BridgeDb: Mapping Gene Identifiers
Using BridgeDb with Python
This tutorial explains how to use the BridgeDb identifier mapping service to translate HGNC names to Ensembl identifiers with Python (using a Jupyter Notebook). This step has been created as a part of the OpenRiskNet use case to link Adverse Outcome Pathways to WikiPathways. The original tutorial can be found here. Additionally, this tutorial can be interactively run through the Google Colab found here (you can also click the Google Colab badge at the top of this page).
First we need to load the Python library to allow calls to the BridgeDb REST webservice:
import requests
Let’s assume we’re interested in the gene with HGNC MECP2, the API call to make mappings is given below as callUrl. Here, the H indicates that the query (MECP2) is an HGNC symbol:
callUrl = 'https://bridgedb.cloud.vhp4safety.nl/Human/xrefs/H/MECP2'
The default call returns all identifiers, not just for Ensembl:
response = requests.get(callUrl)
response.text
'4027037\tAffy\n4027036\tAffy\n4027039\tAffy\nNP_001356323\tRefSeq\n4027038\tAffy\nNP_001356322\tRefSeq\nGO:0042551\tGeneOntology\nNP_001356321\tRefSeq\nuc065car.1\tUCSC Genome Browser\nNP_001356320\tRefSeq\n4204\tWikiGenes\nGO:0051707\tGeneOntology\nGO:0043524\tGeneOntology\nHMNXSV003039744\tAgilent\nILMN_1702715\tIllumina\nGO:0045944\tGeneOntology\nuc065caz.1\tUCSC Genome Browser\nA_33_P3339036\tAgilent\nGO:0006576\tGeneOntology\nuc065cbc.1\tUCSC Genome Browser\n4027031\tAffy\n4027030\tAffy\n4027033\tAffy\n4027032\tAffy\n4027035\tAffy\n4027034\tAffy\nGO:0060090\tGeneOntology\n4027048\tAffy\n4027047\tAffy\n4027049\tAffy\nGO:0090063\tGeneOntology\nGO:0002087\tGeneOntology\nGO:0007416\tGeneOntology\nXP_047298078\tRefSeq\nXP_047298073\tRefSeq\nXP_047298071\tRefSeq\nXP_047298072\tRefSeq\nGO:0007420\tGeneOntology\n4027040\tAffy\n4027042\tAffy\nGO:0046470\tGeneOntology\n4027041\tAffy\n4027044\tAffy\n4027043\tAffy\nGO:0010385\tGeneOntology\nILMN_3310740\tIllumina\n4027046\tAffy\n4027045\tAffy\n11722682_at\tAffy\n4027059\tAffy\n4027058\tAffy\nGO:1990841\tGeneOntology\nGO:0003723\tGeneOntology\nGO:0001666\tGeneOntology\nGO:0003729\tGeneOntology\nuc065cas.1\tUCSC Genome Browser\nGO:0001662\tGeneOntology\nNM_001369391\tRefSeq\nNM_001369392\tRefSeq\nNM_001369393\tRefSeq\nNM_001369394\tRefSeq\nuc065cbd.1\tUCSC Genome Browser\n4027051\tAffy\n4027050\tAffy\n4027053\tAffy\n4027052\tAffy\n4027055\tAffy\n4027057\tAffy\nGO:0016358\tGeneOntology\nNM_004992\tRefSeq\nGO:0003714\tGeneOntology\n4027069\tAffy\nuc004fjv.4\tUCSC Genome Browser\nHGNC:6990\tHGNC Accession number\nD3YJ43\tUniprot-TrEMBL\nGO:0043537\tGeneOntology\nGO:0006541\tGeneOntology\nGO:0040029\tGeneOntology\nA_33_P3317211\tAgilent\nNP_001303266\tRefSeq\n11722683_a_at\tAffy\nGO:0051151\tGeneOntology\n4027060\tAffy\nNM_001110792\tRefSeq\n4027062\tAffy\n4027061\tAffy\n4027063\tAffy\n4027065\tAffy\n4027068\tAffy\nA0A0D9SEX1\tUniprot-TrEMBL\nGO:0098794\tGeneOntology\n5BT2\tPDB\nGO:0006020\tGeneOntology\nGO:0140693\tGeneOntology\nGO:0031175\tGeneOntology\nGO:1905643\tGeneOntology\nuc065cbe.1\tUCSC Genome Browser\n6C1Y\tPDB\nGO:0060291\tGeneOntology\n202618_s_at\tAffy\n17115453\tAffy\n4027079\tAffy\n4027078\tAffy\nGO:0048167\tGeneOntology\nuc004fjw.4\tUCSC Genome Browser\nGO:0031507\tGeneOntology\nGO:0008306\tGeneOntology\nGO:0007219\tGeneOntology\nGO:0010629\tGeneOntology\nuc288oyf.1\tUCSC Genome Browser\nGO:0007585\tGeneOntology\n4027080\tAffy\ng972764_3p_a_at\tAffy\n4027082\tAffy\n4027081\tAffy\nGO:0051570\tGeneOntology\n4027084\tAffy\ng7710148_3p_a_at\tAffy\nuc288pkg.1\tUCSC Genome