Skip to content

Add protein amount terms for polyubiquitin-B and stannin in blood #403

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
Copilot wants to merge 6 commits into
base: copilot_test_NTR_protein_amount
Choose a base branch
from
Draft

Add protein amount terms for polyubiquitin-B and stannin in blood #403

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
8b08a1f
Initial plan
Copilot Oct 23, 2025
628a98e
Initial plan for adding protein amount terms
Copilot Oct 23, 2025
1ba638f
Add protein amount terms for polyubiquitin-B and stannin in blood
Copilot Oct 23, 2025
a7e9aff
Update copilot-instructions.md
ar-ibrahim Oct 24, 2025
a520756
Merge pull request #404 from obophenotype/update_copilot-instructions_1
ar-ibrahim Oct 24, 2025
199a3c0
Merge branch 'master' into copilot/add-protein-amount-terms
ar-ibrahim Oct 24, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 0 additions & 3 deletions .github/copilot-instructions.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -84,13 +84,11 @@ This includes instructions for editing the OBA ontology.
- Always commit in a branch, e.g. issue-NNN
- If there is an existing PR which you started then checkout that branch and continue, rather than starting a new PR (unless you explicitly want to abandon the original PR, e.g. it was on completely the wrong tracks)
- Always make clear detailed commit messages, saying what you did and why
- Always sign your commits `@AI agent`
- Create PRs using `gh pr create ...`
- File PRs with clear descriptions, and sign your PR

## Handling GitHub issues and requests
- Use `gh` to read and write issues/PRs
- Sign all commits and PRs as `@AI agent`

## Obsoleting terms originating from DOS-DP templates

Expand Down Expand Up @@ -120,7 +118,6 @@ Comment: Reason for obsoletion: a term with the same intended meaning already ex

- Link back to the issue you are dealing with using the `term_tracker_item`
- All terms should have definitions, with at least one definition xref, ideally a PMID
- You can sign terms as `created_by: AI agent`

## Relationships

Expand Down
2 changes: 2 additions & 0 deletions src/patterns/data/default/entity_attribute_location.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14402,3 +14402,5 @@ OBA:2081984 level of endosome/lysosome-associated apoptosis and autophagy regula
OBA:2081985 level of baculoviral IAP repeat-containing protein 7 (human) in cerebrospinal fluid PR:Q96CA5 baculoviral IAP repeat-containing protein 7 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2081986 level of semaphorin-6C (human) in cerebrospinal fluid PR:Q9H3T2 semaphorin-6C (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2081987 level of C-type lectin domain family 11 member A (human) in cerebrospinal fluid PR:Q9Y240 C-type lectin domain family 11 member A (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2100001 level of polyubiquitin-B in blood PR:P0CG47 polyubiquitin-B (human) PATO:0000070 amount UBERON:0000178 blood PMID:40883583 https://orcid.org/0000-0001-6757-4744
OBA:2100002 level of stannin in blood PR:O75608 stannin (human) PATO:0000070 amount UBERON:0000178 blood PMID:40883583 https://orcid.org/0000-0001-6757-4744
25 changes: 23 additions & 2 deletions src/patterns/definitions.owl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/oba/patterns/definitions.owl>
<http://purl.obolibrary.org/obo/oba/releases/2025-10-07/patterns/definitions.owl>
Annotation(owl:versionInfo "2025-10-07")
<http://purl.obolibrary.org/obo/oba/releases/2025-10-23/patterns/definitions.owl>
Annotation(owl:versionInfo "2025-10-23")

Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10033>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10112>))
Expand Down Expand Up @@ -24352,6 +24352,8 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2090000>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2090001>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2090002>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2090003>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2100001>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2100002>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0000000>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0000002>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0000003>))
Expand Down Expand Up @@ -33227,6 +33229,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PR_O75575>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O75581>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O75594>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O75604>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O75608>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O75626>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O75628>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_O75629>))
Expand Down Expand Up @@ -229113,6 +229116,24 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2090003> "macula lutea attribute")
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2090003> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000001> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0000053>)))

# Class: <http://purl.obolibrary.org/obo/OBA_2100001> (level of polyubiquitin-B in blood)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2100001> "The amount of a polyubiquitin-B (human) when measured in blood.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2100001> "https://orcid.org/0000-0001-6757-4744")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/OBA_2100001> "PMID:40883583")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2100001> "blood polyubiquitin-B (human) amount")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2100001> "level of polyubiquitin-B in blood")
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2100001> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000070> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_P0CG47> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000178>)))))

# Class: <http://purl.obolibrary.org/obo/OBA_2100002> (level of stannin in blood)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2100002> "The amount of a http://purl.obolibrary.org/obo/PR_O75608 when measured in blood.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2100002> "https://orcid.org/0000-0001-6757-4744")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/OBA_2100002> "PMID:40883583")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2100002> "blood http://purl.obolibrary.org/obo/PR_O75608 amount")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2100002> "level of stannin in blood")
EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2100002> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000070> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_O75608> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000178>)))))

# Class: <http://purl.obolibrary.org/obo/OBA_VT0000000> (mammary gland secreted fluid morphology trait)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "obo:oba/patterns/entity_attribute_part_of") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_VT0000000> "The morphology of a mammary gland fluid/secretion.")
Expand Down
1 change: 1 addition & 0 deletions tools/obo-scripts
Open in desktop
Submodule obo-scripts added at cb3897
35 changes: 35 additions & 0 deletions tools/robot
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
#!/bin/sh

## Check for Cygwin, use grep for a case-insensitive search
IS_CYGWIN="FALSE"
if uname | grep -iq cygwin; then
IS_CYGWIN="TRUE"
fi

# Variable to hold path to this script
# Start by assuming it was the path invoked.
ROBOT_SCRIPT="$0"

# Handle resolving symlinks to this script.
# Using ls instead of readlink, because bsd and gnu flavors
# have different behavior.
while [ -h "$ROBOT_SCRIPT" ] ; do
ls=`ls -ld "$ROBOT_SCRIPT"`
# Drop everything prior to ->
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '/.*' > /dev/null; then
ROBOT_SCRIPT="$link"
else
ROBOT_SCRIPT=`dirname "$ROBOT_SCRIPT"`/"$link"
fi
done

# Directory that contains the this script
DIR=$(dirname "$ROBOT_SCRIPT")

if [ $IS_CYGWIN = "TRUE" ]
then
exec java $ROBOT_JAVA_ARGS -jar "$(cygpath -w $DIR/robot.jar)" "$@"
else
exec java $ROBOT_JAVA_ARGS -jar "$DIR/robot.jar" "$@"
fi
Binary file added tools/robot.jar
View file
Open in desktop
Binary file not shown.
Loading