obsolete-term

name	obsolete-term
description	Obsolete one or more FBbt terms in the fbbt-edit.obo editors file, following the house obsoletion procedure. Handles both 1:1 replacements (term_replaced_by / IAO:0100001) and non-1:1 suggestions (oboInOwl#consider). Surfaces usages in related terms and component files so the curator can decide what to update.
user-invocable	true
argument-hint	["FBbt_ID ..."]
allowed-tools	Read, Edit, Write, Bash, Grep, Glob, AskUserQuestion

Obsolete FBbt Terms

Obsoletes one or more terms in src/ontology/fbbt-edit.obo, following the procedure documented in src/ontology/README-editors.md ("Obsoleting terms", lines 94-112).

Arguments

One or more FBbt IDs separated by spaces (e.g. FBbt:00110069). If no arguments are given, ask the user which terms to obsolete.

Pre-flight reminder

Before making any edits, remind the user: "FlyBase curators must be notified at least a week before term obsoletions are carried out. Confirm that this has been done (or that it is being done in parallel) before merging." Do not block on this — the user is responsible.

Key paths

All paths relative to the repository root.

• Editors file: src/ontology/fbbt-edit.obo
• Components: src/ontology/components/*.owl
• Neuron symbols source: src/ontology/neuron_symbols.tsv
• DOSDP filler TSVs: src/patterns/data/all-axioms/*.tsv, src/patterns/data/logical-only/*.tsv
• Robot template projects: src/patterns/robot_template_projects/**/*.tsv
• EM synonym mapping files (DO NOT remove from these — they are ID-based mappings to external datasets): src/patterns/robot_template_projects/EM_synonyms/*.tsv
• Historical snapshots (never edit): fbbt/releases/**, fbbt/src/tags/**

Workflow

Process each FBbt ID in order. For each:

Step 1: Validate and gather replacement info

1. Confirm the term exists and is not already obsolete:

   grep -n "^id: FBbt:NNNNNNN" src/ontology/fbbt-edit.obo
   

   Read ~20 lines of the stanza and check for is_obsolete: true. If already obsolete, skip and report.

2. If the user did not already specify replacement info for this ID on the command line or in the conversation, use AskUserQuestion to ask:

   • Is there a 1:1 replacement? (options: Yes — use replaced_by, No — use consider, No replacement at all)
   • Replacement FBbt ID(s) (free-text; comma-separated if multiple consider targets)
   • Reason for obsoletion (free-text; becomes the comment)

   Validate replacement IDs by grepping src/ontology/fbbt-edit.obo and src/ontology/components/*.owl so typos surface before any edit.

Step 2: Rewrite the obsolete term's stanza

Re-read the stanza, then rewrite it to keep ONLY these fields (order matters):

[Term]
id: FBbt:NNNNNNN
name: obsolete <original label>
namespace: fly_anatomy.ontology   # only if present in original
def: "<original def>" [<original def xrefs>]
comment: <existing comment (if any), then the reason for obsoletion appended>
synonym: ... (keep all existing synonyms)
property_value: http://purl.org/dc/terms/contributor <orcid>   # keep
property_value: http://purl.org/dc/terms/date "..." xsd:dateTime   # keep
replaced_by: FBbt:XXXXXXX                        # if 1:1
consider: FBbt:XXXXXXX                           # one line per consider target
is_obsolete: true

In obo format, is_obsolete: true is the shorthand for owl:deprecated "true"^^xsd:boolean — the OBO→OWL conversion adds the owl:deprecated annotation automatically, so an editor viewing the file in Protege sees it as owl:deprecated. Do NOT add a separate property_value line for deprecation.

Remove entirely:

• All is_a: lines
• All relationship: lines
• All intersection_of: lines (and any other equivalent-class components: union_of:, disjoint_from:)
• subset: lines (e.g. subset: cur)
• xref: lines that are not def xrefs (def xrefs live inside the def: square brackets and stay)

Keep:

• def: and its xrefs
• All synonym: lines
• The contributor and date property_value: lines

Comment handling: if the stanza already has a comment: line, append the obsoletion reason to it (e.g. <existing comment text> Obsoleted: <reason>.) rather than overwriting it. A single comment: line is allowed in obo; do not add a second one.

