bigbio

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.

Use when the user wants to create or annotate an SDRF file for a proteomics dataset. Triggers on PXD accessions, requests to create SDRF, or annotation tasks.

Use when the user wants to set up SDRF skills dependencies, install parse_sdrf and techsdrf, or configure the environment for the first time.

Onboard, build, or update the ClinGen Gene-Disease Validity resource for hvantk

Onboard, build, or update the ClinVar resource for hvantk

Build a Hail Table from GTEx cis-eQTL summary statistics (per-tissue significant variant-gene pairs) for qtlcascade and variant annotation.

Build a Hail Table from the EBI GWAS Catalog v1.0 full-associations TSV for variant-annotation joins.

Build a Hail Table from the Interactome Insider genomic BED (protein-protein interface residues projected to GRCh38) for interval-based variant annotation.

Build a Hail Table from an MSigDB GMT gene-set file (e.g., C2 Canonical Pathways) for enrichment / burden / overlap analyses.

HGNC gene nomenclature lookup table — authoritative human gene symbols, IDs, and cross-references keyed by hgnc_id.

Build an AnnData object from an EBI Expression Atlas baseline bulk-RNA-seq experiment (TPM expression matrix + SDRF sample metadata).

Reference benchmark datasets for proteomics DEA optimization. Contains ground-truth metadata, expected fold-changes, and best-known method configurations. Used by the evaluator to score candidate workflows against known references.

Domain heuristics for proteomics differential expression analysis. Covers data-type priors (LFQ, TMT, DIA), setting-specific top methods, ensemble strategies, and conditional rules derived from a 34576-experiment benchmark. Used by proposer and reflector to narrow the search space.

LLM prompt templates for proposing proteomics DEA configurations. Provides the system and user prompts used by the proposer to generate candidate analysis pipelines via tool calling.

LLM prompt templates for reflecting on proteomics DEA experiment results. Guides the reflector to analyze score trajectories, identify parameter drivers, declare convergence, and propose targeted perturbations.

LLM prompt templates for generating final analysis reports. Produces a concise Markdown report covering executive summary, recommended configuration rationale, key findings, and caveats.

Create a sample-to-data-relationship format (SDRF) file (usually from another type of samplesheet)

Create a sample-to-data-relationship format (SDRF) file (usually from another type of samplesheet)