Browser\n4027083\tAffy\n4027086\tAffy\n4027085\tAffy\n4027088\tAffy\nHs.3239.0.S2_3p_a_at\tAffy\n4027087\tAffy\n4027089\tAffy\n6OGJ\tPDB\n6OGK\tPDB\nXM_047442122\tRefSeq\nGO:0005829\tGeneOntology\nuc065cau.1\tUCSC Genome Browser\n202616_PM_s_at\tAffy\nGO:0006357\tGeneOntology\nGO:0010971\tGeneOntology\nGO:0099191\tGeneOntology\nGO:0008542\tGeneOntology\nGO:0060079\tGeneOntology\nuc065cbf.1\tUCSC Genome Browser\n4027091\tAffy\n4027090\tAffy\n4027092\tAffy\nC9JH89\tUniprot-TrEMBL\n4027099\tAffy\nGO:0032048\tGeneOntology\nuc288qen.1\tUCSC Genome Browser\nGO:0005813\tGeneOntology\nXM_047442117\tRefSeq\nP51608\tUniprot-TrEMBL\n1QK9\tPDB\nGO:0006349\tGeneOntology\nGO:0000122\tGeneOntology\nNP_001373068\tRefSeq\nGO:0001964\tGeneOntology\nuc065cav.2\tUCSC Genome Browser\nNP_001373066\tRefSeq\nNP_001373067\tRefSeq\n34355_at\tAffy\nGO:0007268\tGeneOntology\nMECP2\tHGNC\nuc065cbg.2\tUCSC Genome Browser\nA0A6Q8PF93\tUniprot-TrEMBL\nGO:0035176\tGeneOntology\nGO:0060252\tGeneOntology\nTC0X002288.hg\tAffy\nGO:0033555\tGeneOntology\nGO:0045892\tGeneOntology\nA_23_P114361\tAgilent\nGO:0045893\tGeneOntology\nENSG00000169057\tEnsembl\nGO:0005515\tGeneOntology\nGO:0005634\tGeneOntology\nGO:0008104\tGeneOntology\nHMNXSV003006762\tAgilent\n300005\tOMIM\nNP_001104262\tRefSeq\nNP_004983\tRefSeq\nGO:0016525\tGeneOntology\nNM_001316337\tRefSeq\nuc065caw.1\tUCSC Genome Browser\nA0A0D9SFX7\tUniprot-TrEMBL\nA0A140VKC4\tUniprot-TrEMBL\nGO:0019233\tGeneOntology\nGO:0045202\tGeneOntology\nGO:0021591\tGeneOntology\nuc288oef.1\tUCSC Genome Browser\n202618_PM_s_at\tAffy\nGO:0019230\tGeneOntology\nGO:0003682\tGeneOntology\n6YWW\tPDB\nuc065cbh.1\tUCSC Genome Browser\nX99687_at\tAffy\nGO:0008344\tGeneOntology\nGO:0009791\tGeneOntology\nGO:0019904\tGeneOntology\nGO:0030182\tGeneOntology\nGO:0035197\tGeneOntology\n8175998\tAffy\nTC0X001524.hg\tAffy\nuc286dlz.1\tUCSC Genome Browser\n8175977\tAffy\nGO:0005615\tGeneOntology\nGO:0005737\tGeneOntology\n202617_s_at\tAffy\nGO:0050905\tGeneOntology\nGO:0008327\tGeneOntology\nGO:0003677\tGeneOntology\nGO:0003676\tGeneOntology\nGO:0008211\tGeneOntology\n17115428\tAffy\nX89430_at\tAffy\nGO:2000820\tGeneOntology\n4027100\tAffy\nA0A6Q8PHQ3\tUniprot-TrEMBL\nGO:0003700\tGeneOntology\nGO:0047485\tGeneOntology\n4204\tEntrez Gene\n202617_PM_s_at\tAffy\n3C2I\tPDB\nGO:0000792\tGeneOntology\nuc065cax.1\tUCSC Genome Browser\nGO:0008283\tGeneOntology\nGO:0008284\tGeneOntology\nuc065cba.1\tUCSC Genome Browser\nGO:0016573\tGeneOntology\nNM_001386139\tRefSeq\nuc286dmb.1\tUCSC Genome Browser\nA0A1B0GTV0\tUniprot-TrEMBL\nuc065cbi.1\tUCSC Genome Browser\nuc286dly.1\tUCSC Genome Browser\nGO:0007616\tGeneOntology\nGO:0016571\tGeneOntology\nGO:0007613\tGeneOntology\nGO:0007612\tGeneOntology\nGO:0021549\tGeneOntology\n11722684_a_at\tAffy\nX94628_rna1_s_at\tAffy\nGO:0010467\tGeneOntology\nGO:0010468\tGeneOntology\nA_24_P237486\tAgilent\nHMNXSV003048644\tAgilent\nGO:0050884\tGeneOntology\nH7BY72\tUniprot-TrEMBL\n202616_s_at\tAffy\nuc065cay.1\tUCSC Genome Browser\nuc065cbb.1\tUCSC Genome Browser\nGO:0007052\tGeneOntology\nuc286dma.1\tUCSC Genome Browser\nB5MCB4\tUniprot-TrEMBL\nGO:0050432\tGeneOntology\n4027026\tAffy\nuc286dlx.1\tUCSC Genome Browser\n4027025\tAffy\nGO:0001976\tGeneOntology\n4027028\tAffy\n4027027\tAffy\nNM_001386138\tRefSeq\n4027029\tAffy\nNM_001386137\tRefSeq\nILMN_1682091\tIllumina\nGO:0005654\tGeneOntology\nGO:1900114\tGeneOntology\nGO:0014009\tGeneOntology\nILMN_1824898\tIllumina\n4027024\tAffy\n0006510725\tIllumina\n4027023\tAffy\n'
You can also see the results are returned as a TSV file, consisting of two columns, the identifier and the matching database.
