Generate Mondo Release Announcement

Instructions

Generate a formatted release announcement markdown file and statistics table for a Mondo ontology release.

Input Documents

Read these source files to extract all data:

1. src/ontology/reports/mondo_release_diff.md — The primary release diff report. Contains:

   • Overview section with summary counts
   • New terms table (with Mondo ID, Label, Definition columns)
   • Changed labels table (renamed terms, with old and new labels)
   • Changed definitions table
   • Obsoleted terms section
   • New obsoletion candidates table
   • Terms no longer obsoletion candidates table

2. src/ontology/reports/difference_release_base.md — The detailed base diff report. Contains:

   • Classes added (for cross-referencing new terms)
   • Text definitions changed
   • Nodes renamed
   • Relationships added/removed
   • Mappings added/removed

3. src/ontology/reports/mondo_obsoletioncandidates.tsv — Current total obsoletion candidates list (needed for the "total number of obsoletion candidates" statistic; count the rows excluding the header).

Reference Examples

Look at the GitHub release notes for the monarch-initiative/mondo repository as formatting examples. To view the most recent release, use:

gh release view --repo monarch-initiative/mondo

Always use the most recent release as the formatting template.

Task 1: Statistics Table

Include a statistics summary table at the top of the release announcement file (before the detailed sections). The table should be in this format:

Statistic	Count
New terms	N
New terms with definitions	N
...	...

Statistics to compute:

Statistic	How to compute
New terms	Count rows in "New terms" table from mondo_release_diff.md
New terms with definitions	Count rows in "New terms" table that have a non-empty Definition column
Terms renamed (including obsolete renames)	Count ALL rows in "Changed labels"/"Nodes renamed" sections
Terms renamed (excluding obsolete renames)	Count rows in "Changed labels" where the new label does NOT start with "obsolete"
Text definitions added (new + existing terms)	Count new terms that have definitions PLUS definitions added to existing terms
Text definitions added to existing terms only	Count entries in "Changed definitions" where the old definition is empty and the new definition is non-empty (excluding new terms)
Text definitions changed (excluding obsolete)	Count entries in "Changed definitions" where BOTH old and new definitions are non-empty, AND the new definition does NOT start with "OBSOLETE."
Text definitions removed	Count entries in "Changed definitions" where the old definition is non-empty and the new definition is empty
Terms obsoleted without replacement	Count obsoleted terms that have NO replaced_by
Terms obsoleted with replacement (merged)	Count obsoleted terms that HAVE a replaced_by
New obsoletion candidates	Count rows in "New obsoletion candidates" table
Terms no longer obsoletion candidates	Count rows in "previously candidates... not anymore" table
Total obsoletion candidates (current)	Count data rows (excluding header) in src/ontology/reports/mondo_obsoletioncandidates.tsv

Task 2: Release Notes Markdown

Create the detailed sections using the exact same format as the most recent GitHub release (with <details>/<summary> collapsible sections and markdown tables).

Sections to include (in this order):

1. New terms — Table with: Mondo ID, Label, Definition. Source: mondo_release_diff.md "New terms" section.

2. Terms renamed (excluding obsoleted terms) — Table with: ID, Old Label, New Label. Source: mondo_release_diff.md "Changed labels" section. Exclude any terms that were renamed only because they were obsoleted (i.e., exclude renames where the new label starts with "obsolete").

3. Text definitions added to existing terms — Table with: Mondo ID, Label, New Text Definition. These are terms that previously had NO definition and now have one (excluding new terms). Source: cross-reference mondo_release_diff.md "Changed definitions" section — entries where the old definition was empty or the term already existed.

4. Text definitions changed — Table with: Mondo ID, Label, Old Text Definition, New Text Definition. Entries where BOTH old and new definitions are non-empty. Exclude obsoleted terms (where the new definition starts with "OBSOLETE."). Source: mondo_release_diff.md "Changed definitions" section.

5. Terms obsoleted with replacement — Table with: Mondo ID, Label, Replacement. These are terms marked obsolete that have a replaced_by tag (i.e., merges). Source: mondo_release_diff.md "Obsolete terms" section, filtered for those with replacements.

6. Terms obsoleted without replacement — Table with: Mondo ID, Label. Obsoleted terms that only have consider tags or no replacement at all. Source: mondo_release_diff.md "Obsolete terms" section, filtered for those without direct replacements.

7. New obsoletion candidates — Table with: Mondo ID, Label. Source: mondo_release_diff.md "New obsoletion candidates" section.

8. Terms that were previously candidates for obsoletion and are now not anymore — Table with: Mondo ID, Label. Source: mondo_release_diff.md corresponding section.

Output file

Save the file as: src/ontology/reports/release_announcement_YYMMDD.md where YYMMDD is today's date.

Important Notes

• The mondo_release_diff.md file begins with a log block between ---START LOG--- and ---END LOG--- markers. Do NOT include this log in the output.
• Each <details>/<summary> section should include the count in the summary line, e.g., <summary>New terms: 11</summary>.
• If a section has zero entries, still include it with an empty table and count of 0.
• Use the same markdown table formatting style as the most recent GitHub release.
• The output file title should be # Mondo Release Statistics.