Use the Edit tool with the full original stanza (from [Term] to the blank line after the last property_value:) as old_string and the rewritten stanza as new_string.

Step 3: Find usages in related terms

Search the editors' file and live components for references to the obsolete ID:

grep -n "FBbt:NNNNNNN" src/ontology/fbbt-edit.obo
grep -rn "FBbt_NNNNNNN\|FBbt:NNNNNNN" src/ontology/components/
grep -rn "FBbt:NNNNNNN\|FBbt_NNNNNNN" src/patterns/data/ src/patterns/robot_template_projects/ src/ontology/neuron_symbols.tsv

Classify each hit:

• In the obsolete term's own stanza — expected, ignore.
• In is_a: / relationship: / equivalent_to: lines of other terms in fbbt-edit.obo — these are live logical references that will break. Report each with file:line and the referring term's ID/name.
• In component .owl files — report file and containing term if determinable.
• In DOSDP / robot-template TSVs — report file and row context. Per README step 4, the term must be removed from any TSV used for axiom generation (otherwise it will be re-generated on the next build).
• In src/patterns/robot_template_projects/EM_synonyms/*.tsv — report but DO NOT propose edits: these mappings are ID-based and should persist (same policy as the move-to-edit skill).
• In src/ontology/neuron_symbols.tsv — report; the symbol entry should usually be removed or transferred to the replacement term.

Print a consolidated Usage report for the term.

Step 4: Ask before updating related items

For each actionable usage found in Step 3, use AskUserQuestion to ask whether to update it. Batch related questions into one AskUserQuestion call where possible. Suggested actions:

• is_a: / relationship: referencing the obsolete ID: options are Re-point to replacement (only offered if a 1:1 replacement exists), Remove the axiom, Leave as-is (I'll handle manually).
• TSV rows (DOSDP / robot template): options are Delete row, Re-point FBbt ID to replacement (if 1:1), Leave as-is.
• neuron_symbols.tsv entry: options are Delete row, Move symbol to replacement ID (if 1:1), Leave as-is.
• Component .owl hits: usually the user should handle these manually (they may be auto-regenerated). Report and ask, but default to Leave as-is.

For each approved edit, apply it with Edit. After editing, re-grep to confirm the old ID no longer appears where it should not.

Step 5: Report

Summarise per term:

• ID and original label
• Obsoletion style applied (replaced_by FBbt:X / consider FBbt:X, FBbt:Y / no replacement)
• Comment used
• Files modified (editors' file + any related-term edits)
• Usages left unmodified (for the curator to review)
• Reminder that FlyBase must be notified if not already done, and that component regeneration (sh run.sh make ...) may be needed before commit.

Sanity checks

Before reporting done, run:

grep -n "^id: FBbt:NNNNNNN" src/ontology/fbbt-edit.obo    # still present, once
grep -n "is_obsolete: true" src/ontology/fbbt-edit.obo | grep -c NNNNNNN  # (if possible) confirm

Re-read the rewritten stanza and verify:

• Label starts with obsolete
• No is_a:, relationship:, subset: or non-def xref: lines remain
• is_obsolete: true is present
• replaced_by: XOR consider: lines are present and match the user's choice
• def:, synonym:, comment:, contributor and date property_values are intact

Troubleshooting

• Parent/related term not found when re-pointing — grep the full ID across src/ontology/ and components; if still missing, report and leave as-is.
• Multiple consider targets — emit one consider: line per target, in numerical ID order.
• obo vs owl deprecation — is_obsolete: true in obo format is the canonical way to mark deprecation; only add an explicit owl:deprecated property_value if surrounding precedent in the file does.
• Stanza ordering in the file — do not move the stanza. Obsolete terms stay in their original numerical position in fbbt-edit.obo.