NTR protoplasmic astrocytes fibrous astrocytes interlaminar astrocytes

[AvolaAmg]

Fixes #2320 #2321 #2322 #2328

[dosumis]

#gogoeditdiff

[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/2024-04-09/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/2024-04-09/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_4042007 http://purl.obolibrary.org/obo/CL_4042007

Added

• CL_4042007 comment "This astrocyte extends its branches to several hundred of dendrites to multiple neurons to envelope 100,000 or more synapses. In humans, a protoplasmic astrocyte has an average diameter of 142 µm, and its diameter ranges between 100 and 400 µm. In rodents the average diameter of a protoplasmic astrocites is 56 µm."

  • database_cross_reference "PMID:20012068"

  • database_cross_reference "PMID:19279265"

• CL_4042007 definition "An astrocyte cell that has highly branched protrusions, its soma is part of a neocortex and it is found between layer 2 and 6. A protoplasmic astrocyte is involved in the formation and elimination of synapses, in the clearance of glutamate, in the modulation of synaptic functions and in the regulation of blood flow in response to synaptic activity."

  • database_cross_reference "PMID:34616062"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:25904839"

  • database_cross_reference "PMID:19279265"

  • database_cross_reference "PMID:37139179"

• CL_4042007 date "2024-04-08T16:01:24Z"^^dateTime

• CL_4042007 contributor 0000-0002-0098-8958

• CL_4042007 label "protoplasmic astrocyte"@en

• Class: CL_4042007

• CL_4042007 SubClassOf astrocyte of the cerebral cortex

• CL_4042007 SubClassOf cerebral cortex neuron

• CL_4042007 SubClassOf neural crest derived neuron

CL_4042008 http://purl.obolibrary.org/obo/CL_4042008

Added

• CL_4042008 contributor 0000-0002-0098-8958

• CL_4042008 date "2024-04-08T16:29:28Z"^^dateTime

• CL_4042008 comment "In humans, a fibrous astrocyte diameter is circa 182 µm. In rodents, a fibrous astrocyte diameter is circa 85 µm."

  • database_cross_reference "PMID:28280934"

• CL_4042008 definition "An astrocyte cell with long fiber-like processes with a soma in the white matter and processes are oriented along the white matter tracts part of a white matter. This astrocyte type has several contacts with the vasculature of a nervous system and is involved in metabolic support."

  • database_cross_reference "PMID:31435019"

  • database_cross_reference "PMID:34616062"

  • database_cross_reference "PMID:28280934"

  • database_cross_reference "PMID:19279265"

  • database_cross_reference "PMID:22144298"

• CL_4042008 label "fibrous astrocyte"@en

• Class: CL_4042008

• CL_4042008 SubClassOf neural crest derived neuron

• CL_4042008 SubClassOf central nervous system neuron

• CL_4042008 SubClassOf astrocyte

CL_4042009 http://purl.obolibrary.org/obo/CL_4042009

Added

• CL_4042009 date "2024-04-08T16:33:45Z"^^dateTime

• CL_4042009 definition "An astrocyte type that presents radial protrusions across the layers of a cortex. The soma of this astrocyte is part of the first layer of a neocortex. This astrocyte extents its protrusions transversally to the deeper layers of a cortex and it creates contact with neurons, the pia matter and capillaries. This astrocyte is involved in facilitating the communication across neurons, astrocytes, capillaries, meninges and the cerebrospinal fluid."

  • database_cross_reference "PMID:31435019"

  • database_cross_reference "PMID:34616062"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:32930323"

  • database_cross_reference "PMID:30552685"

  • database_cross_reference "PMID:19279265"

• CL_4042009 label "interlaminar astrocyte"@en

• CL_4042009 has_related_synonym "ILA"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:30552685"

• CL_4042009 contributor 0000-0002-0098-8958

• Class: CL_4042009

• CL_4042009 SubClassOf neural crest derived neuron

• CL_4042009 SubClassOf cerebral cortex neuron

• CL_4042009 SubClassOf astrocyte of the cerebral cortex

CL_4042010 http://purl.obolibrary.org/obo/CL_4042010

Added

• CL_4042010 date "2024-04-08T16:37:57Z"^^dateTime

• CL_4042010 label "pial interlaminar astrocyte"@en

• CL_4042010 definition "An interlaminar astrocyte whose soma is part of the first layer of a neocortex and is in contact with a pia surface."

