Initial commit

2025-11-29 17:51:42 +08:00
commit 24486941f6
7 changed files with 682 additions and 0 deletions
--- a/.claude-plugin/plugin.json
+++ b/.claude-plugin/plugin.json
@@ -0,0 +1,12 @@
+{
+  "name": "editing-obo-ontologies",
+  "description": "Skills and tools for editing OBO format ontologies",
+  "version": "0.0.0-2025.11.28",
+  "author": {
+    "name": "Chris Mungall",
+    "email": "cjmungall@lbl.gov"
+  },
+  "skills": [
+    "./skills/editing-obo-ontologies"
+  ]
+}
--- a/README.md
+++ b/README.md
@@ -0,0 +1,3 @@
+# editing-obo-ontologies
+
+Skills and tools for editing OBO format ontologies
--- a/plugin.lock.json
+++ b/plugin.lock.json
@@ -0,0 +1,56 @@
+{
+  "$schema": "internal://schemas/plugin.lock.v1.json",
+  "pluginId": "gh:ai4curation/curation-skills:editing-obo-ontologies",
+  "normalized": {
+    "repo": null,
+    "ref": "refs/tags/v20251128.0",
+    "commit": "2e46cb48c132c3e0073b5a32902b1a75911d251b",
+    "treeHash": "8e04abba47a740d345735dd6c73d389dde13ec45d3117b23d4868f0345ee27cc",
+    "generatedAt": "2025-11-28T10:13:06.237881Z",
+    "toolVersion": "publish_plugins.py@0.2.0"
+  },
+  "origin": {
+    "remote": "git@github.com:zhongweili/42plugin-data.git",
+    "branch": "master",
+    "commit": "aa1497ed0949fd50e99e70d6324a29c5b34f9390",
+    "repoRoot": "/Users/zhongweili/projects/openmind/42plugin-data"
+  },
+  "manifest": {
+    "name": "editing-obo-ontologies",
+    "description": "Skills and tools for editing OBO format ontologies"
+  },
+  "content": {
+    "files": [
+      {
+        "path": "README.md",
+        "sha256": "0037bd2663121bc876aa389182b4f78ba7ba0bafab3b2c63ac7971a67637c44c"
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+        "sha256": "87335cfd3ce8c657dac9511fa97142d9791b2e79bd2e35c3a6251e3cd17f19bb"
+      },
+      {
+        "path": "skills/editing-obo-ontologies/obo-grep.pl",
+        "sha256": "7383994a9f6be84943dd2a82544dee33469f096d7d4fb8d0eebae84e544e881a"
+      },
+      {
+        "path": "skills/editing-obo-ontologies/SKILL.md",
+        "sha256": "77aab4f9875dcbaf0b04376073cbb2cd6ad50d63f9371095434f36329ba5747e"
+      },
+      {
+        "path": "skills/editing-obo-ontologies/obo-checkin.pl",
+        "sha256": "7c386bdd2f7ade4a139dce22935472818ba336574227d4d57ad9bdce756c358c"
+      },
+      {
+        "path": "skills/editing-obo-ontologies/obo-checkout.pl",
+        "sha256": "de1c16c2b96ea393d576667dc3eee8954bd6c92bd8d0a2680a2aa267c741628c"
+      }
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+    "flags": []
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+}
--- a/skills/editing-obo-ontologies/SKILL.md
+++ b/skills/editing-obo-ontologies/SKILL.md
@@ -0,0 +1,203 @@
+---
+name: editing-obo-ontologies
+description: Skills and tools for editing OBO format ontologies, including querying terms, checking out/checking in individual terms, and following OBO format conventions. Do not use this if the source for the ontology you are editing is not in obo format (e.g. ofn)
+---
+
+# OBO Ontology Editing Guide
+
+This skill provides guidance and tools for editing ontologies in OBO format.
