NIF-Ontology

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NPOKB

1

added the missing entities

tmsincomb

EDAM ingestion made through http://edamontology.org/EDAM.owl with version 1.25

tmsincomb

interlex uberon, MESH, FMA, etc. deduplication

4

@tmsincomb http://uri.interlex.org/base/ilx_0737716 was not mapped to http://uri.interlex.org/base/ilx_0105730 during import of mesh. There are a number of other cases similar to this. The ilx id for the duplicate mesh terms should...

tgbugs

rename experimental modality -> experimental approach?

7

@UlrikeS91 @lzehl @satra for many people modality => data modality, whereas experimental approach is more nebulous (which we want in this case since approach conflates data modality, technique, paradigm, etc.)....

tgbugs

validate alignment with openMINDS controlled terms

2

https://github.com/HumanBrainProject/openMINDS_controlledTerms/tree/v1/terminologies/ modalities are in, techniques are in a pull request

tgbugs

see title

tgbugs

review old ontology IDs that do not resolve to InterLex

17

There are a number of identifiers in https://github.com/SciCrunch/NIF-Ontology/blob/dev/ttl/generated/NIF-NIFSTD-mapping.ttl that have no corresponding entry in https://github.com/SciCrunch/NIF-Ontology/blob/dev/ttl/generated/NIFSTD-ILX-mapping.ttl nor in https://github.com/SciCrunch/NIF-Ontology/blob/dev/ttl/generated/NIFSTD-SCR-mapping.ttl. @tmsincomb We need to review these and make sure that they resolve....

tgbugs

Martinotti cells no longer classify

1

I suspect it is because the -PV and -VIP have been added as necessary and sufficient conditions: Mammalia neocortex (unionOf L2 L3 L5) Martinotti +Sst -PV -VIP +GABA intrinsic neuron....

memartone

Why are some genes duplicated in names?

2

CRF +Cck +Cck +Cnr1 +Edn3 +Htr3a +Igf1 +VIP +VIP +Vipr1 +ilxtr:LDCV +Adcy9 +Chrm3 +Cplx2 +Htr2c +Pnoc +Npy1r +Tac2 +Cplx3 +Pde7b +Prok2 +Hs6st3 +Syt10 +Rgs12) +Cck +VIP Cck is mentioned 3...

memartone

What are these temporary IDs? And where can I find the compact ID's

4

hasTemporaryId ilxtr-NeuronHuang2017-0-ilxtr-hasExpressionPhenotype-NCBIGene-12308-0-ilxtr-hasExpressionPhenotype-NCBIGene-20604-0-ilxtr-hasInstanceInTaxon-NCBITaxon-10090-0-ilxtr-hasNeurotransmitterPhenotype-CHEBI-16865-0-ilxtr-hasSomaLocatedIn-UBERON-0001950

memartone