Release made on 2023-05-30

What's Changed

This release adds eight new terms for absolute taxonomic abundance analysis and resulting data.

This release uses BFO version 2019-08-26 and OMO version 2023-05-15.

Full Changelog: 2023-05-22...2023-05-30

Release made on 2023-05-22

What's Changed

This release adds 59 new VEuPathDB terms, requested by ClinEpiDB, and 60 new import terms. The design pattern for organism detection data is also modified so multiple hierarchies are inferred through automated reasoning.

Additions

• Updated & added OBI import terms
• Added rdfs:comment values for ENVO imports
• New terms requested by ClinEpiDB
• Updated axioms for organism detection data terms
• Fixes, updates to imports and alternative labels

This release uses BFO version 2019-08-26 and OMO version 2023-05-15.

Full Changelog: 2023-03-20...2023-05-22

Release made on 2023-03-20

What's Changed

This release introduces 21 new VEuPathDB terms and 116 additional imports. This ontology has been refactored so that all terms (whether EUPATH or external) are added or modified only through import modules, without manually editing eupath_dev.owl. Annotations to EUPATH terms are now provided through a single ROBOT template. Axioms for EUPATH terms are provided through multiple ROBOT templates: one template for each set of terms that follow a specific design pattern and one template for the remaining terms.

Additions

• imported 'mass spectrometry assay' #479
• imported 'body morphological measurement' #477
• imported 'cow-baited arthropod trap' #483
• imported NCBITaxon terms for genomics #511
• imported 'caesarean section' #532
• imported phenothrin #530
• imported 'digital object identifier' #531
• imported other terms used in projects #542
• breastfeeding information #482
• collection start & end date terms #533
• units #536
• endemicity terms needed by popBio #538
• taxonomic terms needed by popBio #540

Cleanup and normalization changes

• Refactoring #490

This release uses BFO version 2019-08-26 and OMO version 2023-02-19.

Full Changelog: 2023-01-19...2023-03-20

Release made on 2023-01-19

This release introduces four new VEuPathDB terms and 28 additional import terms. It is the result of ongoing work with OBI to develop a design pattern for terms about the detection of antibodies in specimens, which paves the way for more antibody detection data terms planned to be added to the VEuPathDB ontology.

What's Changed

Additions

• 'parasitemia percentage' #453
• 'Anopheles nuneztovari sensu lato' #444
• 'Anopheles benarrochi B' #456
• Imported 'Mosquito Magnet Liberty Plus trap' #353
• Imported MUAC from OBI (with related fixes) #468
• Anaplasma terms and NCBITaxon import update #463
• Imported antibody assay & related data terms from OBI #459

Cleanup and normalization changes

• Corrected parents of ONTONEO imports #458
• Updated presence_data terms to have organism detection terms as parent #457
• Replaced 'breastfeeding process' with 'suckling behavior' #431
• Removed alternative labels equivalent to labels #460
• Deprecated 'negative blood smear and negative LAMP' #434
• Definition and import fixes #469
• Fixed axiom with deprecated term #455

This release uses BFO version 2019-08-26 and OMO version 2022-04-27.

Full Changelog: 2022-11-04...2023-01-19

Release made on 2022-11-04

This release introduces 154 new VEuPath terms and 24 additional import terms. The most significant changes are many additional bacteria detection terms and the inclusion of synonym annotations from external ontologies to improve searchability.

What's Changed

Additions

• Add metagenomic data term in #395
• Additional term for prevalence of protein variant in #403
• Add bacteria detection data terms in #408
• Add presence of bacteria terms in #412
• Import resistance phenoypte term in #401
• Import 4 animal terms for a genomics dataset in #407
• Inclusion of term synonyms from external ontologies in #410

Cleanup and normalization changes

• Minor fixes and updates from external ontologies in #421

This release uses BFO version 2019-08-26 and OMO version 2022-04-27.

Full Changelog: 2022-08-12...2022-11-03

Release made on 2022-08-12

This release introduces 95 new VEuPath terms and 49 additional imported terms and has a focus on normalizing term labels and definitions and expanding documentation. Changes are now linked directly to pull requests instead of issues.

