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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Uberon ID, incorrect annotation in species #1309

Closed ANiknejad closed 3 years ago

ANiknejad commented 7 years ago

Hello, In recent Bgee check , we retrieve this list (below) of anatomical structures claimed as wrongly annotated in these taxons. However all these anatomical structures exist for these species. We checked without success for obvious Uberon reasons (relationship: only_in_taxon NCBITaxon :) We did not check the inferences.

Uberon ID Uberon name incorrect annotation in species

UBERON:0001264 pancreas Danio rerio

UBERON:0001343 seminiferous tubule of testis Xenopus tropicalis

UBERON:0001953 presubiculum Mus musculus

UBERON:0001987 placenta Monodelphis domestica

UBERON:0002106 spleen Danio rerio

UBERON:0002107 liver Danio rerio,Ornithorhynchus anatinus,Rattus norvegicus

UBERON:0002113 kidney Gallus gallus

UBERON:0002423 hepatobiliary system Danio rerio

UBERON:0002728 entorhinal cortex Mus musculus

UBERON:0002899 hippocampal sulcus Mus musculus

UBERON:0003894 liver primordium Danio rerio

UBERON:0003921 pancreas primordium Danio rerio

UBERON:0003922 pancreatic epithelial bud Danio rerio

UBERON:0007224 medial entorhinal cortex Mus musculus

UBERON:0007225 lateral entorhinal cortex Mus musculus

UBERON:0008933 primary somatosensory cortex Mus musculus

UBERON:0010415 barrel cortex Mus musculus

UBERON:0015793 induseum griseum Mus musculus

UBERON:0015800 taenia tectum of brain Mus musculus

cmungall commented 7 years ago

Hi Ann,

Can you clarify exactly what the check is? Is there an Uberon report that is giving you false positives?

I did a check and spleen and 'part of' some 'Danio rerio' is satisfiable in ext.owl

fbastian commented 7 years ago

These terms were considered as not existing in the provided taxa as inferred by the reasoner, using composite-metazoan.owl from 2016-07-14. We didn't check the source of the inference.

uberon commented 7 years ago

One thing you can try is loading the ontology in Protege, going to DL query, typing

pancreas and 'part of' some 'Danio rerio'

Clicking "Equivalents" and where it says Nothing, click ? for the explanation, and paste that here

On 6 Mar 2017, at 8:32, fbastian wrote:

These terms were considered as not existing in the provided taxa as inferred by the reasoner, using composite-metazoan.owl from 2016-07-14. We didn't check the source of the inference.

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fbastian commented 7 years ago

Don't really have the time to do it sorry :) But this was inferred by the standard OWLTools pipeline so this should really be a problem in the composite-metazoan.

uberon commented 7 years ago

OK, I'll check it out later

On 6 Mar 2017, at 9:56, fbastian wrote:

Don't really have the time to do it sorry :) But this was inferred by the standard OWLTools pipeline so this should really be a problem in the composite-metazoan.

-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/obophenotype/uberon/issues/1309#issuecomment-284477154

cmungall commented 7 years ago

Hmm, sorry about this, but it looks like the 2016-07-14 release didn't get timestamped so it's hard to roll back to.

I'm looking in the next release http://purl.obolibrary.org/obo/uberon/releases/2016-08-12/composite-metazoan.owl and pancreas in Danio rerio seems fine; as does barrel cortex Mus musculus

I'll try and retrospectively tag the 2016-07-14 release...

cmungall commented 7 years ago

OK, http://purl.obolibrary.org/obo/uberon/releases/2016-07-14/composite-metazoan.owl now resolves.

However, I'm not able to replicate the issue. pancreas and 'part of' some 'Danio rerio' is satisfiable in Protege.

also I made a species subset:

wget http://purl.obolibrary.org/obo/uberon/releases/2016-07-14/composite-metazoan.owl -O bgee-cm.owl
owltools  bgee-cm.owl --reasoner elk --make-species-subset -t  NCBITaxon:7955 -o danio.owl

this still has 'pancreas' in it. Can you tell me more about what procedure you're using?

gouttegd commented 3 years ago

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.