+
+## Project Layout Conventions
+
+Most OBO ontologies follow a similar structure:
+- Main development file is typically `src/ontology/{ontology}-edit.obo`
+- Individual terms can be checked out to `terms/` directory for editing
+- Some projects may have different layouts - check the project's documentation
+
+## Querying Ontology Terms
+
+Use the `obo-grep.pl` script for searching OBO files:
+
+- Look at a specific term by ID:
+    - `obo-grep.pl --noheader -r 'id: ONTO:0004177' src/ontology/{ontology}-edit.obo`
+- All mentions of an ID:
+    - `obo-grep.pl --noheader -r 'ONTO:0004177' src/ontology/{ontology}-edit.obo`
+- Search by regex (e.g., all mentions of hand or foot):
+    - `obo-grep.pl --noheader -r '(hand|foot)' src/ontology/{ontology}-edit.obo`
+- Search is much faster than full file reads
+- ONLY search the main edit file (usually `src/ontology/{ontology}-edit.obo`)
+- DO NOT do manual greps or read entire files unless necessary
+
+## Before Making Edits
+
+- Read the request carefully and make a plan, especially if there is nuance
+- If a PMID is mentioned, try to read it using: `aurelian fulltext PMID:NNNNNN`
+- This also works for DOIs and URLs for scientific papers (if accessible)
+- ALWAYS check proposed parent terms for consistency
+- Check project-specific guidelines if available
+
+## Editing Workflow
+
+### IMPORTANT: Use Checkout/Checkin for Large Files
+
+- Do not edit large ontology files directly
+- Use the checkout/checkin workflow for individual terms
+- Check out a term: `obo-checkout.pl src/ontology/{ontology}-edit.obo ONTO:1234567 [OTHER_IDS]`
+- This creates a single stanza file: `terms/{ontology}_1234567.obo` (note: colon replaced with underscore)
+- Edit the small file in the `terms/` folder
+- Check back in: `obo-checkin.pl src/ontology/{ontology}-edit.obo ONTO:1234567 [OTHER_IDS]`
+- Checking in updates the edit file and removes the file from `terms/`
+- You can edit multiple terms in one batch file if needed
+
+### Scripts Available
+
+This skill includes three essential scripts:
+1. `obo-grep.pl` - Fast searching of OBO files
+2. `obo-checkout.pl` - Extract terms to individual files for editing
+3. `obo-checkin.pl` - Merge edited terms back into main file
+
+All scripts are available in your PATH when this skill is loaded.
+
+## OBO Format Guidelines
+
+### Basic Structure
+
+- Term ID format: `ONTO:NNNNNNN` (check project conventions for number of digits)
+- Each term requires:
+  - `id:` - unique identifier
+  - `name:` - human-readable label
+  - `namespace:` - ontology namespace
+  - `def:` - definition with references in square brackets
+- Use standard relationship types: `is_a`, `part_of`, `has_part`, etc.
