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NTR: immunoglobulin superfamily #67

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nataled opened this issue Mar 30, 2012 · 8 comments

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commented Mar 30, 2012

IGSF members are in a flat hierarchy:

....is_a PR:000000001 ! protein
.....is_a PR:000001089 ! immunoglobulin superfamily member 2 ***
.....is_a PR:000001090 ! immunoglobulin superfamily member 8 ***
......is_a PR:000026700 ! immunoglobulin superfamily member 8, signal peptide removed form ***
.....is_a PR:000001304 ! CD300 molecule-like protein
......is_a PR:000001414 ! CMRF35-like molecule 8 ***
......is_a PR:000005165 ! CMRF35-like molecule 6 ***
......is_a PR:000005168 ! CMRF35-like molecule 1 ***
......is_a PR:000006191 ! CMRF35-like molecule ***
.....is_a PR:000004960 ! cell adhesion molecule 1 ***
.....is_a PR:000004961 ! cell adhesion molecule 2 ***
.....is_a PR:000004962 ! cell adhesion molecule 3 ***
.....is_a PR:000004963 ! cell adhesion molecule 4 ***
.....is_a PR:000006304 ! netrin receptor DCC ***
.....is_a PR:000008968 ! immunoglobulin superfamily member 1 ***
.....is_a PR:000008969 ! immunoglobulin superfamily member 10 ***
.....is_a PR:000008970 ! immunoglobulin superfamily member 11 ***
.....is_a PR:000008971 ! immunoglobulin superfamily member 5 ***
.....is_a PR:000008972 ! protein turtle A ***
.....is_a PR:000008973 ! protein turtle B ***
.....is_a PR:000011140 ! neogenin ***

See: http://en.wikipedia.org/wiki/Immunoglobulin\_superfamily

Reported by: cmungall

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commented Feb 11, 2015

Is it possible to fill this term request? This is needed for the Human Phenotype and Mammalian Phenotype ontologies

Original comment by: nicolevasilevsky

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commented Feb 18, 2015

Hi,

Very sorry that this fell through the cracks. The person working on the request left some time ago. My recollection is that this was not an easy case, and include many more proteins than the ones listed. The IGSF proteins are grouped solely on the basis of the presence of an IG-like domain. In PRO, we have not yet focused on grouping by domain--rather, we group by full-length protein similarity. Thus, as a first pass, we've been trying to make the hierarchy on that basis. I'll have to dig out what was already done and carry it to completion myself.

One question: In the context of the phenotype ontologies, what is the use case for the term(s) requested? That would help focus our efforts on the more immediate needs.

Original comment by: nataled

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commented Feb 26, 2015

We want to use this term for equivalence axioms for terms such as these HP terms:
IgA deficiency
IgE deficiency
IgG deficiency
IgM deficiency

We need the terms:
Immunoglobulin A
Immunoglobulin E
Immunoglobulin G
Immunoglobulin M

Original comment by: nicolevasilevsky

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commented Feb 27, 2015

It's a good thing I asked then, as the terms you need would not have been generated by fulfilling this request. It turns out that the original request was indeed partly filled, just not for some of the proteins listed.

As for the phenotype ontologies' needs, that's much easier to do. I'll report back the term identifiers and other information upon completion.

Original comment by: nataled

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commented Feb 27, 2015

A clarification is needed. I see that the Gene Ontology already has the terms you requested. Those terms, however, do not refer to any particular species. The scope of PRO for complexes is such that we would create child terms of those GO terms for individual species. Is that what you need? For example IgA, etc in human?

Original comment by: nataled

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commented Feb 27, 2015

Good question, actually. I'll bring this up with the other Phenotype editors and see if maybe we can use the GO classes instead.
Stay tuned. :)
Thanks!

Original comment by: nicolevasilevsky

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commented Mar 22, 2018

  • Description has changed:

Diff:


--- old
+++ new
@@ -1,4 +1,3 @@
-
 IGSF members are in a flat hierarchy:
 
 ....is\_a PR:000000001 \! protein

  • status: open --> pending
  • assigned_to: Darren Natale
  • Group: -->

Original comment by: nataled

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commented Mar 22, 2018

Going through old requests and closing those that were finished long ago or marking as "pending" those that await input from the requester. If your request is marked Pending, please advise as to whether the request has been satisfactorily addressed or is no longer needed.

Original comment by: nataled

@nataled nataled self-assigned this May 23, 2019

@nataled nataled added Pending and removed sourceforge labels May 23, 2019

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