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Use both SCHPO (deprecated) and SCHPM (preferred) in the taxon checker #4

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selewis opened this issue Oct 25, 2015 · 3 comments
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@selewis
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selewis commented Oct 25, 2015

So that older GAF files with the previous taxon ID 284812 go through the same screening as SCHPM 4896: N=Schizosaccharomyces pombe

@selewis selewis changed the title Use both SCHPO (deprecated) and SCHPM (preferred) to taxon checker Use both SCHPO (deprecated) and SCHPM (preferred) in the taxon checker Oct 25, 2015
@selewis
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selewis commented Oct 25, 2015

Actually there is a deeper problem.
pombe (4896) is a eukaryote (ncbi taxon 2759)
pombe does not have centromeres (GO:0005813)
but http://owlservices.berkeleybop.org/isClassApplicableForTaxon?format=txt&idstyle=obo&id=GO:0005813&taxid=NCBITaxon:2759
returns true

taxonchecker needs to preclude centromeres for eukaryotes

@mah11
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mah11 commented Oct 26, 2015

s/centromeres/centrosomes/g in above comment

@pgaudet
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pgaudet commented Oct 26, 2015

According to wikipedia, centrosomes evolved in metazoa: https://simple.wikipedia.org/wiki/Centrosome
However centrosomes have been described in Dicty: http://www.ncbi.nlm.nih.gov/pubmed/15548420

Thanks,
Pascale

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