ff2d6536b..585bf40f6 100644 --- a/ontology/ecao.md +++ b/ontology/ecao.md @@ -17,6 +17,7 @@ dependencies: - id: uberon description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586). domain: anatomy and development +github_date_added: 2020-05-06 homepage: https://github.com/echinoderm-ontology/ecao_ontology license: label: CC BY 3.0 diff --git a/ontology/eco.md b/ontology/eco.md index a2bd76b12..3b6bc1c8c 100644 --- a/ontology/eco.md +++ b/ontology/eco.md @@ -18,6 +18,7 @@ domain: investigations funded_by: - id: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1458400 title: NSF ABI-1458400 +github_date_added: 2015-07-28 homepage: https://www.evidenceontology.org jobs: - id: https://travis-ci.org/evidenceontology/evidenceontology diff --git a/ontology/ecocore.md b/ontology/ecocore.md index 9256a3144..653f3556a 100644 --- a/ontology/ecocore.md +++ b/ontology/ecocore.md @@ -24,6 +24,7 @@ dependencies: - id: uberon description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. domain: environment +github_date_added: 2017-08-17 homepage: https://github.com/EcologicalSemantics/ecocore jobs: - id: https://travis-ci.org/EcologicalSemantics/ecocore diff --git a/ontology/ecto.md b/ontology/ecto.md index d6b16bb1f..a6bd3f5ef 100644 --- a/ontology/ecto.md +++ b/ontology/ecto.md @@ -28,6 +28,7 @@ dependencies: depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png description: ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). domain: environment +github_date_added: 2019-09-24 homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology jobs: - id: https://travis-ci.org/EnvironmentOntology/environmental-exposure-ontology diff --git a/ontology/ehda.md b/ontology/ehda.md index 22a88a9e8..155888a93 100644 --- a/ontology/ehda.md +++ b/ontology/ehda.md @@ -6,6 +6,7 @@ contact: email: J.Bard@ed.ac.uk label: Jonathan Bard domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://genex.hgu.mrc.ac.uk/ is_obsolete: true replaced_by: ehdaa2 @@ -13,7 +14,6 @@ taxon: id: NCBITaxon:9606 label: Homo sapiens activity_status: inactive -github_date_added: 2015-08-21 --- A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once. diff --git a/ontology/ehdaa.md b/ontology/ehdaa.md index 4bd6680fb..5ca3de017 100644 --- a/ontology/ehdaa.md +++ b/ontology/ehdaa.md @@ -6,6 +6,7 @@ contact: email: J.Bard@ed.ac.uk label: Jonathan Bard domain: anatomy and development +github_date_added: 2015-08-21 homepage: null is_obsolete: true replaced_by: ehdaa2 @@ -13,7 +14,6 @@ taxon: id: NCBITaxon:9606 label: Homo sapiens activity_status: inactive -github_date_added: 2015-08-21 --- A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release. diff --git a/ontology/ehdaa2.md b/ontology/ehdaa2.md index 77113fed0..a6a8e41c4 100644 --- a/ontology/ehdaa2.md +++ b/ontology/ehdaa2.md @@ -16,6 +16,7 @@ dependencies: - id: cl description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology license: label: CC BY 4.0 diff --git a/ontology/emap.md b/ontology/emap.md index 24173dc57..343cae713 100644 --- a/ontology/emap.md +++ b/ontology/emap.md @@ -14,6 +14,7 @@ contact: orcid: 0000-0002-0956-8634 description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://emouseatlas.org is_obsolete: true page: https://www.emouseatlas.org/emap/about/what_is_emap.html @@ -24,7 +25,6 @@ taxon: id: NCBITaxon:10088 label: Mus activity_status: inactive -github_date_added: 2015-07-28 --- ## BACKGROUND diff --git a/ontology/emapa.md b/ontology/emapa.md index 63d57de72..084a4d507 100644 --- a/ontology/emapa.md +++ b/ontology/emapa.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-0956-8634 description: An ontology for mouse anatomy covering embryonic development and postnatal stages. domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://www.informatics.jax.org/expression.shtml license: label: CC BY 4.0 diff --git a/ontology/envo.md b/ontology/envo.md index 99cacc2fe..4084e6b06 100644 --- a/ontology/envo.md +++ b/ontology/envo.md @@ -26,6 +26,7 @@ dependencies: depicted_by: /images/envo.png description: An ontology of environmental systems, components, and processes. domain: environment +github_date_added: 2015-07-28 homepage: http://environmentontology.org/ jobs: - id: https://github.com/EnvironmentOntology/envo/blob/master/.github/workflows/qc.yml diff --git a/ontology/eo.md b/ontology/eo.md index bd5ceb55d..2a94d86ad 100644 --- a/ontology/eo.md +++ b/ontology/eo.md @@ -13,6 +13,7 @@ contact: depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. domain: environment +github_date_added: 2015-07-29 homepage: http://planteome.org/ is_obsolete: true license: diff --git a/ontology/epo.md b/ontology/epo.md index f20eb638f..40417f016 100644 --- a/ontology/epo.md +++ b/ontology/epo.md @@ -7,13 +7,13 @@ build: source_url: http://purl.obolibrary.org/obo/epo.owl description: An ontology designed to support the semantic annotation of epidemiology resources domain: health +github_date_added: 2015-07-29 homepage: https://code.google.com/p/epidemiology-ontology/ in_foundry: false is_obsolete: true products: - id: epo.owl activity_status: inactive -github_date_added: 2015-07-29 --- The Epidemiology Ontology is an ontology designed to support the semantic annotation of epidemiology resources. It is being developed under the EU-funded EPIWORK project, a multidisciplinary research effort which aims at increasing the amount of epidemiological data available, improving disease surveillance systems, and promoting the collaboration among epidemiological researchers. The EO is integrated into NERO (Network of Epidemiology Related Ontologies), a collection of existing ontologies that supports the semantic annotation of epidemiology resources contained in the Epidemic Marketplace (EM), a platform for sharing resources and knowledge within the Epidemiology community. NERO currently includes thirteen external ontologies (the majority are OBO or OBO candidate ontologies) which already provide a high coverage of most epidemiology related areas. As such, the EPO focuses on neglected/highly specific areas of epidemiology and will articulate with other OBO ontologies as needed. diff --git a/ontology/ero.md b/ontology/ero.md index 05a992ec5..210a1ebca 100644 --- a/ontology/ero.md +++ b/ontology/ero.md @@ -11,6 +11,7 @@ contact: description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. documentation: https://open.med.harvard.edu/wiki/display/eaglei/Ontology domain: information +github_date_added: 2015-07-28 homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology is_obsolete: true license: diff --git a/ontology/eupath.md b/ontology/eupath.md index 2cb804da2..5e413b542 100644 --- a/ontology/eupath.md +++ b/ontology/eupath.md @@ -10,6 +10,7 @@ contact: depicted_by: https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). domain: organisms +github_date_added: 2018-01-02 homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology license: label: CC BY 4.0 diff --git a/ontology/ev.md b/ontology/ev.md index 4594a27ae..54a565802 100644 --- a/ontology/ev.md +++ b/ontology/ev.md @@ -6,10 +6,10 @@ contact: email: evoc@sanbi.ac.za label: eVOC mailing list domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://www.evocontology.org/ is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment. diff --git a/ontology/exo.md b/ontology/exo.md index b29009e08..630ac67bc 100644 --- a/ontology/exo.md +++ b/ontology/exo.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-2908-3327 description: Vocabularies for describing exposure data to inform understanding of environmental health. domain: health +github_date_added: 2015-07-28 homepage: https://github.com/CTDbase/exposure-ontology license: label: CC BY 4.0 diff --git a/ontology/fao.md b/ontology/fao.md index fd4892033..b46c61086 100644 --- a/ontology/fao.md +++ b/ontology/fao.md @@ -14,6 +14,7 @@ contact: orcid: 0000-0001-6330-7526 description: A structured controlled vocabulary for the anatomy of fungi. domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ license: label: CC0 1.0 diff --git a/ontology/fbbi.md b/ontology/fbbi.md index 64b880397..346b8c4eb 100644 --- a/ontology/fbbi.md +++ b/ontology/fbbi.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-8841-5870 description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. domain: investigations +github_date_added: 2015-07-28 homepage: http://cellimagelibrary.org/ license: label: CC BY 4.0 diff --git a/ontology/fbbt.md b/ontology/fbbt.md index 4816b54ce..6730c1707 100644 --- a/ontology/fbbt.md +++ b/ontology/fbbt.md @@ -23,6 +23,7 @@ contact: orcid: 0000-0002-1373-1705 description: An ontology representing the gross anatomy of Drosophila melanogaster. domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://purl.obolibrary.org/obo/fbbt license: label: CC BY 4.0 @@ -65,5 +66,4 @@ usages: url: http://flybase.org/cgi-bin/cvreport.html?rel=is_a&id=FBbt:00005106 user: http://flybase.org activity_status: active -github_date_added: 2015-07-28 --- diff --git a/ontology/fbcv.md b/ontology/fbcv.md index f3c73b63c..abf7dab80 100644 --- a/ontology/fbcv.md +++ b/ontology/fbcv.md @@ -17,6 +17,7 @@ contact: orcid: 0000-0002-1373-1705 description: A structured controlled vocabulary used for various aspects of annotation by FlyBase. domain: organisms +github_date_added: 2015-08-06 homepage: http://purl.obolibrary.org/obo/fbcv license: label: CC BY 4.0 diff --git a/ontology/fbdv.md b/ontology/fbdv.md index 0d79fc8b5..be28beb82 100644 --- a/ontology/fbdv.md +++ b/ontology/fbdv.md @@ -17,6 +17,7 @@ contact: orcid: 0000-0002-1373-1705 description: A structured controlled vocabulary of the development of Drosophila melanogaster. domain: anatomy and development +github_date_added: 2015-07-29 homepage: http://purl.obolibrary.org/obo/fbdv license: label: CC BY 4.0 diff --git a/ontology/fbsp.md b/ontology/fbsp.md index 60bf685e3..d4af11968 100644 --- a/ontology/fbsp.md +++ b/ontology/fbsp.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-1373-1705 description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. domain: organisms +github_date_added: 2015-07-28 homepage: http://www.flybase.org/ is_obsolete: true products: @@ -23,7 +24,6 @@ taxon: id: NCBITaxon:7227 label: Drosophila activity_status: inactive -github_date_added: 2015-07-28 --- The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. diff --git a/ontology/fix.md b/ontology/fix.md index 4395e2f0e..d76c85025 100644 --- a/ontology/fix.md +++ b/ontology/fix.md @@ -12,11 +12,11 @@ contact: label: chEBI description: An ontology of physico-chemical methods and properties. domain: chemistry and biochemistry +github_date_added: 2015-07-29 homepage: http://www.ebi.ac.uk/chebi in_foundry: false products: - id: fix.owl - id: fix.obo activity_status: orphaned -github_date_added: 2015-07-29 --- diff --git a/ontology/flopo.md b/ontology/flopo.md index 9d8c798e6..d29d27e2c 100644 --- a/ontology/flopo.md +++ b/ontology/flopo.