---
title: Interpreting genomics outputs
description: >-
  Gene records, pathway results, variant classifications, association scores,
  and cross-database links.
tags:
  - genomics
  - outputs
---

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) |

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