IBL/cBio

All you need is

<script src="https://ibl.github.io/cbio/cbio.js"></script>

Live at: https://ibl.github.io/cbio/

---

Experimenting with the possibility of having cBioPortal Web API as a client side JavaScript library. Since the API is not CORS enabled, a Google Script was implemented as a middle layer. The basic idea is to mimic the query syntax with objects constructed as

cbio.\( callbackFunction , { argument_i : value_i , ... } );

Many thanks to MSKCC's cBioPortal team - this is a great public service !

---

get

cbio.get=function(cmd,fun,parms)

All commands below are a type of bio.get, sy submitting command cmd to cbio WebAPI and process it through callback function fun with option parameters parms. For example

cbio.getTypesOfCanceriscbio.get('getTypesOfCancer')

and

cbio.getProteinArrayData({case_set_id:"coadread_tcga_RPPA",array_info:1},function(x){console.log(cbio.table(x))})

is the same as

cbio.get("getProteinArrayData",{case_set_id:"coadread_tcga_RPPA",array_info:1},function(x){console.log(cbio.table(x))})

or

cbio.get("getProteinArrayData",function(x){console.log(cbio.table(x))},{case_set_id:"coadread_tcga_RPPA",array_info:1})

(note the code will check for switch over vars fun and parms)

getTypesOfCancer

cbio.getTypesOfCancer(callbackFunction);

example:

cbio.getTypesOfCancer()

getCancerStudies

cbio.getCancerStudies(callbackFunction);

example:

cbio.getCancerStudies()

getGeneticProfiles

cbio.getGeneticProfiles("cancer study ID (required)",callbackFunction)

example:

cbio.getGeneticProfiles("gbm_tcga")

getCaseLists

cbio.getCaseLists(cancer_study_id)

example:

cbio.getCaseLists("gbm_tcga")

getProfileData

cbio.getProfileData({case_set_id: "case set ID (required)",genetic_profile_id: "one or more genetic profile IDs (required)",gene_list: "one or more HUGO Gene Symbols or Entrez Gene IDs (required)"})

examples:

cbio.getProfileData({case_set_id:"gbm_tcga_all",genetic_profile_id:"gbm_tcga_mutations",gene_list:["BRCA1","BRCA2","TP53"]})cbio.getProfileData({case_set_id:"gbm_tcga_all",genetic_profile_id:["gbm_tcga_log2CNA","gbm_tcga_gistic"],gene_list:"EGFR"})

getMutationData

cbio.getMutationData({genetic_profile_id: "one or more mutation profile IDs (required)",case_set_id: "case set ID (optional)",gene_list: "one or more HUGO Gene Symbols or Entrez Gene IDs (required)"})

examples:

cbio.getMutationData({case_set_id:"gbm_tcga_all",genetic_profile_id:"gbm_tcga_mutations",gene_list:["EGFR","PTEN"]})cbio.getMutationData({genetic_profile_id:["ov_tcga_mutations","ucec_tcga_mutations"],gene_list:"BRCA1"})

getClinicalData

cbio.getClinicalData("case set ID (required)")

example:

cbio.getClinicalData("ov_tcga_all")

getProteinArrayInfo

cbio.getProteinArrayInfo({cancer_study_id: "cancer study ID (required)",protein_array_type:"protein_level or phosphorylation",gene_list:["one or more HUGO Gene Symbols or Entrez Gene IDs"]})

examples:

cbio.getProteinArrayInfo({cancer_study_id:"coadread_tcga"})cbio.getProteinArrayInfo({cancer_study_id:"coadread_tcga",protein_array_type:"phosphorylation"})cbio.getProteinArrayInfo({cancer_study_id:"coadread_tcga",protein_array_type:"protein_level",gene_list:["ERBB2","TP53"]})

getProteinArrayData

cbio.getProteinArrayData({case_set_id: "case set ID (required)",array_info: “[1or0].If1,antibodyinformationwillalsobe exported”
})

examples:

cbio.getProteinArrayData("coadread_tcga_RPPA")cbio.getProteinArrayData({case_set_id:"coadread_tcga_RPPA"})cbio.getProteinArrayData({case_set_id:"coadread_tcga_RPPA",array_info:1})

---

getLinkStudy

cbio.getLinkStudy(parms)

example:

cbio.getLinkStudy({cancer_study_id:"gbm_tcga",gene_list:["EGFR","NF1"]})// returns URLcbio.getLinkStudy({cancer_study_id:"gbm_tcga",gene_list:["EGFR","NF1"]})// opens URL

getLinkCase

cbio.getLinkCase(parms)

examples:

cbio.getLinkCase({case_id:"TCGA-81-5910",cancer_study_id:"gbm_tcga"})// returns URLcbio.getLinkCase({case_id:"TCGA-81-5910",cancer_study_id:"gbm_tcga"},'cbio')// opens URL

oncoprint

...