SSBD-RDF

What is SSBD-RDF?

Resource Description Framework (RDF) is data model for exchanging data on the Internet. It is part of the family of World Wide Web Consortium (W3C) specifications (http://www.w3.org/TR/rdf11-concepts/). To establish a connection between SSBD and other biological databases, SSBD provides RDF formatted meta-information, which includes quantitative data and their corresponding microscopy images, at RIKEN Meta Database. The SSBD-RDF data currently consists of 18,319 triples (data entities of subject-predicate-object form; ver. 20141003 release 20150911). Table 1 is a list of ontologies/subdomains used to define the specific knowledge in the SSBD-RDF data.

Table 1. The prefixes and corresponding namespaces used in the SSBD-RDF.

PrefixNamespaceOntologies/subdomains
rdfshttp://www.w3.org/2000/01/rdf-schema#RDF Schema
rdfhttp://www.w3.org/1999/02/22-rdf-syntax-ns#RDF
xsdhttp://www.w3.org/2001/XMLSchema#XML Schema
owlhttp://www.w3.org/2002/07/owl#OWL
dctermshttp://purl.org/dc/terms/DCMI Terms
foafhttp://xmlns.com/foaf/0.1FOAF
vcardhttp://www.w3.org/2006/vcard/ns#VCARD
obohttp://purl.obolibrary.org/obo/RO, GO, NCBITaxon
siohttp://semanticscience.org/resource/SIO
ma-onthttp://www.w3.org/ns/ma-ont#Media Resources
bqbiolhttp://biomodels.net/biology-qualifiers/BioModels schema
omehttps://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2015-01/ome_xsd.html#OME schema
ssbdhttp://metadb.riken.jp/db/SSBD/SSBD-RDF

How to use the SSBD-RDF data?

SPARQL query language (SPARQL; http://www.w3.org/TR/rdf-sparql-query/) can be used through the RIKEN Meta Database website to query the SSBD-RDF data. Here you can find some examples of the SPARQL queries.

SPARQL query #1: to find quantitative data and the dataset of microscopy images about M. musculus

PREFIX ssbd: <http://metadb.riken.jp/db/SSBD/>
PREFIX obo:  <http://purl.obolibrary.org/obo/>
SELECT ?s ?desc
FROM
WHERE
{
?s obo:RO_0002162 obo:NCBITaxon_10090 . # M. musculus
?s ssbd:description ?desc .
}

SPARQL query #2: to find quantitative data of nuclear division dynamics obtained from experimental measurements

PREFIX ssbd: <http://metadb.riken.jp/db/SSBD/>
PREFIX obo:  <http://purl.obolibrary.org/obo/>
PREFIX bqbiol: <http://biomodels.net/biology-qualifiers/>
SELECT ?s ?desc
FROM
WHERE
{
?s bqbiol:isPartOf obo:GO_0005634 . # nucleus
?s ssbd:basedOn ?text FILTER regex(?text, "measurement", "i") .
?s ssbd:description ?desc .
}

SPARQL query #3: to find quantitative data of pronuclear migration dynamics in C. elegans obtained from computer simulations

PREFIX ssbd: <http://metadb.riken.jp/db/SSBD/>
PREFIX obo:  <http://purl.obolibrary.org/obo/>
PREFIX bqbiol: <http://biomodels.net/biology-qualifiers/>
SELECT ?s ?desc
FROM
WHERE
{
?s obo:RO_0002162 obo:NCBITaxon_6239 . # C. elegans
?s bqbiol:isVersionOf obo:GO_0035046 . # pronuclear migration
?s ssbd:basedOn ?text FILTER regex(?text, "simulation", "i") .
?s ssbd:description ?desc .
}