literature-taxonomy-curation

Name: literature-taxonomy-curation
Author: KevinSpringer1

30stars0forks

How to install literature-taxonomy-curation?

kevinspringer1/conserved-primer-design/literature-taxonomy-curation

$npx -y skills add KevinSpringer1/conserved-primer-design --skill literature-taxonomy-curation

Installs into the current project.

Summary

Use when an agent must define viral genotype, subtype, clade, lineage, target/background groups, or PhyloGuide groups from cited literature before primer or tNGS panel design.

Files · 1

View on GitHub

SKILL.md

1	# Literature Taxonomy Curation
2
3	Use this skill before `prepare-phylo` or production primer design when group names affect the result. Do not infer genotype/subtype from sequence names alone.
4
5	## Workflow
6
7	1. Identify the exact species/virus, host, region/date scope, and design purpose.
8	2. Search primary taxonomy/genotype papers, ICTV/NCBI/public-health references, and recent surveillance papers.
9	3. Extract group names, representative accessions, distance thresholds or clade criteria, and citations.
10	4. Write a taxonomy JSON with `species`, optional `target_group`, `references`, and `groups`.
11	5. Validate it:
12
13	```bash
14	python agentskill/scripts/curate_references.py validate-taxonomy \
15	--taxonomy-json taxonomy.json \
16	--output taxonomy_report.json
17	```
18
19	Optional PubMed search helper:
20
21	```bash
22	python agentskill/scripts/curate_references.py search-literature \
23	--species "Target virus" \
24	--extra-query "complete genome" \
25	--max-records 20 \
26	--output literature_candidates.json
27	```
28
29	## Required Output
30
31	The downstream agent should receive:
32
33	- `taxonomy.json`: curated groups and references.
34	- `taxonomy_report.json`: validation status, warnings, and errors.
35	- A short rationale explaining why these groups are appropriate for the current species and use case.
36
37	If the species is missing or ambiguous, ask for clarification before assigning groups.

People who liked this also viewed

6 picks

Type

literature-taxonomy-curation

30stars0forks

View on GitHub

How to install literature-taxonomy-curation?

kevinspringer1/conserved-primer-design/literature-taxonomy-curation

$npx -y skills add KevinSpringer1/conserved-primer-design --skill literature-taxonomy-curation

Installs into the current project.

Summary

Use when an agent must define viral genotype, subtype, clade, lineage, target/background groups, or PhyloGuide groups from cited literature before primer or tNGS panel design.

Files · 1

View on GitHub

SKILL.md

1	# Literature Taxonomy Curation
2
3	Use this skill before `prepare-phylo` or production primer design when group names affect the result. Do not infer genotype/subtype from sequence names alone.
4
5	## Workflow
6
7	1. Identify the exact species/virus, host, region/date scope, and design purpose.
8	2. Search primary taxonomy/genotype papers, ICTV/NCBI/public-health references, and recent surveillance papers.
9	3. Extract group names, representative accessions, distance thresholds or clade criteria, and citations.
10	4. Write a taxonomy JSON with `species`, optional `target_group`, `references`, and `groups`.
11	5. Validate it:
12
13	```bash
14	python agentskill/scripts/curate_references.py validate-taxonomy \
15	--taxonomy-json taxonomy.json \
16	--output taxonomy_report.json
17	```
18
19	Optional PubMed search helper:
20
21	```bash
22	python agentskill/scripts/curate_references.py search-literature \
23	--species "Target virus" \
24	--extra-query "complete genome" \
25	--max-records 20 \
26	--output literature_candidates.json
27	```
28
29	## Required Output
30
31	The downstream agent should receive:
32
33	- `taxonomy.json`: curated groups and references.
34	- `taxonomy_report.json`: validation status, warnings, and errors.
35	- A short rationale explaining why these groups are appropriate for the current species and use case.
36
37	If the species is missing or ambiguous, ask for clarification before assigning groups.

People who liked this also viewed

6 picks

Type