| name | claim-disease |
| description | 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. |
claim-disease
Claim the next high-priority uncurated disease(s) from the dismech priority dashboard. Opens GitHub issues and assigns them to whoever is running the skill.
When to use
- "What should I curate next?"
- "Claim the next disease"
- "Pick me the next 3 priority diseases and open issues"
Skip when:
- The user names a specific disease — just open that issue directly, no priority lookup needed.
dashboard/priority.json is missing or stale — regenerate it first with just gen-dashboard.
Inputs
- Optional positional argument N: number of diseases to claim. Defaults to 1, maximum 8.
- Invoked as
/claim-disease (claims 1) or /claim-disease 3 (claims 3). The number, if present, is the only argument and must be a positive integer between 1 and 8 inclusive. The cap exists because filing many issues at once swamps the curation queue and generates more cleanup than throughput.
Workflow
- Read N from the user's argument. If the user passed an integer, use it. If no argument, default to 1.
N is the target number of issues to file and is used in steps 4 and 6. If the argument is non-integer, <= 0, or > 8, stop and ask the user to clarify rather than guess. Never silently cap a request for N > 8 to 8 — the user may be picking diseases for batch handoff and needs to know the limit was hit.
- Verify priority data is fresh. If
dashboard/priority.json is older than 30 days or missing, ask the user whether to regenerate (just gen-dashboard) before continuing. Do not silently use stale data.
- Resolve the current GitHub user:
gh api user -q .login. Use that as the issue assignee.
- Run the candidate finder (Python snippet below) with
LIMIT = N + 50 so there is headroom for candidates that get skipped. The finder reads dashboard/priority.json, builds the set of already-covered MONDO IDs from every YAML in kb/disorders/, and prints the top LIMIT uncovered candidates that have an actionable recommendation (CURATE_ROOT or CURATE_ROOT_WITH_SUBTYPES). Skips LUMP_INTO_PARENT, REVIEW_AGAINST_PARENT, DROP_GROUPING_TERM. Treat the output as an ordered candidate pool.
- Run duplicate preflight for the candidate pool. The
candidate finder covers the local knowledgebase, but each candidate must also
be checked against the most recent upstream knowledgebase plus all PRs and
issues before filing a new issue.
git fetch origin main
git grep -n -i -e "<MONDO_ID>" -e "<label>" origin/main -- kb/disorders || true
gh pr list --repo monarch-initiative/dismech --state all \
--search "\"<MONDO_ID>\" OR \"<label>\"" \
--json number,title,state,url,headRefName --limit 100
gh issue list --repo monarch-initiative/dismech --state all \
--search "\"<MONDO_ID>\" OR \"<label>\"" \
--json number,title,state,url,labels --limit 100
Discard any candidate whose MONDO ID, label, or important synonym appears in
the latest KB, an existing PR, or an existing issue unless the user confirms
it is genuinely distinct.
- Iterate the pool top-down and claim until you have N successful claims (or the pool is exhausted):
- Skip any candidate flagged
possibly_covered_by unless the user has already confirmed it is genuinely uncurated.
- For each remaining candidate, open one issue with the template below. Labels:
curation,enhancement. Assignee: the GitHub user from step 3.
- Stop as soon as you have filed N issues. If the pool runs out before you reach N, report the shortfall and offer to re-run the finder with a larger
LIMIT.
- Report the URLs of every issue filed, plus a short list of candidates that were skipped and why (already in KB / already has PR or issue /
possibly_covered_by / not actionable).
Candidate finder
Run this from the repo root. Pass LIMIT as the first argument — this is not the number of issues to file, it is the size of the candidate pool to draw from. Use LIMIT = N + 50 so there is headroom for candidates that get skipped (already-claimed, possibly_covered_by). The finder filters by MONDO ID, by canonical label, and by synonym list — and additionally surfaces any candidates whose label appears as a substring in an existing entry's label/synonyms (these are flagged as possibly_covered and should be reviewed by hand, not auto-claimed).
