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.
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 |
...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.
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 |
| 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](/forge).
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` tablePathway Diagram
The following diagram shows the key molecular relationships involving Scientific Tool Library discovered through SciDEX knowledge graph analysis:
Mermaid diagram (expand to render)