New patterns for number of GOCC in location.#976
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seger wants to merge 3 commits intoobophenotype:masterfrom
Open
New patterns for number of GOCC in location.#976seger wants to merge 3 commits intoobophenotype:masterfrom
seger wants to merge 3 commits intoobophenotype:masterfrom
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rays22
requested changes
Feb 19, 2025
Comment on lines
+3
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+58
| description: "Abnormal or altered number of cellular components, such as mitochondria, in an anatomical entity/location." | ||
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| contributors: | ||
| - https://orcid.org/0000-0001-5208-3432 | ||
| - https://orcid.org/0000-0002-9611-1279 | ||
|
|
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| classes: | ||
| amount: PATO:0000070 | ||
| abnormal: PATO:0000460 | ||
| cellular component: GO:0005575 | ||
| independent continuant: BFO:0000004 | ||
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| relations: | ||
| inheres_in: RO:0000052 | ||
| has_modifier: RO:0002573 | ||
| has_part: BFO:0000051 | ||
| part_of: BFO:0000050 | ||
|
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| annotationProperties: | ||
| exact_synonym: oio:hasExactSynonym | ||
|
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| vars: | ||
| cellular_component: "'cellular component'" | ||
| location: "'independent continuant'" | ||
|
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| name: | ||
| text: "abnormal number of %s in %s" | ||
| vars: | ||
| - cellular_component | ||
| - location | ||
|
|
||
| annotations: | ||
| - | ||
| annotationProperty: exact_synonym | ||
| text: "altered number of %s in %s" | ||
| vars: | ||
| - cellular_component | ||
| - location | ||
| - | ||
| annotationProperty: exact_synonym | ||
| text: "abnormal number of %s in %s" | ||
| vars: | ||
| - cellular_component | ||
| - location | ||
|
|
||
| def: | ||
| text: "Any anomaly that causes there to be an abnormal number of %s in %s." | ||
| vars: | ||
| - cellular_component | ||
| - location | ||
|
|
||
| equivalentTo: | ||
| text: "'has_part' some ('amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" | ||
| vars: | ||
| - cellular_component | ||
| - location |
Contributor
There was a problem hiding this comment.
Suggested change
| description: "Abnormal or altered number of cellular components, such as mitochondria, in an anatomical entity/location." | |
| contributors: | |
| - https://orcid.org/0000-0001-5208-3432 | |
| - https://orcid.org/0000-0002-9611-1279 | |
| classes: | |
| amount: PATO:0000070 | |
| abnormal: PATO:0000460 | |
| cellular component: GO:0005575 | |
| independent continuant: BFO:0000004 | |
| relations: | |
| inheres_in: RO:0000052 | |
| has_modifier: RO:0002573 | |
| has_part: BFO:0000051 | |
| part_of: BFO:0000050 | |
| annotationProperties: | |
| exact_synonym: oio:hasExactSynonym | |
| vars: | |
| cellular_component: "'cellular component'" | |
| location: "'independent continuant'" | |
| name: | |
| text: "abnormal number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| annotations: | |
| - | |
| annotationProperty: exact_synonym | |
| text: "altered number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| - | |
| annotationProperty: exact_synonym | |
| text: "abnormal number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| def: | |
| text: "Any anomaly that causes there to be an abnormal number of %s in %s." | |
| vars: | |
| - cellular_component | |
| - location | |
| equivalentTo: | |
| text: "'has_part' some ('amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" | |
| vars: | |
| - cellular_component | |
| - location | |
| description: "Abnormal or altered number of cellular components, such as | |
| mitochondria, in an anatomical entity/location." | |
| contributors: | |
| - https://orcid.org/0000-0001-5208-3432 # Nicole Vasilevsky | |
| - https://orcid.org/0000-0002-9611-1279 # Erik Segerdell | |
| classes: | |
| amount: PATO:0000070 | |
| abnormal: PATO:0000460 | |
| cellular component: GO:0005575 | |
| independent continuant: BFO:0000004 | |
| relations: | |
| characteristic_of: RO:0000052 | |
| has_modifier: RO:0002573 | |
| has_part: BFO:0000051 | |
| part_of: BFO:0000050 | |
| annotationProperties: | |
| exact_synonym: oio:hasExactSynonym | |
| vars: | |
| cellular_component: "'cellular component'" | |
| location: "'independent continuant'" | |
| name: | |
| text: "abnormal number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| annotations: | |
| - | |
| annotationProperty: exact_synonym | |
| text: "altered number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| - | |
| annotationProperty: exact_synonym | |
| text: "abnormal number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| def: | |
| text: "Any anomaly that causes there to be an abnormal number of %s in %s." | |
| vars: | |
| - cellular_component | |
| - location | |
| equivalentTo: | |
| text: "'has_part' some ( | |
| 'amount' and | |
| ('characteristic_of' some %s) and | |
| ('part_of' some %s) and | |
| ('has_modifier' some 'abnormal') | |
| )" | |
| vars: | |
| - cellular_component | |
| - location |
- Add names of contributors as comments.
