GPDB Web Service API Manual

1. What is GPDB Web Service?

In GPDB Web Service, various API that can use the data of GPDB is being offered.

The development of the application using every GPDB Web Service becomes possible because it can access the data of GPDB by using API more easily than the outside.

2. With what service are you providing?

In GPDB Web Service, API of the REST/SOAP method is being offered.

Please refer to the following API manuals for details of each API.

3. How do you use it?

In GPDB Web Service, API of the REST/SOAP method is being offered.

The environment that can use the HTTP connection is needed to use REST-API.

Moreover, a browser and the programming language like Perl and Java, etc. are necessary.

The sample program of sample URL and SOAP-API of REST has been described in API manual, and refer, please.

4. API Manual

searchGpdbId
REST Operation	/search/query+gpdb_id[offset,[limit]][/type]
SOAP Operation	searchGpdbId
Description	The entry list is returned by retrieving GPDB_ID.

SOAP

Operation	searchGpdbId
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	gpdb_id (xs:string), type (xs:string), offset (xs:int), limit (xs:int)
Input Description	gpdb_id: keyword (GPDB_ID) type: list or count offset: offset value limit: limit value
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（XML Format）
Sample Code	searchGpdbId.java searchGpdbId.cgi searchGpdbId.php searchGpdbId.rb

REST

Operation	search
URI Convention	/search/query+gpdb_id[offset,[limit]][/type]
Input	query, type, offset, limit
Input Description	query: keyword (GPDB_ID) type: list or count offset: offset value limit: limit value
Output	xml
Output Description	Detailed list of entry（XML Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/GLP-00005e+gpdb_id/ http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/GLP-00005e+gpdb_id/list http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/GLP-00005e+gpdb_id/count http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/GLP-00005e+gpdb_id/1,5 http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/GLP-00005e+gpdb_id/1 http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/GLP-00005e+gpdb_id/1,5/list http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/GLP-00005e+gpdb_id/1,5/count

searchTaxId
REST Operation	/search/query+tax_id[offset,[limit]][/type]
SOAP Operation	searchTaxId
Description	The entry list is returned by retrieving Tax ID.

SOAP

Operation	searchTaxId
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	tax_id (xs:string), type (xs:string), offset (xs:int), limit (xs:int)
Input Description	tax_id: keyword (TAX_ID) type: list or count offset: offset value limit: limit value
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（XML Format）
Sample Code	searchTaxId.java searchTaxId.cgi searchTaxId.php searchTaxId.rb

REST

Operation	search
URI Convention	/search/query+tax_id[offset,[limit]][/type]
Input	query, type, offset, limit
Input Description	query: keyword (TAX_ID) type: list or count offset: offset value limit: limit value
Output	xml
Output Description	Detailed list of entry（XML Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/6239+tax_id/ http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/6239+tax_id/list http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/6239+tax_id/count http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/6239+tax_id/1,5 http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/6239+tax_id/1 http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/6239+tax_id/1,5/list http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/6239+tax_id/1,5/count

searchOrganism
REST Operation	/search/query+organism[offset,[limit]][/type]
SOAP Operation	searchOrganism
Description	The entry list is returned by retrieving Organism.

SOAP

Operation	searchOrganism
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	organism (xs:string), type (xs:string), offset (xs:int), limit (xs:int)
Input Description	organism: keyword (Organism) type: list or count offset: offset value limit: limit value
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（XML Format）
Sample Code	searchOrganism.java searchOrganism.cgi searchOrganism.php searchOrganism.rb

REST

Operation	search
URI Convention	/search/query+organism [/offset,[limit]][/type]
Input	query, type, offset, limit
Input Description	query: keyword (Organism) type: list or count offset: offset value limit: limit value
Output	xml
Output Description	Detailed list of entry（XML Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/Caenorhabditis+organism/ http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/Caenorhabditis+organism/list http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/Caenorhabditis+organism/count http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/Caenorhabditis+organism/1,5 http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/Caenorhabditis+organism/1 http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/Caenorhabditis+organism/1,5/list http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/Caenorhabditis+organism/1,5/count

searchGlycoprotein
REST Operation	/search/query+glycoprotein[offset,[limit]][/type]
SOAP Operation	searchGlycoprotein
Description	The entry list is returned by retrieving Protein Name.

SOAP

Operation	searchGlycoprotein
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	glycoprotein (xs:string), type (xs:string), offset (xs:int), limit (xs:int)
Input Description	glycoprotein: keyword (ProteinName) type: list or count offset: offset value limit: limit value
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（XML Format）
Sample Code	searchGlycoprotein.java searchGlycoprotein.cgi searchGlycoprotein.php searchGlycoprotein.rb

REST

Operation	search
URI Convention	/search/query+glycoprotein[offset,[limit]][/type]
Input	query, type, offset, limit
Input Description	query: keyword (ProteinName) type: list or count offset: offset value limit: limit value
Output	xml
Output Description	Detailed list of entry（XML Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/rig-4+glycoprotein/ http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/rig-4+glycoprotein/list http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/rig-4+glycoprotein/count http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/rig-4+glycoprotein/1,5 http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/rig-4+glycoprotein/1 http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/rig-4+glycoprotein/1,5/list http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/rig-4+glycoprotein/1,5/count

searchDbXref
REST Operation	/search/query+db_xref[offset,[limit]][/type]
SOAP Operation	searchDbXref
Description	The entry list is returned by retrieving ID of each DBs.

