SSBD:database

• Example of using query to retrieve quantitative data using SSBD API in JSON:
  • http://ssbd.qbic.riken.jp/SSBD/api/v3/bd5coords/?format=json;bdmlID=4ed09fa3-7650-45a9-ac55-426980aa7d0a;&ts=1;&limit=2

// 20190104185349
// http://ssbd.qbic.riken.jp/SSBD/api/v3/bd5coords/?format=json;bdmlID=4ed09fa3-7650-45a9-ac55-426980aa7d0a;&ts=1;&limit=2

{
  "meta": {
    "limit": 2,
    "next": "/SSBD/api/v3/bd5coords/?bdmlID=4ed09fa3-7650-45a9-ac55-426980aa7d0a&offset=2&limit=2&ts=1&format=json",
    "offset": 0,
    "previous": null,
    "total_count": 10936
  },
  "objects": [
    {
      "entity": "line",
      "id": "2000",
      "label": "P0",
      "radius": null,
      "sid": 0,
      "t": "2",
      "x": "266",
      "y": "306",
      "z": "15"
    },
    {
      "entity": "line",
      "id": "2000",
      "label": "P0",
      "radius": null,
      "sid": 0,
      "t": "2",
      "x": "265",
      "y": "307",
      "z": "15"
    }
  ]
}

• Example of using query to retrieve scaleUnit quantitative data using SSBD API in JSON:
  • http://ssbd.qbic.riken.jp/SSBD/api/v3/bd5scaleunit/?format=json;bdmlID=4ed09fa3-7650-45a9-ac55-426980aa7d0a;&ts=1;&limit=2

// 20190106144156
// http://ssbd.qbic.riken.jp/SSBD/api/v3/bd5scaleunit/?format=json;bdmlID=4ed09fa3-7650-45a9-ac55-426980aa7d0a;&ts=1;&limit=2

{
  "meta": {
    "limit": 2,
    "next": null,
    "offset": 0,
    "previous": null,
    "total_count": 1
  },
  "objects": [
    {
      "dimension": "3D+T",
      "sUnit": "micrometer",
      "tScale": "40.0",
      "tUnit": "second",
      "xScale": "0.105",
      "yScale": "0.105",
      "zScale": "0.5"
    }
  ]
}    

contact API

Description

Contact information It is normally used together with data, person and affiliation API

Contact Schema

​http://ssbd.qbic.riken.jp/SSBD/api/v3/contact/schema/?format=json

contributor API

Description

Contributor information It is normally used together with data, person and affiliation API

Fields	Description	Usage example	Usage comment
data	meta data stored in SSBD	http://ssbd.qbic.riken.jp/SSBD/api/v3/contributor/?format=json;data__localID__icontains=wt(N2)07	To retrieve Contributor data from SSBD for data's localID which contains 'wt(N2)07'
person	person associated with the data.	http://ssbd.qbic.riken.jp/SSBD/api/v3/contributor/?format=json;person__last_name=Keller	To retrieve Contributor from SSBD for person with the last name Keller
affiliation	affiliation associated with the data.	http://ssbd.qbic.riken.jp/SSBD/api/v3/contributor/?format=json;affiliation__E_mail__icontains=kyoda	To retrieve Contributor information from SSBD with affiliation's email address containing the phrase 'kyoda'

Contact Schema

​http://ssbd.qbic.riken.jp/SSBD/api/v3/contributor/schema/?format=json

data API

Description

Retrieve meta information of the data stored in SSBD.

Fields	Description	Usage example	Usage comment
bdmlID	Retrieve data based on unique BDMLID	http://ssbd.qbic.riken.jp/SSBD/api/v3/data/?format=json;bdmlID__icontains=32	To retrieve summary data from SSBD for bdmlID that matches or contains the phrase "32"
localID	Retreive data based on internal or local identifier	http://ssbd.qbic.riken.jp/SSBD/api/v3/data/?format=json;localID__icontains=wt(N2)07	To retrieve all the meta data from SSBD when localID contains the phrase "wt(N2)07". Note that the field is changed from previous bdml_ID to bdmlUUID in the new API.
organism	Retrieve data based on organism	http://ssbd.qbic.riken.jp/SSBD/api/v3/data/?format=json;organism__icontains=rerio	Return data with organism name containing the phrase "rerio".

Data Schema

• ​http://ssbd.qbic.riken.jp/SSBD/api/v3/data/schema/?format=json

Example of response

• Trying to retrieve meta data from SSBD for bdmlID "320e02ee-1c6c-4e03-a6da-75b5c413b6a3"
• output format is in JSON format
  • http://ssbd.qbic.riken.jp/SSBD/api/v3/data/?format=json;bdmlID=320e02ee-1c6c-4e03-a6da-75b5c413b6a3

    
    / 20190104193200
    // http://ssbd.qbic.riken.jp/SSBD/api/v3/data/?format=json;bdmlID=320e02ee-1c6c-4e03-a6da-75b5c413b6a3
    
    {
      "meta": {
        "limit": 20,
        "next": null,
        "offset": 0,
        "previous": null,
        "total_count": 1
      },
      "objects": [
        {
          "PMID": "18845710",
          "SID": 5,
          "basedon": "Experiment",
          "bdmlID": "320e02ee-1c6c-4e03-a6da-75b5c413b6a3",
          "citation": null,
          "contributors": "Philipp Keller, Annette Schmidt, Joachim Wittbrodt, Ernst Stelzer",
          "datatype": "nuclear positions",
          "dblink": "http://www.embl.de/digitalembryo/fish.html",
          "description": "in toto reconstruction of zebrafish MZoep mutant development",
          "gene": null,
          "license": "CC BY-NC-SA",
          "localID": "zebrafish_in_toto_mzoep.mat",
          "method_summary": "See details in Keller et al. (2008) Science 322, 1065-1069.",
          "orf": null,
          "organism": "D. rerio",
          "release": "2017-12-20",
          "schema_ver": "3.000",
          "title": "BDML file for in toto reconstruction of zebrafish MZoep mutant development"
        }