Gene records, pathway results, variant classifications, association scores, and cross-database links.

Each tool returns structured records with database URLs — gene coordinates, pathway diagrams, variant classifications, or target-disease association scores. These let you take the next step: a strong OpenTargets association score nominates a target worth pursuing, linked protein and structure records feed sequence homology and structure prediction, and a pathogenic ClinVar classification flags a variant for clinical follow-up.

Interpreting genomics outputs

Entrez Search output

Field	Type	Description
`database`	string	Database searched
`query`	string	Search query used
`total_results`	number	Total matching records in the database
`returned_count`	number	Number of records returned (capped by `max_results`)
`hits`	array	Document summaries
`ncbi_url`	string	Link to full NCBI search results

Hit fields (vary by database)

Field	Databases	Description
`uid`	All	NCBI unique identifier
`ncbi_url`	All	Direct link to the record
`title`	All	Record title or description
`organism`	gene, protein, nucleotide	Organism name
`accession`	protein, nucleotide	Accession number
`gene_symbol`	gene	Official gene symbol
`gene_name`	gene	Full gene name
`chromosome`	gene	Chromosome location
`map_location`	gene	Cytogenetic map location
`length`	protein	Sequence length
`pdb_id`	structure	PDB accession code
`method`	structure	Experimental method
`resolution`	structure	Structure resolution

Entrez Link output

Field	Type	Description
`source_db`	string	Source database
`target_db`	string	Target database
`source_ids`	string[]	Input UIDs
`total_linked`	number	Total linked records found
`returned_count`	number	Records returned (capped by `max_results`)
`linked_records`	array	Linked record summaries

Linked record fields

Field	Type	Description
`uid`	string	Target database UID
`title`	string	Record title
`accession`	string	Accession number (if applicable)
`organism`	string	Organism name (if applicable)

Entrez Fetch output

Field	Type	Description
`database`	string	Database fetched from
`ids`	string[]	UIDs retrieved
`format`	string	Format string (e.g., `"fasta/text"`)
`record_count`	number	Number of records
`content`	string	Raw record content (FASTA, GenBank, XML, etc.)
`truncated`	boolean	Whether content was truncated (max 50,000 characters)
`content_length`	number	Original content length

FASTA output example

>NP_000537.3 cellular tumor antigen p53 [Homo sapiens]
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYPQGLNGTVNLPGRNSFEV
...

MeSH Lookup output

Field	Type	Description
`term`	string	Input term
`found`	boolean	Whether an exact match was found
`uid`	string	MeSH descriptor UID
`mesh_term`	string	Official MeSH term
`scope_note`	string	Definition/scope note
`tree_numbers`	string[]	Hierarchical classification codes
`entry_terms`	string[]	Synonyms and related terms (up to 20)
`entry_terms_count`	number	Total number of entry terms
`mesh_url`	string	Link to MeSH Browser

KEGG Pathway Search output

Field	Type	Description
`query`	string	Search query
`operation`	string	Search type performed
`organism`	string	Organism code
`total_found`	number	Number of results
`results`	array	Search results

Result fields

Field	Type	Description
`id`	string	KEGG entry ID (e.g., `path:hsa03440`)
`name`	string	Entry name/description
`url`	string	KEGG entry URL
`diagramUrl`	string	Pathway diagram URL (pathway operation only)

Ensembl Gene Lookup output

Field	Type	Description
`gene`	object	Gene information
`gene.id`	string	Ensembl gene ID
`gene.displayName`	string	Display name (gene symbol)
`gene.description`	string	Gene description
`gene.biotype`	string	Gene biotype (e.g., `protein_coding`)
`gene.chromosome`	string	Chromosome name
`gene.start`	number	Start coordinate (GRCh38)
`gene.end`	number	End coordinate (GRCh38)
`gene.strand`	number	Strand (1 or -1)
`gene.assembly`	string	Assembly name
`gene_length`	number	Gene length in base pairs
`transcript_count`	number	Number of transcript isoforms (if requested)
`transcripts`	array	Transcript details (if `include_transcripts: true`)
`ensembl_url`	string	Link to Ensembl gene page
`ucsc_url`	string	Link to UCSC Genome Browser

Transcript fields

Field	Type	Description
`id`	string	Ensembl transcript ID
`displayName`	string	Transcript name
`biotype`	string	Transcript biotype
`isCanonical`	boolean	Whether this is the canonical transcript
`length`	number	Transcript length in base pairs

ClinVar Search output

Field	Type	Description
`query`	string	Search query
`total_variants`	number	Number of variants returned
`pathogenic_count`	number	Variants classified as pathogenic or likely pathogenic
`vus_count`	number	Variants of uncertain significance
`variants`	array	Variant details

Variant fields

Field	Type	Description
`variationId`	string	ClinVar variation ID
`clinvar_url`	string	Link to ClinVar record
`title`	string	Variant title (typically HGVS expression)
`clinicalSignificance`	string	Classification (pathogenic, likely pathogenic, VUS, etc.)
`reviewStatus`	string	Review confidence level
`gene`	string	Gene symbol
`condition`	string	Associated disease/condition
`rsId`	string	dbSNP rsID (if available)
`dbsnp_url`	string	Link to dbSNP record (if rsID available)

Review status interpretation

Review Status	Stars	Meaning
Practice guideline	4	Professional society guideline
Reviewed by expert panel	3	Expert consensus
Criteria provided, multiple submitters, no conflicts	2	Agreement among labs
Criteria provided, single submitter	1	One lab's interpretation
No assertion criteria provided	0	No evidence description

OpenTargets Associations output

Field	Type	Description
`query`	string	Input query
`query_type`	string	`"target"` or `"disease"`
`resolved_id`	string	Resolved Ensembl or EFO ID
`total_associations`	number	Associations above `min_score`
`avg_score`	number	Average association score
`druggable_count`	number	Associations with known drug evidence
`associations`	array	Association details
`opentargets_url`	string	Link to OpenTargets Platform

Association fields

Field	Type	Description
`targetId`	string	Ensembl gene ID
`targetSymbol`	string	Gene symbol
`diseaseId`	string	EFO disease ID
`diseaseName`	string	Disease name
`overallScore`	number	Combined association score (0-1)
`geneticAssociation`	number	GWAS and rare disease genetics score
`somaticMutation`	number	Cancer somatic mutation score
`knownDrug`	number	Approved/clinical drug evidence score
`literature`	number	Text mining evidence score

Score interpretation

Score Range	Interpretation
0.7 - 1.0	Strong association, well-validated
0.4 - 0.7	Moderate association, emerging evidence
0.1 - 0.4	Weak association, limited evidence
< 0.1	Minimal or no association

Reactome Pathway output

Field	Type	Description
`query`	string	Search query
`species`	string	Species name
`total_pathways`	number	Number of pathways found
`disease_pathways_count`	number	Pathways annotated as disease-related
`pathways`	array	Pathway details

Pathway fields

Field	Type	Description
`stId`	string	Reactome stable identifier
`displayName`	string	Pathway name
`speciesName`	string	Species
`summation`	string	Pathway description
`hasEvent`	boolean	Whether pathway contains events
`isInDisease`	boolean	Disease-related pathway
`diagramUrl`	string	Interactive pathway diagram URL
`imageUrl`	string	Static pathway diagram image (PNG)

Interpreting genomics outputs