SOAP

Operation	searchDbXref
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	ID (xs:string), type (xs:string), offset (xs:int), limit (xs:int)
Input Description	PMID: keyword (ID) type: list or count offset: offset value limit: limit value
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（XML Format）
Sample Code	searchDbXref.java searchDbXref.cgi searchDbXref.php searchDbXref.rb

REST

Operation	search
URI Convention	/search/query+db_xref[offset,[limit]][/type]
Input	query, type, offset, limit
Input Description	query: keyword (ID) type: list or count offset: offset value limit: limit value
Output	xml
Output Description	Detailed list of entry（XML Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/UNP-00001c+db_xref/ http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/UNP-00001c+db_xref/list http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/UNP-00001c+db_xref/count http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/UNP-00001c+db_xref/1,5 http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/UNP-00001c+db_xref/1 http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/UNP-00001c+db_xref/1,5/list http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/search/UNP-00001c+db_xref/1,5/count

getXmlEntry
REST Operation	/entry/gpdb_id[.xml]
SOAP Operation	getXmlEntry
Description	Detailed information on the GPDB entry is returned by the XML form.

SOAP

Operation	getXmlEntry
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	gpdb_id (xs:string)
Input Description	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260,…)
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（XML Format）
Sample Code	getXmlEntry.java getXmlEntry.cgi getXmlEntry.php getXmlEntry.rb

REST

Operation	entry
URI Convention	entry/gpdb_id[.xml]
Input	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260,…)
Input Description	gpdb_id
Output	xml
Output Description	Detailed list of entry （XML Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/entry/GLP-00005e http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/entry/GLP-00005e.xml

getTextEntry
REST Operation	/entry/gpdb_id.txt
SOAP Operation	getTextEntry
Description	Detailed information on the GPDB entry is returned by the Text form.

SOAP

Operation	getTextEntry
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	gpdb_id (xs:string)
Input Description	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260,….)
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（Text Format）
Sample Code	getTextEntry.java getTextEntry.cgi getTextEntry.php getTextEntry.rb

REST

Operation	entry
URI Convention	entry/gpdb_id.txt
Input	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260…)
Input Description	gpdb_id
Output	xml
Output Description	Detailed list of entry （Text Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/entry/GLP-00005e.txt

getDraftEntry
REST Operation	/entry/gpdb_id.he_draft
SOAP Operation	getDraftEntry
Description	Detailed information on the GPDB entry is returned by the Draft Text form.

SOAP

Operation	getDraftEntry
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	gpdb_id (xs:string)
Input Description	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260,…)
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（Draft Text Format）
Sample Code	getDraftEntry.java getDraftEntry.cgi getDraftEntry.php getDraftEntry.rb

REST

Operation	entry
URI Convention	entry/gpdb_id.he_draft
Input	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260,…)
Input Description	gpdb_id
Output	xml
Output Description	Detailed list of entry （Draft Text Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/entry/GLP-00005e.he_draft

getFastaEntry
REST Operation	/entry/gpdb_id.fasta
SOAP Operation	getFastaEntry
Description	Detailed information on the GPDB entry is returned by the Draft Text form.

SOAP

Operation	getFastaEntry
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	gpdb_id (xs:string)
Input Description	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260,…)
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（FASTA Format）
Sample Code	getFastaEntry.java getFastaEntry.cgi getFastaEntry.php getFastaEntry.rb

REST

Operation	entry
URI Convention	entry/gpdb_id.fasta
Input	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260,…)
Input Description	gpdb_id
Output	xml
Output Description	Detailed list of entry （FASTA Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/entry/GLP-00005e.fasta

getGlycoprotein
REST Operation	entry/gpdb_id/glycoprotein
SOAP Operation	getGlycoprotein
Description	Return to Glycosylation information.

SOAP

Operation	getGlycoprotein
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	gpdb_id (xs:string)
Input Description	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260,…)
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（XML Format）
Sample Code	getGlycoprotein.java getGlycoprotein.cgi getGlycoprotein.php getGlycoprotein.rb

REST

Operation	entry
URI Convention	entry/gpdb_id/glycoprotein
Input	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260…)
Input Description	gpdb_id
Output	xml
Output Description	Detailed list of entry（XML Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/entry/GLP-00005e/glycoprotein

getDbXref
REST Operation	entry/gpdb_id/db_xref
SOAP Operation	getDbXref
Description	The entry list is returned by retrieving DB information.

