cadec

Name: cadec
Author: QSong-github

132stars4forks

How to install cadec?

qsong-github/drugclaw/cadec

$npx -y skills add QSong-github/DrugClaw --skill cadec

Installs into the current project.

Summary

Query the CADEC (CSIRO Adverse Drug Event Corpus). Use whenever the user asks about adverse drug event mentions in consumer health text, entity annotations from patient forum posts, MedDRA/SNOMED-CT normalised ADR spans, or wants to look up drugs, symptoms, or coded entities in t

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SKILL.md

1	# CADEC Query Skill
2
3	Search CADEC annotated patient forum posts by any entity. Auto-detects type:
4
5	\| Input Pattern \| Detected As \| Match Logic \|
6	\|---\|---\|---\|
7	\| `10019211` (8 digits) \| MedDRA code \| exact on normalizations.code \|
8	\| `22253000` (6-18 digits) \| SNOMED CT code \| exact on normalizations.code \|
9	\| anything else \| free text \| substring on entity text, type, or doc_id \|
10
11	## API
12
13	\| Function \| Input \| Returns \|
14	\|---\|---\|---\|
15	\| `load_cadec(path)` \| JSON path \| list[dict] (cached) \|
16	\| `search(entity)` \| single entity string \| list[dict] \|
17	\| `search_batch(entities)` \| list of entity strings \| dict[str, list[dict]] \|
18	\| `summarize(hits, entity)` \| hits + label \| compact text \|
19	\| `to_json(hits)` \| list[dict] \| same list (JSON-ready) \|
20
21	## Entity Types in Corpus
22
23	\| Type \| Description \|
24	\|---\|---\|
25	\| ADR \| Adverse Drug Reaction \|
26	\| Drug \| Medication mention \|
27	\| Disease \| Pre-existing condition \|
28	\| Symptom \| Patient-reported symptom \|
29	\| Finding \| Clinical finding \|
30
31	## Usage
32
33	See `if __name__ == "__main__"` block in `34_CADEC.py` for runnable examples:
34	drug name search, ADR text search, MedDRA code lookup, batch search, JSON output.
35
36	## Data
37
38	- Source: CADEC v2, CSIRO (AskaPatient.com forum posts)
39	- Local file: `cadec_combined.json` built from BRAT `.txt` + `.ann` files
40	- Annotations: Original spans + MedDRA + SNOMED CT normalisations
41	- Stats: ~1,250 documents, ~7,600 entity annotations
42	- Path: `DATA_PATH` variable in `34_CADEC.py`
43	- Citation: Karimi et al., 2015. J Biomed Inform 55:73–81

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cadec

132stars4forks

View on GitHub

How to install cadec?

qsong-github/drugclaw/cadec

$npx -y skills add QSong-github/DrugClaw --skill cadec

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# CADEC Query Skill
2
3	Search CADEC annotated patient forum posts by any entity. Auto-detects type:
4
5	\| Input Pattern \| Detected As \| Match Logic \|
6	\|---\|---\|---\|
7	\| `10019211` (8 digits) \| MedDRA code \| exact on normalizations.code \|
8	\| `22253000` (6-18 digits) \| SNOMED CT code \| exact on normalizations.code \|
9	\| anything else \| free text \| substring on entity text, type, or doc_id \|
10
11	## API
12
13	\| Function \| Input \| Returns \|
14	\|---\|---\|---\|
15	\| `load_cadec(path)` \| JSON path \| list[dict] (cached) \|
16	\| `search(entity)` \| single entity string \| list[dict] \|
17	\| `search_batch(entities)` \| list of entity strings \| dict[str, list[dict]] \|
18	\| `summarize(hits, entity)` \| hits + label \| compact text \|
19	\| `to_json(hits)` \| list[dict] \| same list (JSON-ready) \|
20
21	## Entity Types in Corpus
22
23	\| Type \| Description \|
24	\|---\|---\|
25	\| ADR \| Adverse Drug Reaction \|
26	\| Drug \| Medication mention \|
27	\| Disease \| Pre-existing condition \|
28	\| Symptom \| Patient-reported symptom \|
29	\| Finding \| Clinical finding \|
30
31	## Usage
32
33	See `if __name__ == "__main__"` block in `34_CADEC.py` for runnable examples:
34	drug name search, ADR text search, MedDRA code lookup, batch search, JSON output.
35
36	## Data
37
38	- Source: CADEC v2, CSIRO (AskaPatient.com forum posts)
39	- Local file: `cadec_combined.json` built from BRAT `.txt` + `.ann` files
40	- Annotations: Original spans + MedDRA + SNOMED CT normalisations
41	- Stats: ~1,250 documents, ~7,600 entity annotations
42	- Path: `DATA_PATH` variable in `34_CADEC.py`
43	- Citation: Karimi et al., 2015. J Biomed Inform 55:73–81

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