Simple Sloppy Semantic Database (S3DB) is a distributed data management system that relies on
Semantic Web concepts for management of heterogeneous data.
S3DB is
open source software
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open ...
, licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License. It is written in
PHP
PHP is a general-purpose scripting language geared toward web development. It was originally created by Danish-Canadian programmer Rasmus Lerdorf in 1993 and released in 1995. The PHP reference implementation is now produced by The PHP Group. ...
.
History
S3DB was first proposed in 2006, following the argumentation the previous year that
omics
The branches of science known informally as omics are various disciplines in biology whose names end in the suffix '' -omics'', such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the collect ...
data sets would be more easily managed if stored as
RDF triples.
The first version, 1.0, was focused on the support of an indexing engine for
triplestore
A triplestore or RDF store is a purpose-built database for the storage and retrieval of triples through semantic queries. A triple is a data entity composed of subject–predicate–object, like "Bob is 35" or "Bob knows Fred".
Much like a relat ...
management.
The second version, made available in October 2007, added cross-referencing between triples in distinct S3DB deployments to support it as a distributed infrastructure.
The third version was released in July 2008 and exposes its
API
An application programming interface (API) is a way for two or more computer programs to communicate with each other. It is a type of software interface, offering a service to other pieces of software. A document or standard that describes how ...
through a specialized query language, S3QL, accessible as a
REST
Rest or REST may refer to:
Relief from activity
* Sleep
** Bed rest
* Kneeling
* Lying (position)
* Sitting
* Squatting position
Structural support
* Structural support
** Rest (cue sports)
** Armrest
** Headrest
** Footrest
Arts and enter ...
web service. An update of that release (version 3.5) also includes a RESTful
SPARQL
SPARQL (pronounced " sparkle" , a recursive acronym for SPARQL Protocol and RDF Query Language) is an RDF query language—that is, a semantic query language for databases—able to retrieve and manipulate data stored in Resource Description ...
endpoint. This update introduced a self-update feature which replaces version numbers by date of update.
In 2011, S3DB's API was published and was put to use in the management of a clinical trial at
MDAnderson Cancer Center using a web application with a self-assembled interface.
Assessments
The rationale, core data model, and usage in National Cancer Institute (
NIH/NCISPORE awardsare described and illustrated in a 2008
PLoS ONE manuscript and a 2010
BMC Bioinformatics manuscript.
A 2012 survey paper stated, "S3QL supports a permission control mechanism that allows users to specify contextual minutiae such as provenance and access control on the semantic level. The effectiveness of S3QL was illustrated through use cases of IB, such as genomic characterization of cancer and molecular epidemiology of infectious diseases. We expect S3QL or its variations to be accepted as the standard access control mechanism by the SW community".
External links
S3DB homepageS3DB source codeS3QL specificationS3DB tutorial video YouTube, 2008
References
{{Reflist
Types of databases
Distributed data storage
Semantic Web