- Use the current label of RO:0000052 characteristic of.
- Change the grouping (parenthesis) of sub-statements in the EQ.
- Fix yaml syntax:
- 3:81 warning line too long (121 > 80 characters) (line-length)
- 5:14 error trailing spaces (trailing-spaces)
- 31:4 error wrong indentation: expected 4 but found 3 (indentation)
- 39:6 error wrong indentation: expected 6 but found 5 (indentation)
- 45:6 error wrong indentation: expected 6 but found 5 (indentation)
- 55:81 warning line too long (126 > 80 characters) (line-length)
Comment on lines
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| description: "An abnormally decreased number of a cellular component, such as mitochondria, in an anatomical entity/location." | ||
|
|
||
| contributors: | ||
| - https://orcid.org/0000-0001-5208-3432 | ||
| - https://orcid.org/0000-0002-9611-1279 | ||
|
|
||
| classes: | ||
| decreased amount: PATO:0001997 | ||
| abnormal: PATO:0000460 | ||
| cellular component: GO:0005575 | ||
| independent continuant: BFO:0000004 | ||
|
|
||
| relations: | ||
| inheres_in: RO:0000052 | ||
| has_modifier: RO:0002573 | ||
| has_part: BFO:0000051 | ||
| part_of: BFO:0000050 | ||
|
|
||
| annotationProperties: | ||
| exact_synonym: oio:hasExactSynonym | ||
|
|
||
| vars: | ||
| cellular_component: "'cellular component'" | ||
| location: "'independent continuant'" | ||
|
|
||
| name: | ||
| text: "abnormally decreased number of %s in %s" | ||
| vars: | ||
| - cellular_component | ||
| - location | ||
|
|
||
| annotations: | ||
| - annotationProperty: exact_synonym | ||
| text: "reduced number of %s in %s" | ||
| vars: | ||
| - cellular_component | ||
| - location | ||
|
|
||
| def: | ||
| text: "The presence of a reduced number of %s in %s." | ||
| vars: | ||
| - cellular_component | ||
| - location | ||
|
|
||
| equivalentTo: | ||
| text: "'has_part' some ('decreased amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" | ||
| vars: | ||
| - cellular_component | ||
| - location |
Contributor
There was a problem hiding this comment.
Suggested change
| description: "An abnormally decreased number of a cellular component, such as mitochondria, in an anatomical entity/location." | |
| contributors: | |
| - https://orcid.org/0000-0001-5208-3432 | |
| - https://orcid.org/0000-0002-9611-1279 | |
| classes: | |
| decreased amount: PATO:0001997 | |
| abnormal: PATO:0000460 | |
| cellular component: GO:0005575 | |
| independent continuant: BFO:0000004 | |
| relations: | |
| inheres_in: RO:0000052 | |
| has_modifier: RO:0002573 | |
| has_part: BFO:0000051 | |
| part_of: BFO:0000050 | |
| annotationProperties: | |
| exact_synonym: oio:hasExactSynonym | |
| vars: | |
| cellular_component: "'cellular component'" | |
| location: "'independent continuant'" | |
| name: | |
| text: "abnormally decreased number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| annotations: | |
| - annotationProperty: exact_synonym | |
| text: "reduced number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| def: | |
| text: "The presence of a reduced number of %s in %s." | |
| vars: | |
| - cellular_component | |
| - location | |
| equivalentTo: | |
| text: "'has_part' some ('decreased amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" | |
| vars: | |
| - cellular_component | |
| - location | |
| description: "An abnormally decreased number of a cellular component, such as | |
| mitochondria, in an anatomical entity/location." | |
| contributors: | |
| - https://orcid.org/0000-0001-5208-3432 # Nicole Vasilevsky | |
| - https://orcid.org/0000-0002-9611-1279 # Erik Segerdell | |
| classes: | |
| decreased amount: PATO:0001997 | |
| abnormal: PATO:0000460 | |
| cellular component: GO:0005575 | |
| independent continuant: BFO:0000004 | |
| relations: | |
| characteristic_of: RO:0000052 | |
| has_modifier: RO:0002573 | |
| has_part: BFO:0000051 | |
| part_of: BFO:0000050 | |
| annotationProperties: | |
| exact_synonym: oio:hasExactSynonym | |
| vars: | |
| cellular_component: "'cellular component'" | |
| location: "'independent continuant'" | |
| name: | |
| text: "abnormally decreased number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| annotations: | |
| - annotationProperty: exact_synonym | |
| text: "reduced number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| def: | |
| text: "The presence of a reduced number of %s in %s." | |
| vars: | |
| - cellular_component | |
| - location | |
| equivalentTo: | |
| text: "'has_part' some ( | |
| 'decreased amount' and | |
| ('characteristic_of' some %s) and | |
| ('part_of' some %s) and | |
| ('has_modifier' some 'abnormal') | |
| )" | |
| vars: | |
| - cellular_component | |
| - location |
- Add names of contributors as comments.
- Use the current label of RO:0000052 characteristic of.
- Change the grouping (parenthesis) of sub-statements in the EQ.
- Fix yaml syntax:
- 3:81 warning line too long (126 > 80 characters) (line-length)
- 15:11 error trailing spaces (trailing-spaces)
- 22:37 error trailing spaces (trailing-spaces)
- 31:4 error wrong indentation: expected 4 but found 3 (indentation)
- 38:6 error wrong indentation: expected 6 but found 5 (indentation)
- 40:1 error trailing spaces (trailing-spaces)
- 48:81 warning line too long (136 > 80 characters) (line-length)
Comment on lines
+3
to
+52
| description: "An abnormally increased number of a cellular component, such as mitochondria, in an anatomical entity/location." | ||
|
|
||
| contributors: | ||
| - https://orcid.org/0000-0001-5208-3432 | ||
| - https://orcid.org/0000-0002-7356-1779 | ||
| - https://orcid.org/0000-0002-9611-1279 | ||
|
|
||
| classes: | ||
| increased amount: PATO:0000470 | ||
| abnormal: PATO:0000460 | ||
| cellular component: GO:0005575 | ||
| independent continuant: BFO:0000004 | ||
|
|
||
| relations: | ||
| inheres_in: RO:0000052 | ||
| has_modifier: RO:0002573 | ||
| has_part: BFO:0000051 | ||
| part_of: BFO:0000050 | ||
|
|
||
| annotationProperties: | ||
| exact_synonym: oio:hasExactSynonym | ||
|
|
||
| vars: | ||
| cellular_component: "'cellular component'" | ||
| location: "'independent continuant'" | ||
|
|
||
| name: | ||
| text: "increased number of %s in %s" | ||
| vars: | ||
| - cellular_component | ||
| - location | ||
|
|
||
| annotations: | ||
| - annotationProperty: exact_synonym | ||
| text: "extra %s in %s" | ||
| vars: | ||
| - cellular_component | ||
| - location | ||
|
|
||
| def: | ||
| text: "The presence of an increased number of %s in %s." | ||
| vars: | ||
| - cellular_component | ||
| - location | ||
|
|
||
| equivalentTo: | ||
| text: "'has_part' some ('increased amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" | ||
| vars: | ||
| - cellular_component | ||
| - location |
Contributor
There was a problem hiding this comment.
