القائمة
Use when the user needs to find, verify, or compare ontology terms for SDRF columns. Triggers on questions about ontology terms, accessions, or which term to use.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
Independently falsify and review a created, modified, or proposed SDRF against its specification, ontology terms, source evidence, repository files, and experimental design. Use after SDRF annotation or repair, before contribution or completion, when a review gate reports a pending artifact, or whenever an isolated reviewer must distrust the producer's self-assessment and issue a hash-bound verdict.
Create or improve an SDRF through a producer-reviewer workflow with deterministic validation, an evidence manifest, fresh-context adversarial review, repair, and mandatory re-review. Use when an SDRF must be independently verified before completion or contribution, when the user requests adversarial review, or when automated review hooks require a passing hash-bound receipt.
Use when the user wants SDRF annotation to run as an autonomous retained-improvement loop over one dataset, a manifest, or a dataset class such as all PRIDE cell line or crosslinking datasets.
Use when the user has a completed SDRF annotation for a ProteomeXchange dataset and wants to contribute it back to the community via a PR to sdrf-annotated-datasets.
Use when the user wants a comprehensive quality review of an SDRF file, a PR review of an SDRF submission, or a quality score assessment.
Use before sdrf:autoresearch when the user needs to screen or shortlist proteomics studies from PRIDE, MassIVE, ProteomeXchange accessions, or a manifest using detailed user-defined inclusion/exclusion criteria; extract study-level metadata from repository records and publications; and write an evidence-backed TSV for downstream annotation, review, or meta-analysis.
| name | sdrf:terms |
| description | Use when the user needs to find, verify, or compare ontology terms for SDRF columns. Triggers on questions about ontology terms, accessions, or which term to use. |
| user-invocable | true |
| argument-hint | [column name] [search term] |
You are helping the user find the correct ontology term for an SDRF column.
Read spec/sdrf-proteomics/TERMS.tsv and find the row for the column the user is asking about.
The values field tells you which ontology(ies) to search.
Examples from TERMS.tsv:
organism → values: NCBITaxon → search OLS with ontologyId ncbitaxondisease → values: MONDO, EFO, DOID, PATO → search these ontologiesorganism part → values: UBERON, BTO → search UBERON first, BTO as fallbackcell type → values: CL, BTO → search CL first, BTO as fallbackinstrument → values: MS → search MS ontologymodification parameters → values: UNIMOD → use UNIMOD accessionscleavage agent details → values: MS → search MS ontologyAlways read TERMS.tsv rather than relying on memorized ontology mappings — the spec may add new columns or change ontology sources.
Use the OLS MCP tools to find the term:
Primary search:
mcp OLS → searchClasses(query="<user term>", ontologyId="<ontology>")
If no results or too many:
mcp OLS → search(query="<user term>")
Filter results to the correct ontology manually
For broader semantic search:
mcp OLS → searchClassesWithEmbeddingModel(query="<description>", model="<model>")
(Call listEmbeddingModels first to get available models with can_embed=true)
When presenting results, assess specificity:
To check specificity, use hierarchy navigation:
mcp OLS → getAncestors(ontologyId="<ont>", classIri="<iri>")
mcp OLS → getChildren(ontologyId="<ont>", classIri="<iri>")
When the user has a term from one ontology but needs another:
Example: User has DOID term, needs EFO equivalent
1. Get the DOID term details: mcp OLS → fetch(id="doid+<iri>")
2. Search EFO for the same concept: mcp OLS → searchClasses(query="<label>", ontologyId="efo")
3. Present both options with accessions
For disease terms, SDRF accepts EFO, MONDO, or DOID. Recommend:
For each term found, present:
Term: breast carcinoma
Accession: EFO:0000305
Ontology: Experimental Factor Ontology (EFO)
Definition: A carcinoma that arises in the breast region.
Synonyms: breast cancer, mammary carcinoma
Parent: carcinoma (EFO:0000228)
SDRF format: breast carcinoma
Column: characteristics[disease]
Alternative terms:
- invasive breast carcinoma (EFO:0010132) — more specific, if applicable
- breast ductal carcinoma (EFO:0000298) — subtype-specific
normal with accession PATO:0000461not available — the information exists but wasn't capturednot applicable — the property doesn't apply (e.g., cell line for a tissue sample)allow_not_available and allow_not_applicable for the specific columncharacteristics[cell line] — name from CLO, BTO, or EFO ontologycharacteristics[cellosaurus accession] — format: CVCL_XXXX (e.g., CVCL_0030 for HeLa)characteristics[cellosaurus name] — official Cellosaurus nameAC=MS:1001911;NT=Q Exactive HFNT=<name>;AC=UNIMOD:<id>;TA=<amino acid>;MT=<Fixed|Variable>