What is SSBD API?

SSBD API is the Application Programming Interface for accessing the internal data of the SSBD database. The API is based on the web development practice of using RESTFul architecture. A RESTful API call is simply an HTTP request to the SSBD server.

Prerequisite

Before you begin, you need to be familiar with BDML file, its terminology and its schema. Please refer to BDML version 0.18 Specification for more information.
Although the internal data structure is different from the BDML file format, much of its terminology and the data structure are derived from BDML file format.

Summary of SSBD API

API Request Method Functions Status
/SSBD/api/v1/ GET list all the available APIs
/SSBD/api/v1/bdml/ GET retrieve bdmlUUID depreciated; only support BDML v0.15; see data api instead
/SSBD/api/v1/contact/ GET retrieve the contact details of a BDML file record depreciated; only support BDML v0.15; see data api instead
/SSBD/api/v1/coordinates/ GET retrieve the coordinates in the BDML file record Apply to both BDML ver 0.15 and 0.18
/SSBD/api/v1/coordsXYZ/ GET retrieve the coordinates and other details in the BDML file record depreciated; only applicable to BDML ver 0.15
/SSBD/api/v1/data/ GET retrieve all the meta data of a BDML file record replaces info, summay and contact api
/SSBD/api/v1/info/ GET retrieve the info details of a BDML file record depreciated; only support BDML v0.15; see data api instead
/SSBD/api/v1/meta_data/ GET retrieve meta data of a BDML file record similar to data api
/SSBD/api/v1/scale/ GET retrieve the scales used in the BDML file record only applicable to BDML ver 0.15
/SSBD/api/v1/summary/ GET retrieve the summary details of a BDML file record depreciated; only support BDML v0.15; see data api instead

SSBD API Schema

There are two default formats that the API will return. It can either return the data in XML or JSON formats.


<response>
   <bdml type="hash">
      <list_endpoint>/SSBD/api/v1/bdml/</list_endpoint>
      <schema>/SSBD/api/v1/bdml/schema/</schema>
   </bdml>
   <contact type="hash">
      <list_endpoint>/SSBD/api/v1/contact/</list_endpoint>
      <schema>/SSBD/api/v1/contact/schema/</schema>
   </contact>
   <coordinates type="hash">
      <list_endpoint>/SSBD/api/v1/coordinates/</list_endpoint>
      <schema>/SSBD/api/v1/coordinates/schema/</schema>
   </coordsXYZ>
   <coordsXYZ type="hash">
      <list_endpoint>/SSBD/api/v1/coordsXYZ/</list_endpoint>
      <schema>/SSBD/api/v1/coordsXYZ/schema/</schema>
   </coordsXYZ>
   <data type="hash">
      <list_endpoint>/SSBD/api/v1/data/</list_endpoint>
      <schema>/SSBD/api/v1/data/schema/</schema>
   </data>
   <info type="hash">
      <list_endpoint>/SSBD/api/v1/info/</list_endpoint>
      <schema>/SSBD/api/v1/info/schema/</schema>
   </info>
   <meta_data type="hash">
      <list_endpoint>/SSBD/api/v1/meta_data/</list_endpoint>
      <schema>/SSBD/api/v1/meta_data/schema/</schema>
   </meta_data>
   <scale type="hash">
      <list_endpoint>/SSBD/api/v1/scale/</list_endpoint>
      <schema>/SSBD/api/v1/scale/schema/</schema>
   </scale>
   <summary type="hash">
      <list_endpoint>/SSBD/api/v1/summary/</list_endpoint>
      <schema>/SSBD/api/v1/summary/schema/</schema>
   </summary>
</response>