+- Follow existing term patterns for consistency
+
+### Handling New Term Requests (NTRs)
+
+- Check project conventions for temporary ID ranges
+- Example: Some projects use ranges like `ONTO:777xxxx` for new terms
+- Always check for ID clashes: `grep 'id: ONTO:777' src/ontology/{ontology}-edit.obo`
+- NEVER guess ontology IDs - use search tools to find actual terms
+- NEVER guess PMIDs for references - do web searches if needed
+
+### Citations and References
+
+- Cite publications appropriately: `def: "..." [PMID:nnnn, doi:mmmm]`
+- Fetch full text when needed: `aurelian fulltext <PMID:nnn>` (also works with DOIs and URLs)
+- All synonyms should include proper citations
+- Never use empty brackets `[]` without a source
+
+### Synonyms
+
+Synonyms should include proper attribution:
+
+**Correct:**
+```
+synonym: "alternative name" EXACT [PMID:12345678]
+synonym: "abbrev" EXACT ABBREVIATION [PMID:12345678]
+```
+
+### Relationships and Logical Definitions
+
+- All terms should have at least one `is_a` parent
+- Logical definitions follow genus-differentia form
+- Text definitions should mirror logical definitions
+- Include source attribution for relationships when based on literature:
+
+### Logical Definitions (intersection_of)
+
+Example of proper intersection_of usage:
+
+```
+[Term]
+id: ONTO:0000715
+name: specific disease
+def: "A general disease that involves specific location." [PMID:12345678]
+is_a: ONTO:0001082 ! general disease
+intersection_of: ONTO:0004971 ! general disease
+intersection_of: disease_has_location UBERON:0000029 ! specific location
+```
+
+Note that in OWL this corresponds to: `'specific disease' EquivalentTo 'general disease' and 'disease has location' some 'specific location'`
+
+## Obsoleting Terms
+
+- Obsolete terms should have NO logical axioms (`is_a`, `relationship`, `intersection_of`)
+- Obsolete terms may have one `replaced_by` tag (exact replacement)
+- Or multiple `consider` tags (suggested alternatives)
+- Always include obsolescence reason and tracker reference
+
+Example of simple obsolescence:
+
+```
+[Term]
+id: ONTO:0100334
+name: obsolete term name
+property_value: IAO:0000231 OMO:0001000
+property_value: IAO:0000233 "https://github.com/{project}/issues/XXXX" xsd:anyURI
+is_obsolete: true
+replaced_by: ONTO:0100321
+```
+
+Example with considerations instead of replacement:
+
+```
+[Term]
+id: ONTO:0100229
+name: obsolete term name
+def: "OBSOLETE. Original definition here." [original references]
+property_value: IAO:0000231 OMO:0001000
+property_value: IAO:0000233 "https://github.com/{project}/issues/XXXX" xsd:anyURI
+is_obsolete: true
+consider: ONTO:0100259
+consider: ONTO:0100260
+```
+
+### Important Notes on Obsolescence
+
+- Synonyms and xrefs can be migrated to replacement terms judiciously
+- Never do complete merges with `alt_id` - use obsolescence with replacement instead
+- No relationships should point to an obsolete term
+- When obsoleting, you may need to rewire other terms to "skip" the obsoleted term
+
+## Metadata Best Practices
+
+- Link to issue trackers: `property_value: IAO:0000233 "https://github.com/{project}/issues/XXXX" xsd:anyURI`
+- Sign new terms (don't tag pre-existing terms):
+  ```
+  property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-2345-6789
+  ```
+- All terms should have definitions with at least one reference (preferably PMID)
+- Dates are typically auto-generated by build processes
+
+## Syntax Checking
+
+Validate OBO syntax using ROBOT:
+
+```bash
+robot convert --catalog src/ontology/catalog-v001.xml \
+  -i src/ontology/{ontology}-edit.obo \
+  -f obo \
+  -o {ontology}-edit.TMP.obo
+```
+
+Use `-vvv` flag for full stack trace if there are errors.