We will want to convert this reply into a Python dictionary (with the identifier as key, as one database may have multiple identifiers):
lines = response.text.split("\n")
mappings = {}
for line in lines:
if ('\t' in line):
tuple = line.split('\t')
identifier = tuple[0]
database = tuple[1]
if (database == "Ensembl"):
mappings[identifier] = database
print(mappings)
{'ENSG00000169057': 'Ensembl'}
Alternatively, we can restrivct the return values from the BridgeDb webservice to just return Ensembl identifiers (system code En). For this, we add the ?dataSource=En call parameter:
callUrl = 'https://webservice.bridgedb.org/Human/xrefs/H/MECP2?dataSource=En'
response = requests.get(callUrl)
response.text
'ENSG00000169057\tEnsembl\n'
Using BridgeDb with R
Genes can have different identifiers in different databases. BridgeDb is a tool to map the identifiers from different databases. This tutorial presents how an exemplary HGNC symbol can be translated to its Ensembl identifier with BridgeDb. This work is based on the tutorial to show the use case of linking Adverse Outcome Pathways to WikiPathways which was a part of the OpenRiskNet. The original tutorial using the Python language can be found here. This tutorial follows the original one by replicating it in the R language. To do so, the httr R package is required.
The R script for this tutorial can be found here.
# Please install the httr package if it is not installed yet with the next command.
# install.packages("httr")
# Loading the httr package.
library(httr)
The translation of interest will be made by connecting to the BridgeDb’s REST webservice at https://bridgedb.cloud.vhp4safety.nl/ through R.
Setting Up a Query
In this tutorial, the goal is to find the Ensembl identifier(s) for the gene with the HGNC symbol of MECP2. In order to reach the required information, we need to make a query by setting up an URL in R as below.
# Setting up the query url.
query_url <- "https://bridgedb.cloud.vhp4safety.nl/Human/xrefs/H/MECP2"
In the above command, H indicates a query, whereas MECP2 is the HGNC symbol. The HGNC symbol can be replaced with another symbol of interest depending on the user’s needs (please see BridgeDb’s system codes page to see how other databases are coded).
Making the Query
Next, we will make the query to the webservice through R using the GET function in the httr package.
# Making the query.
res <- GET(query_url)
The Raw Content of the Query
The query above, unfortunately, does not return immediately an output that is easy for human reading. This section presents how to see the raw content of the output; please skip to the next section to see how to convert the output into an R data.frame object that is easier to explore and use.
The content of the response is not displayed in the output object immediately.
# The content of the output.
res
## Response [https://bridgedb.cloud.vhp4safety.nl/Human/xrefs/H/MECP2]
## Date: 2023-05-16 09:55
## Status: 200
## Content-Type: text/plain; charset=UTF-8
## Size: 8.5 kB
BridgeDb returns a content in the plain text format. Therefore, this raw content can be displayed with the content function.
content(res, as="text")
## [1] "{\"affy.probeset:202618_PM_s_at\":\"Affy\",\"affy.probeset:8175977\":\"Affy\",\"go:GO:0008283\":\"GeneOntology\",\"go:GO:0008284\":\"GeneOntology\",\"go:GO:1905643\":\"GeneOntology\",\"go:GO:0003700\":\"GeneOntology\",\"ucsc:uc065cbc.1\":\"UCSC Genome Browser\",\"go:GO:0006541\":\"GeneOntology\",\"go:GO:0000792\":\"GeneOntology\",\"illumina.probe:ILMN_1682091\":\"Illumina\",\"go:GO:0031507\":\"GeneOntology\",\"ucsc:uc288qen.1\":\"UCSC Genome Browser\",\"pdb:6C1Y\":\"PDB\",\"go:GO:0060291\":\"GeneOntology\",\"wikigenes:4204\":\"WikiGenes\",\"go:GO:0016573\":\"GeneOntology\",\"go:GO:0016571\":\"GeneOntology\",\"go:GO:0003714\":\"GeneOntology\",\"agilent.probe:HMNXSV003039744\":\"Agilent\",\"pdb:5BT2\":\"PDB\",\"go:GO:0098794\":\"GeneOntology\",\"ucsc:uc065cay.1\":\"UCSC Genome Browser\",\"affy.probeset:11722684_a_at\":\"Affy\",\"go:GO:0032048\":\"GeneOntology\",\"affy.probeset:4027100\":\"Affy\",\"agilent.probe:A_24_P237486\":\"Agilent\",\"affy.probeset:202616_s_at\":\"Affy\",\"go:GO:0007052\":\"GeneOntology\",\"go:GO:0099191\":\"GeneOntology\",\"refseq:NM_001386137\":\"RefSeq\",\"refseq:NM_001386138\":\"RefSeq\",\"ucsc:uc065cbd.1\":\"UCSC