Open Biomedical Ontologies / Cell Ontology (CL) requests / #12 various new terms require for GO xps

Nicole Vasilevsky - 2014-12-02

assigned_to: Chris Mungall
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- Chris Mungall - 2014-12-03
  
  Still need many of these but the list could do with being resynched
  
  On 2 Dec 2014, at 13:30, Nicole Vasilevsky wrote:
  
  assigned_to: Chris Mungall
  
  [cell-ontology-cl-requests:#12] various new terms require for GO
  xps
  
  Status: open
  Group: GO-Cell-XP
  Labels: new term request
  Created: Thu Jul 19, 2007 10:29 PM UTC by Chris Mungall
  Last Updated: Thu Jul 19, 2007 10:29 PM UTC
  Owner: Chris Mungall
  
  paraxial cell
  in: GO:0048343 "paraxial mesodermal cell fate commitment"
  in: GO:0048344 "paraxial mesodermal cell fate determination"
  in: GO:0048348 "paraxial mesodermal cell fate specification"
  female gametophyte central cell
  in: GO:0009559 "embryo sac central cell differentiation"
  in: GO:0009559 "female gametophyte central cell differentiation"
  root epidermal cell
  in: GO:0010053 "root epidermal cell differentiation"
  somatic cell
  in: GO:0016444 "somatic cell DNA recombination"
  ovarian follicle cell
  in: GO:0030707 "ovarian follicle cell development (sensu Insecta)"
  salivary gland cell
  in: GO:0035071 "salivary gland cell autophagic cell death"
  larval midgut cell
  in: GO:0035096 "larval midgut cell programmed cell death"
  embryonic hemocyte
  in: GO:0035163 "embryonic hemocyte differentiation"
  in: GO:0035163 "embryonic hemocyte differentiation (sensu
  Arthropoda)"
  embryonic plasmatocyte
  in: GO:0035164 "embryonic plasmatocyte differentiation"
  sensory organ precursor cell
  in: GO:0045035 "sensory organ precursor cell division"
  activated T cell
  in: GO:0006924 "activated T cell apoptosis"
  R8 cell
  in: GO:0045465 "R8 cell differentiation"
  R7 cell
  in: GO:0045466 "R7 cell differentiation"
  # also: R1 through R6
  
  retinal cell
  in: GO:0046666 "retinal cell programmed cell death"
  in: GO:0046667 "compound eye retinal cell programmed cell death"
  in: GO:0046667 "retinal cell programmed cell death (sensu
  Endopterygota)"
  ## is this a true cell type?
  axial mesodermal cell
  in: GO:0048321 "axial mesodermal cell differentiation"
  lateral mesodermal cell
  in: GO:0048371 "lateral mesodermal cell differentiation"
  intermediate mesodermal cell
  in: GO:0048392 "intermediate mesodermal cell differentiation"
  in: GO:0048393 "intermediate mesodermal cell fate commitment"
  in: GO:0048394 "intermediate mesodermal cell fate determination"
  in: GO:0048398 "intermediate mesodermal cell fate specification"
  inner cell mass cell
  in: GO:0001826 "inner cell mass cell differentiation"
  sebaceous gland cell
  in: GO:0001949 "sebaceous gland cell differentiation"
  cardiac cell
  in: GO:0035051 "cardiac cell differentiation"
  hemocyte
  in: GO:0007516 "hemocyte development"
  in: GO:0007516 "hemocyte development (sensu Arthropoda)"
  in: GO:0035099 "hemocyte migration"
  in: GO:0035099 "hemocyte migration (sensu Arthropoda)"
  in: GO:0035172 "hemocyte proliferation"
  in: GO:0035172 "hemocyte proliferation (sensu Arthropoda)"
  in: GO:0042386 "hemocyte differentiation"
  in: GO:0042386 "hemocyte differentiation (sensu Arthropoda)"
  inflammatory cell
  in: GO:0006925 "inflammatory cell apoptosis"
  late stripe melanocyte cell
  in: GO:0050934 "late stripe melanocyte differentiation"
  early stripe melanocyte cell
  in: GO:0050933 "early stripe melanocyte differentiation"
  polarized epithelial cell
  in: GO:0030859 "polarized epithelial cell differentiation"
  
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  Cell Ontology (CL) requests: ~~#12~~
  
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Nicole Vasilevsky - 2015-06-02

assigned_to: Chris Mungall --> Nicole Vasilevsky
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Nicole Vasilevsky - 2015-06-02

These cells already exist in the CL:

CL_0002371 somatic cell
CL_0000477 ovarian follicle cell
CL_0009005 salivary gland cell
CL_0009003 larval midgut cell
CL_0000896 activated T cell (label is: activated CD4-positive, alpha-beta T cell)
CL_0000709 R8 cell
CL_0000707 R7 cell
CL_0009004 retinal cell
CL_0009002 inflammatory cell

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Nicole Vasilevsky - 2015-06-02

Are these cells equivalent to the requested terms?

Requested term: inner cell mass cell | Term in CL: CL_2000020 inner cell mass native cell
Requested term: sebaceous gland cell | Term in CL: CL_2000021 sebaceous gland native cell
Requested term: cardiac cell | Term in CL:CL_0002494 cardiocyte
Requested term: hemocyte | Term in CL:CL_0000387 hemocyte (sensu Nematoda and Protostomia)

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Nicole Vasilevsky - 2015-06-02

For the term request 'female gametophyte central cell' - I think the GO term should use the PO class: PO_0020090 embryo sac central cell

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Nicole Vasilevsky - 2015-06-02

This term is in PO:
root epidermal cell PO_0025164

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Nicole Vasilevsky - 2015-06-02

I wrote definitions for the outstanding term requests in this google doc: https://docs.google.com/spreadsheets/d/1sNr_Qm9fLsZ7ly-8KRCLD__2nz9QJzZ-Gnv4YuDyYwk/edit#gid=0

If someone could please review/edit, then I'll go ahead and add these new classes and close this ticket.

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Chris Mungall - 2015-06-02

I retract my request for "sensory organ precursor cell"

The rest look good

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Nicole Vasilevsky - 2015-06-02

great! I'll go ahead and add the term requests

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Nicole Vasilevsky - 2015-06-02

added outstanding term requests

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Nicole Vasilevsky - 2015-06-02

status: open --> closed-fixed
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various new terms require for GO xps

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