{
   "bdml"        : {"list_endpoint": "/SSBD/api/v1/bdml/", 
                    "schema": "/SSBD/api/v1/bdml/schema/"}, 
   "contact"     : {"list_endpoint": "/SSBD/api/v1/contact/", 
                    "schema": "/SSBD/api/v1/contact/schema/"}, 
   "coordsXYZ"   : {"list_endpoint": "/SSBD/api/v1/coordsXYZ/", 
                    "schema": "/SSBD/api/v1/coordsXYZ/schema/"}, 
   "data"        : {"list_endpoint": "/SSBD/api/v1/data/", 
                    "schema": "/SSBD/api/v1/data/schema/"}, 
   "info"        : {"list_endpoint": "/SSBD/api/v1/info/", 
                    "schema": "/SSBD/api/v1/info/schema/"}, 
   "meta_data"   : {"list_endpoint": "/SSBD/api/v1/meta_data/", 
                    "schema": "/SSBD/api/v1/meta_data/schema/"}, 
   "scale"       : {"list_endpoint": "/SSBD/api/v1/scale/", 
                    "schema": "/SSBD/api/v1/scale/schema/"}, 
   "summary"     : {"list_endpoint": "/SSBD/api/v1/summary/", 
                    "schema": "/SSBD/api/v1/summary/schema/"}
}

bdml API

Description
Retrieve the unique UUID information for the BDML data. Depreciated; Only supports BDML v0.15; Use data api instead
Fields Description Usage example Usage comment
bdml_ID unique BDML UUID identity number of the BDML data stored in SSBD http://ssbd.qbic.riken.jp/SSBD/api/v1/bdml/?format=xml;bdml_ID__icontains=247 To retrieve bdmlUUID which contains '247' from SSBD
title Title of the BDML data stored in SSBD http://ssbd.qbic.riken.jp/SSBD/api/v1/bdml/?format=xml;title__icontains=coli To retrieve the title which contains the phrase 'coli' from SSBD
id internal unique id for data stored in SSBD http://ssbd.qbic.riken.jp/SSBD/api/v1/bdml/?format=xml;id=1 To retrieve the data with internal id=1 from SSBD
bdml Schema
http://ssbd.qbic.riken.jp/SSBD/api/v1/bdml/schema/?format=xml

contact API

Description
Contact information for the BDML data. Depreciated; only supports BDML v0.15; Use data api instead
Fields Description Usage example Usage comment
bdml unique BDML UUID identity number of the BDML data stored in SSBD http://ssbd.qbic.riken.jp/SSBD/api/v1/contact/?format=xml;bdml__bdml_ID__icontains=247 To retrieve Contact data from SSBD for bdmlUUID which contains '247'
name Name of corresponding author of the BDML data. http://ssbd.qbic.riken.jp/SSBD/api/v1/contact/?format=xml;name__icontains=keller To retrieve Contact data from SSBD for name that contains the phrase keller or Keller;
E_mail E-mail address of the corresponding author. NA cannot be searched; retrieval only
organization Affiliation of the corresponding author. http://ssbd.qbic.riken.jp/SSBD/api/v1/contact/?format=xml;organization__icontains=riken To retrieve Contact data from SSBD for organisation that contains the phrase "riken"
department Department of the organization of the corresponding author. http://ssbd.qbic.riken.jp/SSBD/api/v1/contact/?format=xml;department__icontains=biology To retrieve Contact data from SSBD for department that contains the phrase "dynamics"
laboratory Name of the laboratory of the corresponding author. http://ssbd.qbic.riken.jp/SSBD/api/v1/contact/?format=xml;laboratory__icontains=dynamics To retrieve Contact data from SSBD for laboratory that contains the phrase "dynamics"
address Postal address of the corresponding author. http://ssbd.qbic.riken.jp/SSBD/api/v1/contact/?format=xml;address__icontains=kobe To retrieve Contact data from SSBD for address that contains the phrase "kobe"
phone Phone number of the corresponding author. NA cannot be searched; retrieval only
URL A URL link to corresponding author's laboratory or website. NA cannot be searched; retrieval only
Contact Schema
http://ssbd.qbic.riken.jp/SSBD/api/v1/contact/schema/?format=xml

coordinates API

Description
It provides an interface to retrieve the quantitative numerical data. Support BDML v0.15 and 0.18
Fields Description Usage example Usage comment
bdmlUUID retrieve fields of bdml API including the unique BDML UUID identity number of the BDML data stored in SSBD. http://ssbd.qbic.riken.jp/SSBD/api/v1/coordinates/?format=xml;bdmlUUID=6db18336-e8e9-496e-810b-40298385bbcd;t=10 To retrieve coordinates data from SSBD for bdmlUUID which contains ''6db18336-e8e9-496e-810b-40298385bbcd'.

