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[#58] first draft

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jnguyenx committed Mar 3, 2017
1 parent b4b832f commit a78a6314417e95befe6e75414f6c0f748ce22de5
Showing with 243 additions and 1 deletion.
  1. +35 −0 Dockerfile
  2. +11 −1 README.md
  3. +197 −0 configuration-samples/configuration-all.yaml
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@@ -0,0 +1,35 @@
#
# Oracle Java 8 Dockerfile
#
# https://github.com/dockerfile/java
# https://github.com/dockerfile/java/tree/master/oracle-java8
#
# Pull base image.
FROM ubuntu:16.04
RUN apt-get -y update && apt-get install -y software-properties-common python-software-properties
# Install Java.
RUN \
echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections && \
add-apt-repository -y ppa:webupd8team/java && \
apt-get update && \
apt-get install -y oracle-java8-installer && \
rm -rf /var/lib/apt/lists/* && \
rm -rf /var/cache/oracle-jdk8-installer
# Define commonly used JAVA_HOME variable
ENV JAVA_HOME /usr/lib/jvm/java-8-oracle
# Define working directory.
WORKDIR /data
ADD owlsim-services/target/owlsim-services-3.0-SNAPSHOT.jar /data/
ADD configuration-samples/configuration-all.yaml /data/configuration.yaml
ADD http://ci.monarchinitiative.org/view/dev/job/create-owlsim-files-on-dev/lastSuccessfulBuild/artifact/server/all.owl /data/
ADD https://raw.githubusercontent.com/monarch-initiative/monarch-owlsim-data/master/data/Homo_sapiens/Hs_disease_phenotype.txt /data/
CMD java -jar /data/owlsim-services-3.0-SNAPSHOT.jar server /data/configuration.yaml
EXPOSE 8080
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@@ -56,8 +56,18 @@ Paths:
or for some versions of dropwizard:
* http://localhost:8080/api/docs/
* http://localhost:8080/api/match/matchers
* http://localhost:8080/api/match/matchers
Example query using default config:
http://localhost:8080/api/match/jaccard?id=X:heart-morphology&id=X:brain-morphology
## Build with Docker
Run those commands from the root directory:
```
mvn package
docker build -t owlsim .
docker run -p 8080:8080 owlsim
```
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ontologyUris:
- /data/all.owl
ontologyDataUris: []
dataTsvs: []
curies:
# Skolemize Blank Nodes
# overwrite iri fragment with '' for unresovable bnodes
'_': 'https://monarchinitiative.org/.well-known/genid/'
# Monarch-specific
'': 'https://monarchinitiative.org/'
'MONARCH': 'https://monarchinitiative.org/MONARCH_'
'MonarchData': 'http://data.monarchinitiative.org/ttl/'
'MonarchArchive': 'http://archive.monarchinitiative.org/ttl/'
# other semantic-web items
'Annotation': 'http://www.w3.org/ns/oa#Annotation' # FIXME - i don't think we're using this
'dc': 'http://purl.org/dc/elements/1.1/'
'foaf': 'http://xmlns.com/foaf/0.1/'
# ontologies
# [y] indicates those that the monarch team contributes to
'AQTLTrait': 'http://identifiers.org/animalqtltrait/' # FIXME - should get integrated into Upheno
'BFO': 'http://purl.obolibrary.org/obo/BFO_' # BFO: Basic Formal Ontology
'CHEBI' : 'http://purl.obolibrary.org/obo/CHEBI_' # ChEBI: Chemicals of Biological Interest
'CHR' : 'http://purl.obolibrary.org/obo/CHR_' # CHR: Chromosome Ontology
'CL' : 'http://purl.obolibrary.org/obo/CL_' # CL: Cell Ontology (cell types) [y]
'CLO' : 'http://purl.obolibrary.org/obo/CLO_' # CLO: Cell Line Ontology [y]
'CMO' : 'http://purl.obolibrary.org/obo/CMO_' # CMO: Clinical Measurements Ontology
'DATA' : 'http://edamontology.org/data_' # EDAM: Data and Methods Ontology (data artifacts)