Suggested change
| description: "An abnormally increased number of a cellular component, such as mitochondria, in an anatomical entity/location." | |
| contributors: | |
| - https://orcid.org/0000-0001-5208-3432 | |
| - https://orcid.org/0000-0002-7356-1779 | |
| - https://orcid.org/0000-0002-9611-1279 | |
| classes: | |
| increased amount: PATO:0000470 | |
| abnormal: PATO:0000460 | |
| cellular component: GO:0005575 | |
| independent continuant: BFO:0000004 | |
| relations: | |
| inheres_in: RO:0000052 | |
| has_modifier: RO:0002573 | |
| has_part: BFO:0000051 | |
| part_of: BFO:0000050 | |
| annotationProperties: | |
| exact_synonym: oio:hasExactSynonym | |
| vars: | |
| cellular_component: "'cellular component'" | |
| location: "'independent continuant'" | |
| name: | |
| text: "increased number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| annotations: | |
| - annotationProperty: exact_synonym | |
| text: "extra %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| def: | |
| text: "The presence of an increased number of %s in %s." | |
| vars: | |
| - cellular_component | |
| - location | |
| equivalentTo: | |
| text: "'has_part' some ('increased amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" | |
| vars: | |
| - cellular_component | |
| - location | |
| description: "An abnormally decreased number of a cellular component, such as | |
| mitochondria, in an anatomical entity/location." | |
| contributors: | |
| - https://orcid.org/0000-0001-5208-3432 # Nicole Vasilevsky | |
| - https://orcid.org/0000-0002-9611-1279 # Erik Segerdell | |
| classes: | |
| decreased amount: PATO:0001997 | |
| abnormal: PATO:0000460 | |
| cellular component: GO:0005575 | |
| independent continuant: BFO:0000004 | |
| relations: | |
| characteristic_of: RO:0000052 | |
| has_modifier: RO:0002573 | |
| has_part: BFO:0000051 | |
| part_of: BFO:0000050 | |
| annotationProperties: | |
| exact_synonym: oio:hasExactSynonym | |
| vars: | |
| cellular_component: "'cellular component'" | |
| location: "'independent continuant'" | |
| name: | |
| text: "abnormally decreased number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| annotations: | |
| - annotationProperty: exact_synonym | |
| text: "reduced number of %s in %s" | |
| vars: | |
| - cellular_component | |
| - location | |
| def: | |
| text: "The presence of a reduced number of %s in %s." | |
| vars: | |
| - cellular_component | |
| - location | |
| equivalentTo: | |
| text: "'has_part' some ( | |
| 'decreased amount' and | |
| ('characteristic_of' some %s) and | |
| ('part_of' some %s) and | |
| ('has_modifier' some 'abnormal') | |
| )" | |
| vars: | |
| - cellular_component | |
| - location |
- Add names of contributors as comments.
- Use the current label of RO:0000052 characteristic of.
- Change the grouping (parenthesis) of sub-statements in the EQ.
- Fix yaml syntax:
- 3:81 warning line too long (126 > 80 characters) (line-length)
- 16:11 error trailing spaces (trailing-spaces)
- 23:37 error trailing spaces (trailing-spaces)
- 32:4 error wrong indentation: expected 4 but found 3 (indentation)
- 39:6 error wrong indentation: expected 6 but found 5 (indentation)
- 41:1 error trailing spaces (trailing-spaces)
- 49:81 warning line too long (136 > 80 characters) (line-length)
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These are proposed new patterns for abnormal, increased, and decreased number of cellular components in a location, requested for curation in Xenbase.