dismech

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 availability, and exporting a tab-delimited citation table for downstream phenotype/content gap mining (as was done for Fanconi anemia).

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 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.

Instructions for reviewing a dismech PR, in particular PRs relating to disorder curation, either creating new dismech entries or updating existing ones.

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 for validating and repairing evidence references in the dismech knowledge base. Use this skill when working with evidence items in disorder YAML files, validating that snippet text matches PubMed abstracts, and repairing misquoted or fabricated evidence. Critical for ensuring scientific accuracy and preventing AI hallucinations.

Skill for adding and validating ontology term references in the dismech knowledge base. This skill should be used when working with disorder YAML files that need ontology term annotations (HPO for phenotypes, CL for cell types, GO for biological processes, MONDO for diseases, UBERON for anatomical entities). Use this skill when adding phenotype_term, cell_types term, biological_processes term, or other ontology-bound fields to disorder files.

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. For in-process subagents, use superpowers:dispatching-parallel-agents instead.

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. Covers fusion genes, two-hit hypothesis, oncogene addiction, and precision oncology concepts.

Use when claiming the next high-priority uncurated disease from the dismech priority dashboard. Picks the top-ranked disease in dashboard/priority.json that is not already covered in kb/disorders/, opens a GitHub curation issue, and assigns it to the current GitHub user. Accepts an optional integer 1–8 to claim N diseases at once.

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.

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 dashboards. Replaces the older /pm command with enhanced GitHub integration.

Generate dismech definitions from OHDSI/ATLAS cohort definitions or other computable phenotype logic. Use when converting OMOP cohort JSON, drafting PheKB-style phenotype algorithms, or mapping FHIR/CQL/OMOP rules into dismech `definitions` blocks.

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 for curating microbiome-related pathophysiology in the dismech knowledge base. Use this skill when adding dysbiosis mechanisms, ecological concepts (Anna Karenina, keystone taxa, colonization resistance), SCFA/metabolite pathways, and linking microbial ecology to disease pathophysiology. Covers IBD, C. diff, obesity, and other microbiome-associated conditions.