Reactome Pathway Analysis from command line

Question

[saamar.rajput]

I have a list of genes or may be a file containing a list of genes. I want to see the pathways from Reactome that are enriched with the gene list i have (not just a list of pathway but the visualization from the Reactome Pathway database), But I want to do this by a command line. Is it possible ?

I have tried

curl -X GET "https://reactome.org/ContentService/data/pathways/low/diagram/identifier/IFNB1/allForms?species=9606" -H  "accept: application/json"

But it gives a list of pathways which contain IFNB1 gene, Plus i can only give a single at a time.

[
  {
    "dbId": 2559580,
    "displayName": "Oxidative Stress Induced Senescence",
    "stId": "R-HSA-2559580",
    "isInDisease": false,
    "isInferred": false,
    "name": [
      "Oxidative Stress Induced Senescence"
    ],
    "releaseDate": "2013-09-18",
    "speciesName": "Homo sapiens",
    "hasDiagram": true,
    "schemaClass": "Pathway",
    "className": "Pathway"
  },
  {
    "dbId": 933541,
    "displayName": "TRAF6 mediated IRF7 activation",
    "stId": "R-HSA-933541",
    "isInDisease": false,
    "isInferred": false,
    "name": [
      "TRAF6 mediated IRF7 activation"
    ],
    "releaseDate": "2010-12-14",
    "speciesName": "Homo sapiens",
    "hasDiagram": false,
    "schemaClass": "Pathway",
    "className": "Pathway"
  },
  {
    "dbId": 983231,
    "displayName": "Factors involved in megakaryocyte development and platelet production",
    "stId": "R-HSA-983231",
    "isInDisease": false,
    "isInferred": false,
    "name": [
      "Factors involved in megakaryocyte development and platelet production"
    ]

I also tried

    curl -H "Content-Type: text/plain" --data-binary @genes.txt -X POST --url https://reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1

Which takes in a file with list of genes and gives a TOKEN number for my query and i use this TOKEN to produce pathway analysis list with a command

     https://reactome.org/PathwayBrowser/#/DTAB=AN&ANALYSIS={TOKEN}

All this is very good but i additionally want to open my list of genes in Reactome pathway database and show my genes in the network. Is it possible?

[WouterDeCoster]

Does this help?

https://github.com/wdecoster/enrichr_cli

Answer 1

[darklings]

Can retrieve data/diagrams using the wrapper for the Reactome Content Service in R: https://bioconductor.org/packages/devel/bioc/html/ReactomeContentService4R.html

Also see the vignette.