It has to be used together with t. See below.

entitytype Type of entity that the coordinates belong to, e.g. line, point, sphere, etc. NA cannot be searched; retrieval only
entity entity ID. NA cannot be searched; retrieval only
x x coordinates NA cannot be searched; retrieval only
y y coordinates NA cannot be searched; retrieval only
z z coordinates. NA cannot be searched; retrieval only
t time point http://ssbd.qbic.riken.jp/SSBD/api/v1/coordinates/?format=xml;bdmlUUID=6db18336-e8e9-496e-810b-40298385bbcd;t=10 To retrieve numerical data from SSBD for time t=10 and bdmlUUID is '6db18336-e8e9-496e-810b-40298385bbcd'
coordinates Schema
http://ssbd.qbic.riken.jp/SSBD/api/v1/coordinates/schema/?format=xml

coordsXYZ API

Description
It provides an interface to retrieve the quantitative numerical data. Depreciated; only support BDML v0.15; Use coordinates api instead
Fields Description Usage example Usage comment
bdml retrieve fields of bdml API including the unique BDML UUID identity number of the BDML data stored in SSBD. It uses "bdml__" as prefix for bdml API; Also see bdml API http://ssbd.qbic.riken.jp/SSBD/api/v1/contact/?format=xml;bdml__bdml_ID__icontains=247 To retrieve coordinates data from SSBD for bdmlUUID which contains '247'
entitytype Type of entity that the coordinates belong to, e.g. line, point, sphere, etc. NA cannot be searched; retrieval only
entity entity ID. NA cannot be searched; retrieval only
x x coordinates NA cannot be searched; retrieval only
y y coordinates NA cannot be searched; retrieval only
z z coordinates. NA cannot be searched; retrieval only
t time point http://ssbd.qbic.riken.jp/SSBD/api/v1/coordsXYZ/?format=xml;bdml__bdml_ID__icontains=247;t=10 To retrieve numerical data from SSBD for time t=10 and bdmlUUID contains '247'
coordsXYZ Schema
http://ssbd.qbic.riken.jp/SSBD/api/v1/coordsXYZ/schema/?format=xml

data API

Description
Retrieve all the meta data described in the BDML file stored in SSBD. It replaces contact, info and summary API. It also covers BDML versions including 0.15 and 0.18.
Fields Description Usage example Usage comment
bdmlUUID unique BDML UUID of the BDML data stored in SSBD http://ssbd.qbic.riken.jp/SSBD/api/v1/data/?format=xml;bdmlUUID__icontains=2475d To retrieve all the meta data from SSBD for bdmlUUID which contains "245d". Note that the field is changed from previous bdml_ID to bdmlUUID in the new API.
bdml_multipart_type it denotes whether the bdmlUUID data is part of a series. 1 stands for standalone file and 2 stands for file in a series. NA Cannot be searched; retrieval only
external_bdml link to the actual bdml file NA Cannot be searched; retrieval only
external_pdpml link to the actual pdpml file NA Cannot be searched; retrieval only
external_source link to the actual source of the data NA Cannot be searched; retrieval only
localid Internal or local identifier used to identify the BDML data. http://ssbd.qbic.riken.jp/SSBD/api/v1/data/?format=xml;localid__icontains=B0336 To retrieve summary data from SSBD for localid that contains the phrase "B0336"
release date of the release of the data NA Cannot be searched; retrieval only
schema_ver version of the BDML schema used NA Cannot be searched; retrieval only
status status of the data NA Cannot be searched; retrieval only; only 'available' status is allowed to be retrieved
meta_data other meta-data of the BDML file data on SSBD; Searches require using "meta_data__" as prefix of the fields being search; Also see meta_data API http://ssbd.qbic.riken.jp/SSBD/api/v1/data/?format=xml;meta_data__name__icontains=water To retrieve data given that the "name" field in meta_data API contains the phrase "water"
Data Schema
Example of response
  • Trying to retrieve meta data from SSBD for bdmlUUID that contains the phrase "2475d"
  • output format is in XML format
    • http://ssbd.qbic.riken.jp/SSBD/api/v1/data/?format=xml;bdmlUUID__icontains=2475d
      
