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EBISPOT
FMA Ontology Outdated/Not Indexed
Describe the bug The FMA ontology is not indexed, which is not allowing at least some API searches
To Reproduce Steps to reproduce the behavior:
- Go to https://www.ebi.ac.uk/ols4/ontologies/fma/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FFMA_7312?lang=en
- See the note about outdated.
- Also, if you go to https://www.ebi.ac.uk/ols4/api/terms/findByIdAndIsDefiningOntology?obo_id=FMA:7312, it does not return the term
Expected behavior I would expect this ontology to be indexed as it has been and allow it to be searched via the API
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@JoshuaFortriede this might be related to cloudflare incident yesterday. I've checked today's data release and the latest version of the ontology was successfully processed so it will be available within next 48 hours.
@JoshuaFortriede latest version of FMA ontology is loading empty in OLS. Please see this issue for details: https://github.com/EBISPOT/ols4/issues/1102
@JoshuaFortriede developers/maintainers of FMA ontology need to provide us with the ontology PURL from where we can fetch the OWL file, and only then will it get fully indexed in OLS.
I am one of the maintainers of the FMA Ontology. About Nov 21, 2025 one of us (Onard Mejino) received a notice from OLS stating that the FMA is failing to load into OLS. We weren't aware that the FMA is in OLS, so we looked up the FMA in OLS and found that the link goes to a subset of the FMA that was maintained by the OBO Foundry. It looks like the version maintained by OBO has now been declared inactive, which may be the reason the link in OLS fails to load.
However, even before the loading incident this FMA subset was way out of date. Instead we recommend you link to the latest full version of the FMA, which, as noted by matentzn above, can be found at http://purl.org/sig/ont/fma.owl. More information about the FMA can be found at http://si.washington.edu/info-books/project-details/foundational-model-of-anatomy/summary-of-fma-resources/, including a link to FMA puns, which can make querying via SparQL easier.
This is version 5.0 of the FMA, which is the last one released before the members of our University of Washington Structural Informatics Group retired in 2019. So at least for now this is the last version we expect to release. I will continue to maintain our website for now, but at some point Bioportal https://bioportal.bioontology.org/ontologies/FMAmay become the best place to retrieve it (although at this point they just point to the above Purl).
I hope this helps.
Jim Brinkley Structural Informatics Group University of Washington http://si.washington.edu
Whoops - this is the correct link to Biportal:
https://bioportal.bioontology.org/ontologies/FMA