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0001-8149-5890 description: Traits and phenotypes of flowering plants occurring in digitized Floras domain: phenotype +github_date_added: 2015-12-16 homepage: https://github.com/flora-phenotype-ontology/flopoontology license: label: CC0 1.0 diff --git a/ontology/flu.md b/ontology/flu.md index 2a22729fb..7914a8946 100644 --- a/ontology/flu.md +++ b/ontology/flu.md @@ -9,6 +9,7 @@ contact: email: burkesquires@gmail.com label: Burke Squires domain: health +github_date_added: 2015-07-29 homepage: http://purl.obolibrary.org/obo/flu/ in_foundry: false is_obsolete: true @@ -16,5 +17,4 @@ products: - id: flu.owl tracker: http://purl.obolibrary.org/obo/flu/tracker activity_status: inactive -github_date_added: 2015-07-29 --- diff --git a/ontology/fma.md b/ontology/fma.md index 20e9fae09..af7e608df 100644 --- a/ontology/fma.md +++ b/ontology/fma.md @@ -11,6 +11,7 @@ contact: label: Onard Mejino description: This is currently a slimmed down version of FMA domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://si.washington.edu/projects/fma license: label: CC BY 3.0 diff --git a/ontology/fobi.md b/ontology/fobi.md index c5bfa362c..201039b49 100644 --- a/ontology/fobi.md +++ b/ontology/fobi.md @@ -12,6 +12,7 @@ dependencies: - id: foodon description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data domain: diet, metabolomics, and nutrition +github_date_added: 2019-12-04 homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology license: label: CC BY 3.0 diff --git a/ontology/foodon.md b/ontology/foodon.md index 09b42c225..36fe6bb48 100644 --- a/ontology/foodon.md +++ b/ontology/foodon.md @@ -18,6 +18,7 @@ dependencies: - id: uberon description: A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research domain: diet, metabolomics, and nutrition +github_date_added: 2016-07-25 homepage: https://foodon.org/ license: label: CC BY 3.0 diff --git a/ontology/fovt.md b/ontology/fovt.md index 445dd739d..58e28817a 100644 --- a/ontology/fovt.md +++ b/ontology/fovt.md @@ -22,6 +22,7 @@ dependencies: - id: uberon description: FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA). domain: phenotype +github_date_added: 2020-05-06 homepage: https://github.com/futres/fovt jobs: - id: https://travis-ci.org/futres/fovt diff --git a/ontology/fypo.md b/ontology/fypo.md index b0f5aa559..9a4a0cc5c 100644 --- a/ontology/fypo.md +++ b/ontology/fypo.md @@ -14,6 +14,7 @@ contact: depicted_by: https://github.com/pombase/website/blob/master/src/assets/FYPO_logo_tiny.png description: FYPO is a formal ontology of phenotypes observed in fission yeast. domain: phenotype +github_date_added: 2015-07-29 homepage: https://github.com/pombase/fypo license: label: CC BY 4.0 diff --git a/ontology/gaz.md b/ontology/gaz.md index d10454cb1..54177e0c5 100644 --- a/ontology/gaz.md +++ b/ontology/gaz.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0001-8910-9851 description: A gazetteer constructed on ontological principles domain: environment +github_date_added: 2015-07-28 homepage: http://environmentontology.github.io/gaz/ license: label: CC0 1.0 diff --git a/ontology/gecko.md b/ontology/gecko.md index edbe65296..80105e3ba 100644 --- a/ontology/gecko.md +++ b/ontology/gecko.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0003-4871-5569 description: An ontology to represent genomics cohort attributes domain: organisms +github_date_added: 2020-08-11 homepage: https://github.com/IHCC-cohorts/GECKO license: label: CC BY 4.0 diff --git a/ontology/genepio.md b/ontology/genepio.md index b8df4876f..c808bb0b1 100644 --- a/ontology/genepio.md +++ b/ontology/genepio.md @@ -15,6 +15,7 @@ dependencies: - id: uberon description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. domain: health +github_date_added: 2016-07-25 homepage: http://genepio.org/ license: label: CC BY 3.0 diff --git a/ontology/geno.md b/ontology/geno.md index 7f2eb123c..c11752c4d 100644 --- a/ontology/geno.md +++ b/ontology/geno.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-1048-5019 description: An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases. domain: biological systems +github_date_added: 2017-01-05 homepage: https://github.com/monarch-initiative/GENO-ontology/ license: label: CC BY 4.0 diff --git a/ontology/geo.md b/ontology/geo.md index c4ced9700..1e63a7859 100644 --- a/ontology/geo.md +++ b/ontology/geo.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-9881-1017 description: An ontology of geographical entities domain: environment +github_date_added: 2015-07-28 homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki license: label: CC BY 4.0 diff --git a/ontology/gno.md b/ontology/gno.md index e1c791d47..79167e64a 100644 --- a/ontology/gno.md +++ b/ontology/gno.md @@ -20,6 +20,7 @@ contact: orcid: 0000-0001-5168-3196 description: GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels. domain: chemistry and biochemistry +github_date_added: 2019-08-15 homepage: https://gnome.glyomics.org/ license: label: CC BY 4.0 diff --git a/ontology/go.md b/ontology/go.md index a862c3305..d7e57bc55 100644 --- a/ontology/go.md +++ b/ontology/go.md @@ -33,6 +33,7 @@ dependencies: depicted_by: http://geneontology.org/assets/go-logo-icon.mini.png description: An ontology for describing the function of genes and gene products domain: biological systems +github_date_added: 2015-07-28 homepage: http://geneontology.org/ in_foundry_order: 1 integration_server: http://build.berkeleybop.org/view/GO diff --git a/ontology/gro.md b/ontology/gro.md index c65df6122..6cc2b095d 100644 --- a/ontology/gro.md +++ b/ontology/gro.md @@ -6,10 +6,10 @@ contact: email: po-discuss@plantontology.org label: Plant Ontology Administrators domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://www.gramene.org/plant_ontology/ is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the Plant Ontology. diff --git a/ontology/gsso.md b/ontology/gsso.md index 2a21785e7..bb5eca273 100644 --- a/ontology/gsso.md +++ b/ontology/gsso.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0001-8397-8810 description: The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences. domain: organisms +github_date_added: 2020-10-01 homepage: https://gsso.research.cchmc.org/ license: label: Apache 2.0 License diff --git a/ontology/habronattus.md b/ontology/habronattus.md index 3d867104f..f38612b29 100644 --- a/ontology/habronattus.md +++ b/ontology/habronattus.md @@ -7,10 +7,10 @@ contact: label: Peter Midford orcid: 0000-0001-6512-3296 domain: organisms +github_date_added: 2015-08-21 homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for courtship behavior of the spider Habronattus californicus. diff --git a/ontology/hancestro.md b/ontology/hancestro.md index 0231584c7..59edbbc30 100644 --- a/ontology/hancestro.md +++ b/ontology/hancestro.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0003-1058-2668 description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. domain: organisms +github_date_added: 2018-07-13 homepage: https://github.com/EBISPOT/ancestro license: label: CC BY 4.0 diff --git a/ontology/hao.md b/ontology/hao.md index da572e470..ab7b0f9c6 100644 --- a/ontology/hao.md +++ b/ontology/hao.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-5640-5491 description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://hymao.org license: label: CC0 1.0 diff --git a/ontology/hom.md b/ontology/hom.md index 11c2409ea..51fb4b149 100644 --- a/ontology/hom.md +++ b/ontology/hom.md @@ -14,6 +14,7 @@ contact: orcid: 0000-0002-9415-5104 description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://github.com/BgeeDB/homology-ontology license: label: CC0 1.0 diff --git a/ontology/hp.md b/ontology/hp.md index 2d648c0e6..445dba708 100644 --- a/ontology/hp.md +++ b/ontology/hp.md @@ -22,6 +22,7 @@ contact: depicted_by: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png description: A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. domain: phenotype +github_date_added: 2015-07-28 homepage: http://www.human-phenotype-ontology.org/ jobs: - id: https://travis-ci.org/obophenotype/human-phenotype-ontology diff --git a/ontology/hsapdv.md b/ontology/hsapdv.md index 5a8d36325..4dad9b63d 100644 --- a/ontology/hsapdv.md +++ b/ontology/hsapdv.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-9415-5104 description: Life cycle stages for Human domain: anatomy and development +github_date_added: 2015-08-21 homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv license: label: CC BY 3.0 diff --git a/ontology/hso.md b/ontology/hso.md index babaff536..bac97a371 100644 --- a/ontology/hso.md +++ b/ontology/hso.md @@ -15,6 +15,7 @@ dependencies: - id: uberon description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. domain: health +github_date_added: 2020-11-28 homepage: https://w3id.org/hso license: label: CC BY 3.0 diff --git a/ontology/htn.md b/ontology/htn.md index 268b2495c..093da9876 100644 --- a/ontology/htn.md +++ b/ontology/htn.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-1795-5570 description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines domain: health +github_date_added: 2019-06-05 homepage: https://github.com/aellenhicks/htn_owl license: label: CC BY 4.0 diff --git a/ontology/iao.md b/ontology/iao.md index c795e3607..f2543f475 100644 --- a/ontology/iao.md +++ b/ontology/iao.md @@ -13,6 +13,7 @@ contact: depicted_by: https://avatars0.githubusercontent.com/u/13591168?v=3&s=200 description: An ontology of information entities. domain: information +github_date_added: 2015-07-28 homepage: https://github.com/information-artifact-ontology/IAO/ license: label: CC BY 4.0 diff --git a/ontology/iceo.md b/ontology/iceo.md index 10b59d3de..4a089ddee 100644 --- a/ontology/iceo.md +++ b/ontology/iceo.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0003-3781-6962 description: ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs). domain: microbiology +github_date_added: 2019-09-02 homepage: https://github.com/ontoice/ICEO license: label: CC BY 4.0 diff --git a/ontology/ico.md b/ontology/ico.md index 570dbf954..1d78e91a9 100644 --- a/ontology/ico.md +++ b/ontology/ico.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-9189-9661 description: An ontology of clinical informed consents domain: investigations +github_date_added: 2015-08-21 homepage: https://github.com/ICO-ontology/ICO license: label: CC BY 3.0 diff --git a/ontology/ido.md b/ontology/ido.md index 38344af6c..b68e01a92 100644 --- a/ontology/ido.md +++ b/ontology/ido.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0003-1617-8244 description: A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain. domain: health +github_date_added: 2015-07-28 homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology license: label: CC BY 3.0 diff --git a/ontology/idomal.md b/ontology/idomal.md index a5968b266..9f94c2371 100644 --- a/ontology/idomal.md +++ b/ontology/idomal.md @@ -7,6 +7,7 @@ contact: label: Pantelis Topalis description: An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. domain: health +github_date_added: 2015-07-28 homepage: https://www.vectorbase.org/ontology-browser license: label: CC0 1.0 diff --git a/ontology/iev.md b/ontology/iev.md index 515d6547d..9b1eb558b 100644 --- a/ontology/iev.md +++ b/ontology/iev.md @@ -7,10 +7,10 @@ build: method: obo2owl source_url: http://download.baderlab.org/INOH/ontologies/EventOntology_172.obo domain: chemistry and biochemistry +github_date_added: 2015-08-21 homepage: http://www.inoh.org is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- A structured controlled vocabulary of pathway centric biological processes. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate biological processes, pathways, sub-pathways in the INOH pathway data.
