Hyperlink management system
ID converter system
[Japanese]

About web service

The web service is provided REST API, to use the function of Hyperlink management system and ID converter system in your programs.

Web service usage

API provides "convert" and "entry" methods. "convert" method provides that does the batch conversion to ID of the form that specifies the input ID list and that extracts the relation with ID of the data base besides ID of a certain database. "entry" method provides collected data IDs, collected databases, update information or the number of link URLs. [ ]element is optional. API samples
		http://biodb.jp/convert/id_type/id_type or db_type/entry_id[,entry_id2,...][format]/
		[output][count][format]/[offset,limit][format]
	

		http://biodb.jp/entry/method[format]/[count][format]
	

  • Elements list
  • ElementsArgumentsDescriptions
    id_type,db_typeRefer to the table 
    entry_idex(AB210043)Input data ID(s) that corresponds to "id_type" is specified(max is 100 IDs)
    outputidReturn IDs list.
    urlReturn link URLs list.
    format.txtReturn as text format.
    .jsonReturn as json format.
    countcountReturn the number of results.
    offset,limitInteger ex(5,10)Return the range of results. In example, Return the results between 5 to 14.(limit max is 100).
    methodid_typeReturn the list of collected data IDs.
    db_typeReturn the list of collected databases.
    updateReturn the update information of collected databases.
    urlReturn the hyperlinks number between collected data IDs and databases.

    This web service response is Text or Json format.
    If you send a query including wrong arguments, this web service returns HTTP code 404.
    If "entry_id" corresponding data is not exist、this web service returns json format ["err":"Not Found"] or text format "Not Found" in Text format.


  • Table of id_type and db_type lists for human
  • id_typeType of data ID
    acc_idAccession Number
    hit_idH-Inv transcript ID (HIT)
    hix_idH-Inv cluster ID (HIX)
    hip_idH-Inv protein ID (HIP)
    uniprot_idUniProt Accession Number
    gene_symbolHUGO gene symbol
    ref_seqRefSeq
    omim_idOMIM ID
    gene_idGeneID
    pubmed_idPubMed ID
    jsnp_iddbSNP rs# (GemDBJ)
    ms_idH-GOLD Marker ID
    pdb_idPDB ID
    fr_idfRNAdb ID
    enst_idEnsembl Transcript ID
    ensg_idEnsembl Gene ID
    clone_idClone ID (NBRC)
    flj_idFLJ ID (NBRC)
    kegg_idKEGG Gene ID
    pathway_idKEGG Pathway ID
    hprd_idHPRD ID
    protein_idRefSeq Protein ID
    cipro_idCIPRO ID
    cco_pdbechem_idPdbeChem ID
    cco_drugbank_idDrugBank ID
    dgv_idDGV ID
    peptide_idPeptide Accession
    ensp_idEnsembl Protein ID
    db_typeDatabase name
    transcriptviewH-InvDB Transcript view
    locusviewH-InvDB Locus view
    gintegraH-InvDB G-integra
    ppiH-InvDB PPI view
    nucleotideNCBI Sequence Viewer
    genbankGenBank
    entrezgeneEntrez Gene
    omimOMIM
    pubmedPubMed
    gemdbjGeMDBJ
    hugoHUGO HGNC
    mutationviewMutationView
    hgoldH-GOLD
    pdbjPDBj
    uniprotUniProt
    ggdbGGDB
    frnadbfRNAdb
    enstEnsembl Transcript
    ensgEnsembl Gene
    nbrcNBRC
    hgpdHGPD
    keggKEGG
    pathwayKEGG Pathway
    hprdHPRD
    legendaLEGENDA
    evolaEVOLA
    hdbasHDBAS
    gcompassGCOMPASS
    proteinviewPROTEINVIEW
    ciproCIPRO
    hangelHANGEL
    fljhFLJH
    varysysdbVARYSYSDB
    pdbechemPDBECHEM
    drugbank_hDRUGBANK_H
    wikipedia_hpWIKIPEDIA_HP
    jsnpJSNP
    proteinPROTEIN
    dgvDGV
    coxpresCOXPRES
    atlasHuman Protein ATLAS
    peptidePeptide Atlas
    enspEnsembl Protein

