2460 revise def multiciliated epithelial cell #2482

Caroline-99 · 2024-08-08T12:36:58Z

Pato term (PATO_0010007 multiciliated) is imported into CL
text definition updated and references added
logical definition updated

Related to pato-ontology/pato#561 - PATO term has been approved and the imports have been refreshed

- Pato term (PATO_0010007 multiciliated) is imported into CL (note this term has not been approved by PATO yet) -text defintion updates and references added -logical defintion updated

anitacaron · 2024-08-12T12:47:47Z

#gogoeditdiff

anitacaron · 2024-08-12T12:52:35Z

Do you need help updating imports to have PATO correctly imported?

github-actions · 2024-08-12T12:52:46Z

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/2024-09-06/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/2024-09-06/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_4047001 `http://purl.obolibrary.org/obo/CL_4047001`

Added

Class: CL_4047001

created by `http://www.geneontology.org/formats/oboInOwl#created_by`

Removed

created by label "created by"

creation date `http://www.geneontology.org/formats/oboInOwl#creation_date`

Removed

creation date label "creation date"

has part `http://purl.obolibrary.org/obo/BFO_0000051`

Removed

has part label "has_part"
has part has_obo_namespace "quality"

id `http://www.geneontology.org/formats/oboInOwl#id`

Removed

id label "id"

multi-ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005012`

Removed

multi-ciliated epithelial cell definition "A ciliated epithelial cell with many cilia."
- database_cross_reference "CL:CVS"

Added

multi-ciliated epithelial cell comment "While the term 'multi-ciliated epithelial cell' refers to cells with multiple motile cilia, there are exceptions where epithelial cells may have multiple non-motile cilia. Examples include olfactory sensory neurons, which have non-motile cilia for sensory detection, and choroid plexus epithelial cells, which possess multiple non-motile cilia with transient motility during development. Multiciliated cells are essential for human health, and their dysfunction can lead to various diseases known as ciliopathies, such as primary ciliary dyskinesia. This condition affects the respiratory system, brain ventricles, and reproductive system, leading to chronic respiratory infections, hydrocephalus, and infertility"
- database_cross_reference "PMID:23959957"
- database_cross_reference "PMID:25729351"
- database_cross_reference "PMID:26378583"
- database_cross_reference "PMID:22118931"
multi-ciliated epithelial cell definition "A columnar/cuboidal epithelial cell with multiple motile cilia on its apical surface. These cells facilitate the movement of liquids such as mucus or cerebrospinal fluid across the epithelial surface."
- database_cross_reference "PMID:38032388"
- database_cross_reference "CL:CVS"
- database_cross_reference "PMID:28400610"
multi-ciliated epithelial cell SubClassOf columnar/cuboidal epithelial cell

part of `http://purl.obolibrary.org/obo/BFO_0000050`

Removed

part of label "part_of"
part of has_obo_namespace "quality"

github-actions · 2024-08-12T12:52:48Z

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

PATO_0010007 `http://purl.obolibrary.org/obo/PATO_0010007`

Added

Class: PATO_0010007

multi-ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005012`

Removed

multi-ciliated epithelial cell definition "A ciliated epithelial cell with many cilia."
- database_cross_reference "CL:CVS"
multi-ciliated epithelial cell SubClassOf has part some cilium
multi-ciliated epithelial cell SubClassOf epithelial cell

Added

multi-ciliated epithelial cell comment "While the term 'multi-ciliated epithelial cell' refers to cells with multiple motile cilia, there are exceptions where epithelial cells may have multiple non-motile cilia. Examples include olfactory sensory neurons, which have non-motile cilia for sensory detection, and choroid plexus epithelial cells, which possess multiple non-motile cilia with transient motility during development. Multiciliated cells are essential for human health, and their dysfunction can lead to various diseases known as ciliopathies, such as primary ciliary dyskinesia. This condition affects the respiratory system, brain ventricles, and reproductive system, leading to chronic respiratory infections, hydrocephalus, and infertility"
- database_cross_reference "PMID:23959957"
- database_cross_reference "PMID:25729351"
- database_cross_reference "PMID:26378583"
- database_cross_reference "PMID:22118931"
multi-ciliated epithelial cell definition "A columnar/cuboidal epithelial cell with multiple motile cilia on its apical surface. These cells facilitate the movement of liquids such as mucus or cerebrospinal fluid across the epithelial surface."
- database_cross_reference "PMID:38032388"
- database_cross_reference "CL:CVS"
- database_cross_reference "PMID:28400610"
multi-ciliated epithelial cell EquivalentTo columnar/cuboidal epithelial cell and (has part some motile cilium) and (bearer of some PATO_0010007)

JABelfiore

Definition and references look good, one minor amend.

src/ontology/cl-edit.owl

AvolaAmg

in this paper they are referring to Multiciliated ependymal (E1) cells and (and other two type of ciliated cell E2, E3).
Would you like to have a look at this paper to see if Mutliciliated ependymal cell should be added as an NTR with parent term multi-ciliated epithelial cell ?

src/ontology/cl-edit.owl

AvolaAmg

Please see in line comments.