'DC' : 'http://purl.obolibrary.org/obo/DC_' # TODO
'DECIPHER' : 'http://purl.obolibrary.org/obo/DECIPHER_' # DECIPHER: Deciphering Developmental Disease
'DOID': 'http://purl.obolibrary.org/obo/DOID_' # DOID: Human Disease Ontology [y]
'ECO': 'http://purl.obolibrary.org/obo/ECO_' # ECO: Evidence Code Ontology [y]
'EFO' : 'http://www.ebi.ac.uk/efo/EFO_' # EFO: Experimental Factor Ontology (all kinds of stuff) [y]
'ENVO' : 'http://purl.obolibrary.org/obo/ENVO_' # ENVO: Environment Ontology
'EOM' : 'http://purl.obolibrary.org/obo/EOM_' # elements of morphology phentoypes
'ERO' : 'http://purl.obolibrary.org/obo/ERO_' # ERO: eagle-i resource ontology [y]
'faldo' : 'http://biohackathon.org/resource/faldo#' # FALDO: Feature Annotation Location Description Ontology (genomic feature properties) [y]
'FBcv' : 'http://purl.obolibrary.org/obo/FBcv_' # FBcv: flybase CV (includes phenotypes)
'FBbt': 'http://purl.obolibrary.org/obo/FBbt_' # FBbt: flybase anatomy
'FBdv': 'http://purl.obolibrary.org/obo/FBdv_' # FBdv: flybase developmental stages
'GENO': 'http://purl.obolibrary.org/obo/GENO_' # GENO: Genotype Partonomy Ontology [y]
'GO' : 'http://purl.obolibrary.org/obo/GO_' # GO: Gene Ontology [y]
'HP': 'http://purl.obolibrary.org/obo/HP_' # HP: Human Phenotype Ontology [y]
'IAO': 'http://purl.obolibrary.org/obo/IAO_' # IAO: Information Artifact Ontology [y]
'KEGG-ds' : 'http://purl.obolibrary.org/KEGG-ds_' # KEGG-ds: KEGG Disease Ontology
'LPT': 'http://purl.obolibrary.org/obo/LPT_' # LPT: Livestock Phenotypic Trait Ontology
'MA': 'http://purl.obolibrary.org/obo/MA_' # MA: Mouse Anatomy Ontology [y]
'MedGen' : 'http://www.ncbi.nlm.nih.gov/medgen/' # a vocabulary - should this be in purl?
'MESH': 'http://purl.obolibrary.org/obo/MESH_' # MeSH: Medical Subject Headings (medical diseases, phenotypes, and drugs)
'MP': 'http://purl.obolibrary.org/obo/MP_' # MP: Mammalian Phenotype Ontology [y]
'MPATH': 'http://purl.obolibrary.org/obo/MPATH_' # MPATH: Mammalian Pathology Ontology
'NBO': 'http://purl.obolibrary.org/obo/NBO_' # NBO: NeuroBehavior Ontology [y]
'OBA': 'http://purl.obolibrary.org/obo/OBA_' # OBA: Ontology of Biological Attributes (traits)
'OBAN': 'http://purl.org/oban/' # OBAN: Open Biomedical Annotation Model [y]
'OBI': 'http://purl.obolibrary.org/obo/OBI_' # OBI: Ontology of Biomedical Investigations [y]
'OBO': 'http://purl.obolibrary.org/obo/' # all ontologies in the OBO namespace (this is not itself an ontology)
'OIO': 'http://www.geneontology.org/formats/oboInOwl#' # oboInOwl: obo-specific annotation properties, like synonym types
'OMIA' : 'http://purl.obolibrary.org/obo/OMIA_' # OMIA: Online Mendelian Inheritance in Animals (animal diseases)
'OMIM' : 'http://purl.obolibrary.org/obo/OMIM_' # OMIM: Online Mendelian Inheritance in Man (human disease and variants)
'Orphanet' : 'http://www.orpha.net/ORDO/Orphanet_' # Orphanet: rare diseases and orphan drugs
'PATO': 'http://purl.obolibrary.org/obo/PATO_' # PATO: Phenotypic Quality Ontology [y]
'PCO': 'http://purl.obolibrary.org/obo/PCO_' # PCO: Population and Community Ontology [y]
'PR': 'http://purl.obolibrary.org/obo/PR_' # PRO: protein ontology
'PW' : 'http://purl.obolibrary.org/obo/PW_' # PW: pathway ontology
'RO': 'http://purl.obolibrary.org/obo/RO_' # RO: Relationship Ontology [y]
'SIO' : 'http://semanticscience.org/resource/SIO_' # SIO: SemanticScience Integrated Ontology (information artifacts)
'SNOMED' : 'http://purl.obolibrary.org/obo/SNOMED_' # SNOMED:diseases and phenotypes