What's Changed

Additional terms

• Terms for citizen science collection in #363
• Geolocation provenance value terms in #364
• Addition of 'information on putatively essential gene' in #373
• Newly defined terms from project placeholders in #378
• New template terms (mostly presence data) in #383
• Update to UBERON imports in #371

Cleanup and normalization changes

Label and definition normalization

• Normalize and add axioms to diagnosis categories in #362
• Fixes to indicator terms under 'household asset information' in #376
• Update to terms for time spent in an occupation in #377
• Typo fixes and corrections to specimen collection terms in #379
• Update to diagnosis term labels/definitions in #382
• Normalize information content entity labels in #384
• Remove term missing definition (to be restored in future release) in #386

Hierarchy changes

• Update protein variant hierarchy #366

Design pattern diagrams for wiki

• Cmap diagrams in #369
• Clinical-chemistry-data diagram in #375

This release uses BFO version 2019-08-26 and OMO version 2022-04-27.

Full Changelog: 2022-06-08...2022-08-12

Release made on 2022-06-08

This release adds 386 new VEuPath terms and 61 added imports. The major changes in this release are the additions of three ROBOT templates/modules that provide many new organism identification data classes as the bulk of the new terms. Another ROBOT template/module, along with a new annotation property, is added so that web display labels can be added as a type of alternative label and updated by script. An existing ROBOT template/module was changed to correct clinical chemistry data terms, so that the axioms and hierarchy for this part of the ontology provide for more efficient reasoning and match those of the new templates added in this release.

OBI imports requested by VEuPath for organism identification data were added, and 'threshold cycle' from the raw data template to the threshold cycle template. Definition corrections to other OBI organism detection terms appear in this release; these corrections are in obi-dev (but not yet in the latest OBI release as of this posting). ERO imports were removed since those were either no longer in use or could be replaced with matching OBI terms, which effected one existing term. Other added imports include tick species and bacteria found in ticks, requested by PopBio. Configuration changes ensure the latest OMO version is loaded.

Changes were also made to existing VEuPath terms. There are corrections due to terms that should have been redefined instead of deprecated, corrections resulting from dropping a web display category, and one IRI reassignment. Consistent labeling is imposed for time and date information.

This release uses BFO version 2019-08-26 and OMO version 2022-04-27.

Release made on 2022-02-15

This release adds 33 new VEuPath terms and 118 additional import terms. These include OBI terms for assays on specimens and data generated from them, which are used in axioms for data terms about the detection of organisms in specimens. Also imported from OBI is its term for process in which a collection becomes a specimen.

Terms curated from VectorBase are added about pyrethroid resistance, mosquito monitoring, blood meal, and genetics of Anopheles gambiae. Additional Anopheles species are also imported. Terms from MicrobiomeDB were curated for taxondetection, and terms were curated from FungiDB for resistance to antifungal drugs. Terms curated for administrative regions of specific states are added, based on administrative terms from ENVO (also imported for this release. Imports from OBIB which replaced OMIABIS IDs with their own IDs, are updated.

Besides the added terms, other improvements have been made. All deprecated terms, including object properties and annotation properties, have been moved to a separate module. The Makefile is updated for automatic and consistent building of modules from templates. The common 'definition source' replaces our internal annotation for identifying a VectorBase ID that a EUPATH ID replaces. Lastly, a new annotation property is added.