      <response>
      <meta type="hash">
         <limit type="integer">20</limit>
         <next type="null"/>
         <offset type="integer">0</offset>
         <previous type="null"/>
         <total_count type="integer">1</total_count>
      </meta>
      <objects type="list">
      <object>
         <bdmlUUID>bb7f643a-f50b-4552-bd23-a7f267e2475d</bdmlUUID>
         <bdml_multipart_type>2</bdml_multipart_type>
         <external_bdml>
            http://ssbd.qbic.riken.jp/data/bdml/ZF_PJK/0011_zebrafish_animal_a.bdml0.18.xml
         </external_bdml>
         <external_pdpml>
            http://ssbd.qbic.riken.jp/data/pdpml/keller2008.pdpml0.06.xml
         </external_pdpml>
         <external_source type="null"/>
         <localid>zebrafish_animal_a.mat</localid>
         <meta_data>
            <E_mail>keller@embl.de</E_mail>
            <PMID type="integer">18845710</PMID>
            <URL type="null"/>
            <address type="null"/>
            <basedon>Measurement</basedon>
            <citation type="null"/>
            <contributors>
               Keller, P.J., Schmidt, A.D., Wittbrodt, J. and Stelzer, E.H.K.
            </contributors>
            <datatype>nuclear positions</datatype>
            <dblink>http://www.embl.de/digitalembryo/fish.html</dblink>
            <department>Cell Biology and Biophysics Unit</department>
            <description>
               reconstruction of the zebrafish animal hemisphere (A)
            </description>
            <gene type="null"/>
            <laboratory>Stelzer Laboratory</laboratory>
            <license>CC BY-NC-SA</license>
            <localid>zebrafish_animal_a.mat</localid>
            <method_summary>
               See details in Keller et al. (2008) Science 322, 1065-1069.
            </method_summary>
            <name>Philipp J. Keller</name>
            <organism>zebrafish</organism>
            <organization>European Molecular Biology Laboratory</organization>
            <phone type="null"/>
            <title>
               BDML file for reconstruction of the zebrafish animal hemisphere (A)
            </title>
         </meta_data>
         <release>2008-09-01</release>
         <resource_uri>/SSBD/api/v1/data/510/</resource_uri>
         <schema_ver>0.180</schema_ver>
         <status>available</status>
      </object>
      </objects>
      </response>
      
      

info API

Description
Information about the BDML data stored in SSBD. Depreciated; Only supports BDML v0.15; Use data API instead
Fields Description Usage example Usage comment
id unique internal ID of the BDML data stored in SSBD http://ssbd.qbic.riken.jp/SSBD/api/v1/info/?format=xml;id=1 To retrieve info data from SSBD for id=1
bdmlID Unique ID of the BDML data. http://ssbd.qbic.riken.jp/SSBD/api/v1/info/?format=xml;bdmlID__icontains=705c To retrieve info data from SSBD for bdmlID that contains the phrase 705c or 705C;
title Title of the BDML data. http://ssbd.qbic.riken.jp/SSBD/api/v1/info/?format=xml;title__contains=wild-type To retrieve info data from SSBD for all the titles that contains the phrase "wild-type"
license License information of the BDML data NA cannot be searched; retrieval only
release Release date of the BDML data NA cannot be searched; retrieval only
version local version of the BDML data NA cannot be searched; retrieval only
Info Schema
Example of response
  • Trying to retrieve Info data from SSBD with a title that contains the word "705c"
  • output format is in JSON (for easier formatting and viewing)
    • http://ssbd.qbic.riken.jp/SSBD/api/v1/info/?format=json;bdmlID__icontains=705c
         
