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terminologies.txt
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terminologies.txt
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Abbrev: ChEBI
Name : Chemical Entities of Biological Interest
Server: https://www.ebi.ac.uk/chebi/
Db_URL: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=%s
Term. : Yes
Use : https://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi_lite.obo.gz
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Abbrev: CL
Name : Cell Ontology
Server: https://obophenotype.github.io/cell-ontology/
Db_URL: https://www.ebi.ac.uk/ols4/ontologies/cl/classes?iri=http://purl.obolibrary.org/obo/%s
Term. : Yes
Use : https://github.com/obophenotype/cell-ontology/releases/latest ... redirected then then: cl-simple.obo
Note : cl-base.obo and cl-basic.obo are very similar with a bit of references to external terms
Note : cl-full.obo and cl.obo contain a lot of references to external terms
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Abbrev: NCBI_TaxID
Name : NCBI taxonomy database
Server: https://www.ncbi.nlm.nih.gov/taxonomy
Db_URL: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=%s&lvl=3
Term. : Yes
Use: : curl -o taxdump.tar.gz https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
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Abbrev: UBERON
Name : Uber-anatomy ontology
Server: https://uberon.github.io/
Db_URL: https://www.ebi.ac.uk/ols4/ontologies/uberon/classes/http://purl.obolibrary.org/obo/%s
Term. : Yes
Use : https://github.com/obophenotype/uberon/releases/latest/download/uberon-simple.obo
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Abbrev: NCIt
Name : NCI thesaurus
Server: https://ncit.nci.nih.gov/ncitbrowser
Db_URL: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=%s
Term. : Yes
Use : https://purl.obolibrary.org/obo/ncit.obo
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Abbrev: ORDO
Name : Orphanet Rare Disease Ontology
Server: https://www.ebi.ac.uk/ols4/ontologies/ordo
Db_URL: https://www.ebi.ac.uk/ols4/ontologies/ordo/classes?iri=http://www.orpha.net/ORDO/%s
Term. : Yes
Use : Link to latest OWL version from page https://bioportal.bioontology.org/ontologies/ORDO/?p=summary
Use : Example: https://data.bioontology.org/ontologies/ORDO/submissions/28/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
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Abbrev: VBO
Name : Vertebrate Breed Ontology
Server: https://monarch-initiative.github.io/vertebrate-breed-ontology/
Db_URL: https://www.ebi.ac.uk/ols4/ontologies/vbo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F%s
Term. : Yes
Use : https://raw.githubusercontent.com/monarch-initiative/vertebrate-breed-ontology/master/vbo.obo
Use : redirected from http://purl.obolibrary.org/obo/vbo.owl
Use : info from https://github.com/monarch-initiative/vertebrate-breed-ontology
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Abbrev: RS
Name : Rat Strain Ontology
Server: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology
Db_URL: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=%s
Term : Yes
Remark: with 47 distinct ACs
Use : From https://bioportal.bioontology.org/ontologies/RS
Use : OBO link with NO deprecation info: https://data.bioontology.org/ontologies/RS/submissions/267/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
Use : Use RDF/XML link to OWL version with deprecation info: https://data.bioontology.org/ontologies/RS/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=rdf
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Abbrev: UniProtKB
Name : UniProt knowledgebase
Server https://www.uniprot.org
Db_URL: https://www.uniprot.org/uniprotkb/%s/entry
Term. : Yes
Remark: Use protein families / domains ? NO, do not use it as terminology
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