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Additional Biomedical Databases

Quick reference for other available databases in the toolkit.

Reactome — Pathway Analysis

What it does: Curated pathways, protein interactions, disease mechanisms.

Key tools:

  • reactome_query_pathways — Find pathways by keyword/gene
  • reactome_get_pathway — Get pathway details
  • reactome_get_disease_pathways — Find disease-specific pathways

Use case: Understanding biological mechanisms:

{
  "name": "reactome_get_disease_pathways",
  "arguments": {
    "disease_name": "myasthenia gravis"
  }
}

Returns: Immune system pathways relevant to MG

Data: Manually curated pathway diagrams, peer-reviewed

UniProt — Protein Database

What it does: Protein sequences, annotations, disease associations, cross-references.

Key tools:

  • uniprot_search_proteins — Search by name, function, disease
  • uniprot_get_protein — Get protein details
  • uniprot_get_disease_associations — Disease links for protein
  • uniprot_map_ids — Convert between database IDs

Use case: Get protein details for a gene:

{
  "name": "uniprot_search_proteins",
  "arguments": {
    "query": "acetylcholine receptor",
    "reviewed": true
  }
}

Returns: Curated Swiss-Prot entries (high quality)

Data: Functional annotations, disease associations, subcellular location, interaction partners

KEGG — Pathways and Systems

What it does: Metabolic pathways, disease pathways, drug-target networks.

Key tools:

  • kegg_list_pathways — Browse available pathways
  • kegg_get_pathway_info — Get pathway diagram info
  • kegg_find_pathways — Search by keyword
  • kegg_get_disease — Disease-specific pathways
  • kegg_get_gene — Gene annotation

Use case: Find metabolic pathways for a drug target:

{
  "name": "kegg_get_pathway_info",
  "arguments": {
    "pathway_id": "hsa04115"
  }
}

Returns: Pathway diagram with all genes/proteins/compounds

Data: Metabolic, signaling, and disease pathway maps

GWAS Catalog — Genetic Associations

What it does: Genome-wide association studies linking variants to traits/diseases.

Key tools:

  • gwas_search_associations — Find variants associated with trait
  • gwas_search_traits — Find traits/diseases
  • gwas_get_variant — Details for specific variant (rsID)
  • gwas_search_studies — Find studies for disease

Use case: Find genetic variants associated with disease:

{
  "name": "gwas_search_associations",
  "arguments": {
    "query": "myasthenia gravis",
    "p_upper": 0.00001
  }
}

Returns: Significant variants (p < 0.00001) with effect sizes

Data: Meta-analysis of 10,000+ studies; population frequency; effect sizes

Pathway Commons — Integrated Pathways

What it does: Aggregated pathway data from Reactome, BioPAX, NCI PID, etc.

Key tools:

  • pathwaycommons_search — Search pathways/proteins
  • pathwaycommons_graph — Get network graph (neighborhood, paths)
  • pathwaycommons_traverse — Query using graph expressions

Use case: Find protein interaction networks:

{
  "name": "pathwaycommons_graph",
  "arguments": {
    "source": "TP53",
    "kind": "neighborhood",
    "limit": 20
  }
}

Returns: Proteins interacting with TP53

Data: Multi-source pathway integration

MyGene.info — Gene Annotations

What it does: Unified gene information across multiple databases.

Key tools:

  • mygene_get_gene — Get gene by symbol/ID
  • mygene_search_genes — Search by gene name/synonym

Use case: Get full gene info (location, aliases, external IDs):

{
  "name": "mygene_get_gene",
  "arguments": {
    "gene_id_or_symbol": "TP53"
  }
}

Returns: Gene location, aliases, Uniprot ID, Mouse/Rat orthologs, etc.

Data: Cross-references to Ensembl, Uniprot, NCBI, OMIM, etc.

MyDisease.info — Disease Annotations

What it does: Unified disease information across multiple sources.

Key tools:

  • mydisease_get_disease — Get disease by MONDO/name
  • mydisease_search_diseases — Search disease database

Use case: Get disease details:

{
  "name": "mydisease_get_disease",
  "arguments": {
    "disease_id": "MONDO_0005179"
  }
}

Returns: Disease synonyms, associations, cross-references

Data: MONDO terminology, linked databases

MyChem.info — Chemical/Drug Info

What it does: Unified chemical and drug information.

Key tools:

  • mychem_get_drug — Get drug by name/ID
  • mychem_search_drugs — Search chemical database

Use case: Find chemical compound details:

{
  "name": "mychem_get_drug",
  "arguments": {
    "drug_id": "aspirin"
  }
}

Returns: Chemical structure, synonyms, pharmacology, external IDs

Data: SMILES, InChI, PubChem, DrugBank integration

Node Normalization API — ID Mapping

What it does: Convert between database identifiers (CURIE normalization).

Key tools:

  • nodenorm_get_normalized_nodes — Map IDs across databases
  • nodenorm_get_curie_prefixes — List supported databases
  • nodenorm_get_semantic_types — Supported entity types

Use case: Convert gene IDs:

{
  "name": "nodenorm_get_normalized_nodes",
  "arguments": {
    "curie": "HGNC:11998",
    "conflation": null
  }
}

Returns: Equivalent IDs in NCBI Gene, Uniprot, Ensembl, etc.

Data: Cross-database identifier mappings

MyVariant.info — Variant Annotations

What it does: Genetic variant effect predictions and annotations.

Key tools:

  • myvariant_get_variant — Get variant details by ID
  • myvariant_search_variants — Search variants by gene, rsID, consequence

Use case: Get variant effect prediction:

{
  "name": "myvariant_search_variants",
  "arguments": {
    "query": "TP53",
    "filter": "consequence:missense"
  }
}

Returns: Variants with SIFT/PolyPhen predictions, clinical significance

Data: dbSNP, ClinVar, gnomAD population frequencies, CADD scores

Combination Strategies

Gene → Protein → Pathways → Drug Targets

  1. mygene_get_gene — Get gene info
  2. uniprot_get_protein — Get protein function
  3. reactome_query_pathways — Find pathways
  4. chembl_find_drugs_by_target — Find drugs

Disease → Targets → Drugs → Trials

  1. opentargets_search — Find disease targets
  2. opentargets_get_associations — Rank by evidence
  3. chembl_find_drugs_by_target — Find drugs
  4. ctg_search_by_intervention — Find trials

Variant → Gene → Disease → Treatments

  1. myvariant_get_variant — Get variant effects
  2. mygene_get_gene — Get gene info
  3. omim_search_genes — Check disease link
  4. chembl_find_drugs_by_target — Treatment options

API Key Requirements

Database Key Required? How to Get
Reactome No Public
UniProt No Public
KEGG No Public
GWAS No Public
Pathway Commons No Public
MyGene.info No Public
MyDisease.info No Public
MyChem.info No Public
Node Normalization No Public
MyVariant.info No Public
OMIM Yes https://omim.org/api
NCI Clinical Trials Optional https://clinicaltrialsapi.cancer.gov
OpenFDA Optional https://open.fda.gov/apis

Choosing Which Database

Goal Use This
Find disease targets OpenTargets, OMIM
Find drugs for disease ChEMBL, clinical trials
Check safety profile OpenFDA, PubMed
Understand mechanism Reactome, KEGG, Pathway Commons
Find genetic variants GWAS, MyVariant, OMIM
Get protein info UniProt, MyGene.info
Review literature PubMed, preprints
Map IDs between databases Node Normalization

Performance Tips

  1. Cache results — 30-day TTL, no need to re-query often
  2. Batch queries — Combine multiple criteria in single call
  3. Combine databases — Use one to find IDs for another
  4. Filter early — Reduce results before detailed queries
  5. Use disease ontology — MONDO IDs are standardized

Troubleshooting

No results?

  • Try alternative terms (gene symbol vs protein name)
  • Check spelling
  • Use disease ontology IDs (MONDO, OMIM numbers)
  • Try related keywords

Too many results?

  • Add filters (phase, recruitment status, etc.)
  • Limit result count
  • Sort by relevance/evidence score
  • Focus on specific domain

ID format issues?

  • Use Node Normalization API to convert IDs
  • Prefix with database (e.g., HGNC:TP53)
  • Check which ID format each database expects