Genome Browser\",\"refseq:NM_001386139\":\"RefSeq\",\"uniprot:H7BY72\":\"Uniprot-TrEMBL\",\"go:GO:0007613\":\"GeneOntology\",\"go:GO:0007612\":\"GeneOntology\",\"affy.probeset:X89430_at\":\"Affy\",\"go:GO:0021591\":\"GeneOntology\",\"go:GO:0007616\":\"GeneOntology\",\"uniprot:C9JH89\":\"Uniprot-TrEMBL\",\"go:GO:0010467\":\"GeneOntology\",\"go:GO:0010468\":\"GeneOntology\",\"affy.probeset:8175998\":\"Affy\",\"affy.probeset:17115428\":\"Affy\",\"hgnc:HGNC:6990\":\"HGNC Accession number\",\"go:GO:0060079\":\"GeneOntology\",\"illumina.probe:0006510725\":\"Illumina\",\"pdb:1QK9\":\"PDB\",\"pdb:6OGJ\":\"PDB\",\"pdb:6OGK\":\"PDB\",\"ucsc:uc065caz.1\":\"UCSC Genome Browser\",\"uniprot:A0A6Q8PF93\":\"Uniprot-TrEMBL\",\"refseq:NM_001369392\":\"RefSeq\",\"refseq:NM_001369391\":\"RefSeq\",\"uniprot:P51608\":\"Uniprot-TrEMBL\",\"refseq:NM_001369394\":\"RefSeq\",\"refseq:NM_001369393\":\"RefSeq\",\"ucsc:uc065car.1\":\"UCSC Genome Browser\",\"go:GO:0043524\":\"GeneOntology\",\"go:GO:0045944\":\"GeneOntology\",\"go:GO:0042551\":\"GeneOntology\",\"ucsc:uc065cbi.1\":\"UCSC Genome Browser\",\"go:GO:0051707\":\"GeneOntology\",\"go:GO:0001964\":\"GeneOntology\",\"ucsc:uc286dlx.1\":\"UCSC Genome Browser\",\"ucsc:uc065cba.1\":\"UCSC Genome Browser\",\"ncbigene:4204\":\"Entrez Gene\",\"ucsc:uc286dma.1\":\"UCSC Genome Browser\",\"go:GO:0005654\":\"GeneOntology\",\"go:GO:0046470\":\"GeneOntology\",\"go:GO:2000820\":\"GeneOntology\",\"go:GO:0051151\":\"GeneOntology\",\"illumina.probe:ILMN_1702715\":\"Illumina\",\"go:GO:0014009\":\"GeneOntology\",\"go:GO:0043537\":\"GeneOntology\",\"refseq:NP_001373068\":\"RefSeq\",\"refseq:NP_001373067\":\"RefSeq\",\"refseq:NP_001373066\":\"RefSeq\",\"go:GO:0001976\":\"GeneOntology\",\"go:GO:0007268\":\"GeneOntology\",\"go:GO:0040029\":\"GeneOntology\",\"ucsc:uc065caw.1\":\"UCSC Genome Browser\",\"illumina.probe:ILMN_3310740\":\"Illumina\",\"affy.probeset:4027023\":\"Affy\",\"affy.probeset:4027024\":\"Affy\",\"affy.probeset:4027025\":\"Affy\",\"affy.probeset:4027026\":\"Affy\",\"affy.probeset:4027027\":\"Affy\",\"affy.probeset:4027028\":\"Affy\",\"go:GO:0009791\":\"GeneOntology\",\"affy.probeset:4027029\":\"Affy\",\"refseq:XM_024452383\":\"RefSeq\",\"agilent.probe:A_33_P3339036\":\"Agilent\",\"affy.probeset:34355_at\":\"Affy\",\"go:GO:0008344\":\"GeneOntology\",\"go:GO:0008104\":\"GeneOntology\",\"ucsc:uc065cbb.1\":\"UCSC Genome Browser\",\"go:GO:0005634\":\"GeneOntology\",\"go:GO:0003682\":\"GeneOntology\",\"affy.probeset:TC0X002288.hg\":\"Affy\",\"go:GO:0005515\":\"GeneOntology\",\"go:GO:0019230\":\"GeneOntology\",\"affy.probeset:4027030\":\"Affy\",\"go:GO:0019233\":\"GeneOntology\",\"affy.probeset:4027031\":\"Affy\",\"affy.probeset:4027032\":\"Affy\",\"go:GO:0016525\":\"GeneOntology\",\"affy.probeset:4027033\":\"Affy\",\"go:GO:0050884\":\"GeneOntology\",\"affy.probeset:4027034\":\"Affy\",\"affy.probeset:4027035\":\"Affy\",\"affy.probeset:4027036\":\"Affy\",\"go:GO:0021549\":\"GeneOntology\",\"affy.probeset:4027037\":\"Affy\",\"uniprot:A0A6Q8PHQ3\":\"Uniprot-TrEMBL\",\"affy.probeset:4027038\":\"Affy\",\"affy.probeset:4027039\":\"Affy\",\"go:GO:0019904\":\"GeneOntology\",\"refseq:XM_011531166\":\"RefSeq\",\"uniprot:A0A1B0GTV0\":\"Uniprot-TrEMBL\",\"go:GO:0090063\":\"GeneOntology\",\"uniprot:D3YJ43\":\"Uniprot-TrEMBL\",\"ensembl:ENSG00000169057\":\"Ensembl\",\"go:GO:0008211\":\"GeneOntology\",\"affy.probeset:TC0X001524.hg\":\"Affy\",\"ucsc:uc065cax.1\":\"UCSC Genome Browser\",\"affy.probeset:4027040\":\"Affy\",\"affy.probeset:4027041\":\"Affy\",\"affy.probeset:4027042\":\"Affy\",\"affy.probeset:4027043\":\"Affy\",\"affy.probeset:4027044\":\"Affy\",\"affy.probeset:4027045\":\"Affy\",\"affy.probeset:4027046\":\"Affy\",\"affy.probeset:4027047\":\"Affy\",\"affy.probeset:4027048\":\"Affy\",\"affy.probeset:4027049\":\"Affy\",\"uniprot:A0A0D9SEX1\":\"Uniprot-TrEMBL\",\"go:GO:0006020\":\"GeneOntology\",\"ucsc:uc065cbg.2\":\"UCSC Genome Browser\",\"ucsc:uc286dlz.1\":\"UCSC Genome