+
+## Design Patterns
+
+Many OBO ontologies use DOSDP (Dead Simple Ontology Design Patterns):
+- Check `src/patterns/dosdp-patterns/*.yaml` for project-specific patterns
+- Follow existing patterns when creating similar terms
+- Common patterns include:
+  - Location-based disease patterns
+  - Gene-related disease patterns
+  - Part-of hierarchies
+  - Abnormality patterns
+
+
+## Important Reminders
+
+- NEVER guess identifiers of any kind
+- If you include an identifier not provided by the user, you MUST verify it
+- PMIDs can be checked with `aurelian` or web search
+- Always follow project-specific conventions and check existing examples
+- When in doubt, ask for clarification rather than making assumptions
--- a/skills/editing-obo-ontologies/obo-checkin.pl
+++ b/skills/editing-obo-ontologies/obo-checkin.pl
@@ -0,0 +1,201 @@
+#!/usr/bin/perl -w
+
+use strict;
+use FileHandle;
+my $outdir = "terms";
+my $cmd;
+my $dry_run = 0;
+my $preserve_files = 0;
+while ($ARGV[0] =~ /^\-/) {
+    my $opt = shift @ARGV;
+    if ($opt eq '-h' || $opt eq '--help') {
+        print usage();
+        exit 0;
+    }
+    if ($opt eq '-d' || $opt eq '--outdir') {
+        $outdir = shift @ARGV;
+    }
+    if ($opt eq '-n' || $opt eq '--dry-run') {
+        $dry_run = 1;
+    }
+    if ($opt eq '-p' || $opt eq '--preserve-files') {
+        $preserve_files = 1;
+    }
+}
+`mkdir -p $outdir`;
+my $id;
+my $stanza = "";
+my @alt_ids = ();
+my $fn = shift @ARGV;
+# ensure ids are sorted
+my @ids = sort @ARGV;
+
+my %new_stanza_map = ();
+
+foreach my $id (@ids) {
+    my $path = get_path($id);
+    # check if $id is a path to a file that exists
+    if ($id =~ m@[\./]@ && -e $id) {
+        open(F, $id) || die "no such file $id";
+        my @lines = <F>;
+        close(F);
+        my $uber_stanza = join("", @lines);
+        my @stanzas_in_block = split(/\n\n/, $uber_stanza);
+        foreach my $stanza (@stanzas_in_block) {
+            # trim whitespace
+            $stanza =~ s/\s+$//;
+            if (!length($stanza)) {
+                next;
+            }
+            # check if stanza has id (note that stanza is multi-line)
+            if ($stanza =~ /id:\s+(\S+)/) {
+                my $stanza_id = $1;
+                $new_stanza_map{$stanza_id} = "$stanza\n\n";
+            }
+            else {
+                die "no id found in $stanza";
+            }
+        }
+    }
+    else {
+        open(F, $path) || die "no such file $path";
+        my $stanza = "";
+        while(<F>) {
+            chomp;
+            $stanza .= "$_\n";
+        }
+        close(F);
+        if ($stanza =~ /id: (\S+)/) {
+            # check id matches
+            if ($1 ne $id) {
+                die "id mismatch $1 ne $id";
+            }
+        }
+        else {
+            die "no id found in $path";
+        }
+        $new_stanza_map{$id} = $stanza;
+    }
+}
+
+open(W, ">$fn.tmp") || die "cannot write tp $fn.tmp";
+
+my %stanza_map = ();
+my %stanza_type_map = (); # To track stanza type (Term or Typedef)
+$/ = "\n\n";
+open(F, $fn) || die "cannot open $fn";
+while(<F>) {
+    if ($_ =~ /id: (\S+)/) {
+        my $id = $1;
+        $stanza_map{$id} = $_;
+        
+        # Determine stanza type
+        if ($_ =~ /\[(\w+)\]/) {
+            $stanza_type_map{$id} = $1;
+        }
+        else {
+            # Default to Term if type not specified
+            $stanza_type_map{$id} = "Term";
+        }
+    }
+    else {
+        print W $_;
+    }
+}
+close(F);
+
+# combine old and new stanzas
+foreach my $id (sort keys %new_stanza_map) {
+    $stanza_map{$id} = $new_stanza_map{$id};
+    
+    # Update stanza type for new stanzas
+    if ($new_stanza_map{$id} =~ /\[(\w+)\]/) {
+        my $s = $1;
+        $stanza_type_map{$id} = $s;
+    }
+    else {
+        # Default to Term if type not specified
+        $stanza_type_map{$id} = "Term";
+    }
+}
+
+# Sort ids by stanza type (Term first, then Typedef) and then alphabetically within each type
+my @sorted_ids = sort {
+    # First compare stanza types (Term comes before Typedef)
+    my $type_compare = ($stanza_type_map{$a} eq "Typedef") <=> ($stanza_type_map{$b} eq "Typedef");
+    
+    # If same type, sort alphabetically by ID
+    return $type_compare || $a cmp $b;
+} keys %stanza_map;
+
+foreach my $id (@sorted_ids) {
+    my $s = $stanza_map{$id};
+    # normalize line endings to strip trailing whitespace
+    $s =~ s@[\r\n]+$@\n\n@;
+    print W $s;
+}
+close(W);
+
+if ($dry_run) {
+    print "dry run, no changes made\n";
+}
+else {
+    `mv $fn.tmp $fn`;
+    # clear out @ids from $outdir
+    foreach my $id (@ids) {
+        my $path = get_path($id);
+        if (!$preserve_files) {
+            unlink $path;
+        }
+    }
+}
+
+# get the path for an id
+# the ID should be either:
+# - an ontology curie, e.g. GO:0000001, in which case the path is terms/GO_0000001.obo
+# - an OWL local name, e.g. GO_0000001, in which case the path is terms/GO_0000001.obo
+# - a file name, e.g. terms/my_terms.obo, in which case the path is terms/my_terms.obo
+sub get_path {
+    my ($id) = @_;
+    my $fn = "$id";
+    $fn =~ s@:@_@;
+    # if the id has : or / in it and is a path to a file that exists, return it
+    if ($fn =~ m@[\./]@ && -e $fn) {
+        return $fn;
+    }
+    return "$outdir/$fn.obo"
+    
+}
+
+sub w {
+    my ($id, $stanza) = @_;
+    my $path = get_path($id);
+    open(F, ">$path") || die($path);
+    print F $stanza;
+    close(F)
+}
+
+sub scriptname {
+    my @p = split(/\//,$0);
+    pop @p;
+}
+
+
+sub usage {
+    my $sn = scriptname();
+
+    <<EOM;
+$sn  OBO-FILE [ -d TERM-DIR ] TERM1 TERM2 ...
+
+Checks in obo files from TERM-DIR into the OBO-FILE
+
+Example:
+
+$sn src/ontology/foo-edit.obo FOO:0000087 FOO:0000081
+
+This will check in the FOO:0000087 and FOO:0000081 terms from the terms directory
+into the foo-edit.obo file.
+
+EOM
+}
+
--- a/skills/editing-obo-ontologies/obo-checkout.pl
+++ b/skills/editing-obo-ontologies/obo-checkout.pl
@@ -0,0 +1,94 @@
+#!/usr/bin/perl -w
+
+use strict;
+use FileHandle;
+my $outdir = "terms";
+my $cmd;
+while ($ARGV[0] =~ /^\-/) {
+    my $opt = shift @ARGV;
+    if ($opt eq '-h' || $opt eq '--help') {
+        print usage();
+        exit 0;
+    }
+    if ($opt eq '-d' || $opt eq '--outdir') {
+        $outdir = shift @ARGV;
+    }
+}
+`mkdir -p $outdir`;
+my $id;
+my $stanza = "";
+my @alt_ids = ();
+my $fn = shift @ARGV;
+my @ids = @ARGV;
+my %idmap = map {$_ => 1} @ids;
+my $num_ids = scalar(@ids);
+
+my $n = 0;
+print "Reading $fn\n";
+open(F, $fn) || die "no such file $fn";
+while(<F>) {
+    if (m@^\[@) {
+        $n++;
+        if ($id) {
+            # check if id is in %idmap
+            if ($idmap{$id}) {
+                w($id, $stanza);
+            }
+        }
+        $stanza = "";
+        $id = "";
+    }
+    if (m@^id: (\S+)@) {
+        $id = $1;
+    }
+    if (m@^alt_id: (\S+)@) {
+        push(@alt_ids, $1);
+    }
+    $stanza .= $_;
+}
+close(F);
+#print "n: $n\n";
+sub get_path {
+    my ($id) = @_;
+    my $fn = "$id";
+    $fn =~ s@:@_@;
+    return "$outdir/$fn.obo"
+    
+}
+
+sub w {
+    my ($id, $stanza) = @_;
+    my $path = get_path($id);
+    print "Checking out $id to $path\n";
+    open(W, ">$path") || die($path);
+    print W $stanza;
+    close(W)
+}
+
+sub scriptname {
+    my @p = split(/\//,$0);
+    pop @p;
+}
+
+
+sub usage {
+    my $sn = scriptname();
+
+    <<EOM;
+$sn  OBO-FILE [ -d TERM-DIR ] TERM1 TERM2 ...