      {
          "meta": {   "limit": 20, 
                       "next": null, 
                     "offset": 0, 
                   "previous": null, 
                "total_count": 1
                }, 
       "objects": [{
                     "bdmlID": "eb16443f-1956-48eb-8510-5f1ddc3b705c", 
                         "id": 188, 
                    "license": "CC BY-NC-SA", 
                    "release": "2013-09-02", 
                      "title": "BDML file for the result of computer simulation of male pronuclear migration in C. elegans embryo", 
                    "version": 1}]
      }
      
      

meta_data API

Description
Summary of the meta data described in the BDML file in SSBD
Fields Description Usage example Usage comment
E_mail E-mail address of the corresponding author. NA cannot be searched; retrieval only
PMID PubMed ID of the original published paper. NA cannot be searched; retrieval only
URL A URL link to corresponding author's laboratory or website. NA cannot be searched; retrieval only
address Postal address of the corresponding author. http://ssbd.qbic.riken.jp/SSBD/api/v1/meta_data/?format=xml;address__icontains=kobe To retrieve Contact data from SSBD for address that contains the phrase "kobe"
basedon Speficify whether the data was gathered from an in vivo measurement or from a computer simulation. http://ssbd.qbic.riken.jp/SSBD/api/v1/meta_data/?format=xml;basedon__icontains=measurement To retrieve summary data from SSBD for basedon that contains the name "measurement or Measurement"; icontains mean that it is case insensitive
citation Detailed information about the original published paper. NA cannot be searched; retrieval only
contributors Names of contributors who produce/collect the data. http://ssbd.qbic.riken.jp/SSBD/api/v1/meta_data/?format=xml;contributors__icontains=keller To retrieve meta data from SSBD for contributors that contains the name "keller or Keller or KELLER"; icontains mean that it is case insensitive
datatype Describes specific type of data that was represented in the BDML data http://ssbd.qbic.riken.jp/SSBD/api/v1/meta_data/?format=xml;;datatype__contains=dynamics To retrieve meta data from SSBD for datatype that contains the phrase "dynamics"
dblink A URL link to the original database. NA cannot be searched; retrieval only
department Department of the organization of the corresponding author. http://ssbd.qbic.riken.jp/SSBD/api/v1/meta_data/?format=xml;department__icontains=biology To retrieve meta data from SSBD for department that contains the phrase "dynamics"
description Detailed information about the data described in the BDML file. http://ssbd.qbic.riken.jp/SSBD/api/v1/meta_data/?format=xml;description__icontains=simulation To retrieve summary data from SSBD for description that contain the word "simulation"
laboratory Name of the laboratory of the corresponding author. http://ssbd.qbic.riken.jp/SSBD/api/v1/meta_data/?format=xml;laboratory__icontains=dynamics To retrieve meta data from SSBD for laboratory that contains the phrase "dynamics"
license License information of the data NA cannot be searched; retrieval only
localid Internal or local identifier used to identify the BDML data. http://ssbd.qbic.riken.jp/SSBD/api/v1/meta_data/?format=xml;localid__contains=wt To retrieve meta data from SSBD for local identifier or ID that contains the phrase "wt"
method_summary Summary of the method used in preparing for the data NA cannot be searched; retrieval only
organism Name of a targeted organism being described. Name is based on the NCBI taxonomy definition. http://ssbd.qbic.riken.jp/SSBD/api/v1/meta_data/?format=xml;organism__contains=elegans To retrieve meta data from SSBD for organism that contains the phrase "elegans"
organization Affiliation of the corresponding author. http://ssbd.qbic.riken.jp/SSBD/api/v1/meta_data/?format=xml;organization__icontains=riken To retrieve meta data from SSBD for organisation that contains the phrase "riken"
phone Phone number of the corresponding author. NA cannot be searched; retrieval only
Meta_data Schema
Example of response
  • Trying to retrieve summary data from SSBD for basedon that contains the word "coli" as in E.coli
  • output format is in XML format
    • http://ssbd.qbic.riken.jp/SSBD/api/v1/meta_data/?format=xml;organism__icontains=coli
      