INOH is part of the BioPAX working group. diff --git a/ontology/imr.md b/ontology/imr.md index bef7cb70a..33557cb21 100644 --- a/ontology/imr.md +++ b/ontology/imr.md @@ -10,10 +10,10 @@ contact: email: curator@inoh.org label: INOH curators domain: chemistry and biochemistry +github_date_added: 2015-08-21 homepage: http://www.inoh.org is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- A structured controlled vocabulary of concrete protein names and generic (abstract) protein names. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. This ontology is used to annotate protein names, protein family names, generic/concrete protein names in the INOH pathway data.
INOH is part of the BioPAX working group. diff --git a/ontology/ino.md b/ontology/ino.md index d2486c5c0..54e270343 100644 --- a/ontology/ino.md +++ b/ontology/ino.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-9189-9661 description: An ontology of interactions and interaction networks domain: biological systems +github_date_added: 2018-03-10 homepage: https://github.com/INO-ontology/ino license: label: CC BY 3.0 diff --git a/ontology/ipr.md b/ontology/ipr.md index 949c2e296..c9b75ddae 100644 --- a/ontology/ipr.md +++ b/ontology/ipr.md @@ -6,10 +6,10 @@ contact: email: interhelp@ebi.ac.uk label: InterPro Help domain: chemistry and biochemistry +github_date_added: 2015-08-21 homepage: http://www.ebi.ac.uk/interpro/index.html is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- A database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. diff --git a/ontology/kisao.md b/ontology/kisao.md index ada4f660f..48e75c3dc 100644 --- a/ontology/kisao.md +++ b/ontology/kisao.md @@ -27,6 +27,7 @@ funded_by: title: NIH P41EB023912 - id: https://grantome.com/search?q=R35GM119771 title: NIH R35GM119771 +github_date_added: 2015-07-28 homepage: https://github.com/SED-ML/KiSAO license: label: Artistic License 2.0 diff --git a/ontology/labo.md b/ontology/labo.md index 814af94dc..0682a12f0 100644 --- a/ontology/labo.md +++ b/ontology/labo.md @@ -16,6 +16,7 @@ dependencies: - id: opmi description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. domain: information +github_date_added: 2019-08-29 homepage: https://github.com/OpenLHS/LABO license: label: CC BY 4.0 diff --git a/ontology/lepao.md b/ontology/lepao.md index 185184a92..76b65ae32 100644 --- a/ontology/lepao.md +++ b/ontology/lepao.md @@ -17,6 +17,7 @@ dependencies: - id: uberon description: The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research). domain: anatomy and development +github_date_added: 2021-12-14 homepage: https://github.com/insect-morphology/lepao license: label: CC BY 4.0 diff --git a/ontology/lipro.md b/ontology/lipro.md index 71b231930..266bb3060 100644 --- a/ontology/lipro.md +++ b/ontology/lipro.md @@ -10,12 +10,12 @@ contact: label: Christipher Baker description: An ontology representation of the LIPIDMAPS nomenclature classification. domain: chemistry and biochemistry +github_date_added: 2015-07-29 in_foundry: false is_obsolete: true tags: - lipids activity_status: inactive -github_date_added: 2015-07-29 --- Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. The ontology describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. diff --git a/ontology/loggerhead.md b/ontology/loggerhead.md index 9862b8189..536088bf6 100644 --- a/ontology/loggerhead.md +++ b/ontology/loggerhead.md @@ -7,10 +7,10 @@ contact: label: Peter Midford orcid: 0000-0001-6512-3296 domain: organisms +github_date_added: 2015-08-21 homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for Loggerhead sea turtle (Caretta caretta) nesting behavior, based on the published ethogram of Hailman and Elowson. diff --git a/ontology/ma.md b/ontology/ma.md index 7fac77980..4814c7b18 100644 --- a/ontology/ma.md +++ b/ontology/ma.md @@ -14,6 +14,7 @@ contact: orcid: 0000-0002-0956-8634 description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus). domain: anatomy and development +github_date_added: 2015-07-29 homepage: https://github.com/obophenotype/mouse-anatomy-ontology license: label: CC BY 4.0 diff --git a/ontology/mamo.md b/ontology/mamo.md index 85c1fc7f0..76f0b57e9 100644 --- a/ontology/mamo.md +++ b/ontology/mamo.md @@ -7,6 +7,7 @@ build: source_url: https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. domain: simulation +github_date_added: 2015-07-28 homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/ license: label: Artistic License 2.0 diff --git a/ontology/mao.md b/ontology/mao.md index 9f7d9985c..afe6af8d6 100644 --- a/ontology/mao.md +++ b/ontology/mao.md @@ -6,10 +6,10 @@ contact: email: julie@igbmc.u-strasbg.fr label: Julie Thompson domain: chemistry and biochemistry +github_date_added: 2015-08-21 homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment. diff --git a/ontology/mat.md b/ontology/mat.md index df4c36094..fbc8ea637 100644 --- a/ontology/mat.md +++ b/ontology/mat.md @@ -6,10 +6,10 @@ contact: email: j.bard@ed.ac.uk label: Jonathan Bard domain: anatomy and development +github_date_added: 2015-08-21 homepage: null is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- Minimal set of terms for anatomy diff --git a/ontology/maxo.md b/ontology/maxo.md index dd403eecb..1339aea04 100644 --- a/ontology/maxo.md +++ b/ontology/maxo.md @@ -21,6 +21,7 @@ dependencies: depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png description: Medical Action Ontology is an ontology... domain: health +github_date_added: 2020-02-12 homepage: https://github.com/monarch-initiative/MAxO jobs: - id: https://travis-ci.org/monarch-initiative/MAxO diff --git a/ontology/mco.md b/ontology/mco.md index 6cf15786b..94687f0cb 100644 --- a/ontology/mco.md +++ b/ontology/mco.md @@ -28,6 +28,7 @@ dependencies: - id: zeco description: Microbial Conditions Ontology is an ontology... domain: investigations +github_date_added: 2019-02-15 homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology jobs: - id: https://travis-ci.org/microbial-conditions-ontology/microbial-conditions-ontology diff --git a/ontology/mf.md b/ontology/mf.md index 03e33fd1e..8c0f6a154 100644 --- a/ontology/mf.md +++ b/ontology/mf.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-3469-4923 description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. domain: health +github_date_added: 2015-07-28 homepage: https://github.com/jannahastings/mental-functioning-ontology license: label: CC BY 3.0 diff --git a/ontology/mfmo.md b/ontology/mfmo.md index afcc79b2e..1764a6519 100644 --- a/ontology/mfmo.md +++ b/ontology/mfmo.md @@ -11,6 +11,7 @@ dependencies: - id: uberon description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. domain: anatomy and development +github_date_added: 2015-08-11 homepage: https://github.com/rdruzinsky/feedontology license: label: CC BY 3.0 diff --git a/ontology/mfo.md b/ontology/mfo.md index cb75a5cd6..5f1b4285d 100644 --- a/ontology/mfo.md +++ b/ontology/mfo.md @@ -7,6 +7,7 @@ contact: label: Thorsten Henrich description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. domain: anatomy and development +github_date_added: 2015-07-28 is_obsolete: true products: - id: mfo.owl @@ -15,7 +16,6 @@ taxon: id: NCBITaxon:8089 label: Oryzias activity_status: inactive -github_date_added: 2015-07-28 --- A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. diff --git a/ontology/mfoem.md b/ontology/mfoem.md index 265342cc9..fcbdc0c91 100644 --- a/ontology/mfoem.md +++ b/ontology/mfoem.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-3469-4923 description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. domain: health +github_date_added: 2015-07-28 homepage: https://github.com/jannahastings/emotion-ontology license: label: CC BY 3.0 diff --git a/ontology/mfomd.md b/ontology/mfomd.md index e6c1cd29c..4d748b39c 100644 --- a/ontology/mfomd.md +++ b/ontology/mfomd.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-3469-4923 description: An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable domain: health +github_date_added: 2015-08-21 homepage: https://github.com/jannahastings/mental-functioning-ontology license: label: CC BY 3.0 diff --git a/ontology/mi.md b/ontology/mi.md index b441f6367..ca3e2ea47 100644 --- a/ontology/mi.md +++ b/ontology/mi.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-8429-8793 description: A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. domain: investigations +github_date_added: 2015-07-28 homepage: https://github.com/HUPO-PSI/psi-mi-CV license: label: CC BY 4.0 diff --git a/ontology/miapa.md b/ontology/miapa.md index 37d8b5b09..f2025128c 100644 --- a/ontology/miapa.md +++ b/ontology/miapa.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-9107-0714 description: An application ontology to formalize annotation of phylogenetic data. domain: information +github_date_added: 2015-07-28 homepage: http://www.evoio.org/wiki/MIAPA license: label: CC0 1.0 diff --git a/ontology/micro.md b/ontology/micro.md index 6144b75b8..72e6fc7a0 100644 --- a/ontology/micro.md +++ b/ontology/micro.