New VEuPath terms:

term	ID	label
class	EUPATH_0000808	16S rRNA sequencing assay targeting V1-V2 region
class	EUPATH_0000809	16S rRNA sequencing assay targeting V1-V3 region
class	EUPATH_0000810	16S rRNA sequencing assay targeting V2 region
class	EUPATH_0000811	16S rRNA sequencing assay targeting V3-V4 region
class	EUPATH_0000812	16S rRNA sequencing assay targeting V3-V5 region
class	EUPATH_0000813	16S rRNA sequencing assay targeting V4 region
annotation property	EUPATH_0001020	force string type
class	EUPATH_0009264	plant taxon detected by sequence match
class	EUPATH_0009265	animal taxon detected by sequence match
class	EUPATH_0009266	protist taxon detected by sequence match
class	EUPATH_0009267	taxon detected by sequence match
class	EUPATH_0009268	fungal taxon detected by sequence match
class	EUPATH_0009269	normalized number of taxon-specific sequence matches
class	EUPATH_0021095	state of India
class	EUPATH_0026002	subdistrict of Thailand
class	EUPATH_0026006	district of Thailand
class	EUPATH_0026007	province of Thailand
class	EUPATH_0028020	parish of Uganda
class	EUPATH_0035013	union council of Bangladesh
class	EUPATH_0038721	zone of Ethiopia
class	EUPATH_0038722	kebele of Ethiopia
class	EUPATH_0038723	woreda of Ethiopia
class	EUPATH_0043227	female insect feeding status
class	EUPATH_0043228	gravid female insect feeding status
class	EUPATH_0043229	fed gravid female insect status
class	EUPATH_0043230	unfed gravid female insect status
class	EUPATH_0043231	unfed female insect status
class	EUPATH_0043232	fed female insect status
individual	EUPATH_0043233	Florida Keys Mosquito Control district organization
class	EUPATH_0043234	prevalence of Cyp4J5 L43F
class	EUPATH_0044179	district of Uganda
class	EUPATH_0044180	region of Uganda
class	EUPATH_0049405	ward of Tanzania

Release made on 2021-09-09

This release introduces 58 new VEuPath terms. 259 additional terms are imported, many of which have defining axioms also included in the import. This release is the result of deeper collaboration with OBI. VEuPath terms have been submitted and accepted in the latest OBI release, with many hierarchy, annotation and axiom changes to match OBI organization. Some of these submitted terms are revised for clarity from the original VEuPath terms. Deprecated classes are now organized into a ROBOT template that places them under an 'Obsolete Class' parent for easier ontology browsing. Terms about arthropod specimens and PopBio migration terms were also submitted to OBI at our request and imported into this release.

Imports also include terms for diseases and abnormalities identified in diagnoses and autopsy reports, a term for a multi-species collection needed by VectorBase, and terms recently included in ClinEpi projects.

Other changes include requiring "indicator" in labels of boolean data terms, removal of unused terms, revising the hierarchy for consistency, and the addition of defined annotation properties needed for exploratory data analysis (EDA). Definitions for measurement terms were also revised to not specify units.

Release made on 2021-04-28

This release introduces 16 new VEuPath terms, 146 additional imported terms, and 210 additional axioms. Its development was focused on improving the organization, consistency, and browsing experience of the ontology. Changes were made to the hierarchy, especially under the terms that were immediate parent to a large number of children, e.g. 'material entity' and 'information content entity'.

The ChEBI import hierarchy underwent the following improvements. Mixture terms were separated from 'molecular entity' terms. More categorical terms (e.g. 'fatty acid') were added to balance the hierarchy. ChEBI terms with labels containing "insecticide", "drug", or "antibiotic" were only kept if they were roles (rather than material entities), for clarity.

Other label changes for clarity include ensuring that "location" only refers to a site, standardizing children of 'count', distinguishing a memory of diagnosis from a diagnosis, and removing units of measurement from labels

Many OBI terms were imported for arthropod collection and specimen types (some of which replaced VEuPath terms in the previous release). Imports were also added for chemical entities, drug products, cells, and organisms mentioned in ClinEpiDB, for ONTONEO obstetric terms.

This release adds most of the axioms for the terms imported from OBI; these axioms define the terms logically and prevent inconsistent use. Other added axioms identify ChEBI entities as insecticides or antimicrobial agents or were added to information content entities.

New VEuPath terms include geohash terms for MapVEu and more arthropod collection terms.

Terms no longer needed were deprecated, and deprecated terms that had replacements were standardized with the 'term replaced by' annotation.