Browser\",\"go:GO:1900114\":\"GeneOntology\",\"refseq:XP_011529468\":\"RefSeq\",\"go:GO:0008327\":\"GeneOntology\",\"affy.probeset:g7710148_3p_a_at\":\"Affy\",\"agilent.probe:HMNXSV003006762\":\"Agilent\",\"go:GO:0005615\":\"GeneOntology\",\"go:GO:0005737\":\"GeneOntology\",\"go:GO:0047485\":\"GeneOntology\",\"affy.probeset:4027050\":\"Affy\",\"affy.probeset:4027051\":\"Affy\",\"affy.probeset:4027052\":\"Affy\",\"affy.probeset:4027053\":\"Affy\",\"refseq:NM_001316337\":\"RefSeq\",\"affy.probeset:4027055\":\"Affy\",\"affy.probeset:4027057\":\"Affy\",\"affy.probeset:4027058\":\"Affy\",\"affy.probeset:4027059\":\"Affy\",\"pdb:3C2I\":\"PDB\",\"go:GO:0007585\":\"GeneOntology\",\"go:GO:0003677\":\"GeneOntology\",\"affy.probeset:g972764_3p_a_at\":\"Affy\",\"agilent.probe:A_33_P3317211\":\"Agilent\",\"affy.probeset:4027060\":\"Affy\",\"affy.probeset:4027061\":\"Affy\",\"affy.probeset:4027062\":\"Affy\",\"affy.probeset:4027063\":\"Affy\",\"ucsc:uc065cau.1\":\"UCSC Genome Browser\",\"affy.probeset:4027065\":\"Affy\",\"affy.probeset:4027068\":\"Affy\",\"affy.probeset:4027069\":\"Affy\",\"refseq:NP_001104262\":\"RefSeq\",\"refseq:NM_001110792\":\"RefSeq\",\"affy.probeset:11722682_at\":\"Affy\",\"affy.probeset:202617_PM_s_at\":\"Affy\",\"go:GO:0008542\":\"GeneOntology\",\"ucsc:uc065cbh.1\":\"UCSC Genome Browser\",\"ucsc:uc286dly.1\":\"UCSC Genome Browser\",\"go:GO:0008306\":\"GeneOntology\",\"go:GO:0007219\":\"GeneOntology\",\"go:GO:0010629\":\"GeneOntology\",\"ucsc:uc286dmb.1\":\"UCSC Genome Browser\",\"affy.probeset:4027078\":\"Affy\",\"affy.probeset:4027079\":\"Affy\",\"affy.probeset:202617_s_at\":\"Affy\",\"go:GO:0035176\":\"GeneOntology\",\"go:GO:0045893\":\"GeneOntology\",\"go:GO:0045892\":\"GeneOntology\",\"affy.probeset:X99687_at\":\"Affy\",\"ucsc:uc288oef.1\":\"UCSC Genome Browser\",\"go:GO:0006357\":\"GeneOntology\",\"affy.probeset:4027080\":\"Affy\",\"affy.probeset:4027081\":\"Affy\",\"affy.probeset:4027082\":\"Affy\",\"affy.probeset:4027083\":\"Affy\",\"go:GO:0010971\":\"GeneOntology\",\"affy.probeset:4027084\":\"Affy\",\"ucsc:uc065cav.2\":\"UCSC Genome Browser\",\"affy.probeset:4027085\":\"Affy\",\"go:GO:0005829\":\"GeneOntology\",\"affy.probeset:4027086\":\"Affy\",\"affy.probeset:4027087\":\"Affy\",\"go:GO:0050432\":\"GeneOntology\",\"affy.probeset:4027088\":\"Affy\",\"affy.probeset:4027089\":\"Affy\",\"go:GO:0033555\":\"GeneOntology\",\"refseq:XP_024308151\":\"RefSeq\",\"ucsc:uc065cbe.1\":\"UCSC Genome Browser\",\"ucsc:uc004fjv.4\":\"UCSC Genome Browser\",\"affy.probeset:202616_PM_s_at\":\"Affy\",\"omim:300005\":\"OMIM\",\"go:GO:0006349\":\"GeneOntology\",\"affy.probeset:4027090\":\"Affy\",\"affy.probeset:4027091\":\"Affy\",\"go:GO:0005813\":\"GeneOntology\",\"affy.probeset:4027092\":\"Affy\",\"ucsc:uc288oyf.1\":\"UCSC Genome Browser\",\"agilent.probe:HMNXSV003048644\":\"Agilent\",\"affy.probeset:4027099\":\"Affy\",\"go:GO:0030182\":\"GeneOntology\",\"go:GO:0060252\":\"GeneOntology\",\"go:GO:0035197\":\"GeneOntology\",\"go:GO:0007420\":\"GeneOntology\",\"agilent.probe:A_23_P114361\":\"Agilent\",\"uniprot:B5MCB4\":\"Uniprot-TrEMBL\",\"go:GO:0006576\":\"GeneOntology\",\"go:GO:0000122\":\"GeneOntology\",\"refseq:NP_001303266\":\"RefSeq\",\"ucsc:uc065cas.1\":\"UCSC Genome Browser\",\"go:GO:0003729\":\"GeneOntology\",\"uniprot:A0A140VKC4\":\"Uniprot-TrEMBL\",\"refseq:NM_004992\":\"RefSeq\",\"go:GO:1990841\":\"GeneOntology\",\"go:GO:0003723\":\"GeneOntology\",\"go:GO:0001666\":\"GeneOntology\",\"ucsc:uc065cbf.1\":\"UCSC Genome Browser\",\"go:GO:0045202\":\"GeneOntology\",\"uniprot:A0A0D9SFX7\":\"Uniprot-TrEMBL\",\"ucsc:uc004fjw.4\":\"UCSC Genome Browser\",\"go:GO:0001662\":\"GeneOntology\",\"refseq:NP_001356320\":\"RefSeq\",\"go:GO:0007416\":\"GeneOntology\",\"go:GO:0051570\":\"GeneOntology\",\"affy.probeset:X94628_rna1_s_at\":\"Affy\",\"go:GO:0010385\":\"GeneOntology\",\"affy.probeset:11722683_a_at\":\"Affy\",\"hgnc.symbol:MECP2\":\"HGNC\",\"illumina.probe:ILMN_1824898\":\"Illumina\",\"go:GO:0050905\":\"GeneOntology\",\"refseq:NP_001356321\":\"RefSeq\",\"refseq:NP_001356322\":\"RefSeq\",\"refseq:NP_001356323\":\"RefSeq\",\"ucsc:uc288pkg.1\":\"UCSC Genome Browser\",\"go:GO:0002087\":\"GeneOntology\",\"affy.probeset:202618_s_at\":\"Affy\",\"go:GO:0048167\":\"GeneOntology\",\"refseq:NP_004983\":\"RefSeq\",\"affy.probeset:Hs.3239.0.S2_3p_a_at\":\"Affy\",\"affy.probeset:17115453\":\"Affy\",\"go:GO:0031175\":\"GeneOntology\",\"go:GO:0016358\":\"GeneOntology\"}"
Processing the Raw Content to Get a Data Frame
The raw content of the response can be converted into a data frame by managing the text in the response. The commands below show these steps to process the raw content.
