protein-data-service

Collects some data from different resources about genes/proteins

Install

yarn

Run

node server.js

Usage

http://localhost:2999/?ensemblGeneId=ENSG00000000003&ensemblTranscriptId=ENST00000373020

• ensemblGeneId: required
• ensemblTranscriptId: optional, is a filter, cannot be specified without a gene id

The reason a transcript ID cannot be specified by itself is that the variation biomart only filters on gene ID

Data sources

Accesses protein domains and COSMIC variants from BioMart

The count level information is parsed from CosmicCodingMuts.vcf from release v87, 13th November 2018. It is pre-processed and loaded into sqlite

Currently accessing Ensembl 95 from biomart

Sample

Returns JSON object of format

{
  variants: [],
  domains: [],
  protein: []
}

A sample element of the variant array is

{
  "uniqueId": "COSM1736737",
  "start": 236,
  "end": 237,
  "seq_id": "TSPAN6",
  "score": 1
}

A sample element of the domain array is

{
  "uniqueId": "IPR000301_8_245",
  "start": 8,
  "end": 245,
  "seq_id": "TSPAN6",
  "type": "Tetraspanin"
}

A sample sequence is

{
  "name": "TSPAN6",
  "sequences": {
    "aminoAcid": "MASPSRRLQTKPVITCFKSVLLIYTFIFWITGVILLAVGIWGKVSLENYFSLLNEKATNVPFVLIATGTVIILLGTFGCFATCRASAWMLKLYAMFLTLVFLVELVAAIVGFVFRHEIKNSFKNNYEKALKQYNSTGDYRSHAVDKIQNTLHCCGVTDYRDWTDTNYYSEKGFPKSCCKLEDCTPQRDADKVNNEGCFIKVMTIIESEMGVVAGISFGVACFQLIGIFLAYCLSRAITNNQYEIV",
    "translatedDna": "ATGGCGTCCCCGTCTCGGAGACTGCAGACTAAACCAGTCATTACTTGTTTCAAGAGCGTTCTGCTAATCTACACTTTTATTTTCTGGATCACTGGCGTTATCCTTCTTGCAGTTGGCATTTGGGGCAAGGTGAGCCTGGAGAATTACTTTTCTCTTTTAAATGAGAAGGCCACCAATGTCCCCTTCGTGCTCATTGCTACTGGTACCGTCATTATTCTTTTGGGCACCTTTGGTTGTTTTGCTACCTGCCGAGCTTCTGCATGGATGCTAAAACTGTATGCAATGTTTCTGACTCTCGTTTTTTTGGTCGAACTGGTCGCTGCCATCGTAGGATTTGTTTTCAGACATGAGATTAAGAACAGCTTTAAGAATAATTATGAGAAGGCTTTGAAGCAGTATAACTCTACAGGAGATTATAGAAGCCATGCAGTAGACAAGATCCAAAATACGTTGCATTGTTGTGGTGTCACCGATTATAGAGATTGGACAGATACTAATTATTACTCAGAAAAAGGATTTCCTAAGAGTTGCTGTAAACTTGAAGATTGTACTCCACAGAGAGATGCAGACAAAGTAAACAATGAAGGTTGTTTTATAAAGGTGATGACCATTATAGAGTCAGAAATGGGAGTCGTTGCAGGAATTTCCTTTGGAGTTGCTTGCTTCCAACTGATTGGAATCTTTCTCGCCTACTGCCTCTCTCGTGCCATAACAAATAACCAGTATGAGATAGTG"
  }
}