SOAP

Operation	getDbXref
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	gpdb_id (xs:string)
Input Description	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260…)
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（XML Format）
Sample Code	getDbXref.java getDbXref.cgi getDbXref.php getDbXref.rb

REST

Operation	entry
URI Convention	entry/gpdb_id/db_xref
Input	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260…)
Input Description	gpdb_id
Output	xml
Output Description	Detailed list of entry（XML Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/entry/GLP-00005e/db_xref

getGlycosylationSite
REST Operation	entry/gpdb_id/glycosylation_site
SOAP Operation	getGlycosylationSite
Description	Return to Glycosylation information.

SOAP

Operation	getGlycosylationSite
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	gpdb_id (xs:string)
Input Description	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260…)
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（XML Format）
Sample Code	getGlycosylationSite.java getGlycosylationSite.cgi getGlycosylationSite.php getGlycosylationSite.rb

REST

Operation	entry
URI Convention	entry/gpdb_id/glycosylation_site
Input	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260…)
Input Description	gpdb_id
Output	xml
Output Description	Detailed list of entry（XML Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/entry/GLP-00005e/glycosylation_site

getSequence
REST Operation	entry/gpdb_id/sequence
SOAP Operation	getSequence
Description	Return to Sequence information.

SOAP

Operation	getSequence
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	gpdb_id (xs:string)
Input Description	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260…)
WSDL Output	return (xs:string)
Output Description	Detailed list of entry（XML Format）
Sample Code	getSequence.java getSequence.cgi getSequence.php getSequence.rb

REST

Operation	entry
URI Convention	entry/gpdb_id/sequence
Input	gpdb_id (more entry acquisition: GLP-00005E,GLP-000260…)
Input Description	gpdb_id
Output	xml
Output Description	Detailed list of entry（XML Format）
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/entry/GLP-00005e/sequence

getIdList
REST Operation	getIdList[/type[.format]]
SOAP Operation	getIdList
Description	Return to the list of GPDB_ID, Tax ID and Organism.

SOAP

Operation	getIdList
WSDL	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/services/GPDB.wsdl
WSDL Input	type (xs:string), format (xs:string)
Input Description	type: list or count format: xml or txt
WSDL Output	return (xs:string)
Output Description	GPDB_IDとTax_IDとORGANISMの一覧
Sample Code	getIdList.java getIdList.cgi getIdList.php getIdList.rb

REST

Operation	getIdList
URI Convention	getIdList[/type[.format]]
Input	type, format
Input Description	type: list or count format: xml or txt
Output	xml
Output Description	The list of GPDB_ID, Tax_ID and ORGANISM
Sample URI	http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/getIdList http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/getIdList/list http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/getIdList/list.txt http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/getIdList/count http://riodb.ibase.aist.go.jp/rcmg/ws/gpdb/getIdList/count.txt

5. Common specification

5.1. When the result when it processes it is 0

When Search and Entry is processed, the empty entries of 0 the result are returned. As for REST, status becomes 404.

5.2. Processing of error when being executing it

REST returns 500 status when the error occurs when executing it, and the error screen is displayed.

5.3. SOAP Fault

The processing of the error is left to the client though SOAP returns SOAP Fault.

SOAP Input Normal Status

<?xml version='1.0' encoding='utf-8'?>
<soap:Envelope xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/"
        xmlns:typens=http://webservice.jcgpdb.jp
        xmlns:xsi=http://www.w3.org/2001/XMLSchema-instance
        xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/"
        xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/"
        xmlns:xsd="http://www.w3.org/2001/XMLSchema"
        soap:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
<soap:Body>
  <typens:getIdList>
   <format xsi:type="xsd:string">text</format>
   <type xsi:type="xsd:string">list</type>
  </typens:getIdList>
</soap:Body>
</soap:Envelope>

SOAP Output Normal Status

<?xml version='1.0' encoding='utf-8'?>
<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/">
<soapenv:Body>
  <ns:getIdListResponse xmlns:ns="http://webservice.jcGPDB.jp">
   <ns:return>
    FUT1 NM_000148
    FUT2 NM_000511
    …
    SLC35D2 NM_007001
    beta3Glc-T NM_194318
   </ns:return>
  </ns:getIdListResponse>
</soapenv:Body>
</soapenv:Envelope>

SOAP Input Error Status
※ Lack the parameter of Request

SOAP Output Error Status
※ Return to SOAP Fault

<?xml version='1.0' encoding='utf-8'?>
<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/">
<soapenv:Body>
  <soapenv:Fault>
   <faultcode>soapenv:Server</faultcode>
   <faultstring>
    Exception occurred while trying to invoke service method getIdList
   </faultstring>
   <detail />
  </soapenv:Fault>
</soapenv:Body>
</soapenv:Envelope>