diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md index 21eba09d..d2caf082 100644 --- a/.github/copilot-instructions.md +++ b/.github/copilot-instructions.md @@ -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 @@ -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 diff --git a/src/patterns/data/default/entity_attribute_location.tsv b/src/patterns/data/default/entity_attribute_location.tsv index fb71bdca..520ebb8b 100644 --- a/src/patterns/data/default/entity_attribute_location.tsv +++ b/src/patterns/data/default/entity_attribute_location.tsv @@ -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 diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 5c6169d6..c23d33fd 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2025-10-07") + +Annotation(owl:versionInfo "2025-10-23") Declaration(Class()) Declaration(Class()) @@ -24352,6 +24352,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -33227,6 +33229,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -229113,6 +229116,24 @@ AnnotationAssertion(Annotation( "macula lutea attribute") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (level of polyubiquitin-B in blood) + +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute_location") "The amount of a polyubiquitin-B (human) when measured in blood.") +AnnotationAssertion( "https://orcid.org/0000-0001-6757-4744") +AnnotationAssertion( "PMID:40883583") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute_location") "blood polyubiquitin-B (human) amount") +AnnotationAssertion(rdfs:label "level of polyubiquitin-B in blood") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (level of stannin in blood) + +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute_location") "The amount of a http://purl.obolibrary.org/obo/PR_O75608 when measured in blood.") +AnnotationAssertion( "https://orcid.org/0000-0001-6757-4744") +AnnotationAssertion( "PMID:40883583") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute_location") "blood http://purl.obolibrary.org/obo/PR_O75608 amount") +AnnotationAssertion(rdfs:label "level of stannin in blood") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + # Class: (mammary gland secreted fluid morphology trait) AnnotationAssertion(Annotation( "obo:oba/patterns/entity_attribute_part_of") "The morphology of a mammary gland fluid/secretion.") diff --git a/tools/obo-scripts b/tools/obo-scripts new file mode 160000 index 00000000..cb38971c --- /dev/null +++ b/tools/obo-scripts @@ -0,0 +1 @@ +Subproject commit cb38971ce39654bc9e4e96efcd22e950c3561f5d diff --git a/tools/robot b/tools/robot new file mode 100755 index 00000000..5408a051 --- /dev/null +++ b/tools/robot @@ -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 diff --git a/tools/robot.jar b/tools/robot.jar new file mode 100644 index 00000000..9a3a8f88 Binary files /dev/null and b/tools/robot.jar differ