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Term issue: CD45/PTPRC term realignments needed #167

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addiehl opened this issue Oct 24, 2019 · 0 comments
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@addiehl addiehl commented Oct 24, 2019

The following entries for CD45 isoforms in the Protein Ontology need to be related due to automated import of recent UniProt sequence entries related to CD45:

(1) CD45RA
http://purl.obolibrary.org/obo/PR_000001015
receptor-type tyrosine-protein phosphatase C isoform CD45RA
PRO-short-label: PTPRC/iso:CD45RA
EXACT: CD45RA
Definition: A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C). [PMID:1351092, PRO:CNA]

AND

http://purl.obolibrary.org/obo/PR_P08575-8
receptor-type tyrosine-protein phosphatase C isoform h6 (human)
PRO-short-label: hPTPRC/iso:h6
EXACT: receptor-type tyrosine-protein phosphatase C isoform CD45RA (human)
Definition: A receptor-type tyrosine-protein phosphatase C (human) that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-8. [PRO:DNx, UniProtKB:P08575]

Although PR:0000001015 was initially created to represent the human CD45RA isoform, as there is evidence for a CD45RA isoform in chimpanzee and perhaps other species, it should remain as the parent term for this isoform. However, an inferred (or asserted) is_a relationship of PR:P08575-8 to PR:0000001015 needs to be created to reflect that PR:P08575-8 is the human specific form of PR:0000001015.

Also http://purl.obolibrary.org/obo/PR_P08575-8 should receive the exact synonym "CD45RA (human)" in line with the "CD45RA" synonym of the parent.

(2) CD45RO
http://purl.obolibrary.org/obo/PR_000001017
receptor-type tyrosine-protein phosphatase C isoform CD45RO

AND

http://purl.obolibrary.org/obo/PR_P08575-4
receptor-type tyrosine-protein phosphatase C isoform h2 (human)
PRO-short-label: hPTPRC/iso:h2
EXACT: receptor-type tyrosine-protein phosphatase C isoform CD45R0 (human)

need to have a parent-child relationship for similar reasons. Currently PRO lists http://purl.obolibrary.org/obo/PR_P08575-2 as the human specific child of http://purl.obolibrary.org/obo/PR_000001017 but the UniProt entry for P08575 no longer includes a P08575-2 isoform.

This should be corrected in PRO.

Also http://purl.obolibrary.org/obo/PR_000001017 should receive the exact synonym "CD45RO" and http://purl.obolibrary.org/obo/PR_P08575-4 should receive the exact synonym "CD45RO (human)" in line with the "CD45RO" synonym of the parent.

(3) CD45RB
http://purl.obolibrary.org/obo/PR_000001016 should be the parent of http://purl.obolibrary.org/obo/PR_P08575-9. These are the entries for CD45RB and both should also receive the CD45RB synonyms in line with the other CD45 entries.

(4) CD45RAC
http://purl.obolibrary.org/obo/PR_000025803 should be the parent of http://purl.obolibrary.org/obo/PR_P08575-6. These are the entries for CD45RAC and both should also receive the CD45RAC synonyms in line with the other CD45 entries.

(5) CD45RAB
http://purl.obolibrary.org/obo/PR_000025802 should be the parent of http://purl.obolibrary.org/obo/PR_P08575-5 These are the entries for CD45RAB and both should also receive the CD45RAB synonyms in line with the other CD45 entries.

(6) CD45R
B220/CD45R is not a specific isoform of CD45, but rather refers to any isoform that contains exon 'A' (both in human and mouse, technically exon 4). In human, CD45R is thus the combination of CD45RAB (PR:P08575-5), CD45RAC (PR:P08575-6), and CD45RA (PR:P08575-8). The Protein Ontology should create a human entry for CD45R that reflects this, perhaps as a union class (yum).

Alex

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