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Addresses #2354 to create a design pattern for cycling/proliferating …
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…cells (#2419)

* Create DOSDP for cycling cells

* Create table for DOSDP of cycling cells

* Fix issues and make patterns

- Synonyms can't be made a pattern like the labels and they need a new variable.
- Minor fixes in the yaml file

* Add GO term and refresh imports

* Fix missing punctuation in definition

* Add DOSDP in editing_guidelines

* Remove extra empty rows in tsv file

* Synonyms are now created by generate_synonyms

* Integrate guidelines suggestions.

* Fix yaml syntax

* cycling stromal cells added

cycling stromal cells added

* Revert "cycling stromal cells added"

This reverts commit 1049f1d.

* Incorporate changes for new EquivalentTo

- Imports terms:
    - 'has quality'
    - 'active'
- New EquivalentTo as discussed in the ticket

* cycling cells gut added

* Update guidelines with new pattern

* PMID and CL ID updated

* PMID update

* spaces removed

* Remove cycling naive B cell and follicular DC

This commit also updates the pattern

* Fix plasma cell, and fix neuroblast label

---------

Co-authored-by: Ray Stefancsik <[email protected]>
Co-authored-by: JABelfiore <[email protected]>
Co-authored-by: David Osumi-Sutherland <[email protected]>
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@aleixpuigb @rays22
@JABelfiore @dosumis
4 people authored Aug 9, 2024
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18 changes: 18 additions & 0 deletions docs/editing_guidelines.md
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Expand Up @@ -178,3 +178,21 @@ The textual definition of a logically defined class should be a plain English eq
### Asserting relationships

Please refer to the [relations guide](relations_guide.md) for detailled guidelines about which relations to use for most cases.

## Design Pattern Usage with DOSDP


The cell ontology contains a large number of terms, classifications, and relationships that are constantly expanding. Manually maintaining all these elements would be a daunting task, so a substantial portion of the maintenance is automated. This automation heavily relies on the systematic use of design patterns.

CL uses **Dead simple OWL design patterns** (DOSDP, [Osumi-Sutherland *et al.*, 2017](https://doi.org/10.1186/s13326-017-0126-0)) to document simple patterns, as they require minimal programming expertise, and once implemented, it is easy to edit.

All patterns are stored in [/src/patterns/dosdp-patterns](https://github.com/obophenotype/cell-ontology/tree/master/src/patterns/dosdp-patterns), while the editable tables are located in [/src/patterns/data/default](https://github.com/obophenotype/cell-ontology/tree/master/src/patterns/data/default).

### Cycling cell states
Pattern name: cyclingCellStates.yaml

Cell cycling is a fundamental biological mechanism that brings a cell to divide and duplicate into two daughter cells. This process is carried out by a large number of cells, and cells undergoing cell cycling have a distinct transcriptional profile compared to non cycling cells. Cycling cells need to be annotated and described by CL terms as these cells have been identified in a multitude of single-cell transcriptional datasets.

The terms created with this pattern are labeled as **'cycling X'**, being *X* the parent term, and have an exact synonym **'proliferating X'**. These cell terms can be logically defined as a `'cell' and 'participates in' some 'cell cycle process' and 'has quality' some 'active'`. Ex:

'cycling B cell' *SubClassOf* ['B cell](http://purl.obolibrary.org/obo/CL_0000236) and ['participates in'](http://purl.obolibrary.org/obo/RO_0000056) some ['cell cycle process'](http://purl.obolibrary.org/obo/GO_0022402) and ['has quality'](http://purl.obolibrary.org/obo/RO_0000086) some ['active'](http://purl.obolibrary.org/obo/PATO_0002354)
1 change: 1 addition & 0 deletions src/ontology/catalog-v001.xml
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<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl/imports/nif_import.owl" uri="imports/nif_import.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl/imports/nif_cell.owl" uri="imports/nif_cell.owl"/>
<uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Cell.owl" uri="mirror/NIF-Cell.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl/patterns/definitions.owl" uri="../patterns/definitions.owl"/>
<uri name="http://purl.obolibrary.org/obo/cl/components/hra_subset.owl" uri="components/hra_subset.owl"/>
<uri name="http://purl.obolibrary.org/obo/cl/components/mappings.owl" uri="components/mappings.owl"/>
<uri name="http://purl.obolibrary.org/obo/cl/components/blood_and_immune_upper_slim.owl" uri="components/blood_and_immune_upper_slim.owl"/>
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1 change: 1 addition & 0 deletions src/ontology/cl-edit.owl
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Expand Up @@ -30,6 +30,7 @@ Import(<http://purl.obolibrary.org/obo/cl/components/hra_subset.owl>)
Import(<http://purl.obolibrary.org/obo/cl/components/kidney_upper_slim.owl>)
Import(<http://purl.obolibrary.org/obo/cl/components/mappings.owl>)
Import(<http://purl.obolibrary.org/obo/cl/imports/merged_import.owl>)
Import(<http://purl.obolibrary.org/obo/cl/patterns/definitions.owl>)
Annotation(obo:IAO_0000700 obo:CL_0000000)
Annotation(dc:description "An ontology of cell types.")
Annotation(dc:title "Cell Ontology")
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1 change: 0 additions & 1 deletion src/ontology/components/mappings.owl
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<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->


