Error with config/version not updating

markmcdowall commented 3 years ago

Hi,

When looking at the version of PRIDE that is available in OLS, the latest version of PRIDE seems to have been loaded at 2020-09-25, but the config/version described via the REST API still references an older version (05-11-2019):

https://www.ebi.ac.uk/ols/api/ontologies?page=2&size=100

{
      "ontologyId" : "pride",
      "loaded" : "2020-09-25T03:21:11.082+0000",
      "updated" : "2020-12-02T23:35:58.842+0000",
      "status" : "LOADED",
      "message" : "",
      "version" : null,
      "fileHash" : "d94da5bda5d098bb752a42ff51d67cf8fbf360dd",
      "loadAttempts" : 0,
      "numberOfTerms" : 3705,
      "numberOfProperties" : 56,
      "numberOfIndividuals" : 0,
      "config" : {
        "id" : "http://purl.obolibrary.org/obo/pride_cv.obo",
        "versionIri" : null,
        "title" : "PRIDE Controlled Vocabulary",
        "namespace" : "pride",
        "preferredPrefix" : "PRIDE",
        "description" : "The PRIDE PRoteomics IDEntifications (PRIDE) database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence.",
        "homepage" : "https://github.com/PRIDE-Utilities/pride-ontology",
        "version" : "05-11-2019",
        "mailingList" : "https://github.com/PRIDE-Utilities/pride-ontology/issues",
        "creators" : [ ],
        "annotations" : {
          "date" : [ "06:03:2012 11:34" ],
          "saved-by" : [ "jg" ],
          "default-namespace" : [ "PRIDE" ],
          "has_obo_format_version" : [ "1.2" ],
          "auto-generated-by" : [ "OBO-Edit 2.3" ],
          "comment" : [ "I would set treat-xrefs-as-equivalent but there are some weird xrefs that would break that behaviour (PRIDE:PRIDE, value-type:xsd:string, ...)" ]
        },
        "fileLocation" : "https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.obo",
        "reasonerType" : "NONE",
        "oboSlims" : false,
        "labelProperty" : "http://www.w3.org/2000/01/rdf-schema#label",
        "definitionProperties" : [ "http://purl.obolibrary.org/obo/def" ],
        "synonymProperties" : [ "http://www.geneontology.org/formats/oboInOWL#hasExactSynonym" ],
        "hierarchicalProperties" : [ "http://purl.obolibrary.org/obo/pride_cv.obo#part_of" ],
        "baseUris" : [ "http://purl.obolibrary.org/obo/PRIDE_" ],
        "hiddenProperties" : [ ],
        "preferredRootTerms" : [ ],
        "allowDownload" : true,
        "internalMetadataProperties" : [ ],
        "skos" : false
      },
      "_links" : {
        "self" : {
          "href" : "https://www.ebi.ac.uk/ols/api/ontologies/pride"
        },
        "terms" : {
          "href" : "https://www.ebi.ac.uk/ols/api/ontologies/pride/terms"
        },
        "properties" : {
          "href" : "https://www.ebi.ac.uk/ols/api/ontologies/pride/properties"
        },
        "individuals" : {
          "href" : "https://www.ebi.ac.uk/ols/api/ontologies/pride/individuals"
        }
      }
    }

jamesamcl commented 3 years ago

Hi Mark - thanks for reporting. We had a couple of issues with our last indexer run, but they are now resolved and it's running again today, so PRIDE should be updated to the latest version by tomorrow.

jamesamcl commented 3 years ago

I think the issue is actually that we have at some point saved an old version number from the OBO, but as the OBO file does not currently contain a version, the old version is persisted in the OLS database. We will change this behaviour to remove the old version number if no version number is present during an indexer run.

markmcdowall commented 3 years ago

Was looking at the PRotein ontology and there appeas to be the same issue.

https://www.ebi.ac.uk/ols/ontologies/pr

The linked version of pr.owl is for version 62.0, but the version value in the box and when using the REST API lists it as 02-10-2019

markmcdowall commented 3 years ago

It looks like there is a similar issue with ChEBI as well. The listed version is 01-01-2020, but the ChEBI version 196 is from 30-01-2021:

jamesamcl commented 3 years ago

This should now be resolved, in that versions are no longer returned for these ontologies as they are not provided in the upstream ontology files.

EBISPOT / OLS

Error with config/version not updating #446