Addresses #1759 NTR valve endothelial cell

[ghost]

Addresses #1759 NTR valve endothelial cell
#gogoeditdiff

Appears to contain some extra changes from the recently merged PR #1727. (EDIT: these have been removed)

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2022-12-09/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2022-12-09/cl-simple.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

CL_4030033 http://purl.obolibrary.org/obo/CL_4030033

Added

• CL_4030033 definition "An endothelial cell that lines a surface of a cardiac valve leaflet. Along with valve interstitial cells, a valve endothelial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes."

  • database_cross_reference "PMID:25311230"

• CL_4030033 comment "At least in some mammalian species, a valve endothelial cell expresses CD31. Valve endothelial cells can undergo an endothelial to mesenchymal transition to acquire a fibroblast or myofibroblast phenotype that leads to changes in the microenvironmental signals and facilitates tissue regeneration."

  • database_cross_reference "PMID:25311230"

• CL_4030033 contributor 0000-0002-1773-2692

• CL_4030033 label "valve endothelial cell"

• CL_4030033 has_exact_synonym "valvular endothelial cell"

  • database_cross_reference "PMID:25311230"

• CL_4030033 date "2022-12-09T11:58:49Z"^^dateTime

• CL_4030033 has_exact_synonym "VEC"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:25311230"

  • database_cross_reference "PMID:30796046"

• Class: CL_4030033

• CL_4030033 SubClassOf cardiac endothelial cell

• CL_4030033 SubClassOf cardiac valve cell

cardiac valve cell http://purl.obolibrary.org/obo/CL_1000147

Removed

• cardiac valve cell SubClassOf cell

Added

• cardiac valve cell SubClassOf native cell

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

CL_4030033 http://purl.obolibrary.org/obo/CL_4030033

Added

• CL_4030033 definition "An endothelial cell that lines a surface of a cardiac valve leaflet. Along with valve interstitial cells, a valve endothelial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes."^^string

  • database_cross_reference "PMID:25311230"^^string

• CL_4030033 comment "At least in some mammalian species, a valve endothelial cell expresses CD31. Valve endothelial cells can undergo an endothelial to mesenchymal transition to acquire a fibroblast or myofibroblast phenotype that leads to changes in the microenvironmental signals and facilitates tissue regeneration."^^string

  • database_cross_reference "PMID:25311230"^^string

• CL_4030033 contributor 0000-0002-1773-2692

• CL_4030033 label "valve endothelial cell"

• CL_4030033 has_exact_synonym "valvular endothelial cell"^^string

  • database_cross_reference "PMID:25311230"^^string

• CL_4030033 date "2022-12-09T11:58:49Z"^^dateTime

• CL_4030033 has_exact_synonym "VEC"^^string

  • database_cross_reference "PMID:25311230"^^string

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:30796046"^^string

• Class: CL_4030033

• CL_4030033 EquivalentTo endothelial cell and (part_of some cardial valve)

cardiac valve cell http://purl.obolibrary.org/obo/CL_1000147

Removed

• cardiac valve cell EquivalentTo cell and (part_of some cardial valve)

Added

• cardiac valve cell EquivalentTo native cell and (part_of some cardial valve)

[dosumis]

Declarations can happen depending on how you add new terms for import. If you paste the IRIs straight into Protege, that => a declaration in the edit file.

[ghost]

Declarations can happen depending on how you add new terms for import. If you paste the IRIs straight into Protege, that => a declaration in the edit file.

Yes, I have done that for other tickets as it is listed as the first option here. The page says this method is "to be avoided" but does not give a reason and it has consistently worked for prior tickets.

The declarations appearing in this PR, however, are a surprise since I did not add them. If I had to guess, they may be coming from PR #1727 since they all seem to appear there.
Regardless, I'll delete the declarations in this PR and then merge.

[shawntanzk]

OH! yeah I rmbr writing that, the reason its there was this:

This workflow is to be avoided, but may be appropriate if the editor does not have access to the ODK docker container. 

We should consider removing that whole part and just saying make a request for someone to import the term for you >.<

But yeah, probs best not to use it, its a hacky work around that might cause issues down the road

[dosumis]

{ Off topic for this PR but: adding IRIs directly has the great advantage that it can be used instantly without having to wait for someone to help or disrupting your editing flow run a slow import update. I wonder if we should tolerate it and have a clean-up job that removes stray declarations from the edtor's file. Alternatively maybe we could have some super minimal temp import update (say IRI + label only) that editors can use rapidly while working on a PR, postponing a full update to later - Maybe add to agenda for Monday tech call? }

[ghost]

The following new term has been added to CL and will be available in the next release:

CL:4030033 'valve endothelial cell'

[shawntanzk]

Should this have the GO term attached to it like in #1761?

[ghost]

Should this have the GO term attached to it like in #1761?

Not totally sure about this... the reference notes they secrete paracrine molecules, but I have not found a reference that explicitly states VECs secrete extracellular matrix constituents. Activated VICs are noted explicitly to secrete fibrous matrix proteins (collagen), which is why the GO axiom was added to that term.

From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4485434/:

"VECs also secrete paracrine factors, including nitric oxide, endothelin-1, and C-type natriuretic peptide. Most biochemical factors secreted by VECs (except endothelin-1) function to reduce the pathogenic phenotypes of VICs."

vs.

"In addition, VICs secrete fibrous matrix proteins, matrix metalloproteinases (such as MMP1 and MMP2), biochemical factors, and can differentiate into myofibroblasts or osteoblast-like cells or undergo cell death-mediated calcification"

If you think appropriate, I could edit the text definition and/or add a less specific axiom regarding secretion.