3 changes: 2 additions & 1 deletion src/ontology/imports/go_terms.txt
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Expand Up @@ -7,4 +7,5 @@ GO:0043679
GO:0043195
GO:0099096
GO:0004990
GO:0070278
GO:0070278
GO:0000279
103 changes: 103 additions & 0 deletions src/ontology/imports/merged_import.owl
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3 changes: 2 additions & 1 deletion src/ontology/imports/pato_terms.txt
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Expand Up @@ -33,4 +33,5 @@ PATO:0002094
PATO:0070046
PATO:0070047
PATO:0070061
PATO:0040072
PATO:0040072
PATO:0002354
3 changes: 2 additions & 1 deletion src/ontology/imports/ro_terms.txt
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Expand Up @@ -4,4 +4,5 @@ RO:0013001
RO:0002175
RO:0013007
RO:0015015
RO:0015016
RO:0015016
RO:0000086
21 changes: 21 additions & 0 deletions src/patterns/data/default/cyclingCellStates.tsv
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defined_class defined_class_label cell pubs synonym_xrefs creator date_created
CL:4033068 cycling B cell CL:0000236 PMID:31348891 PMID:31348891 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033069 cycling T cell CL:0000084 PMID:37291214 PMID:37291214 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033070 cycling dendritic cell CL:0000451 PMID:32066951 PMID:32066951 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033071 cycling NK cell CL:0000623 PMID:34062119 PMID:34062119 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033072 cycling gamma-delta T cell CL:0000798 PMID:32066951 PMID:32066951 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033073 cycling monocyte CL:0000576 PMID:31348891 PMID:31348891 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033074 "cycling CD8-positive, alpha-beta T cell" CL:0000625 PMID:34062119 PMID:34062119 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033075 "cycling CD4-positive, alpha-beta T cell" CL:0000624 PMID:34062119 PMID:34062119 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033076 cycling macrophage CL:0000235 PMID:33208946 PMID:33208946 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033077 cycling alveolar macrophage CL:0000583 PMID:37291214 PMID:37291214 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033078 cycling mononuclear phagocyte CL:0000113 PMID:37468583 PMID:37468583 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033079 cycling endothelial cell of lymphatic vessel CL:0002138 PMID:37291214 PMID:37291214 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033080 cycling pulmonary alveolar type 2 cell CL:0002063 PMID:37291214 PMID:37291214 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033081 cycling myeloid cell CL:0000763 PMID:38301653 PMID:38301653 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4033082 cycling basal cell CL:0000646 PMID:33208946 PMID:33208946 https://orcid.org/0000-0001-6677-8489 2024-07-02T09:14:23Z
CL:4047001 cycling stromal cell CL:0000499 PMID:34497389 PMID:34497389 https://orcid.org/0009-0005-7919-4905 2024-07-19T09:14:23Z
CL:4047002 cycling glial cell CL:0000125 PMID:34497389 PMID:34497389 https://orcid.org/0009-0005-7919-4905 2024-07-19T09:14:23Z
CL:4047003 cycling plasma cell CL:0000786 PMID:34497389 PMID:34497389 https://orcid.org/0009-0005-7919-4905 2024-07-19T09:14:23Z
CL:4047004 cycling type EC enteroendocrine cell CL:0000577 PMID:34497389 PMID:34497389 https://orcid.org/0009-0005-7919-4905 2024-07-19T09:14:23Z
CL:4047005 cycling neuroblast (sensu Vertebrata) CL:0000031 PMID:34497389 PMID:34497389 https://orcid.org/0009-0005-7919-4905 2024-07-19T09:14:23Z
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