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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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linking CL terms to UBERON terms #430

Closed jahilton closed 2 years ago

jahilton commented 8 years ago

The following terms are lacking a connection to UBERON terms, and I have suggested a part_of for each term.

CL:0000553 (megakaryocyte progenitor cell) - bone marrow (UBERON:0002371) Ref: http://www.ncbi.nlm.nih.gov/pubmed/9685164

CL:0000038 (erythroid progenitor cell) - bone marrow (UBERON:0002371) Ref: http://www.bloodjournal.org/content/bloodjournal/79/3/657.full.pdf?sso-checked=true

CL:0000050 (megakaryocyte-erythroid progenitor cell) - bone marrow (UBERON:0002371) Ref: https://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Megakaryocyte-erythroid+progenitor+cells

CL:0000049 (common myeloid progenitor) - bone marrow (UBERON:0002371) Ref: http://www.bloodjournal.org/content/bloodjournal/79/3/657.full.pdf?sso-checked=true

CL:0000765 (erythroblast) - blood (UBERON:0000178) Ref: http://medical-dictionary.thefreedictionary.com/erythroblast

CL:0000037 (hematopoietic stem cell) - bone marrow (UBERON:0002371) Ref: https://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Hematopoietic+stem+cells

CL:0000598 (pyramidal neuron) - brain (UBERON:0000955) Ref: http://www.nature.com/nrn/journal/v9/n3/full/nrn2286.html

cerivs commented 8 years ago

Most of these are also found in zebrafish which doesn't have a bone marrow so they cannot be part_of bone marrow.

jahilton commented 8 years ago

Thank you for bringing that to my attention. I think 'blood (UBERON:0000178)' would be the most appropriate term instead of bone marrow.

jahilton commented 8 years ago

Is there any progress with linking these terms to UBERON?

cricketsloan commented 8 years ago

It seems that we cannot use the links to UBERON as it is generic for all anatomies.

addiehl commented 2 years ago

I disagree with the linkages to 'blood' as as inappropriate on several levels, not least of which is that 'blood' in Uberon is defined as "A fluid that is composed of blood plasma and erythrocytes," which seems to exclude the possibilities of other cells being part of blood. Although the Uberon definition seems wrong in that blood clearly has additional cell types such as platelets and various leukocytes, I suppose in a pan-species way having erythrocytes is a minimal requirement.

Also, CL:0000598 (pyramidal neuron) is 'part of' some 'central nervous system' already.

Anyway, closing for lack of recent activity and questionable reasoning.