  • database_cross_reference "PMID:32930323"

  • database_cross_reference "PMID:37139179"

• CL_4042010 contributor 0000-0002-0098-8958

• Class: CL_4042010

• CL_4042010 SubClassOf CL_4042009

CL_4042011 http://purl.obolibrary.org/obo/CL_4042011

Added

• CL_4042011 contributor 0000-0002-0098-8958

• CL_4042011 label "subpial Interlaminar astrocyte"@en

• CL_4042011 definition "An interlaminar astrocyte type whose soma is part of the upper first layer of the neocortex and its processes extend to a pia surface."

  • database_cross_reference "PMID:32930323"

  • database_cross_reference "PMID:37139179"

• CL_4042011 date "2024-04-08T16:39:09Z"^^dateTime

• Class: CL_4042011

• CL_4042011 SubClassOf CL_4042009

[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/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

CL_4042007 http://purl.obolibrary.org/obo/CL_4042007

Added

• CL_4042007 comment "This astrocyte extends its branches to several hundred of dendrites to multiple neurons to envelope 100,000 or more synapses. In humans, a protoplasmic astrocyte has an average diameter of 142 µm, and its diameter ranges between 100 and 400 µm. In rodents the average diameter of a protoplasmic astrocites is 56 µm."

  • database_cross_reference "PMID:20012068"

  • database_cross_reference "PMID:19279265"

• CL_4042007 definition "An astrocyte cell that has highly branched protrusions, its soma is part of a neocortex and it is found between layer 2 and 6. A protoplasmic astrocyte is involved in the formation and elimination of synapses, in the clearance of glutamate, in the modulation of synaptic functions and in the regulation of blood flow in response to synaptic activity."

  • database_cross_reference "PMID:34616062"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:25904839"

  • database_cross_reference "PMID:19279265"

  • database_cross_reference "PMID:37139179"

• CL_4042007 date "2024-04-08T16:01:24Z"^^dateTime

• CL_4042007 contributor 0000-0002-0098-8958

• CL_4042007 label "protoplasmic astrocyte"@en

• Class: CL_4042007

• CL_4042007 SubClassOf astrocyte of the cerebral cortex

• CL_4042007 SubClassOf has soma location some neocortex

• CL_4042007 SubClassOf part of some neocortex

CL_4042008 http://purl.obolibrary.org/obo/CL_4042008

Added

• CL_4042008 contributor 0000-0002-0098-8958

• CL_4042008 date "2024-04-08T16:29:28Z"^^dateTime

• CL_4042008 comment "In humans, a fibrous astrocyte diameter is circa 182 µm. In rodents, a fibrous astrocyte diameter is circa 85 µm."

  • database_cross_reference "PMID:28280934"

• CL_4042008 definition "An astrocyte cell with long fiber-like processes with a soma in the white matter and processes are oriented along the white matter tracts part of a white matter. This astrocyte type has several contacts with the vasculature of a nervous system and is involved in metabolic support."

  • database_cross_reference "PMID:31435019"

  • database_cross_reference "PMID:34616062"

  • database_cross_reference "PMID:28280934"

  • database_cross_reference "PMID:19279265"

  • database_cross_reference "PMID:22144298"

• CL_4042008 label "fibrous astrocyte"@en

• Class: CL_4042008

• CL_4042008 SubClassOf part of some white matter

• CL_4042008 SubClassOf has soma location some white matter

• CL_4042008 SubClassOf astrocyte

CL_4042009 http://purl.obolibrary.org/obo/CL_4042009

Added

• CL_4042009 date "2024-04-08T16:33:45Z"^^dateTime

• CL_4042009 definition "An astrocyte type that presents radial protrusions across the layers of a cortex. The soma of this astrocyte is part of the first layer of a neocortex. This astrocyte extents its protrusions transversally to the deeper layers of a cortex and it creates contact with neurons, the pia matter and capillaries. This astrocyte is involved in facilitating the communication across neurons, astrocytes, capillaries, meninges and the cerebrospinal fluid."

