B. Ogan Mancarcı

Origin of terms in the inferredTerms component

3

In the current design all inferred terms are returned in a single array https://staging-gemma.msl.ubc.ca/rest/v2/datasets?filter=allCharacteristics.valueUri%20%3D%20http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000540 This means it is not possible to identify which term an inferred term originated from without...

http://purl.obolibrary.org/obo/CLO_0037279 is an up to date ontology term. we have datasets annotated with it https://gemma.msl.ubc.ca/rest/v2/datasets?filter=allCharacteristics.valueUri%20%3D%20http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCLO_0037279 though we don't seem to be propagating to it's child terms. but annotations/children endpoint claims...

Removal of discrete geeq fields and their replacements

3

@ppavlidis wanted to have the discrete geeq fields removed from the dataset endpoints. However the wrapper packages uses some components, so ideally they would be replaced. These fields are -...

- Success/failure counts fail to account for compunding dice (`!!`) when used with a `>[integer]` range specification

FactorValueValue objects are not fully populated for experimentalFactors for getDatasetDifferentialExpressionAnalyses endpoint

7

According to the API specification, getDatasetDifferentialExpressionAnalyses endpoint is supposed to return `ExperimentalFactorValueObjects` as values of `experimentalFactors` of the returned `resultSets` However an [actual call](https://gemma.msl.ubc.ca/rest/v2/datasets/GSE48962/analyses/differential) to the endpoint would show that...

/annotations/search endpoint returns incorrect results

1

It appears that /annotations/search endpoint returns incorrect value-value.URI pairings on occasion. Some examples are - [http://www.ebi.ac.uk/efo/EFO_0004425](https://gemma.msl.ubc.ca/rest/v2/annotations/search?query=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0004425) - initial time point, returns other specific time points like 6h. - [http://purl.obolibrary.org/obo/OBI_0000025](https://gemma.msl.ubc.ca/rest/v2/annotations/search?query=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000025) -...

Offset and limit getDatasetDifferentialExpressionAnalyses endpoint

2

I am a bit unclear on what offset and limit arguments are doing in this enpoint. It seems like unlike all other enpdoints with an offset and limit, they don't...

Ideally turning this into a more generalised package rather than strictly focusing on mouse images at an opportune time, possibly under a new repo entirely. Current documentation is [here](https://community.brain-map.org/c/how-to/brain-atlas-api/35) some...