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-2100-6351 description: An ontology of prokaryotic phenotypic and metabolic characters domain: phenotype +github_date_added: 2015-10-20 homepage: https://github.com/carrineblank/MicrO license: label: CC BY 2.0 diff --git a/ontology/mirnao.md b/ontology/mirnao.md index 3efb82501..1d48778bc 100644 --- a/ontology/mirnao.md +++ b/ontology/mirnao.md @@ -7,6 +7,7 @@ contact: label: Pantelis Topalis description: An application ontology for use with miRNA databases. domain: chemistry and biochemistry +github_date_added: 2015-07-28 homepage: http://code.google.com/p/mirna-ontology/ is_obsolete: true license: @@ -15,7 +16,6 @@ license: products: - id: mirnao.owl activity_status: inactive -github_date_added: 2015-07-28 --- microRNA Ontology (miRNAO) is an application ontology and it has been developed in order to drive miRNA databases. diff --git a/ontology/miro.md b/ontology/miro.md index e761c8079..718a01cbb 100644 --- a/ontology/miro.md +++ b/ontology/miro.md @@ -7,6 +7,7 @@ contact: label: Christos (Kitsos) Louis description: Application ontology for entities related to insecticide resistance in mosquitos domain: environment +github_date_added: 2015-07-28 products: - id: miro.owl - id: miro.obo diff --git a/ontology/mmo.md b/ontology/mmo.md index ca33a5959..1564bc50b 100644 --- a/ontology/mmo.md +++ b/ontology/mmo.md @@ -16,6 +16,7 @@ contact: orcid: 0000-0002-6443-9376 description: 'A representation of the variety of methods used to make clinical and phenotype measurements. ' domain: health +github_date_added: 2015-07-28 homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 license: label: CC0 1.0 diff --git a/ontology/mmusdv.md b/ontology/mmusdv.md index 8ea598d35..27177d604 100644 --- a/ontology/mmusdv.md +++ b/ontology/mmusdv.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-9415-5104 description: Life cycle stages for Mus Musculus domain: anatomy and development +github_date_added: 2015-08-21 homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv license: label: CC BY 3.0 diff --git a/ontology/mo.md b/ontology/mo.md index f3052b785..0509470b1 100644 --- a/ontology/mo.md +++ b/ontology/mo.md @@ -8,6 +8,7 @@ contact: orcid: 0000-0002-5714-991X description: A standardized description of a microarray experiment in support of MAGE v.1. domain: investigations +github_date_added: 2015-07-28 homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php is_obsolete: true page: http://mged.sourceforge.net/software/downloads.php @@ -15,7 +16,6 @@ products: - id: mo.owl replaced_by: obi activity_status: inactive -github_date_added: 2015-07-28 --- Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. diff --git a/ontology/mod.md b/ontology/mod.md index 1b7366950..dfa486e98 100644 --- a/ontology/mod.md +++ b/ontology/mod.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-0045-7698 description: PSI-MOD is an ontology consisting of terms that describe protein chemical modifications domain: chemistry and biochemistry +github_date_added: 2015-07-28 homepage: http://www.psidev.info/MOD license: label: CC BY 4.0 diff --git a/ontology/mondo.md b/ontology/mondo.md index 6873368ed..e7aec87b1 100644 --- a/ontology/mondo.md +++ b/ontology/mondo.md @@ -15,6 +15,7 @@ contact: depicted_by: https://raw.githubusercontent.com/monarch-initiative/mondo/master/docs/images/mondo_logo_black-stacked-small.png description: A global community effort to harmonize multiple disease resources to yield a coherent merged ontology. domain: health +github_date_added: 2016-07-12 homepage: https://monarch-initiative.github.io/mondo label: Mondo license: diff --git a/ontology/mop.md b/ontology/mop.md index f23895aad..61f394687 100644 --- a/ontology/mop.md +++ b/ontology/mop.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0001-5985-7429 description: Processes at the molecular level domain: chemistry and biochemistry +github_date_added: 2015-08-17 homepage: https://github.com/rsc-ontologies/rxno license: label: CC BY 4.0 diff --git a/ontology/mp.md b/ontology/mp.md index fa2b71e91..6ae7b7f7a 100644 --- a/ontology/mp.md +++ b/ontology/mp.md @@ -23,6 +23,7 @@ contact: orcid: 0000-0003-4606-0597 description: Standard terms for annotating mammalian phenotypic data. domain: phenotype +github_date_added: 2015-07-28 homepage: http://www.informatics.jax.org/searches/MP_form.shtml jobs: - id: http://build.berkeleybop.org/job/build-mp-edit diff --git a/ontology/mpath.md b/ontology/mpath.md index 6f6621686..73158324d 100644 --- a/ontology/mpath.md +++ b/ontology/mpath.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-5111-7263 description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes domain: health +github_date_added: 2015-07-28 homepage: http://www.pathbase.net license: label: CC BY 3.0 diff --git a/ontology/mpio.md b/ontology/mpio.md index 0fce44315..dbdc98b54 100644 --- a/ontology/mpio.md +++ b/ontology/mpio.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0003-1834-3856 description: An ontology of minimum information regarding potential drug-drug interaction information. domain: health +github_date_added: 2017-11-02 homepage: https://github.com/MPIO-Developers/MPIO license: label: CC BY 4.0 diff --git a/ontology/mro.md b/ontology/mro.md index 8d2f3d182..92f1fae1a 100644 --- a/ontology/mro.md +++ b/ontology/mro.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-8457-6693 description: An ontology for Major Histocompatibility Complex (MHC) restriction in experiments domain: chemistry and biochemistry +github_date_added: 2015-09-17 homepage: https://github.com/IEDB/MRO license: label: CC BY 3.0 diff --git a/ontology/ms.md b/ontology/ms.md index 269c716e1..8b8747c7f 100644 --- a/ontology/ms.md +++ b/ontology/ms.md @@ -15,6 +15,7 @@ dependencies: - id: uo description: A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. domain: investigations +github_date_added: 2015-07-28 homepage: http://www.psidev.info/groups/controlled-vocabularies integration_server: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master label: MS diff --git a/ontology/nbo.md b/ontology/nbo.md index e1b5b337b..21a6979f9 100644 --- a/ontology/nbo.md +++ b/ontology/nbo.md @@ -16,6 +16,7 @@ contact: orcid: 0000-0002-2061-091X description: An ontology of human and animal behaviours and behavioural phenotypes domain: biological systems +github_date_added: 2015-07-28 homepage: https://github.com/obo-behavior/behavior-ontology/ license: label: CC BY 3.0 diff --git a/ontology/ncbitaxon.md b/ontology/ncbitaxon.md index da58f0a2e..bbc929d08 100644 --- a/ontology/ncbitaxon.md +++ b/ontology/ncbitaxon.md @@ -18,6 +18,7 @@ contact: orcid: 0000-0002-9415-5104 description: An ontology representation of the NCBI organismal taxonomy domain: organisms +github_date_added: 2015-07-28 homepage: https://github.com/obophenotype/ncbitaxon jobs: - id: http://build.berkeleybop.org/job/build-ncbitaxon/ diff --git a/ontology/ncro.md b/ontology/ncro.md index a7622af42..246faa929 100644 --- a/ontology/ncro.md +++ b/ontology/ncro.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0003-2408-2883 description: An ontology for non-coding RNA, both of biological origin, and engineered. domain: investigations +github_date_added: 2015-11-18 homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology license: label: CC BY 4.0 diff --git a/ontology/nif_cell.md b/ontology/nif_cell.md index acb521dc4..4fefae102 100644 --- a/ontology/nif_cell.md +++ b/ontology/nif_cell.md @@ -7,11 +7,11 @@ contact: label: Fahim Imam description: Neuronal cell types domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://neuinfo.org/ is_obsolete: true replaced_by: cl activity_status: inactive -github_date_added: 2015-08-21 --- Cell types from NIFSTD diff --git a/ontology/nif_dysfunction.md b/ontology/nif_dysfunction.md index 76e5da0a0..f1fb87822 100644 --- a/ontology/nif_dysfunction.md +++ b/ontology/nif_dysfunction.md @@ -6,11 +6,11 @@ contact: email: smtifahim@gmail.com label: Fahim Imam domain: health +github_date_added: 2015-08-21 homepage: http://neuinfo.org/ is_obsolete: true replaced_by: doid activity_status: inactive -github_date_added: 2015-08-21 --- This ontology contains the former BIRNLex-Disease, version 1.3.2. diff --git a/ontology/nif_grossanatomy.md b/ontology/nif_grossanatomy.md index d44ac1d07..c23b5ece1 100644 --- a/ontology/nif_grossanatomy.md +++ b/ontology/nif_grossanatomy.md @@ -6,11 +6,11 @@ contact: email: smtifahim@gmail.com label: Fahim Imam domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://neuinfo.org/ is_obsolete: true replaced_by: uberon activity_status: inactive -github_date_added: 2015-08-21 --- NIF-GrossAnatomy: anatomical entities of relevance to neuroscience. Contains most classes from BIRNLex-Anatomy diff --git a/ontology/nmr.md b/ontology/nmr.md index d99e7b4a6..a1ccf85bc 100644 --- a/ontology/nmr.md +++ b/ontology/nmr.md @@ -10,13 +10,13 @@ contact: label: Schober Daniel description: Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation. domain: investigations +github_date_added: 2015-07-28 homepage: http://msi-ontology.sourceforge.net/ is_obsolete: true page: http://msi-ontology.sourceforge.net/ontology/NMR.owlDocument.doc products: - id: nmr.owl activity_status: inactive -github_date_added: 2015-07-28 --- Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation. diff --git a/ontology/nomen.md b/ontology/nomen.md index 04ca43a2a..3daf7d084 100644 --- a/ontology/nomen.md +++ b/ontology/nomen.md @@ -16,6 +16,7 @@ domain: information funded_by: - id: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1356381 title: NSF ABI-1356381 +github_date_added: 2019-01-11 homepage: https://github.com/SpeciesFileGroup/nomen label: NOMEN license: diff --git a/ontology/oae.md b/ontology/oae.md index 99a6ab8a0..a903b41d8 100644 --- a/ontology/oae.md +++ b/ontology/oae.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0001-9189-9661 description: A biomedical ontology in the domain of adverse events domain: health +github_date_added: 2015-07-28 homepage: https://github.com/OAE-ontology/OAE/ license: label: CC BY 3.0 diff --git a/ontology/oarcs.md b/ontology/oarcs.md index cc7a21d08..0a81f6449 100644 --- a/ontology/oarcs.md +++ b/ontology/oarcs.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-5640-5491 description: OArCS is an ontology describing the Arthropod ciruclatory system. domain: anatomy and development +github_date_added: 2017-02-10 homepage: https://github.com/aszool/oarcs license: label: CC BY 3.0 diff --git a/ontology/oba.md b/ontology/oba.md index b89090961..db4c81630 100644 --- a/ontology/oba.md +++ b/ontology/oba.md @@ -14,6 +14,7 @@ contact: orcid: 0000-0002-6601-2165 description: A collection of biological attributes (traits) covering all kingdoms of life. domain: phenotype +github_date_added: 2015-07-28 homepage: https://github.com/obophenotype/bio-attribute-ontology jobs: - id: https://travis-ci.org/obophenotype/bio-attribute-ontology diff --git a/ontology/obcs.md b/ontology/obcs.md index 0bb4f0c33..d4ebfd64a 100644 --- a/ontology/obcs.md +++ b/ontology/obcs.