+
+Checks out obo files into TERM-DIR from the OBO-FILE
+
+Example:
+
+$sn src/ontology/foo-edit.obo FOO:0000087 FOO:0000081
+
+This will extract the FOO:0000087 and FOO:0000081 terms from the foo-edit.obo file
+and write them to the terms directory, as files:
+
+terms/FOO_0000087.obo
+terms/FOO_0000081.obo
+
+EOM
+}
+
--- a/skills/editing-obo-ontologies/obo-grep.pl
+++ b/skills/editing-obo-ontologies/obo-grep.pl
@@ -0,0 +1,113 @@
+#!/usr/bin/perl -w
+
+use strict;
+my %tag_h=();
+my $regexp = '';
+my $noheader;
+my $negate;
+my $count;
+my $idfile;
+while ($ARGV[0] =~ /^\-.+/) {
+    my $opt = shift @ARGV;
+    if ($opt eq '-h' || $opt eq '--help') {
+        print usage();
+        exit 0;
+    }
+    if ($opt eq '-r' || $opt eq '--regexp') {
+        $regexp = shift @ARGV;
+    }
+    if ($opt eq '--regexp-file') {
+        my $f = shift @ARGV;
+        my @or = ();
+        open(F,$f);
+        while(<F>) {
+            chomp;
+            push(@or,$_);
+        }
+        close(F);
+        $regexp = sprintf('id: (%s)\n', join('|',@or));
+    }
+    if ($opt eq '-c' || $opt eq '--count') {
+        $count = 1;
+    }
+    if ($opt eq '--noheader') {
+        $noheader = 1;
+    }
+    if ($opt eq '--idfile') {
+        my $idfile = shift;
+        open(F,$idfile) || die $idfile;
+        my @ids = ();
+        while(<F>) {
+            chomp;
+            s@\s.*@@;
+            push(@ids, $_);
+        }
+        close(F);
+        $regexp = "id: (" .  join("|", @ids) . ")\n";
+    }
+    if ($opt eq '-v' || $opt eq '--neg') {
+        $negate = 1;
+    }
+}
+
+
+$/ = "\n\n";
+
+my $n = 0;
+while (@ARGV) {
+    my $f = pop @ARGV;
+    if ($f eq '-') {
+        *F=*STDIN;
+    }
+    else {
+        open(F,$f) || die "cannot open $f";
+    }
+    my $hdr = 0;
+    while(<F>) {
+        if (!$hdr && $_ !~ /^\[/) {
+            print unless $noheader || $count;
+            $hdr = 1;
+        }
+        else {
+            if ($negate) {
+                if ($_ !~ /$regexp/) {
+                    $n++;
+                    print unless $count;
+                }
+            }
+            else {
+                if (/$regexp/) {
+                    $n++;
+                    print unless $count;
+                }
+            }
+        }
+    }
+}
+if ($count) {
+    print "$n\n";
+}
+
+exit 0;
+
+sub scriptname {
+    my @p = split(/\//,$0);
+    pop @p;
+}
+
+
+sub usage {
+    my $sn = scriptname();
+
+    <<EOM;
+$sn [--noheader] [--neg] [--r REGULAR-EXPRESSION] [--regexp-file FILE] OBO-FILE
+
+filters out stanzas from obo files
+
+Example:
+
+$sn -r 'def:.*transcript' go.obo
+
+EOM
+}
+