ols-mcp
01MCP server Claude CodeCodexCursor +2
MCP for retrieving things from the Ontology Lookup Service. Runs locally from the ols-mcp Python package.
56 yesterday A
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original BSD-3-Clause
pubmed
02MCP server Claude CodeCodexCursor +2
Anthropic's hosted PubMed server: lets the agent search biomedical literature and read abstracts and citations from PubMed. Remote server at pubmed.mcp.claude.com.
56 yesterday A
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copy · 100% BSD-3-Clause
create-pr
03Command Claude Code
Create a pull request (PR) from some work.
56 yesterday A 10 tokens
original BSD-3-Clause
curate
04Command Claude Code
Curate a given disorder, either de-novo, or augment an existing one. A list of deep research providers may be specified.
56 yesterday A 27 tokens
original BSD-3-Clause
pm
05Command Claude Code
You should find either a file or a folder.
56 yesterday A 15 tokens
original BSD-3-Clause
PreToolUse
06Hook Claude Code
Runs before the agent uses a tool for Edit, MultiEdit and Write tool calls, executing validate_disorder_hook.py (2 commands). From monarch-initiative/dismech.
56 yesterday A
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original BSD-3-Clause
dismech
07Settings file Claude Code
Agent settings declaring 1 hook event (PreToolUse) and 35 allowed tools.
56 yesterday A
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original BSD-3-Clause
boss
08Skill Claude CodeCodex
Use ONLY when the user explicitly asks to orchestrate parallel external agents (Codex or Claude Code) in tmux sessions via tp (tmux-pilot). Or when a user tells you that you're the boss or orchestrator. You can also use this if you are an operclaw agent. NEVER auto-invoke for a generic "do this in parallel" request.…
56 yesterday A 95 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Skill for curating cancer and neoplastic disease entries in the dismech knowledge base. Use this skill when creating or enhancing cancer entries, adding oncogene/tumor suppressor pathophysiology, curating histopathology findings, adding targeted therapy information, and linking genetic drivers to treatment responses.…
56 yesterday A 83 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Use when claiming the next disease to curate in dismech. Two-phase pick — open claim-labelled issues for what is already taken, then the stubs/ queue for what is left — then files a Curate (MONDO:NNNNNNN) claim issue assigned to the current GitHub user. Accepts an optional integer 1–8 to claim N diseases at once. The…
56 yesterday A 102 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Skill for collecting recent clinical Practice Guideline citations from PubMed for dismech disorder entries. Use this skill when building or refreshing a care-guideline citation set — searching PubMed by disorder for Publication Type "Practice Guideline" within a recent time window, prioritizing disorders by guideline…
56 yesterday A 87 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Generate dismech definitions from OHDSI/ATLAS cohort definitions or other computable phenotype logic. Use when converting OMOP cohort JSON, drafting PheKB-/OHDSI-style phenotype algorithms, or mapping FHIR/CQL/OMOP rules into dismech definitions blocks.
56 yesterday A 68 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Skill for creating a new mechanism module in kb/modules/ (a conserved pathological process that recurs across disorders). Use when the user asks to create/curate a module, add an Xogenesis (pathological-structure-formation) module, or factor a recurrent mechanism out of several disorders. Covers the module schema…
56 yesterday A 102 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Create, edit, review, or audit dismech disease groupings in kb/groupings/.yaml. Use for Grouping records, member unions, groupingbasis and groupingrationale, membershipcriteria boolean logic, criteriasemantics, differentiatingmechanisms, grouping foreign keys, ontology-closure audits, or grouping validation and…
56 yesterday A 91 tokens
original BSD-3-Clause
curate-next
15Skill Claude CodeCodex
Use when asked to curate the next N disease curation issues already assigned to the current GitHub user. Filters open issues to those where the user is the sole assignee and no PR exists yet, picks the first N, then dispatches /curate in parallel for each. Accepts a positional integer N between 1 and 8.
56 yesterday A 73 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Skill for populating the classifications top-level block of a dismech Disease entry. Covers Harrison's Part assignment, mechanistic nosology, lysosomal storage, IUIS immunodeficiency, channelopathy, and ICD-O morphology fields, with a lookup table from common clinical phrasing to controlled-vocabulary keys.
56 yesterday A 70 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Mine Disease Trajectories (DT/DisTraj) outputs for comorbidity/trajectory candidates, including parsing DT JSON/TSV, extracting directed pairs, filtering by sex or significance, and mapping signals into dismech comorbidity YAML.
56 yesterday A 57 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Skill for analyzing and improving compliance in the dismech knowledge base. Use this skill when checking disorder file completeness, identifying missing fields (ontology terms, evidence, descriptions), understanding weighted priority scoring, and systematically improving knowledge base coverage.
56 yesterday A 52 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Instructions for reviewing a dismech PR, in particular PRs relating to disorder curation, either creating new dismech entries or updating existing ones.
56 yesterday A 37 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Add, validate, repair, or review evidence references and exact-quote snippets in dismech KB YAML and deep-research reports. Use for PMID, DOI, NCT, ICTRP, or structured-source evidence; reference-cache generation; snippet failures; title snippets; bracket normalization; deep-research citation validation; Named Entity…
56 yesterday A 88 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Select, add, validate, review, or repair ontology bindings and derived term caches in dismech. Use when changing term IDs, canonical labels, preferredterm values, enum meaning mappings, phenotype, cell-type, biological-process, disease, anatomy, exposure, or treatment annotations; choosing an OAK adapter; resolving…
56 yesterday A 92 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Write the prose of a GitHub PR body, issue comment, review body, or review reply in this repo. Use before posting anything to GitHub — opening a PR, summarizing or triaging an issue, replying to a reviewer, reporting what a scan found, or explaining why you did not make a change. Covers audience calibration, leading…
56 yesterday A 114 tokens
original BSD-3-Clause
Skill Claude CodeCodex
Skill for initiating new disorder YAML files in the dismech knowledge base. Use this skill when the user asks to create a new disorder entry. Also useful for enhancing existing entries.
56 yesterday A 44 tokens
original BSD-3-Clause
projman
24Skill Claude CodeCodex
Project management skill for markdown-based projects with GitHub Project sync. Use when: (1) viewing/managing projects in projects/ folder, (2) syncing project checkboxes to GitHub Projects, (3) picking up next work item from a project, (4) updating project status after completing work, (5) generating project…
56 yesterday A 85 tokens
original BSD-3-Clause