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-2999-0103 description: A biomedical ontology in the domain of biological and clinical statistics. domain: information technology +github_date_added: 2015-07-31 homepage: https://github.com/obcs/obcs in_foundry: false license: diff --git a/ontology/obi.md b/ontology/obi.md index 577a04ca0..0fa7443a9 100644 --- a/ontology/obi.md +++ b/ontology/obi.md @@ -16,6 +16,7 @@ contact: depicted_by: https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png description: An integrated ontology for the description of life-science and clinical investigations domain: investigations +github_date_added: 2015-07-28 homepage: http://obi-ontology.org in_foundry_order: 1 integration_server: http://build.berkeleybop.org/job/build-obi/ diff --git a/ontology/obib.md b/ontology/obib.md index 1f3b5f7a7..1189a3210 100644 --- a/ontology/obib.md +++ b/ontology/obib.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-2999-0103 description: An ontology built for annotation and modeling of biobank repository and biobanking administration domain: investigations +github_date_added: 2015-08-17 homepage: https://github.com/biobanking/biobanking license: label: CC BY 4.0 diff --git a/ontology/obo_rel.md b/ontology/obo_rel.md index 160c6f6a3..208599fe7 100644 --- a/ontology/obo_rel.md +++ b/ontology/obo_rel.md @@ -7,11 +7,11 @@ contact: label: Chris Mungall orcid: 0000-0002-6601-2165 domain: upper +github_date_added: 2015-08-21 homepage: http://www.obofoundry.org/ro is_obsolete: true replaced_by: ro activity_status: inactive -github_date_added: 2015-08-21 --- Defines core relations used in all OBO ontologies. Importand note: this ontology is now deprecated - use RO instead diff --git a/ontology/ogg.md b/ontology/ogg.md index d8190eb84..7bf18ea27 100644 --- a/ontology/ogg.md +++ b/ontology/ogg.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-9189-9661 description: A formal ontology of genes and genomes of biological organisms. domain: biological systems +github_date_added: 2015-07-29 homepage: https://bitbucket.org/hegroup/ogg license: label: CC BY 3.0 diff --git a/ontology/ogi.md b/ontology/ogi.md index 2972cf9ce..35eb3e9e7 100644 --- a/ontology/ogi.md +++ b/ontology/ogi.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-5379-5359 description: An ontology that formalizes the genomic element by defining an upper class genetic interval domain: chemistry and biochemistry +github_date_added: 2015-07-28 homepage: https://code.google.com/p/ontology-for-genetic-interval/ is_obsolete: true products: diff --git a/ontology/ogms.md b/ontology/ogms.md index 3ec6935f8..f7fb0c98d 100644 --- a/ontology/ogms.md +++ b/ontology/ogms.md @@ -10,6 +10,7 @@ contact: depicted_by: https://avatars2.githubusercontent.com/u/12973154?s=200&v=4 description: An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities domain: health +github_date_added: 2015-07-29 homepage: https://github.com/OGMS/ogms license: label: CC BY 4.0 diff --git a/ontology/ogsf.md b/ontology/ogsf.md index e423bc7a3..21453275f 100644 --- a/ontology/ogsf.md +++ b/ontology/ogsf.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-5379-5359 description: An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. domain: investigations +github_date_added: 2015-07-28 homepage: https://github.com/linikujp/OGSF license: label: CC BY 3.0 diff --git a/ontology/ohd.md b/ontology/ohd.md index dc66e0e94..08758acfb 100644 --- a/ontology/ohd.md +++ b/ontology/ohd.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0001-9625-1899 description: The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies. domain: health +github_date_added: 2016-12-01 homepage: https://purl.obolibrary.org/obo/ohd/home license: label: CC BY 4.0 diff --git a/ontology/ohmi.md b/ontology/ohmi.md index 3c7a8671c..2dbca1581 100644 --- a/ontology/ohmi.md +++ b/ontology/ohmi.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-9189-9661 description: The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions. domain: organisms +github_date_added: 2017-04-21 homepage: https://github.com/ohmi-ontology/ohmi license: label: CC BY 4.0 diff --git a/ontology/ohpi.md b/ontology/ohpi.md index 5d40fbd3a..ff98d7b9e 100644 --- a/ontology/ohpi.md +++ b/ontology/ohpi.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-5159-414X description: OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is developed to represent manually curated HPI knowledge available in the PHIDIAS resource. domain: biological systems +github_date_added: 2019-07-22 homepage: https://github.com/OHPI/ohpi license: label: CC BY 4.0 diff --git a/ontology/olatdv.md b/ontology/olatdv.md index 520fa57a5..040cfbc9b 100644 --- a/ontology/olatdv.md +++ b/ontology/olatdv.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-9415-5104 description: Life cycle stages for Medaka domain: anatomy and development +github_date_added: 2015-08-21 homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv license: label: CC BY 3.0 diff --git a/ontology/omiabis.md b/ontology/omiabis.md index 0d2aea528..4fcc64903 100644 --- a/ontology/omiabis.md +++ b/ontology/omiabis.md @@ -8,6 +8,7 @@ contact: orcid: 0000-0003-1834-3856 description: An ontological version of MIABIS (Minimum Information About BIobank data Sharing) domain: health +github_date_added: 2016-02-05 homepage: https://github.com/OMIABIS/omiabis-dev is_obsolete: true license: diff --git a/ontology/omit.md b/ontology/omit.md index 9508cd99c..b45c8f15a 100644 --- a/ontology/omit.md +++ b/ontology/omit.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0003-2408-2883 description: Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain domain: chemistry and biochemistry +github_date_added: 2015-07-29 homepage: http://omit.cis.usouthal.edu/ in_foundry: false license: diff --git a/ontology/omp.md b/ontology/omp.md index caee6d0c5..d58d667ea 100644 --- a/ontology/omp.md +++ b/ontology/omp.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0001-9016-2684 description: An ontology of phenotypes covering microbes domain: phenotype +github_date_added: 2015-08-21 homepage: http://microbialphenotypes.org license: label: CC BY 3.0 diff --git a/ontology/omrse.md b/ontology/omrse.md index 31a00e014..80355d72b 100644 --- a/ontology/omrse.md +++ b/ontology/omrse.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-9881-1017 description: This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations. domain: health +github_date_added: 2015-07-28 homepage: https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview license: label: CC BY 4.0 diff --git a/ontology/one.md b/ontology/one.md index 4f88ed9a4..a5569d18a 100644 --- a/ontology/one.md +++ b/ontology/one.md @@ -13,6 +13,7 @@ dependencies: - id: ons description: An ontology to standardize research output of nutritional epidemiologic studies. domain: diet, metabolomics, and nutrition +github_date_added: 2020-11-17 homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies label: Ontology for Nutritional Epidemiology license: diff --git a/ontology/ons.md b/ontology/ons.md index 68b4b6b61..c38926fcc 100644 --- a/ontology/ons.md +++ b/ontology/ons.md @@ -18,6 +18,7 @@ dependencies: - id: uberon description: An ontology for description of concepts in the nutritional studies domain. domain: diet, metabolomics, and nutrition +github_date_added: 2020-05-28 homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies label: Ontology for Nutritional Studies license: diff --git a/ontology/ontoavida.md b/ontology/ontoavida.md index 7c8fb4441..0c582f914 100644 --- a/ontology/ontoavida.md +++ b/ontology/ontoavida.md @@ -15,6 +15,7 @@ dependencies: - id: stato description: OntoAvida develops an integrated vocabulary for the description of the most widely-used computational approach for studying evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment). domain: simulation +github_date_added: 2021-12-01 homepage: https://gitlab.com/fortunalab/ontoavida license: label: CC BY 4.0 diff --git a/ontology/ontoneo.md b/ontology/ontoneo.md index ca25ceb76..4676c0c47 100644 --- a/ontology/ontoneo.md +++ b/ontology/ontoneo.md @@ -15,6 +15,7 @@ contact: orcid: 0000-0003-2338-8872 description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. domain: health +github_date_added: 2016-11-22 homepage: ontoneo.com license: label: CC BY 3.0 diff --git a/ontology/opl.md b/ontology/opl.md index 38a878dd3..11eb0e8d2 100644 --- a/ontology/opl.md +++ b/ontology/opl.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-2999-0103 description: A reference ontology for parasite life cycle stages. domain: organisms +github_date_added: 2015-07-28 homepage: https://github.com/OPL-ontology/OPL license: label: CC BY 4.0 diff --git a/ontology/opmi.md b/ontology/opmi.md index 8f29216ea..b182125b2 100644 --- a/ontology/opmi.md +++ b/ontology/opmi.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-9189-9661 description: The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions. domain: investigations +github_date_added: 2018-08-30 homepage: https://github.com/OPMI/opmi license: label: CC BY 4.0 diff --git a/ontology/ornaseq.md b/ontology/ornaseq.md index c5b04e1b8..611820624 100644 --- a/ontology/ornaseq.md +++ b/ontology/ornaseq.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-8034-7685 description: An application ontology designed to annotate next-generation sequencing experiments performed on RNA. domain: investigations +github_date_added: 2019-06-20 homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml license: label: CC BY 4.0 diff --git a/ontology/ovae.md b/ontology/ovae.md index 3962dd7d8..09787c760 100644 --- a/ontology/ovae.md +++ b/ontology/ovae.