      <response>
         <meta type="hash">
            <limit type="integer">20</limit>
            <next type="null"/>
            <offset type="integer">0</offset>
            <previous type="null"/>
            <total_count type="integer">2</total_count>
         </meta>
         <objects type="list">
            <object>
               <E_mail>satya.arjunan@riken.jp</E_mail>
               <PMID type="integer">20012222</PMID>
               <URL type="null"/>
               <address>6-2-3 Furuedai, Suita, Osaka 565-0874, Japan</address>
               <basedon>Simulation</basedon>
               <citation type="null"/>
               <contributors>Arjunan, S. N. V. and Tomita, M.</contributors>
               <datatype>single molecule dynamics</datatype>
               <dblink>http://www.ncbi.nlm.nih.gov/pubmed/20012222</dblink>
               <department>Quantitative Biology Center</department>
               <description>
                  quantitative single molecule dynamics of Min proteins (MinEE, MinDEE, MinDEED, and MinD) in E. coli wild-type
               </description>
               <laboratory>Laboratory for Biochemical Simulation</laboratory>
               <license>CC BY-NC-SA</license>
               <localid>Eco_MinE_AS</localid>
               <method_summary>
                  See details in Arjunan et al. (2010) Syst Synth Biol 4, 35-53.
               </method_summary>
               <name>Satya Nanda Vel Arjunan</name>
               <organism>E. coli</organism>
               <organization>RIKEN</organization>
               <phone type="null"/>
               <title>
                  BDML file for quantitative information about single molecule dynamics of E. coli wild-type
               </title>
            </object>
            <object>
               <E_mail>satya.arjunan@riken.jp</E_mail>
               <PMID type="integer">20012222</PMID>
               <URL type="null"/>
               <address>6-2-3 Furuedai, Suita, Osaka 565-0874, Japan</address>
               <basedon>Simulation</basedon>
               <citation type="null"/>
               <contributors>Arjunan, S. N. V. and Tomita, M.</contributors>
               <datatype>single molecule dynamics</datatype>
               <dblink>http://www.ncbi.nlm.nih.gov/pubmed/20012222</dblink>
               <department>Quantitative Biology Center</department>
               <description>
                  quantitative single molecule dynamics of Min proteins (MinEE, MinDEE, MinDEED, and MinD) in E. coli wild-type
               </description>
               <laboratory>Laboratory for Biochemical Simulation</laboratory>
               <license>CC BY-NC-SA</license>
               <localid>Eco_MinE_AS</localid>
               <method_summary>
                  See details in Arjunan et al. (2010) Syst Synth Biol 4, 35-53.
               </method_summary>
               <name>Satya Nanda Vel Arjunan</name>
               <organism>E. coli</organism>
               <organization>RIKEN</organization>
               <phone type="null"/>
               <title>
                  BDML file for quantitative information about single molecule dynamics of E. coli wild-type
               </title>
            </object>
         </objects>
      </response>
      
      

scale API

Description
Scale and unit of coordinates and time. Only support BDML v0.15
Fields Description Usage example Usage comment
bdml retrieve fields of bdml API including the unique BDML UUID identity number of the BDML data stored in SSBD. It uses "bdml__" as prefix for bdml API; Also see bdml API http://ssbd.qbic.riken.jp/SSBD/api/v1/scale/?format=xml;bdml__bdml_ID__icontains=705c To retrieve Scale data from SSBD for bdmlUUID containing the phrase "705c"
tUnit Measurement unit of time. http://ssbd.qbic.riken.jp/SSBD/api/v1/scale/?format=xml;tUnit=minute To retrieve Scale data from SSBD for tUnit that is "minute";
tScale Time scale. NA cannot be searched; retrieval only
xScale Scale in x dimension. NA cannot be searched; retrieval only
yScale Scale in y dimension. NA cannot be searched; retrieval only
zScale Scale in z dimension. NA cannot be searched; retrieval only
xyzUnit Measurement unit of x, y and z dimensions. http://ssbd.qbic.riken.jp/SSBD/api/v1/scale/?format=xml;xyzUnit=meter To retrieve Scale data from SSBD for xyzUnit that is "meter"
Scale Schema
http://ssbd.qbic.riken.jp/SSBD/api/v1/scale/schema/?format=xml