  • database_cross_reference "PMID:31435019"

  • database_cross_reference "PMID:34616062"

  • database_cross_reference "PMID:37824655"

  • database_cross_reference "PMID:32930323"

  • database_cross_reference "PMID:30552685"

  • database_cross_reference "PMID:19279265"

• CL_4042009 label "interlaminar astrocyte"@en

• CL_4042009 has_related_synonym "ILA"

  • has_synonym_type abbreviation

  • database_cross_reference "PMID:30552685"

• CL_4042009 contributor 0000-0002-0098-8958

• Class: CL_4042009

• CL_4042009 SubClassOf part of some neocortex

• CL_4042009 SubClassOf has soma location some neocortex

• CL_4042009 SubClassOf astrocyte of the cerebral cortex

CL_4042010 http://purl.obolibrary.org/obo/CL_4042010

Added

• CL_4042010 date "2024-04-08T16:37:57Z"^^dateTime

• CL_4042010 label "pial interlaminar astrocyte"@en

• CL_4042010 definition "An interlaminar astrocyte whose soma is part of the first layer of a neocortex and is in contact with a pia surface."

  • database_cross_reference "PMID:32930323"

  • database_cross_reference "PMID:37139179"

• CL_4042010 contributor 0000-0002-0098-8958

• Class: CL_4042010

• CL_4042010 SubClassOf CL_4042009

CL_4042011 http://purl.obolibrary.org/obo/CL_4042011

Added

• CL_4042011 contributor 0000-0002-0098-8958

• CL_4042011 label "subpial Interlaminar astrocyte"@en

• CL_4042011 definition "An interlaminar astrocyte type whose soma is part of the upper first layer of the neocortex and its processes extend to a pia surface."

  • database_cross_reference "PMID:32930323"

  • database_cross_reference "PMID:37139179"

• CL_4042011 date "2024-04-08T16:39:09Z"^^dateTime

• Class: CL_4042011

• CL_4042011 SubClassOf CL_4042009

[dosumis]

Please add part relationships (e.g. to cortex). Should be able to get some inferred classification from these. (Note: This looks like a case where has_soma_location would be useful, but this is currently restricted to neurons).

Besides that- please see minor correction/suggestions to text

(I'm also seeing something odd with APs in robot diffs. Investigating)

[dosumis]

@anitacaron - is there something odd going on with the ROBOT diff? I'm seeing different APs on ROBOT diff vs functional syntax text diff

e.g.

CL_4042009 comment "An astrocyte type that presents radial protrusions across the layers of a cortex. The soma of this astrocyte is part of the first layer of a neocortex. This astrocyte extents its protrusions transversally to the deeper layers of a cortex and it creates contact with neurons, a pia matter and capillaries. This astrocyte is involved in facilitating the communication across neurons, astrocytes, capillaries, meninges and the cerebrospinal fluid."

vs:

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19279265") Annotation(oboInOwl:hasDbXref "PMID:30552685") Annotation(oboInOwl:hasDbXref "PMID:31435019") Annotation(oboInOwl:hasDbXref "PMID:32930323") Annotation(oboInOwl:hasDbXref "PMID:34616062") Annotation(oboInOwl:hasDbXref "PMID:37824655") obo:IAO_0000115 obo:CL_4042009 "An astrocyte type that presents radial protrusions across the layers of a cortex. The soma of this astrocyte is part of the first layer of a neocortex. This astrocyte extents its protrusions transversally to the deeper layers of a cortex and it creates contact with neurons, the pia matter and capillaries. This astrocyte is involved in facilitating the communication across neurons, astrocytes, capillaries, meninges and the cerebrospinal fluid.")

IAO_0000115 = definition

Looks correct on loading in Protege.

[AvolaAmg]

#gogoeditdiff

[dosumis]

@JABelfiore can you review text on this PR? Given your Comms background I'm hoping you might be able to help polish/subedit definitions and comments.

[dosumis]

Please make minor changes in text before merge. Thanks!

[aleixpuigb]

I would suggest to change "A cell type..." to "An astrocyte..."