  • Table of id_type and db_type lists for mouse
  • id_typeType of data ID
    MMU_MGI_IDMGI ID
    MMU_ACC_IDAccession Number
    HIT_IDH-Inv transcript ID (HIT)
    MMU_UNIPROT_IDUniProt Accession Number
    MMU_REF_SEQRefSeq
    MMU_GENE_IDGeneID
    MMU_PUBMED_IDPubMed ID
    MMU_ENST_IDEnsembl Transcript ID
    MMU_ENSG_IDEnsembl Gene ID
    db_typeDatabase name
    transcriptviewH-InvDB Transcript view
    locusviewH-InvDB Locus view
    gintegraH-InvDB G-integra
    ppiH-InvDB PPI view
    nucleotideNCBI Sequence Viewer
    genbankGenBank
    entrezgeneEntrez Gene
    nucleotideOMIM
    pubmedPubMed
    gemdbjGeMDBJ
    hugoHUGO HGNC
    mutationviewMutationView
    hgoldH-GOLD
    pdbjPDBj
    uniprotUniProt
    ggdbGGDB
    frnadbfRNAdb
    enstEnsembl Transcript
    ensgEnsembl Gene
    nbrcNBRC
    hgpdHGPD
    keggKEGG
    pathwayKEGG Pathway
    hprdHPRD

  • Table of sample API
  • DescriptionAPI
    Return link URL information from Accession Number AB210043 to H-InvDB Locusview.(json format)http://biodb.jp/convert/acc_id/locusview/AB210043
    Return IDs list of UniProt Accession Number O43278 and P56555 converting into H-Inv Transcript ID (HIT).(text format)http://biodb.jp/convert/uniprot_id/hit_id/O43278,P56555/id.txt
    Return link URLs information from UniProt Accession Number O43278 and P56555 to H-InvDB Transcript View.(text format)http://biodb.jp/convert/uniprot_id/transcriptview/O43278,P56555/url.txt
    Return first results of link URLs information lists from UniProt Accession Number O43278 and P56555 to H-InvDB Transcript View.(txt format)http://biodb.jp/convert/uniprot_id/transcriptview/O43278,P56555/url/1,1.txt
    Return list of collected databases(txt)http://biodb.jp/entry/db_type.txt
    Return list of collected data IDs(txt)http://biodb.jp/entry/id_type.txt
    Return update information of collected databases(txt)http://biodb.jp/entry/update.txt
    Return link URLs list between collected databases(txt)http://biodb.jp/entry/url.txt

    Sample codes

    Sample codes of perl, java, ruby and python using this API.
    This sample codes return following results

    Response
    {hfs:{"query":{"id_type":"acc_id","id":"AB058780"},"result":{"id_type":"hit_id","id":["HIT000001592"]}}}
    


    perl 5.8.0
    #!/usr/bin/perl
    
    use LWP::UserAgent;
    
    ## set URL 
    my $url = "http://biodb.jp/convert/acc_id/hit_id/AB058780";        
    my $ua = LWP::UserAgent->new();
    my $res = $ua->get($url);
    my $json = $res->content;
    
    ## view
    print "$json\n";
    

    java 1.6.0
    import java.io.BufferedReader;
    import java.io.IOException;
    import java.io.InputStreamReader;
    import java.net.HttpURLConnection;
    import java.net.URL;
    
    public class Sample {
    
    	public static void main(String[] args) throws IOException{	
    		//set URL
    		URL url = new URL("http://biodb.jp/convert/acc_id/locusview/AB210043");
    		HttpURLConnection con = (HttpURLConnection)url.openConnection();
    		con.setRequestMethod("GET");
    		con.connect();
    		
    		BufferedReader reader =
    			new BufferedReader(new InputStreamReader(con.getInputStream()));	
    		//view
    		String line;
    		while ((line = reader.readLine())!= null){
    			System.out.println(line);
    		}	
    		reader.close();
    		con.disconnect();
    	}
    }
    

    ruby 1.6.8
    #!/usr/bin/ruby
    
    require 'net/http'
    
    Net::HTTP.version_1_2
    
    ##set host
    host='biodb.jp'
    
    ##set URL
    path='/convert/acc_id/locusview/AB210043'
    
    Net::HTTP.start(host, 80) {|http|
    response = http.get(path)
    
    ##view
    puts response.body
    }
    

    python 2.2.3
    #!/usr/bin/python
    
    import httplib
    
    ##set host
    host = "biodb.jp"
    
    ##set URL
    path = "/convert/acc_id/locusview/AB210043"
    
    con = httplib.HTTPConnection(host)
    con.request('GET', path, body='')
    response = con.getresponse()
    
    ##view
    print response.read()