LIMIT=${1:-51} python3 - <<'PY'
import json, os, glob, yaml, re
n = int(os.environ.get("LIMIT", "51"))
def norm(s):
return re.sub(r"\s+", " ", s.lower().strip()) if s else ""
covered_ids = set()
covered_labels = set()
covered_label_corpus = []
for path in glob.glob("kb/disorders/*.yaml"):
try:
with open(path) as fh:
d = yaml.safe_load(fh)
except Exception:
continue
if not isinstance(d, dict):
continue
dt = (d.get("disease_term") or {}).get("term") or {}
if dt.get("id"):
covered_ids.add(dt["id"])
for m in (d.get("mappings") or {}).get("mondo_mappings") or []:
tid = ((m or {}).get("term") or {}).get("id")
if tid:
covered_ids.add(tid)
for sub in d.get("has_subtypes") or []:
st = ((sub or {}).get("disease_term") or {}).get("term") or {}
if st.get("id"):
covered_ids.add(st["id"])
# labels & synonyms for fuzzy matching
for s in filter(None, [d.get("name"), dt.get("label"), (d.get("disease_term") or {}).get("preferred_term")]):
covered_labels.add(norm(s))
covered_label_corpus.append((norm(s), path))
for syn in d.get("synonyms") or []:
if isinstance(syn, str):
covered_labels.add(norm(syn))
covered_label_corpus.append((norm(syn), path))
elif isinstance(syn, dict) and syn.get("name"):
covered_labels.add(norm(syn["name"]))
covered_label_corpus.append((norm(syn["name"]), path))
try:
with open("dashboard/priority.json") as fh:
priority = json.load(fh)
except FileNotFoundError:
raise SystemExit(
"dashboard/priority.json not found — run `just gen-dashboard` first"
)
actionable = {"CURATE_ROOT", "CURATE_ROOT_WITH_SUBTYPES"}
picks = []
for row in priority["rows"]:
if row.get("recommended_action") not in actionable:
continue
if row["mondo_id"] in covered_ids:
continue
label_n = norm(row["label"])
if label_n in covered_labels:
continue
possibly = []
if len(label_n.split()) >= 2 and len(label_n) >= 8:
for cn, src in covered_label_corpus:
if len(cn.split()) < 2 or len(cn) < 8:
continue
if label_n in cn or cn in label_n:
possibly.append(src)
pick = {
"mondo_id": row["mondo_id"],
"label": row["label"],
"score": row["score"],
"recommended_action": row["recommended_action"],
}
if possibly:
pick["possibly_covered_by"] = sorted(set(possibly))[:3]
picks.append(pick)
if len(picks) >= n:
break
print(json.dumps(picks, indent=2))
PY
If a candidate has possibly_covered_by, do not auto-claim it — show the user, confirm whether the existing entry already covers it, and skip if so. Only claim candidates with no possibly_covered_by flag without confirmation.
Issue template
Title:
Curate <label> (<MONDO_ID>)
Body:
Curate a dismech entry for **<label>** ([<MONDO_ID>](https://monarchinitiative.org/<MONDO_ID>)) — <one-sentence biomedical context>.
<If recommended_action is CURATE_ROOT_WITH_SUBTYPES, add a paragraph noting that subtypes should be modelled with `has_subtypes`. Mention any obvious subtypes you know of, or note that they should be identified during curation.>
Source: top of [priority dashboard](https://dismech.monarchinitiative.org/dashboard/priority.html) (`<recommended_action>`, score <score>).
Tracker: part of #1079.
Create with:
gh issue create \
--title "Curate <label> (<MONDO_ID>)" \
--assignee "$(gh api user -q .login)" \
--label curation,enhancement \
--body "$(cat <<'EOF'
...body...
EOF
)"
Common mistakes
Tracker
The umbrella issue for priority curation is #1079. Always link new curation issues back to it.