'SO' : 'http://purl.obolibrary.org/obo/SO_' # SO: Sequence Ontology [y]
'STATO': 'http://purl.obolibrary.org/obo/STATO_' # Statistics Ontology
'UBERON' : 'http://purl.obolibrary.org/obo/UBERON_' # UBERON: integrated anatomy ontology (metazoans, mostly) [y]
'UPHENO' : 'http://purl.obolibrary.org/obo/UPHENO_' # UPHENO: integrated phenotype ontology, and normal traits [y]
'UMLS' : 'http://purl.obolibrary.org/obo/UMLS_' # UMLS: unified medical language system
'UO' : 'http://purl.obolibrary.org/obo/UO_' # UO: units of measurements
'VT' : 'http://purl.obolibrary.org/obo/VT_' # VT: Vertebrate Trait Ontology
'WBPhenotype': 'http://purl.obolibrary.org/obo/WBPhenotype_' # WBPhenotype: WormBase phenotypes (nematode) [y]
'XCO' : 'http://purl.obolibrary.org/obo/XCO_' # XCO: Experimental Conditions Ontology
'ZFA': 'http://purl.obolibrary.org/obo/ZFA_' # ZFA: Zebrafish Anatomy Ontology [y]
'ZFS': 'http://purl.obolibrary.org/obo/ZFS_' # ZFS: Zebrafish Staging [y]
'ZP': 'http://purl.obolibrary.org/obo/ZP_' # ZP: Zebrafish Phenotype Ontology [y]
'WBbt': 'http://purl.obolibrary.org/obo/WBbt_' #WBbt: C. elegans gross anatomy
'EMAPA': 'http://purl.obolibrary.org/obo/EMAPA_' # EMAPA: Mouse gross anatomy and development, timed
'XAO': 'http://purl.obolibrary.org/obo/XAO_' # XAO: Xenopus anatomy and development
# publication/reference sources
'DOI' : 'http://dx.doi.org/'
'GeneReviews' : 'http://www.ncbi.nlm.nih.gov/books/' # diseases too
'ISBN': 'https://monarchinitiative.org/ISBN_'
'ISBN-10': 'https://monarchinitiative.org/ISBN10_'
'ISBN-13': 'https://monarchinitiative.org/ISBN13_'
'ISBN-15': 'https://monarchinitiative.org/ISBN15_'
'J' : 'http://www.informatics.jax.org/reference/J:' # MGI-internal identifiers for pubs
'MPD': 'http://phenome.jax.org/'
'MPD-assay': 'http://phenome.jax.org/db/qp?rtn=views/catlines&keymeas='
'PMID': 'http://www.ncbi.nlm.nih.gov/pubmed/'
'PMCID' : 'http://www.ncbi.nlm.nih.gov/pmc/'
'AQTLPub' : 'http://www.animalgenome.org/cgi-bin/QTLdb/BT/qabstract?PUBMED_ID='
'GO_REF' : 'http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:'
'HPO' : 'http://human-phenotype-ontology.org/' # to be used for persons, though they don't resolve with this
# strains, lines, or organismal reagents
'APB': 'http://pb.apf.edu.au/phenbank/strain.html?id='
'CMMR': 'http://www.cmmr.ca/order.php?t=m&id='
'Coriell' : 'https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref='
'CoriellCollection' : 'https://catalog.coriell.org/1/'
'CoriellFamily' : 'https://catalog.coriell.org/0/Sections/BrowseCatalog/FamilyTypeSubDetail.aspx?fam='
'CoriellIndividual' : 'https://catalog.coriell.org/Search?q='
'dbSNPIndividual' : 'http://www.ncbi.nlm.nih.gov/SNP/snp_ind.cgi?ind_id=' # FIXME
'EMMA' : 'https://www.infrafrontier.eu/search?keyword=EM:'
'JAX' : 'http://jaxmice.jax.org/strain/'
'MMRRC' : 'https://www.mmrrc.org/catalog/sds.php?mmrrc_id='
'MPD-strain': 'http://phenome.jax.org/db/q?rtn=strains/details&strainid='
'MUGEN': 'http://bioit.fleming.gr/mugen/Controller?workflow=ViewModel&expand_all=true&name_begins=model.block&eid='
'NCIMR': 'https://mouse.ncifcrf.gov/available_details.asp?ID='
'RBRC': 'http://www2.brc.riken.jp/lab/animal/detail.php?brc_no=RBRC'
# organisms and genome builds (also NCBITaxon)
'NCBIAssembly': 'http://www.ncbi.nlm.nih.gov/assembly/'
'NCBIGenome' : 'http://www.ncbi.nlm.nih.gov/genome/'
'NCBITaxon' : 'http://purl.obolibrary.org/obo/NCBITaxon_'
'OMIA-breed': 'https://monarchinitiative.org/model/OMIA-breed:'
'UCSC' : 'ftp://hgdownload.cse.ucsc.edu/goldenPath/'
# homology
'HOMOLOGENE' : 'http://www.ncbi.nlm.nih.gov/homologene/'
'KEGG-ko' : 'http://www.kegg.jp/dbget-bin/www_bget?ko:'
'PANTHER' : 'http://www.pantherdb.org/panther/family.do?clsAccession=' # protein/orthologous families
# variants
'AQTL' : 'http://identifiers.org/animalqtl/' # FIXME temporary # traits
'CGD' : 'http://ohsu.edu/cgd/' # diseases, variant instances
'ClinVar' : 'http://www.ncbi.nlm.nih.gov/clinvar/' # variant+condition
'ClinVarVariant' : 'http://www.ncbi.nlm.nih.gov/clinvar/variation/'
'ClinVarSubmitters' : 'http://www.ncbi.nlm.nih.gov/clinvar/submitters/'
'COSMIC' : 'http://cancer.sanger.ac.uk/cosmic/mutation/overview?id='
'HGMD' : 'http://identifiers.org/hgmd/'
'dbSNP' : 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs='
'dbVar' : 'http://www.ncbi.nlm.nih.gov/dbvar/'
# pathways
'KEGG-path' : 'http://www.kegg.jp/dbget-bin/www_bget?path:'
'REACT' : 'http://www.reactome.org/PathwayBrowser/#/'
# genes (and RNAs and transcripts)
'BIOGRID' : 'http://thebiogrid.org/' # also interactions
'CCDS' : 'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=' # transcripty things
'dictyBase' : 'http://dictybase.org/gene/'
'EcoGene' : 'http://ecogene.org/gene/'
'ENSEMBL' : 'http://identifiers.org/ensembl/'
'FlyBase' : 'http://flybase.org/reports/' # also variants, pubs, genotypes, strains
'GenBank' : 'http://www.ncbi.nlm.nih.gov/nuccore/'
'HGNC' : 'http://identifiers.org/hgnc/HGNC:'
'IMPC' : 'http://www.mousephenotype.org/data/genes/' # FIXME
'KEGG-hsa' : 'http://www.kegg.jp/dbget-bin/www_bget?hsa:'
'MGI': 'http://www.informatics.jax.org/accession/MGI:' # also variants, pubs, genotypes
'miRBase' : 'http://identifiers.org/mirbase/' # microRNA genes
'NCBIGene' : 'http://www.ncbi.nlm.nih.gov/gene/'
'PomBase' : 'http://identifiers.org/PomBase:'
'RefSeq' : 'http://www.ncbi.nlm.nih.gov/refseq/?term='
'RGD' : 'http://rgd.mcw.edu/rgdweb/report/gene/main.html?id='
'SGD' : 'http://identifiers.org/SGD:'
'TAIR' : 'http://identifiers.org/TAIR:'
'WormBase' : 'http://identifiers.org/wormbase/' # also variants, pubs, genotypes
'Xenbase' : 'http://identifiers.org/xenbase/'
'ZFIN' : 'http://zfin.org/' # also variants, pubs, genotypes
# proteins
'EC' : 'http://identifiers.org/ec-code/'
'HPRD' : 'http://www.hprd.org/protein/'
'NCBIProtein' : 'http://www.ncbi.nlm.nih.gov/protein/'
'PDB' : 'http://identifiers.org/PDB:'
'SwissProt' : 'http://identifiers.org/SwissProt:'
'TrEMBL' : 'http://www.uniprot.org/uniprot/'
'UniProtKB' : 'http://identifiers.org/uniprot/'
# SEPIO: Scientific Evidence and Provenance Information Ontology
'SEPIO': 'http://purl.obolibrary.org/obo/SEPIO_'
'VIVO': 'http://vivoweb.org/ontology/core#'
#Procedures/protocols
'IMPRESS-procedure' : 'https://www.mousephenotype.org/impress/procedures/'
'IMPRESS-protocol' : 'https://www.mousephenotype.org/impress/protocol/'
'IMPRESS-parameter' : 'https://www.mousephenotype.org/impress/parameterontologies/'
#Drugs, chemicals, compounds
'CID' : 'http://pubchem.ncbi.nlm.nih.gov/compound/'
'DrugBank' : 'http://www.drugbank.ca/drugs/'
'SIO': 'http://semanticscience.org/resource/SIO_'
'OAE': 'http://purl.obolibrary.org/obo/OAE_'
'RXCUI': 'http://purl.bioontology.org/ontology/RXNORM/'
'MEDDRA': 'http://purl.bioontology.org/ontology/MEDDRA/'
'FDADrug': 'http://www.fda.gov/Drugs/InformationOnDrugs/'
'BT': 'http://c.biothings.io/#'
'UNII': 'http://fdasis.nlm.nih.gov/srs/unii/'
'GINAS' : 'http://tripod.nih.gov/ginas/app/substance#'

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