Skill 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.…
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.…
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…
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…
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.
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…
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…
Skill 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.
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.
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.
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.
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.
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…
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…
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…
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.
Skill 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…
Skill Claude CodeCodex
Review one provider-generated mechanistic-hypothesis exploration report, including its dataset use, analyses, and artifacts, or reconcile multiple separately assessed reports for one hypothesis. Use when assessing or comparing Biomni, OpenScientist, Kosmos, or another provider's hypothesis report or computational…
Skill Claude CodeCodex
Query the AOP-Wiki XML export — Adverse Outcome Pathways, Key Events, and Key Event Relationships — through the installable aop-wiki-cli module. Use when asked to find the AOP/KE/KER for a mechanism, stressor, or adverse outcome; to run or write an AOP-Wiki term search config; to pull KER weight-of-evidence, empirical…
Skill Claude CodeCodex
Assess how much evidence AOP-Wiki actually carries for a Key Event Relationship before curating from it. Use when judging whether a KER, or a set of them, is backed by literature; when reading completionscore, weightofevidence, empiricalsupport, or oecdstatus off a KER or its parent AOP; when deciding how much…
Skill Claude CodeCodex
Turn a set of AOP-Wiki Key Events into a verified set of dismech causal edges. Use when an issue, pilot mapping, or project page names Key Events (especially Molecular Initiating Events) with no dismech counterpart and you need to find what each one leads to, judge whether the AOP-Wiki record supports the claim, and…
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: