Gemma propagation doesn't recognise substantia nigra as part of the brain and

[oganm]

When using the term for brain (http://purl.obolibrary.org/obo/UBERON_000095) to fetch datasets from all brain regions, the propagation seems to be missing a few terms, most but not all of the missing items can be explained with missing terms in the propagated filter term the endpoint returns

Attempted query: https://gemma.msl.ubc.ca/rest/v2/datasets/?filter=allCharacteristics.valueUri%20%3D%20http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0000955

Missing results that should have been in there

• GSE8397: https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=873
  • This dataset is annotated with various substantia related termsUBERON_0001965, UBERON_0002661, UBERON_0001966. None of these appear in the returned filter despite being part of brain as also supported by the ontology
• GSE166024: https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=18019
  • has UBERON_0001965 (substantia nigra pars compacta)
• GSE206308.2: https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=25992
  • has UBERON_0001965 (substantia nigra pars compacta)
• GSE168496: https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=26791
  • has UBERON_0002038 (substantia nigra). This term is also missing from the propagated filter
• GSE161045: https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=27018
  • this one is an outlier because it is annotated with UBERON_0001874 (putamen) and this term does appear in the returned filter. I have no idea why the dataset is left behind

[ppavlidis]

Thanks for pointing this out. Substantia nigra should definitely be included in "brain" as it is a child term.

But for GSE161045, UBERON_0002038 is not putamen, it's substantia nigra.

Putamen is http://purl.obolibrary.org/obo/UBERON_0001874

[oganm]

Yep. Pasted the wrong term. It is UBERON_0001874

[arteymix]

The inference is working as expected:

Is it possible that a free-term is used in the dataset?

[ppavlidis]

The inference is working as expected:

Is it possible that a free-term is used in the dataset?

Not for the examples Ogan gave. They are annotated with an ontology term that is a subclass of Brain.

[ppavlidis]

Confirmation in the Browser that something isn't working right, directly searching for a dataset mentioned while having "brain" checked yields:

[oganm]

The annotations do appear to be ontology terms and not free text. UBERON_0002038 does appear in the propagated filter despite missing the dataset annotated with it, similar to the putamen term. UBERON_0001965, UBERON_0002661 and UBERON_0001966 however do not appear in the propagated filter at all

https://gemma.msl.ubc.ca/rest/v2/datasets/GSE168496/annotations
https://gemma.msl.ubc.ca/rest/v2/datasets/GSE161045/annotations

[arteymix]

Ok, substantia nigra is inferred, but not substantia nigra pars compacta which is a children as per the "part of" relation. I'll debug that...

[oganm]

just to make sure, while substantia nigra is inferred, the dataset annotated with it still isn't within the results

[arteymix]

It looks like a bug in the inference code. I can reproduce this.

With Uberon base OWL, I get none of the terms and regular Uberon only returns "substantia nigra"

[arteymix]

This could be due to the fact we're only using the transitive inference instead of the full OWL inference.