Hyperlink management system

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

Elements	Arguments	Descriptions
id_type,db_type	Refer to the table
entry_id	ex(AB210043)	Input data ID(s) that corresponds to "id_type" is specified（max is 100 IDs）
output	id	Return IDs list.
output	url	Return link URLs list.
format	.txt	Return as text format.
format	.json	Return as json format.
count	count	Return the number of results.
offset,limit	Integer ex(5,10)	Return the range of results. In example, Return the results between 5 to 14.（limit max is 100）.
method	id_type	Return the list of collected data IDs.
	db_type	Return the list of collected databases.
	update	Return the update information of collected databases.
	url	Return the hyperlinks number between collected data IDs and databases.

This web service response is Text or Json format.

The example of text format

API

	http://biodb.jp/convert/acc_id/locusview/AB210043.txt

Response

	##query_id,result_id,state,url
	AB210043,HIX0026954,1,http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0026954

"query_id" is query data ID、"result_id" is converting data IDs、"url" is link URL of query data ID of database.

This example of link URL to "locusview".

"state" is 1 or 0. This value means server state of a collected database.

When updating this system every day, each state of collected databases is checked. "1" means connectable to the databases at that time. Meanwhile, "0" means no connection.

The example of json format

API

	http://biodb.jp/convert/acc_id/locusview/AB210043.json

Response

{
hfs:{
	"query":{
		"id_type":"acc_id",
		"id":"AB210043"
		},
	"result":{
		"id_type":"hix_id",
		"db_type":"locusview",
		"url":["http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0026954"],
		"id":["HIX0026954"],
		"state":"1"
		}
	}
}

"id_type" is a type of data ID, "id" is a data ID, "db_type" is a type of database,

"url" is a link from input query ID to database. "id" and "url" return array in "result".

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

id_type	Type of data ID
acc_id	Accession Number
hit_id	H-Inv transcript ID (HIT)
hix_id	H-Inv cluster ID (HIX)
hip_id	H-Inv protein ID (HIP)
uniprot_id	UniProt Accession Number
gene_symbol	HUGO gene symbol
ref_seq	RefSeq
omim_id	OMIM ID
gene_id	GeneID
pubmed_id	PubMed ID
jsnp_id	dbSNP rs# (GemDBJ)
ms_id	H-GOLD Marker ID
pdb_id	PDB ID
fr_id	fRNAdb ID
enst_id	Ensembl Transcript ID
ensg_id	Ensembl Gene ID
clone_id	Clone ID (NBRC)
flj_id	FLJ ID (NBRC)
kegg_id	KEGG Gene ID
pathway_id	KEGG Pathway ID
hprd_id	HPRD ID

db_type	Database name
transcriptview	H-InvDB Transcript view
locusview	H-InvDB Locus view
gintegra	H-InvDB G-integra
ppi	H-InvDB PPI view
nucleotide	NCBI Sequence Viewer
genbank	GenBank
entrezgene	Entrez Gene
nucleotide	OMIM
pubmed	PubMed
gemdbj	GeMDBJ
hugo	HUGO HGNC
mutationview	MutationView
hgold	H-GOLD
pdbj	PDBj
uniprot	UniProt
ggdb	GGDB
frnadb	fRNAdb
enst	Ensembl Transcript
ensg	Ensembl Gene
nbrc	NBRC
hgpd	HGPD
kegg	KEGG
pathway	KEGG Pathway
hprd	HPRD

Table of sample API

Description	API
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 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";

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(); } }

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 }

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()

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()

About web service

Web service usage

Sample codes