# Assigning the raw content to an object.
dat <- content(res, as="text")
# Splitting the raw output into lines that are separated with a comma.
dat <- as.data.frame(strsplit(dat, ",")[[1]])
# Splitting the two columns in the data set and convert the output into a data.frame.
dat <- unlist(apply(dat, 1, strsplit, '":"'))
# Converting the data into a matrix.
dat <- matrix(dat, ncol=2, byrow=TRUE)
# Cleaning unnecessary characters in the raw output.
dat <- gsub("\\{", "", dat)
dat <- gsub("}", "", dat)
dat <- gsub('\\"', "", dat)
# Converting the output into a data frame and naming its columns.
dat <- as.data.frame(dat)
colnames(dat) <- c("identifier", "database")
dat # The processed data frame
## identifier database
## 1 affy.probeset:202618_PM_s_at Affy
## 2 affy.probeset:8175977 Affy
## 3 go:GO:0008283 GeneOntology
## 4 go:GO:0008284 GeneOntology
## 5 go:GO:1905643 GeneOntology
## 6 go:GO:0003700 GeneOntology
## 7 ucsc:uc065cbc.1 UCSC Genome Browser
## 8 go:GO:0006541 GeneOntology
## 9 go:GO:0000792 GeneOntology
## 10 illumina.probe:ILMN_1682091 Illumina
## 11 go:GO:0031507 GeneOntology
## 12 ucsc:uc288qen.1 UCSC Genome Browser
## 13 pdb:6C1Y PDB
## 14 go:GO:0060291 GeneOntology
## 15 wikigenes:4204 WikiGenes
## 16 go:GO:0016573 GeneOntology
## 17 go:GO:0016571 GeneOntology
## 18 go:GO:0003714 GeneOntology
## 19 agilent.probe:HMNXSV003039744 Agilent
## 20 pdb:5BT2 PDB
## 21 go:GO:0098794 GeneOntology
## 22 ucsc:uc065cay.1 UCSC Genome Browser
## 23 affy.probeset:11722684_a_at Affy
## 24 go:GO:0032048 GeneOntology
## 25 affy.probeset:4027100 Affy
## 26 agilent.probe:A_24_P237486 Agilent
## 27 affy.probeset:202616_s_at Affy
## 28 go:GO:0007052 GeneOntology
## 29 go:GO:0099191 GeneOntology
## 30 refseq:NM_001386137 RefSeq
## 31 refseq:NM_001386138 RefSeq
## 32 ucsc:uc065cbd.1 UCSC Genome Browser
## 33 refseq:NM_001386139 RefSeq
## 34 uniprot:H7BY72 Uniprot-TrEMBL
## 35 go:GO:0007613 GeneOntology
## 36 go:GO:0007612 GeneOntology
## 37 affy.probeset:X89430_at Affy
## 38 go:GO:0021591 GeneOntology
## 39 go:GO:0007616 GeneOntology
## 40 uniprot:C9JH89 Uniprot-TrEMBL
## 41 go:GO:0010467 GeneOntology
## 42 go:GO:0010468 GeneOntology
## 43 affy.probeset:8175998 Affy
## 44 affy.probeset:17115428 Affy
## 45 hgnc:HGNC:6990 HGNC Accession number
## 46 go:GO:0060079 GeneOntology
## 47 illumina.probe:0006510725 Illumina
## 48 pdb:1QK9 PDB
## 49 pdb:6OGJ PDB
## 50 pdb:6OGK PDB
## 51 ucsc:uc065caz.1 UCSC Genome Browser
## 52 uniprot:A0A6Q8PF93 Uniprot-TrEMBL
## 53 refseq:NM_001369392 RefSeq
## 54 refseq:NM_001369391 RefSeq
## 55 uniprot:P51608 Uniprot-TrEMBL
## 56 refseq:NM_001369394 RefSeq
## 57 refseq:NM_001369393 RefSeq
## 58 ucsc:uc065car.1 UCSC Genome Browser
## 59 go:GO:0043524 GeneOntology
## 60 go:GO:0045944 GeneOntology
## 61 go:GO:0042551 GeneOntology
## 62 ucsc:uc065cbi.1 UCSC Genome Browser
## 63 go:GO:0051707 GeneOntology
## 64 go:GO:0001964 GeneOntology
## 65 ucsc:uc286dlx.1 UCSC Genome Browser
## 66 ucsc:uc065cba.1 UCSC Genome Browser
## 67 ncbigene:4204 Entrez Gene
## 68 ucsc:uc286dma.1 UCSC Genome Browser
## 69 go:GO:0005654 GeneOntology
## 70 go:GO:0046470 GeneOntology
## 71 go:GO:2000820 GeneOntology
## 72 go:GO:0051151 GeneOntology
## 73 illumina.probe:ILMN_1702715 Illumina
## 74 go:GO:0014009 GeneOntology
## 75 go:GO:0043537 GeneOntology
## 76 refseq:NP_001373068 RefSeq
## 77 refseq:NP_001373067 RefSeq
## 78 refseq:NP_001373066 