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Linking to PRO Terms and Files

PRO identifiers are URIs, globally unique identifiers, given as persistent URLs (PURLs).

PURLs for ontology terms

The URIs for individual terms have one of two forms:

  1. http://purl.obolibrary.org/obo/PR_ddddddddd where d is a digit.
  2. http://purl.obolibrary.org/obo/PR_<uniprot accession>

In the second case, the identifiers denote the class of proteins that the UniProt accession is about. PRO uses these identifiers for the organism-level gene and isoform terms. For example, http://purl.obolibrary.org/obo/PR_Q10322 is the class of proteins known as E3 ubiquitin-protein ligase dma1 in Schizosaccharomyces pombe 972h-. To be precise, this class of proteins includes any that is a gene product of the gene dma1, or of a population variant at the same locus, e.g. some mutation of dma1.


PURLs for ontology files

Current releases

    http://purl.obolibrary.org/obo/pr.owl will always point to the current release of the Protein Ontology in OWL 2 RDF/XML syntax. This is the reasoned-over version, which has additional axioms inferred from the original edited ontology. Appending ".gz" to the end will retrieve the compressed version.

    http://purl.obolibrary.org/obo/pr.obo will always point to the current release of the Protein Ontology in OBO format. This is the reasoned-over version, which has additional axioms inferred from the original edited ontology.

    http://purl.obolibrary.org/obo/pr/pr-asserted.owl will always point to the asserted version of the current release of PRO in OWL2 RDF/XML syntax; that is, without additional axioms inferred by reasoning. Appending ".gz" to the end will retrieve the compressed version.

    http://purl.obolibrary.org/obo/pr/pr-asserted.obo will always point to the asserted version of the current release of PRO in OBO format; that is, without additional axioms inferred by reasoning.

Previous releases

PRO is released using a major/minor versioning system. However, previous releases for all files given above can be found at PURLs that contain either the release number or the release date. Versioned PURLS can be counted on to be stable even when new versions are released. Note that reasoned-over files and/or OWL files were not produced for some earlier releases, so these might be missing.

Using release number:
 Release number versioned PURLs require that the major and minor release is indicated, separated by a single dot.
 
     http://purl.obolibrary.org/obo/pr/<major><dot><minor>/pr.owl
    example: http://purl.obolibrary.org/obo/pr/51.0/pr.owl
     http://purl.obolibrary.org/obo/pr/<major><dot><minor>/pr-asserted.owl
    example: http://purl.obolibrary.org/obo/pr/51.0/pr-asserted.owl
 
Using date:
 Date versioned PURLs require that the date be given in yyyy-mm-dd format. In each case the file returned is the one released on day number dd of month number mm of the year yyyy.
 
     http://purl.obolibrary.org/obo/pr/yyyy-mm-dd/pr.owl
    example: http://purl.obolibrary.org/obo/pr/2016-12-23/pr.owl
     http://purl.obolibrary.org/obo/pr/yyyy-mm-dd/pr-asserted.owl
    example: http://purl.obolibrary.org/obo/pr/2016-12-23/pr-asserted.owl

Note that ontology files for specific versions will still show the ontology IRI as that of the current release (namely, http://purl.obolibrary.org/obo/<file><dot><format>). However, the stable version-specific IRI will always be that of the official major/minor type (http://purl.obolibrary.org/obo/pr/<major><dot><minor>/<file><dot><format>) even when retrieved via date versioned PURLs.

Pre-release

http://purl.obolibrary.org/obo/pr/pr-dev.obo is the current development version (asserted) of PRO in OBO format. Note that day-to-day development for PRO is done using OBO format, so there is no corresponding OWL PURL. A corresponding GPI file is also available using http://purl.obolibrary.org/obo/pr/pr-dev.gpi.

Caution: As this version is not part of an official release, correct syntax and/or stability of identifiers are not guaranteed.

Other project-related PURLs

    http://purl.obolibrary.org/obo/pr points to the PRO Project Home Page

    http://purl.obolibrary.org/obo/pr/downloads points to the downloads folder for the current release

    http://purl.obolibrary.org/obo/pr/browse points the PRO ontology browsable using OntoBee

    http://purl.obolibrary.org/obo/pr/gpi points to the GPI file for the current release

    http://purl.obolibrary.org/obo/pr/tracker points the PRO ontology issue tracker

    http://purl.obolibrary.org/obo/pr/wiki points to the PRO wiki (on which this page is kept)

    http://purl.obolibrary.org/obo/pr/purls points to this page


PURL administration

PURLs for the project, all of which begin with http://www.obolibrary.org/obo/pr, are maintained by the OBO Foundry Technical Working Group and by dnatale (Darren Natale).

PURLS are managed at http://purl.obolibrary.org.

The OBO Foundry ID Policy is documented at http://obofoundry.org/id-policy.html.