Tark Tools

Configuration File: tark_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the tark_tools.json configuration file.

Available Tools

Tark_get_mane_transcripts (Type: TarkManeTranscriptsTool)

Look up the MANE (Matched Annotation from NCBI and EMBL-EBI) transcript(s) for a gene, mapping th…

Tark_get_mane_transcripts tool specification

Tool Information:

  • Name: Tark_get_mane_transcripts

  • Type: TarkManeTranscriptsTool

  • Description: Look up the MANE (Matched Annotation from NCBI and EMBL-EBI) transcript(s) for a gene, mapping the Ensembl transcript (ENST) to its equivalent RefSeq transcript (NM_). Returns MANE Select and, where defined, MANE Plus Clinical pairings from the Ensembl Tark transcript archive. Query by HGNC gene symbol, an Ensembl transcript id, or a RefSeq transcript id (versions optional — they are matched on the base id). Use to find the clinically-recommended representative transcript for a gene and to convert between RefSeq and Ensembl transcript namespaces. No API key required.

Parameters:

  • gene ([‘string’, ‘null’]) (optional) HGNC gene symbol, e.g. ‘BRCA2’, ‘CFTR’.

  • ensembl_id ([‘string’, ‘null’]) (optional) Ensembl transcript id, e.g. ‘ENST00000380152’ (version optional).

  • refseq_id ([‘string’, ‘null’]) (optional) RefSeq transcript id, e.g. ‘NM_000059’ (version optional).

Example Usage:

query = {
    "name": "Tark_get_mane_transcripts",
    "arguments": {
    }
}
result = tu.run(query)

Tark_get_transcript (Type: TarkTranscriptTool)

Get the archived transcript record for an Ensembl transcript id (ENST) from the Ensembl Tark tran…

Tark_get_transcript tool specification

Tool Information:

  • Name: Tark_get_transcript

  • Type: TarkTranscriptTool

  • Description: Get the archived transcript record for an Ensembl transcript id (ENST) from the Ensembl Tark transcript archive: assembly, biotype, genomic location (region/start/end/strand), the transcript sequence checksum, and the Ensembl release versions in which the transcript appears. Use to resolve transcript versions and verify transcript identity/equivalence across releases. No API key required.

Parameters:

  • stable_id (string) (required) Ensembl transcript stable id, e.g. ‘ENST00000380152’ (version optional).

Example Usage:

query = {
    "name": "Tark_get_transcript",
    "arguments": {
        "stable_id": "example_value"
    }
}
result = tu.run(query)