RefSeq
## 79 go:GO:0001976 GeneOntology
## 80 go:GO:0007268 GeneOntology
## 81 go:GO:0040029 GeneOntology
## 82 ucsc:uc065caw.1 UCSC Genome Browser
## 83 illumina.probe:ILMN_3310740 Illumina
## 84 affy.probeset:4027023 Affy
## 85 affy.probeset:4027024 Affy
## 86 affy.probeset:4027025 Affy
## 87 affy.probeset:4027026 Affy
## 88 affy.probeset:4027027 Affy
## 89 affy.probeset:4027028 Affy
## 90 go:GO:0009791 GeneOntology
## 91 affy.probeset:4027029 Affy
## 92 refseq:XM_024452383 RefSeq
## 93 agilent.probe:A_33_P3339036 Agilent
## 94 affy.probeset:34355_at Affy
## 95 go:GO:0008344 GeneOntology
## 96 go:GO:0008104 GeneOntology
## 97 ucsc:uc065cbb.1 UCSC Genome Browser
## 98 go:GO:0005634 GeneOntology
## 99 go:GO:0003682 GeneOntology
## 100 affy.probeset:TC0X002288.hg Affy
## 101 go:GO:0005515 GeneOntology
## 102 go:GO:0019230 GeneOntology
## 103 affy.probeset:4027030 Affy
## 104 go:GO:0019233 GeneOntology
## 105 affy.probeset:4027031 Affy
## 106 affy.probeset:4027032 Affy
## 107 go:GO:0016525 GeneOntology
## 108 affy.probeset:4027033 Affy
## 109 go:GO:0050884 GeneOntology
## 110 affy.probeset:4027034 Affy
## 111 affy.probeset:4027035 Affy
## 112 affy.probeset:4027036 Affy
## 113 go:GO:0021549 GeneOntology
## 114 affy.probeset:4027037 Affy
## 115 uniprot:A0A6Q8PHQ3 Uniprot-TrEMBL
## 116 affy.probeset:4027038 Affy
## 117 affy.probeset:4027039 Affy
## 118 go:GO:0019904 GeneOntology
## 119 refseq:XM_011531166 RefSeq
## 120 uniprot:A0A1B0GTV0 Uniprot-TrEMBL
## 121 go:GO:0090063 GeneOntology
## 122 uniprot:D3YJ43 Uniprot-TrEMBL
## 123 ensembl:ENSG00000169057 Ensembl
## 124 go:GO:0008211 GeneOntology
## 125 affy.probeset:TC0X001524.hg Affy
## 126 ucsc:uc065cax.1 UCSC Genome Browser
## 127 affy.probeset:4027040 Affy
## 128 affy.probeset:4027041 Affy
## 129 affy.probeset:4027042 Affy
## 130 affy.probeset:4027043 Affy
## 131 affy.probeset:4027044 Affy
## 132 affy.probeset:4027045 Affy
## 133 affy.probeset:4027046 Affy
## 134 affy.probeset:4027047 Affy
## 135 affy.probeset:4027048 Affy
## 136 affy.probeset:4027049 Affy
## 137 uniprot:A0A0D9SEX1 Uniprot-TrEMBL
## 138 go:GO:0006020 GeneOntology
## 139 ucsc:uc065cbg.2 UCSC Genome Browser
## 140 ucsc:uc286dlz.1 UCSC Genome Browser
## 141 go:GO:1900114 GeneOntology
## 142 refseq:XP_011529468 RefSeq
## 143 go:GO:0008327 GeneOntology
## 144 affy.probeset:g7710148_3p_a_at Affy
## 145 agilent.probe:HMNXSV003006762 Agilent
## 146 go:GO:0005615 GeneOntology
## 147 go:GO:0005737 GeneOntology
## 148 go:GO:0047485 GeneOntology
## 149 affy.probeset:4027050 Affy
## 150 affy.probeset:4027051 Affy
## 151 affy.probeset:4027052 Affy
## 152 affy.probeset:4027053 Affy
## 153 refseq:NM_001316337 RefSeq
## 154 affy.probeset:4027055 Affy
## 155 affy.probeset:4027057 Affy
## 156 affy.probeset:4027058 Affy
## 157 affy.probeset:4027059 Affy
## 158 pdb:3C2I PDB
## 159 go:GO:0007585 GeneOntology
## 160 go:GO:0003677 GeneOntology
## 161 affy.probeset:g972764_3p_a_at Affy
## 162 agilent.probe:A_33_P3317211 Agilent
## 163 affy.probeset:4027060 Affy
## 164 affy.probeset:4027061 Affy
## 165 affy.probeset:4027062 Affy
## 166 affy.probeset:4027063 Affy
## 167 ucsc:uc065cau.1 UCSC Genome Browser
## 168 affy.probeset:4027065 Affy
## 169 affy.probeset:4027068 Affy
## 170 affy.probeset:4027069 Affy
## 171 refseq:NP_001104262 RefSeq
## 172 refseq:NM_001110792 RefSeq
## 173 affy.probeset:11722682_at Affy
## 174 affy.probeset:202617_PM_s_at