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-9189-9661 description: A biomedical ontology in the domain of vaccine adverse events. domain: health +github_date_added: 2015-07-28 homepage: http://www.violinet.org/ovae/ license: label: CC BY 3.0 diff --git a/ontology/pao.md b/ontology/pao.md index 08686a3ab..5df16ca32 100644 --- a/ontology/pao.md +++ b/ontology/pao.md @@ -8,13 +8,13 @@ contact: label: Pankaj Jaiswal orcid: 0000-0002-1005-8383 domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://www.plantontology.org is_obsolete: true taxon: id: NCBITaxon:33090 label: Viridiplantae activity_status: inactive -github_date_added: 2015-08-21 --- REPLACED BY: PO. A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization. Note that this has been subsumed into the PO diff --git a/ontology/pato.md b/ontology/pato.md index 23a9dd141..a83d2ae86 100644 --- a/ontology/pato.md +++ b/ontology/pato.md @@ -17,6 +17,7 @@ contact: orcid: 0000-0002-2061-091X description: An ontology of phenotypic qualities (properties, attributes or characteristics) domain: phenotype +github_date_added: 2015-07-28 homepage: https://github.com/pato-ontology/pato/ in_foundry_order: 1 jobs: diff --git a/ontology/pcl.md b/ontology/pcl.md index 0f868f07d..9705a720f 100644 --- a/ontology/pcl.md +++ b/ontology/pcl.md @@ -22,6 +22,7 @@ dependencies: - id: uberon description: Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties. domain: phenotype +github_date_added: 2022-01-25 homepage: https://github.com/obophenotype/provisional_cell_ontology license: label: CC BY 4.0 diff --git a/ontology/pco.md b/ontology/pco.md index 0ff03810b..72a70e231 100644 --- a/ontology/pco.md +++ b/ontology/pco.md @@ -22,6 +22,7 @@ dependencies: - id: ro description: An ontology about groups of interacting organisms such as populations and communities domain: environment +github_date_added: 2015-07-28 homepage: https://github.com/PopulationAndCommunityOntology/pco jobs: - id: https://travis-ci.org/PopulationAndCommunityOntology/pco diff --git a/ontology/pd_st.md b/ontology/pd_st.md index 65cad6a04..759bcd814 100644 --- a/ontology/pd_st.md +++ b/ontology/pd_st.md @@ -6,6 +6,7 @@ contact: email: henrich@embl.de label: Thorsten Heinrich domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://4dx.embl.de/platy is_obsolete: true replaced_by: pdumdv @@ -13,5 +14,4 @@ taxon: id: NCBITaxon:6358 label: Platynereis activity_status: inactive -github_date_added: 2015-08-21 --- diff --git a/ontology/pdro.md b/ontology/pdro.md index bf5fd067b..5c1576280 100644 --- a/ontology/pdro.md +++ b/ontology/pdro.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-3336-2476 description: An ontology to describe entities related to prescription of drugs domain: information +github_date_added: 2016-11-11 homepage: https://github.com/OpenLHS/PDRO license: label: CC BY 4.0 diff --git a/ontology/pdumdv.md b/ontology/pdumdv.md index 69c5cad0f..c9c118fdb 100644 --- a/ontology/pdumdv.md +++ b/ontology/pdumdv.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-9415-5104 description: Life cycle stages for Platynereis dumerilii domain: anatomy and development +github_date_added: 2015-08-21 homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv license: label: CC BY 3.0 diff --git a/ontology/peco.md b/ontology/peco.md index acbd917ae..74d46fb5c 100644 --- a/ontology/peco.md +++ b/ontology/peco.md @@ -10,6 +10,7 @@ contact: depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. domain: investigations +github_date_added: 2017-06-05 homepage: http://planteome.org/ license: label: CC BY 4.0 diff --git a/ontology/pgdso.md b/ontology/pgdso.md index f100de649..f1efc35cf 100644 --- a/ontology/pgdso.md +++ b/ontology/pgdso.md @@ -6,13 +6,13 @@ contact: email: po-discuss@plantontology.org label: Plant Ontology Administrators domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://www.plantontology.org is_obsolete: true taxon: id: NCBITaxon:33090 label: Viridiplantae activity_status: inactive -github_date_added: 2015-08-21 --- REPLACED BY: PO. A controlled vocabulary of growth and developmental stages in various plants. Note that this has been subsumed into the PO diff --git a/ontology/phipo.md b/ontology/phipo.md index 2c99508cd..7637bb982 100644 --- a/ontology/phipo.md +++ b/ontology/phipo.md @@ -15,6 +15,7 @@ dependencies: - id: pato description: PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions. domain: phenotype +github_date_added: 2018-08-15 homepage: https://github.com/PHI-base/phipo jobs: - id: https://travis-ci.org/PHI-base/phipo diff --git a/ontology/plana.md b/ontology/plana.md index b85ecd87e..40e172bcb 100644 --- a/ontology/plana.md +++ b/ontology/plana.md @@ -16,6 +16,7 @@ dependencies: - id: uberon description: PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes. domain: anatomy and development +github_date_added: 2017-02-07 homepage: https://github.com/obophenotype/planaria-ontology jobs: - id: https://travis-ci.org/obophenotype/planaria-ontology diff --git a/ontology/planp.md b/ontology/planp.md index f56bd0c8c..1ee3e6ee3 100644 --- a/ontology/planp.md +++ b/ontology/planp.md @@ -18,6 +18,7 @@ dependencies: - id: ro description: Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. domain: phenotype +github_date_added: 2018-11-19 homepage: https://github.com/obophenotype/planarian-phenotype-ontology jobs: - id: https://travis-ci.org/obophenotype/planarian-phenotype-ontology diff --git a/ontology/plo.md b/ontology/plo.md index 33d9e29b6..0acb5a371 100644 --- a/ontology/plo.md +++ b/ontology/plo.md @@ -6,10 +6,10 @@ contact: email: mb4@sanger.ac.uk label: Matt Berriman domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://www.sanger.ac.uk/Users/mb4/PLO/ is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- A structured controlled vocabulary for the life cycle of the malaria parasite Plasmodium. diff --git a/ontology/po.md b/ontology/po.md index 2c21e7781..5ea63c13d 100644 --- a/ontology/po.md +++ b/ontology/po.md @@ -19,6 +19,7 @@ contact: depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://browser.planteome.org/amigo in_foundry_order: 1 jobs: diff --git a/ontology/poro.md b/ontology/poro.md index 1f90a93a8..5d985381f 100644 --- a/ontology/poro.md +++ b/ontology/poro.md @@ -18,6 +18,7 @@ dependencies: - id: uberon description: An ontology covering the anatomy of the taxon Porifera (sponges) domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://github.com/obophenotype/porifera-ontology jobs: - id: https://travis-ci.org/obophenotype/porifera-ontology diff --git a/ontology/ppo.md b/ontology/ppo.md index 4a27fca7b..ee6eaca43 100644 --- a/ontology/ppo.md +++ b/ontology/ppo.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0001-8815-0078 description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. domain: phenotype +github_date_added: 2016-12-30 homepage: https://github.com/PlantPhenoOntology/PPO license: label: CC BY 3.0 diff --git a/ontology/pr.md b/ontology/pr.md index 6623346ec..c126bffe9 100644 --- a/ontology/pr.md +++ b/ontology/pr.md @@ -23,6 +23,7 @@ depicted_by: https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo description: An ontological representation of protein-related entities documentation: https://proconsortium.org/download/current/pro_readme.txt domain: chemistry and biochemistry +github_date_added: 2015-07-28 homepage: http://proconsortium.org in_foundry_order: 1 license: diff --git a/ontology/proco.md b/ontology/proco.md index 03159c702..84dad6635 100644 --- a/ontology/proco.md +++ b/ontology/proco.md @@ -16,6 +16,7 @@ dependencies: - id: sbo description: PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes. domain: chemistry and biochemistry +github_date_added: 2022-04-19 homepage: https://github.com/proco-ontology/PROCO license: label: CC BY 4.0 diff --git a/ontology/propreo.md b/ontology/propreo.md index 77c88d0b5..17861c218 100644 --- a/ontology/propreo.md +++ b/ontology/propreo.md @@ -6,10 +6,10 @@ contact: email: satya30@uga.edu label: Satya S. Sahoo domain: chemistry and biochemistry +github_date_added: 2015-08-21 homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/ is_obsolete: true activity_status: inactive -github_date_added: 2015-08-21 --- A comprehensive proteomics data and process provenance ontology. diff --git a/ontology/psdo.md b/ontology/psdo.md index a393e1444..5db81fd52 100644 --- a/ontology/psdo.md +++ b/ontology/psdo.md @@ -18,6 +18,7 @@ dependencies: - id: stato description: Ontology to reproducibly study visualizations of clinical performance domain: information +github_date_added: 2019-04-04 homepage: https://github.com/Display-Lab/psdo license: label: CC BY 3.0 diff --git a/ontology/pso.md b/ontology/pso.md index b442224c2..7841322bd 100644 --- a/ontology/pso.md +++ b/ontology/pso.md @@ -15,6 +15,7 @@ dependencies: - id: ro description: The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter. domain: agriculture +github_date_added: 2020-05-14 homepage: https://github.com/Planteome/plant-stress-ontology jobs: - id: https://travis-ci.org/Planteome/plant-stress-ontology diff --git a/ontology/pw.md b/ontology/pw.md index 9a082ceb5..8730d0fc3 100644 --- a/ontology/pw.md +++ b/ontology/pw.md @@ -17,6 +17,7 @@ contact: depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif description: A controlled vocabulary for annotating gene products to pathways. domain: biological systems +github_date_added: 2015-07-28 homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html license: label: CC BY 4.0 diff --git a/ontology/rbo.md b/ontology/rbo.md index cf3b66361..565ec5f0b 100644 --- a/ontology/rbo.md +++ b/ontology/rbo.md @@ -21,6 +21,7 @@ dependencies: - id: uo description: RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. domain: environment +github_date_added: 2021-01-28 homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO jobs: - id: https://travis-ci.org/DanBerrios/RBO diff --git a/ontology/resid.md b/ontology/resid.md index dd4e74988..30ef13c6f 100644 --- a/ontology/resid.md +++ b/ontology/resid.md @@ -7,12 +7,12 @@ contact: label: John Garavelli description: For the description of covalent bonds in proteins. domain: chemistry and biochemistry +github_date_added: 2015-07-28 homepage: http://www.ebi.ac.uk/RESID/ is_obsolete: true tags: - proteins activity_status: inactive -github_date_added: 2015-07-28 --- For the description of covalent bonds in proteins. diff --git a/ontology/rex.md b/ontology/rex.md index 5e31dc4c3..2404c354b 100644 --- a/ontology/rex.md +++ b/ontology/rex.md @@ -8,10 +8,10 @@ build: source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. domain: chemistry and biochemistry +github_date_added: 2015-07-28 products: - id: rex.owl activity_status: orphaned -github_date_added: 2015-07-28 --- REX is an ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. REX includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX. diff --git a/ontology/rnao.md b/ontology/rnao.md index 6c3ec266f..1900fa464 100644 --- a/ontology/rnao.md +++ b/ontology/rnao.md @@ -16,6 +16,7 @@ contact: orcid: 0000-0001-5985-7429 description: Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. domain: chemistry and biochemistry +github_date_added: 2015-07-28 homepage: https://github.com/bgsu-rna/rnao license: label: CC0 1.0 diff --git a/ontology/ro.md b/ontology/ro.md index 097d10f08..e3a124c45 100644 --- a/ontology/ro.md +++ b/ontology/ro.md @@ -16,6 +16,7 @@ contact: description: Relationship types shared across multiple ontologies documentation: https://oborel.github.io/obo-relations/ domain: upper +github_date_added: 2015-07-28 homepage: https://oborel.github.io/ jobs: - id: https://travis-ci.org/oborel/obo-relations diff --git a/ontology/rs.md b/ontology/rs.md index cb5f8006c..6f8c27ed8 100644 --- a/ontology/rs.md +++ b/ontology/rs.md @@ -17,6 +17,7 @@ contact: depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif description: Ontology of rat strains domain: organisms +github_date_added: 2015-07-28 homepage: http://rgd.mcw.edu/rgdweb/search/strains.html license: label: CC BY 4.0 diff --git a/ontology/rxno.md b/ontology/rxno.md index c3e14f3c8..6996a74a1 100644 --- a/ontology/rxno.md +++ b/ontology/rxno.