https://github.com/cmdcolin/protein_data_service

https://github.com/cmdcolin/protein_data_service

Last synced: 25 days ago
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• Host: GitHub
• URL: https://github.com/cmdcolin/protein_data_service
• Owner: cmdcolin
• Created: 2019-02-23T23:42:33.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2019-03-01T02:25:25.000Z (over 7 years ago)
• Last Synced: 2025-01-15T08:44:07.355Z (over 1 year ago)
• Language: JavaScript
• Size: 51.9 MB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md

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README

          
# 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"

      }

    }