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:
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
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
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):
New terms — Table with: Mondo ID, Label, Definition. Source: mondo_release_diff.md "New terms" section.
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").
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.
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.
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.
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.
New obsoletion candidates — Table with: Mondo ID, Label. Source: mondo_release_diff.md "New obsoletion candidates" section.
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.
1---2name: release-announcement3description: Generate a formatted Mondo release announcement with statistics table from release diff reports4---56# Generate Mondo Release Announcement78## Instructions910Generate a formatted release announcement markdown file and statistics table for a Mondo ontology release.1112## Input Documents1314Read these source files to extract all data:15161. **`src/ontology/reports/mondo_release_diff.md`** — The primary release diff report. Contains:17 - Overview section with summary counts18 - New terms table (with Mondo ID, Label, Definition columns)19 - Changed labels table (renamed terms, with old and new labels)20 - Changed definitions table21 - Obsoleted terms section22 - New obsoletion candidates table23 - Terms no longer obsoletion candidates table24252. **`src/ontology/reports/difference_release_base.md`** — The detailed base diff report. Contains:26 - Classes added (for cross-referencing new terms)27 - Text definitions changed28 - Nodes renamed29 - Relationships added/removed30 - Mappings added/removed31323. **`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).3334## Reference Examples3536Look at the GitHub release notes for the `monarch-initiative/mondo` repository as formatting examples. To view the most recent release, use:37```38gh release view --repo monarch-initiative/mondo39```40Always use the most recent release as the formatting template.4142## Task 1: Statistics Table4344Include a **statistics summary table** at the top of the release announcement file (before the detailed sections). The table should be in this format:4546| Statistic | Count |47|:---|---:|48| New terms | N |49| New terms with definitions | N |50| ... | ... |5152### Statistics to compute:5354| Statistic | How to compute |55|:---|:---|56| New terms | Count rows in "New terms" table from `mondo_release_diff.md` |57| New terms with definitions | Count rows in "New terms" table that have a non-empty Definition column |58| Terms renamed (including obsolete renames) | Count ALL rows in "Changed labels"/"Nodes renamed" sections |59| Terms renamed (excluding obsolete renames) | Count rows in "Changed labels" where the new label does NOT start with "obsolete" |60| Text definitions added (new + existing terms) | Count new terms that have definitions PLUS definitions added to existing terms |61| 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) |62| 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." |63| Text definitions removed | Count entries in "Changed definitions" where the old definition is non-empty and the new definition is empty |64| Terms obsoleted without replacement | Count obsoleted terms that have NO `replaced_by` |65| Terms obsoleted with replacement (merged) | Count obsoleted terms that HAVE a `replaced_by` |66| New obsoletion candidates | Count rows in "New obsoletion candidates" table |67| Terms no longer obsoletion candidates | Count rows in "previously candidates... not anymore" table |68| Total obsoletion candidates (current) | Count data rows (excluding header) in `src/ontology/reports/mondo_obsoletioncandidates.tsv` |6970## Task 2: Release Notes Markdown7172Create the detailed sections using the **exact same format** as the most recent GitHub release (with `<details>/<summary>` collapsible sections and markdown tables).7374### Sections to include (in this order):75761. **New terms** — Table with: Mondo ID, Label, Definition. Source: `mondo_release_diff.md` "New terms" section.77782. **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").79803. **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.81824. **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.83845. **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.85866. **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.87887. **New obsoletion candidates** — Table with: Mondo ID, Label. Source: `mondo_release_diff.md` "New obsoletion candidates" section.89908. **Terms that were previously candidates for obsoletion and are now not anymore** — Table with: Mondo ID, Label. Source: `mondo_release_diff.md` corresponding section.9192### Output file9394Save the file as: `src/ontology/reports/release_announcement_YYMMDD.md` where YYMMDD is today's date.9596## Important Notes9798- 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.99- Each `<details>/<summary>` section should include the count in the summary line, e.g., `<summary>New terms: 11</summary>`.100- If a section has zero entries, still include it with an empty table and count of 0.101- Use the same markdown table formatting style as the most recent GitHub release.102- The output file title should be `# Mondo Release Statistics`.
monarch-initiative