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0001-5985-7429 description: Connects organic name reactions to their roles in an organic synthesis and to processes in MOP domain: chemistry and biochemistry +github_date_added: 2015-08-17 homepage: https://github.com/rsc-ontologies/rxno license: label: CC BY 4.0 diff --git a/ontology/sao.md b/ontology/sao.md index 555c24d89..83f932caf 100644 --- a/ontology/sao.md +++ b/ontology/sao.md @@ -6,6 +6,7 @@ contact: email: slarson@ncmir.ucsd.edu label: Stephen Larson domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html is_obsolete: true replaced_by: go @@ -13,7 +14,6 @@ taxon: id: NCBITaxon:9606 label: Homo sapiens activity_status: inactive -github_date_added: 2015-08-21 --- We have developed the Subcellular Anatomy Ontology for the Nervous System (SAO) to provide a formal ontology to describe structures from the dimensional range known as the “mesoscale,” encompassing cellular and subcellular structure, supracellular domains, and macromolecules. The SAO describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil (Fong et al., submitted). Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their approporiate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration. diff --git a/ontology/sbo.md b/ontology/sbo.md index f746dcaa2..552c95cae 100644 --- a/ontology/sbo.md +++ b/ontology/sbo.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0003-0705-9809 description: Terms commonly used in Systems Biology, and in particular in computational modeling. domain: chemistry and biochemistry +github_date_added: 2015-07-28 homepage: http://www.ebi.ac.uk/sbo/ license: label: Artistic License 2.0 diff --git a/ontology/scdo.md b/ontology/scdo.md index 6b8fa3573..ccfe33beb 100644 --- a/ontology/scdo.md +++ b/ontology/scdo.md @@ -45,6 +45,7 @@ dependencies: - id: vt description: An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. domain: health +github_date_added: 2021-04-16 homepage: https://scdontology.h3abionet.org/ license: label: GPL-3.0 diff --git a/ontology/sep.md b/ontology/sep.md index ef56ce7f9..177afd7e6 100644 --- a/ontology/sep.md +++ b/ontology/sep.md @@ -11,6 +11,7 @@ contact: label: SEP developers via the PSI and MSI mailing lists description: A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments. domain: investigations +github_date_added: 2015-07-28 homepage: http://psidev.info/index.php?q=node/312 is_obsolete: true page: http://psidev.info/index.php?q=node/312 diff --git a/ontology/sepio.md b/ontology/sepio.md index 334277340..ba0d3045d 100644 --- a/ontology/sepio.md +++ b/ontology/sepio.md @@ -14,6 +14,7 @@ contact: depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/SEPIO-LOGOS/sepio_logo_black-banner.png description: An ontology for representing the provenance of scientific claims and the evidence that supports them. domain: investigations +github_date_added: 2017-06-30 homepage: https://github.com/monarch-initiative/SEPIO-ontology license: label: CC BY 3.0 diff --git a/ontology/sibo.md b/ontology/sibo.md index 67ea02bd6..287d2bc53 100644 --- a/ontology/sibo.md +++ b/ontology/sibo.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-6601-2165 description: Social Behavior in insects domain: biological systems +github_date_added: 2015-07-29 homepage: https://github.com/obophenotype/sibo license: label: CC BY 3.0 diff --git a/ontology/so.md b/ontology/so.md index cc8c6e17a..a55ae1808 100644 --- a/ontology/so.md +++ b/ontology/so.md @@ -14,6 +14,7 @@ contact: depicted_by: http://sequenceontology.org/img/so_icon.png description: A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. domain: chemistry and biochemistry +github_date_added: 2015-07-28 homepage: http://www.sequenceontology.org/ license: label: CC BY 4.0 diff --git a/ontology/sopharm.md b/ontology/sopharm.md index 4b4236100..91f0a2cde 100644 --- a/ontology/sopharm.md +++ b/ontology/sopharm.md @@ -6,13 +6,13 @@ contact: email: Adrien.Coulet@loria.fr label: Adrien Coulet domain: chemistry and biochemistry +github_date_added: 2015-08-21 homepage: http://www.loria.fr/~coulet/sopharm2.0_description.php is_obsolete: true taxon: id: NCBITaxon:9606 label: Homo sapiens activity_status: inactive -github_date_added: 2015-08-21 --- SO-Pharm is a formal ontology that represent domain knowledge in pharmacogenomics. To achieve this goal SO-Pharm articulates ontologies from sub domains of phamacogenomics (i.e. genotype, phenotype, drug, trial representations). SO-Pharm enables to support knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. diff --git a/ontology/spd.md b/ontology/spd.md index f0fa194de..fc596c802 100644 --- a/ontology/spd.md +++ b/ontology/spd.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-0358-0130 description: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://research.amnh.org/atol/files/ license: label: CC BY 3.0 diff --git a/ontology/stato.md b/ontology/stato.md index d088c3eed..35395cc3a 100644 --- a/ontology/stato.md +++ b/ontology/stato.md @@ -10,6 +10,7 @@ contact: depicted_by: https://raw.githubusercontent.com/ISA-tools/stato/dev/images/stato-logo-3.png description: STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of application, and information needed or resulting from statistical methods, such as probability distributions, variables, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results. domain: information technology +github_date_added: 2015-08-17 homepage: http://stato-ontology.org/ in_foundry: false license: diff --git a/ontology/swo.md b/ontology/swo.md index 6563970c5..60c7cc329 100644 --- a/ontology/swo.md +++ b/ontology/swo.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-7702-4495 description: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. domain: information technology +github_date_added: 2015-07-28 homepage: https://github.com/allysonlister/swo license: label: CC BY 4.0 diff --git a/ontology/symp.md b/ontology/symp.md index 3b433aca5..84f4673e0 100644 --- a/ontology/symp.md +++ b/ontology/symp.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0001-8910-9851 description: An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease. domain: health +github_date_added: 2015-07-28 homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page license: label: CC0 1.0 diff --git a/ontology/tads.md b/ontology/tads.md index fcd4f7178..6c5058847 100644 --- a/ontology/tads.md +++ b/ontology/tads.md @@ -7,6 +7,7 @@ contact: label: Daniel Sonenshine description: 'The anatomy of the Tick, Families: Ixodidae, Argassidae' domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://www.vectorbase.org/ontology-browser license: label: CC BY 4.0 diff --git a/ontology/tahe.md b/ontology/tahe.md index ea7dc496e..4de84f192 100644 --- a/ontology/tahe.md +++ b/ontology/tahe.md @@ -6,11 +6,11 @@ contact: email: pierre.sprumont@unifr.ch label: Pierre Sprumont domain: anatomy and development +github_date_added: 2015-08-21 homepage: null is_obsolete: true taxon: id: NCBITaxon:9606 label: Homo sapiens activity_status: inactive -github_date_added: 2015-08-21 --- diff --git a/ontology/tahh.md b/ontology/tahh.md index fea505dd5..706e71fe7 100644 --- a/ontology/tahh.md +++ b/ontology/tahh.md @@ -6,11 +6,11 @@ contact: email: pierre.sprumont@unifr.ch label: Pierre Sprumont domain: health +github_date_added: 2015-08-21 homepage: null is_obsolete: true taxon: id: NCBITaxon:9606 label: Homo sapiens activity_status: inactive -github_date_added: 2015-08-21 --- diff --git a/ontology/tao.md b/ontology/tao.md index b1f229996..e5b252f49 100644 --- a/ontology/tao.md +++ b/ontology/tao.md @@ -11,6 +11,7 @@ contact: orcid: 0000-0003-3162-7490 description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology is_obsolete: true license: @@ -26,7 +27,6 @@ taxon: id: NCBITaxon:32443 label: Teleostei activity_status: inactive -github_date_added: 2015-07-28 --- Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa. diff --git a/ontology/taxrank.md b/ontology/taxrank.md index 9769a2d12..186f1d565 100644 --- a/ontology/taxrank.md +++ b/ontology/taxrank.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-8688-6599 description: A vocabulary of taxonomic ranks (species, family, phylum, etc) domain: organisms +github_date_added: 2015-07-28 homepage: https://github.com/phenoscape/taxrank jobs: - id: https://travis-ci.org/phenoscape/taxrank diff --git a/ontology/tgma.md b/ontology/tgma.md index a4b08c7fa..bf8deb567 100644 --- a/ontology/tgma.md +++ b/ontology/tgma.md @@ -7,6 +7,7 @@ contact: label: Pantelis Topalis description: A structured controlled vocabulary of the anatomy of mosquitoes. domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://www.vectorbase.org/ontology-browser license: label: CC0 1.0 diff --git a/ontology/to.md b/ontology/to.md index 64e6098ee..d9f9bb88b 100644 --- a/ontology/to.md +++ b/ontology/to.md @@ -20,6 +20,7 @@ contact: depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG description: A controlled vocabulary to describe phenotypic traits in plants. domain: phenotype +github_date_added: 2015-07-28 homepage: http://browser.planteome.org/amigo jobs: - id: https://travis-ci.org/Planteome/plant-trait-ontology diff --git a/ontology/trans.md b/ontology/trans.md index 7ec005dcd..fee9fe450 100644 --- a/ontology/trans.md +++ b/ontology/trans.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0001-8910-9851 description: An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. domain: health +github_date_added: 2015-07-28 homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology license: label: CC0 1.0 diff --git a/ontology/tto.md b/ontology/tto.md index 6d401bed9..3e76fb36d 100644 --- a/ontology/tto.md +++ b/ontology/tto.