Affy
## 175 go:GO:0008542 GeneOntology
## 176 ucsc:uc065cbh.1 UCSC Genome Browser
## 177 ucsc:uc286dly.1 UCSC Genome Browser
## 178 go:GO:0008306 GeneOntology
## 179 go:GO:0007219 GeneOntology
## 180 go:GO:0010629 GeneOntology
## 181 ucsc:uc286dmb.1 UCSC Genome Browser
## 182 affy.probeset:4027078 Affy
## 183 affy.probeset:4027079 Affy
## 184 affy.probeset:202617_s_at Affy
## 185 go:GO:0035176 GeneOntology
## 186 go:GO:0045893 GeneOntology
## 187 go:GO:0045892 GeneOntology
## 188 affy.probeset:X99687_at Affy
## 189 ucsc:uc288oef.1 UCSC Genome Browser
## 190 go:GO:0006357 GeneOntology
## 191 affy.probeset:4027080 Affy
## 192 affy.probeset:4027081 Affy
## 193 affy.probeset:4027082 Affy
## 194 affy.probeset:4027083 Affy
## 195 go:GO:0010971 GeneOntology
## 196 affy.probeset:4027084 Affy
## 197 ucsc:uc065cav.2 UCSC Genome Browser
## 198 affy.probeset:4027085 Affy
## 199 go:GO:0005829 GeneOntology
## 200 affy.probeset:4027086 Affy
## 201 affy.probeset:4027087 Affy
## 202 go:GO:0050432 GeneOntology
## 203 affy.probeset:4027088 Affy
## 204 affy.probeset:4027089 Affy
## 205 go:GO:0033555 GeneOntology
## 206 refseq:XP_024308151 RefSeq
## 207 ucsc:uc065cbe.1 UCSC Genome Browser
## 208 ucsc:uc004fjv.4 UCSC Genome Browser
## 209 affy.probeset:202616_PM_s_at Affy
## 210 omim:300005 OMIM
## 211 go:GO:0006349 GeneOntology
## 212 affy.probeset:4027090 Affy
## 213 affy.probeset:4027091 Affy
## 214 go:GO:0005813 GeneOntology
## 215 affy.probeset:4027092 Affy
## 216 ucsc:uc288oyf.1 UCSC Genome Browser
## 217 agilent.probe:HMNXSV003048644 Agilent
## 218 affy.probeset:4027099 Affy
## 219 go:GO:0030182 GeneOntology
## 220 go:GO:0060252 GeneOntology
## 221 go:GO:0035197 GeneOntology
## 222 go:GO:0007420 GeneOntology
## 223 agilent.probe:A_23_P114361 Agilent
## 224 uniprot:B5MCB4 Uniprot-TrEMBL
## 225 go:GO:0006576 GeneOntology
## 226 go:GO:0000122 GeneOntology
## 227 refseq:NP_001303266 RefSeq
## 228 ucsc:uc065cas.1 UCSC Genome Browser
## 229 go:GO:0003729 GeneOntology
## 230 uniprot:A0A140VKC4 Uniprot-TrEMBL
## 231 refseq:NM_004992 RefSeq
## 232 go:GO:1990841 GeneOntology
## 233 go:GO:0003723 GeneOntology
## 234 go:GO:0001666 GeneOntology
## 235 ucsc:uc065cbf.1 UCSC Genome Browser
## 236 go:GO:0045202 GeneOntology
## 237 uniprot:A0A0D9SFX7 Uniprot-TrEMBL
## 238 ucsc:uc004fjw.4 UCSC Genome Browser
## 239 go:GO:0001662 GeneOntology
## 240 refseq:NP_001356320 RefSeq
## 241 go:GO:0007416 GeneOntology
## 242 go:GO:0051570 GeneOntology
## 243 affy.probeset:X94628_rna1_s_at Affy
## 244 go:GO:0010385 GeneOntology
## 245 affy.probeset:11722683_a_at Affy
## 246 hgnc.symbol:MECP2 HGNC
## 247 illumina.probe:ILMN_1824898 Illumina
## 248 go:GO:0050905 GeneOntology
## 249 refseq:NP_001356321 RefSeq
## 250 refseq:NP_001356322 RefSeq
## 251 refseq:NP_001356323 RefSeq
## 252 ucsc:uc288pkg.1 UCSC Genome Browser
## 253 go:GO:0002087 GeneOntology
## 254 affy.probeset:202618_s_at Affy
## 255 go:GO:0048167 GeneOntology
## 256 refseq:NP_004983 RefSeq
## 257 affy.probeset:Hs.3239.0.S2_3p_a_at Affy
## 258 affy.probeset:17115453 Affy
## 259 go:GO:0031175 GeneOntology
## 260 go:GO:0016358 GeneOntology
Finally, the respective Ensemble identifier for the HGNC symbol asked in the beginning of the tutorial can be found by checking the Ensembl database in the output.
dat[which(dat$database == "Ensembl"), ]
## identifier database
## 123 ensembl:ENSG00000169057 Ensembl