Scientific Tool Library

SciDEX agents have access to 118 scientific data retrieval tools spanning literature, genomics, proteomics, disease biology, pharmacogenomics, and more. All tools are registered in the skills table and invoked via the @log_tool_call decorator for full provenance tracking.

Tool Categories

Literature & Citations

Tool	Source	Description
PubMed Search	NCBI	Search 36M+ biomedical articles by query
PubMed Abstract	NCBI	Fetch full abstract by PMID
Semantic Scholar	Semantic Scholar	Search with citation graph context
Europe PMC Search	Europe PMC	40M+ articles with MeSH terms, citation counts
Europe PMC Citations	Europe PMC	Get citing articles for a PMID
OpenAlex Works	OpenAlex	250M+ works with bibliometrics, open access status

Gene & Protein Annotation

Tool	Source	Description
Gene Info	MyGene.info	Gene aliases, chromosomal location, Entrez ID
UniProt Protein Info	UniProt REST	Protein function, sequence, disease associations
Ensembl Gene Info	Ensembl REST	Genomic coordinates, cross-refs (OMIM, HGNC, RefSeq)
Human Protein Atlas	HPA	RNA/protein expression by tissue and cell type
AlphaFold Structure	AlphaFold DB	3D structure predictions with confidence scores
InterPro Domains	InterPro	Protein domain/family annotations with GO terms
EBI Protein Variants	EBI Proteins API	Disease-associated protein variants

Disease & Phenotype

Tool	Source	Description
Disease Info	NLP/curated	Disease synonyms, MeSH mapping
DisGeNET Gene-Disease	DisGeNET	Gene-disease associations from curated databases
DisGeNET Disease-Gene	DisGeNET	Disease → gene associations
Open Targets Associations	Open Targets	Evidence-weighted gene-disease links
Monarch Disease-Gene	Monarch Initiative	Cross-database phenotype associations (OMIM, HPO, MGI)
OMIM Gene Phenotypes	NCBI/OMIM	Mendelian disease phenotypes and MIM numbers
ClinVar Variants	ClinVar	Clinical significance of genetic variants
gnomAD Gene Variants	gnomAD v4	Population genetics: pLI, o/e LoF, allele frequencies

Pathways & Networks

Tool	Source	Description
KEGG Pathways	KEGG REST	Gene pathway associations with diagram links
Reactome Pathways	Reactome	Pathway associations via UniProt cross-refs
Enrichr Pathway Analysis	Enrichr	GO/pathway enrichment for gene lists
STRING Protein Interactions	STRING	PPI networks with confidence scores
STRING Enrichment	STRING	Functional enrichment for gene sets
IntAct Molecular Interactions	EBI IntAct	Experimentally validated molecular interactions
Pathway Commons Search	Pathway Commons	Meta-search across Reactome, KEGG, PANTHER, NCI-PID

Gene Expression & Epigenomics

Tool	Source	Description
GTEx Tissue Expression	GTEx Portal	Tissue-specific eQTL and expression data
Allen Brain Expression	Allen Brain Atlas	ISH expression across brain structures
BrainSpan Expression	Allen/BrainSpan	Developmental transcriptome across brain structures
Allen Cell Types	Allen Brain Cell Atlas	Cell-type level expression (SEA-AD dataset)
Human Protein Atlas	HPA	Brain cell type expression in nCPM
CellxGene Gene Expression	CZI CellxGene	Single-cell gene expression across organisms
Expression Atlas Differential	EMBL-EBI	Differential expression experiments across conditions
MethBase Suite (10 tools)	MethBase	Methylation profiling: tissue, disease, age correlation

Drugs & Compounds

Tool	Source	Description
ChEMBL Drug Targets	ChEMBL	Drug-target interactions with activity data
PubChem Compound	PubChem	Molecular formula, weight, SMILES, InChI
DrugBank Drug Info	OpenFDA + PubChem	Brand names, indications, mechanism of action
DGIdb Drug-Gene	DGIdb v5	Drug-gene interactions aggregating 40+ sources
STITCH Chemical Interactions	STITCH	Chemical-protein interactions with confidence scores
PharmGKB Pharmacogenomics	PharmGKB	CPIC tier, VIP gene status, and drug-gene associations for pharmacogenomic decisions

Datasets & Registries

Tool	Source	Description
GEO Dataset Search	NCBI GEO	Search 4M+ gene expression and genomics datasets by query and organism

Clinical Gene-Disease Validity

Tool	Source	Description
ClinGen Gene-Disease Validity	ClinGen	Expert-panel curated validity (Definitive to Refuted) with mode of inheritance

Genetics & Population

Tool	Source	Description
GWAS Genetic Associations	NHGRI-EBI GWAS Catalog	SNP associations with chromosomal positions
Clinical Trials Search	ClinicalTrials.gov	Active/completed trials by query

Model Organisms

Tool	Source	Description
MGI Mouse Models	IMPC	Mouse gene info, alleles, phenotypes with p-values

Cancer & Somatic Mutations

Tool	Source	Description
COSMIC Gene Mutations	COSMIC/Open Targets	Somatic cancer mutations and Cancer Gene Census

Gene Ontology

Tool	Source	Description
QuickGO Gene Ontology	EBI QuickGO	GO annotations: biological process, molecular function, cellular component

Meta Tools

Tool	Description
Research Topic	Orchestrates multiple tools around a gene/topic for comprehensive summaries

Usage

Tools are invoked automatically by debate agents and analysis pipelines. Each call is logged:

Tool name, inputs, outputs (truncated)
Duration, success/failure, error messages
Usage count increments in skills.times_used

View tool usage statistics at /forge.

Adding New Tools

Implement function in tools.py with @log_tool_call decorator
Add entry to TOOL_NAME_MAPPING in tools.py
Add registration entry to TOOLS list in forge_tools.py
Run python3 forge_tools.py to register in skills table

Pathway Diagram

The following diagram shows the key molecular relationships involving Scientific Tool Library discovered through SciDEX knowledge graph analysis:

graph TD
    APOE["APOE"] -->|"co associated with"| Multiple["Multiple"]
    IGFBPL1["IGFBPL1"] -->|"co associated with"| Multiple["Multiple"]
    C1QA["C1QA"] -->|"co associated with"| Multiple["Multiple"]
    Multiple["Multiple"] -->|"co associated with"| Multiple["Multiple"]
    h_6f21f62a["h-6f21f62a"] -->|"targets"| Multiple["Multiple"]
    h_8f9633d9["h-8f9633d9"] -->|"targets"| Multiple["Multiple"]
    style APOE fill:#ce93d8,stroke:#333,color:#000
    style Multiple fill:#ce93d8,stroke:#333,color:#000
    style IGFBPL1 fill:#ce93d8,stroke:#333,color:#000
    style C1QA fill:#ce93d8,stroke:#333,color:#000
    style h_6f21f62a fill:#4fc3f7,stroke:#333,color:#000
    style h_8f9633d9 fill:#4fc3f7,stroke:#333,color:#000

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