summary API

Description
Summary of the data described in the BDML file which is stored in SSBD. Depreciated; Only supports BDML v0.15; Use data api instead
Fields Description Usage example Usage comment
bdml retrieve fields of bdml API including the unique BDML UUID identity number of the BDML data stored in SSBD. It uses "bdml__" as prefix for bdml API; Also see bdml API http://ssbd.qbic.riken.jp/SSBD/api/v1/summary/?format=xml;bdml__bdml_ID__icontains=705c To retrieve summary data from SSBD for bdmlUUID containing the phrase "705c"
description Detailed information about the data described in the BDML file. http://ssbd.qbic.riken.jp/SSBD/api/v1/summary/?format=xml;description__icontains=simulation To retrieve summary data from SSBD for description containing the word "simulation"
datatype Describes specific type of data that was represented in the BDML data http://ssbd.qbic.riken.jp/SSBD/api/v1/summary/?format=xml;;datatype__contains=dynamics To retrieve summary data from SSBD for datatype that contains the phrase "dynamics"
identifier Internal or local identifier used to identify the BDML data. http://ssbd.qbic.riken.jp/SSBD/api/v1/summary/?format=xml;identifier__contains=wt To retrieve summary data from SSBD for identifier that contains the phrase "wt"
organism Name of a targeted organism being described. Name is based on the NCBI taxonomy definition. http://ssbd.qbic.riken.jp/SSBD/api/v1/summary/?format=xml;organism__contains=elegans To retrieve summary data from SSBD for organism that contains the phrase "elegans"
contributors Names of contributors who produce/collect the data. http://ssbd.qbic.riken.jp/SSBD/api/v1/summary/?format=xml;contributors__icontains=keller To retrieve summary data from SSBD for contributors that contains the name "keller or Keller or KELLER"; icontains mean that it is case insensitive
basedon Speficify whether the data was gathered from an in vivo measurement or from a computer simulation. http://ssbd.qbic.riken.jp/SSBD/api/v1/summary/?format=xml;basedon__icontains=measurement To retrieve summary data from SSBD for basedon that contains the name "measurement or Measurement"; icontains mean that it is case insensitive
PMID PubMed ID of the original published paper. NA cannot be searched; retrieval only
citation Detailed information about the original published paper. NA cannot be searched; retrieval only
dblink A URL link to the original database. NA cannot be searched; retrieval only
Summary Schema
Example of response
  • Trying to retrieve summary data from SSBD for organism that contains the word "mus" and datatype which contains the phrase "pos"
  • output format is in XML format
    • http://ssbd.qbic.riken.jp/SSBD/api/v1/summary/?format=xml;organism__icontains=mus;datatype__icontains=pos
      
      <response>
         <meta type="hash">
            <limit type="integer">20</limit>
            <next type="null"/>
            <offset type="integer">0</offset>
            <previous type="null"/>
            <total_count type="integer">1</total_count>
         </meta>
         <objects type="list">
            <object>
               <PMID type="integer">22590505</PMID>
               <basedon>Measurement</basedon>
               <bdml>
                  <bdml_ID>745645af-8d54-4320-9027-a7520ca9c17f</bdml_ID>
                  <id type="integer">300</id>
                  <title>
                     BDML file for quantitative information about nuclei centroids of mouse embryonic cells
                  </title>
               </bdml>
               <citation>
                  Bashar, M.K., Komatsu, K., Fujimori, T., Kobayashi, T.J. (2012) Automatic extraction of nuclei centroids of mouse embryonic cells from fluorescence microscopy images. PLoS One 7: e35550.
               </citation>
               <contributors>
                  Bashar M.K., Komatsu, K., Fujimori, T., Kobayashi, T.J.
               </contributors>
               <datatype>nuclear positions</datatype>
               <dblink type="null"/>
               <description>
                  quantitative information about nuclei centroids of mouse embryonic cells
               </description>
               <identifier>088044_L1</identifier>
               <organism>Mus musculus</organism>
            </object>
         </objects>
      </response>