Caroline-99 · 2024-09-06T15:15:25Z

#gogoeditdiff

src/ontology/cl-edit.owl

…://github.com/obophenotype/cell-ontology into 2460-revise-def-multiciliated-epithelial-cell

Caroline-99 added 2 commits August 8, 2024 13:35

Fixes #2460

2d58d0c

- Pato term (PATO_0010007 multiciliated) is imported into CL (note this term has not been approved by PATO yet) -text defintion updates and references added -logical defintion updated

Update cl-edit.owl

07c6d44

Caroline-99 linked an issue Aug 8, 2024 that may be closed by this pull request

Revise def multiciliated epithelial cell #2460

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Caroline-99 requested review from AvolaAmg and JABelfiore August 9, 2024 13:35

Caroline-99 added 2 commits August 9, 2024 14:35

Merge branch 'master' into 2460-revise-def-multiciliated-epithelial-cell

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Merge branch 'master' into 2460-revise-def-multiciliated-epithelial-cell

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anitacaron added the update-imports-required Imports need to be refreshed before this PR can be merged. label Aug 16, 2024

Caroline-99 and others added 9 commits August 16, 2024 14:26

expanded the comments section

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Update cl-edit.owl

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Merge branch 'master' into 2460-revise-def-multiciliated-epithelial-cell

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Merge branch 'master' into 2460-revise-def-multiciliated-epithelial-cell

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Merge branch 'master' into 2460-revise-def-multiciliated-epithelial-cell

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Merge branch 'master' into 2460-revise-def-multiciliated-epithelial-cell

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refreshed the imports

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Update definitions.owl

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Merge branch 'master' into 2460-revise-def-multiciliated-epithelial-cell

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aleixpuigb added 2 commits September 6, 2024 17:05

Update PATO imports

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Merge branch 'master' into 2460-revise-def-multiciliated-epithelial-cell

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Caroline-99 added 2 commits September 9, 2024 09:59

Merge branch 'master' into 2460-revise-def-multiciliated-epithelial-cell

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Merge branch 'master' into 2460-revise-def-multiciliated-epithelial-cell

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Caroline-99 requested review from AvolaAmg and JABelfiore September 12, 2024 13:11

Caroline-99 and others added 3 commits September 16, 2024 16:09

Merge branch 'master' into 2460-revise-def-multiciliated-epithelial-cell

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added references

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Merge branch '2460-revise-def-multiciliated-epithelial-cell' of https…

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…://github.com/obophenotype/cell-ontology into 2460-revise-def-multiciliated-epithelial-cell

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Caroline-99 merged commit 83c9e2f into master Sep 16, 2024
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Caroline-99 deleted the 2460-revise-def-multiciliated-epithelial-cell branch September 16, 2024 15:58

2460 revise def multiciliated epithelial cell #2482

2460 revise def multiciliated epithelial cell #2482

Conversation

Caroline-99 commented Aug 8, 2024 • edited Loading

anitacaron commented Aug 12, 2024

anitacaron commented Aug 12, 2024

github-actions bot commented Aug 12, 2024 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

CL_4047001 http://purl.obolibrary.org/obo/CL_4047001

Added

created by http://www.geneontology.org/formats/oboInOwl#created_by

Removed

creation date http://www.geneontology.org/formats/oboInOwl#creation_date

Removed

has part http://purl.obolibrary.org/obo/BFO_0000051

Removed

id http://www.geneontology.org/formats/oboInOwl#id

Removed

multi-ciliated epithelial cell http://purl.obolibrary.org/obo/CL_0005012

Removed

Added

part of http://purl.obolibrary.org/obo/BFO_0000050

Removed

github-actions bot commented Aug 12, 2024 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

PATO_0010007 http://purl.obolibrary.org/obo/PATO_0010007

Added

multi-ciliated epithelial cell http://purl.obolibrary.org/obo/CL_0005012

Removed

Added

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Caroline-99 commented Sep 6, 2024

Caroline-99 commented Aug 8, 2024 •

edited

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github-actions bot commented Aug 12, 2024 •

edited

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CL_4047001 `http://purl.obolibrary.org/obo/CL_4047001`

created by `http://www.geneontology.org/formats/oboInOwl#created_by`

creation date `http://www.geneontology.org/formats/oboInOwl#creation_date`

has part `http://purl.obolibrary.org/obo/BFO_0000051`

id `http://www.geneontology.org/formats/oboInOwl#id`

multi-ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005012`

part of `http://purl.obolibrary.org/obo/BFO_0000050`

github-actions bot commented Aug 12, 2024 •

edited

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PATO_0010007 `http://purl.obolibrary.org/obo/PATO_0010007`

multi-ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005012`