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-8688-6599 description: An ontology covering the taxonomy of teleosts (bony fish) domain: organisms +github_date_added: 2015-07-28 homepage: https://github.com/phenoscape/teleost-taxonomy-ontology license: label: CC0 1.0 diff --git a/ontology/txpo.md b/ontology/txpo.md index 3f778e300..15330ec7c 100644 --- a/ontology/txpo.md +++ b/ontology/txpo.md @@ -16,6 +16,7 @@ contact: orcid: 0000-0002-9673-1283 description: TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. domain: chemistry and biochemistry +github_date_added: 2019-09-26 homepage: https://toxpilot.nibiohn.go.jp/ license: label: CC BY 3.0 diff --git a/ontology/uberon.md b/ontology/uberon.md index b1ab6e5bb..e76a0045c 100644 --- a/ontology/uberon.md +++ b/ontology/uberon.md @@ -51,6 +51,7 @@ funded_by: title: NIH P41-HG002273 - id: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0956049 title: NSF DEB-0956049 +github_date_added: 2015-07-28 homepage: http://uberon.org label: Uberon license: diff --git a/ontology/uo.md b/ontology/uo.md index 9990edb88..68b79333c 100644 --- a/ontology/uo.md +++ b/ontology/uo.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-2061-091X description: Metrical units for use in conjunction with PATO domain: phenotype +github_date_added: 2015-07-29 homepage: https://github.com/bio-ontology-research-group/unit-ontology in_foundry: false license: diff --git a/ontology/upa.md b/ontology/upa.md index 93158894e..905750a37 100644 --- a/ontology/upa.md +++ b/ontology/upa.md @@ -15,6 +15,7 @@ dependencies: - id: ro description: A manually curated resource for the representation and annotation of metabolic pathways domain: biological systems +github_date_added: 2018-12-12 homepage: https://github.com/geneontology/unipathway jobs: - id: https://travis-ci.org/geneontology/unipathway diff --git a/ontology/upheno.md b/ontology/upheno.md index 7b38b5e9d..3654bc5c5 100644 --- a/ontology/upheno.md +++ b/ontology/upheno.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0001-5208-3432 description: The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. domain: phenotype +github_date_added: 2015-08-21 homepage: https://github.com/obophenotype/upheno license: label: CC0 1.0 diff --git a/ontology/vario.md b/ontology/vario.md index 6b6a75c9c..2fe4104a4 100644 --- a/ontology/vario.md +++ b/ontology/vario.md @@ -10,13 +10,13 @@ contact: label: Mauno Vihinen description: Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. domain: biological systems +github_date_added: 2015-07-28 homepage: http://variationontology.org preferredPrefix: VariO products: - id: vario.owl - id: vario.obo activity_status: orphaned -github_date_added: 2015-07-28 --- Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. diff --git a/ontology/vhog.md b/ontology/vhog.md index ebd8552d8..bdf34e8e5 100644 --- a/ontology/vhog.md +++ b/ontology/vhog.md @@ -4,6 +4,7 @@ id: vhog title: Vertebrate Homologous Ontology Group Ontology depicted_by: http://bgee.org/img/logo/bgee13_logo.png domain: anatomy and development +github_date_added: 2015-07-28 is_obsolete: true products: - id: vhog.owl diff --git a/ontology/vo.md b/ontology/vo.md index d3af4450c..a35b9ed5d 100644 --- a/ontology/vo.md +++ b/ontology/vo.md @@ -11,6 +11,7 @@ contact: orcid: 0000-0001-9189-9661 description: VO is a biomedical ontology in the domain of vaccine and vaccination. domain: health +github_date_added: 2015-07-29 homepage: http://www.violinet.org/vaccineontology license: label: CC BY 3.0 diff --git a/ontology/vsao.md b/ontology/vsao.md index ae6a58f10..e70a208e9 100644 --- a/ontology/vsao.md +++ b/ontology/vsao.md @@ -11,6 +11,7 @@ contact: orcid: 0000-0003-3162-7490 description: Vertebrate skeletal anatomy ontology. domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://www.nescent.org/phenoscape/Main_Page is_obsolete: true page: https://www.phenoscape.org/wiki/Skeletal_Anatomy_Jamboree @@ -21,7 +22,6 @@ taxon: id: NCBITaxon:7742 label: Vertebrata activity_status: inactive -github_date_added: 2015-07-28 --- Vertebrate skeletal anatomy ontology. diff --git a/ontology/vt.md b/ontology/vt.md index d6967b3c8..7e86d820f 100644 --- a/ontology/vt.md +++ b/ontology/vt.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-2346-5201 description: An ontology of traits covering vertebrates domain: phenotype +github_date_added: 2015-08-21 homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology license: label: CC BY 4.0 diff --git a/ontology/vto.md b/ontology/vto.md index b3307cc8a..4951b3956 100644 --- a/ontology/vto.md +++ b/ontology/vto.md @@ -9,6 +9,7 @@ contact: orcid: 0000-0002-8688-6599 description: Comprehensive hierarchy of extinct and extant vertebrate taxa. domain: organisms +github_date_added: 2015-07-28 homepage: https://github.com/phenoscape/vertebrate-taxonomy-ontology license: label: CC0 1.0 diff --git a/ontology/wbbt.md b/ontology/wbbt.md index df8c1940b..2ec731ec3 100644 --- a/ontology/wbbt.md +++ b/ontology/wbbt.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-8151-7479 description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology license: label: CC BY 4.0 diff --git a/ontology/wbls.md b/ontology/wbls.md index a96e64697..2d768b9d2 100644 --- a/ontology/wbls.md +++ b/ontology/wbls.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0001-9076-6015 description: A structured controlled vocabulary of the development of Caenorhabditis elegans. domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://github.com/obophenotype/c-elegans-development-ontology license: label: CC BY 4.0 diff --git a/ontology/wbphenotype.md b/ontology/wbphenotype.md index 80ffd9163..104167e1c 100644 --- a/ontology/wbphenotype.md +++ b/ontology/wbphenotype.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0001-9076-6015 description: A structured controlled vocabulary of Caenorhabditis elegans phenotypes domain: phenotype +github_date_added: 2015-07-28 homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology license: label: CC BY 4.0 diff --git a/ontology/xao.md b/ontology/xao.md index 2e6eb8f6d..99452f8b6 100644 --- a/ontology/xao.md +++ b/ontology/xao.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-9611-1279 description: XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis. domain: anatomy and development +github_date_added: 2015-07-28 homepage: http://www.xenbase.org/anatomy/xao.do?method=display in_foundry_order: 1 license: diff --git a/ontology/xco.md b/ontology/xco.md index 4ed14055f..7030dcfb6 100644 --- a/ontology/xco.md +++ b/ontology/xco.md @@ -17,6 +17,7 @@ contact: depicted_by: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif description: Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. domain: health +github_date_added: 2015-07-29 homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 license: label: CC0 1.0 diff --git a/ontology/xpo.md b/ontology/xpo.md index bbccfe508..e1855a49e 100644 --- a/ontology/xpo.md +++ b/ontology/xpo.md @@ -22,6 +22,7 @@ dependencies: - id: xao description: XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. domain: phenotype +github_date_added: 2018-11-30 homepage: https://github.com/obophenotype/xenopus-phenotype-ontology jobs: - id: https://travis-ci.org/obophenotype/xenopus-phenotype-ontology diff --git a/ontology/ypo.md b/ontology/ypo.md index fc7cc3e9c..883a11477 100644 --- a/ontology/ypo.md +++ b/ontology/ypo.md @@ -7,6 +7,7 @@ contact: label: Mike Cherry orcid: 0000-0001-9163-5180 domain: phenotype +github_date_added: 2015-08-21 homepage: http://www.yeastgenome.org/ is_obsolete: true replaced_by: apo @@ -14,7 +15,6 @@ taxon: id: NCBITaxon:4932 label: Saccharomyces cerevisiae activity_status: inactive -github_date_added: 2015-08-21 --- A structured controlled vocabulary for the phenotypes of budding yeast. diff --git a/ontology/zea.md b/ontology/zea.md index 0fdc141f3..e2a6f2ec0 100644 --- a/ontology/zea.md +++ b/ontology/zea.md @@ -7,13 +7,13 @@ contact: label: Leszek Vincent orcid: 0000-0002-9316-2919 domain: anatomy and development +github_date_added: 2015-08-21 homepage: http://www.maizemap.org/ is_obsolete: true taxon: id: NCBITaxon:4575 label: Zea activity_status: inactive -github_date_added: 2015-08-21 --- A structured controlled vocabulary for the anatomy of Zea mays. diff --git a/ontology/zeco.md b/ontology/zeco.md index 6e4a4c1cb..dacfd2edc 100644 --- a/ontology/zeco.md +++ b/ontology/zeco.md @@ -12,6 +12,7 @@ contact: orcid: 0000-0002-9900-7880 description: Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN domain: environment +github_date_added: 2016-07-28 homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology license: label: CC BY 3.0 diff --git a/ontology/zfa.md b/ontology/zfa.md index 949de1d57..ce2ff170c 100644 --- a/ontology/zfa.md +++ b/ontology/zfa.md @@ -14,6 +14,7 @@ contact: orcid: 0000-0002-2244-7917 description: A structured controlled vocabulary of the anatomy and development of the Zebrafish domain: anatomy and development +github_date_added: 2015-07-28 homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources in_foundry_order: 1 license: diff --git a/ontology/zfs.md b/ontology/zfs.md index b254fa381..ccb2567a1 100644 --- a/ontology/zfs.md +++ b/ontology/zfs.md @@ -13,6 +13,7 @@ contact: orcid: 0000-0002-2244-7917 description: Developmental stages of the Zebrafish domain: anatomy and development +github_date_added: 2015-07-29 homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources in_foundry: false license: diff --git a/ontology/zp.md b/ontology/zp.md index 4de4dab2a..63e948b75 100644 --- a/ontology/zp.md +++ b/ontology/zp.md @@ -21,6 +21,7 @@ dependencies: - id: zfa description: The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism. domain: phenotype +github_date_added: 2019-01-02 homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology jobs: - id: https://travis-ci.org/obophenotype/zebrafish-phenotype-ontology diff --git a/util/add_dates.py b/util/add_dates.py index 17610289f..36ed70dd6 100644 --- a/util/add_dates.py +++ b/util/add_dates.py @@ -52,7 +52,7 @@ def update_markdown(path: pathlib.Path, date: datetime.datetime) -> None: with path.open() as file: lines = [line.rstrip("\n") for line in file] - if any(line.startswith("added:") for line in lines): + if any(line.startswith("github_date_added:") for line in lines): # No need to add duplicates return @@ -63,7 +63,7 @@ def update_markdown(path: pathlib.Path, date: datetime.datetime) -> None: print("---", file=file) for line in lines[1:idx]: print(line, file=file) - print("added:", date.strftime("%Y-%m-%d"), file=file) + print("github_date_added:", date.strftime("%Y-%m-%d"), file=file) print("---", file=file) for line in lines[idx + 1 :]: print(line, file=file)