Simple Sloppy Semantic Database

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, licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License. It is written in PHP.

History

S3DB was first proposed in 2006,[1] following the argumentation the previous year that omics data sets would be more easily managed if stored as RDF triples.[2]

The first version, 1.0, was focused on the support of an indexing engine for triplestore 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 through a specialized query language, S3QL,[3] accessible as a REST web service. An update of that release (version 3.5) also includes a RESTful SPARQL endpoint. This update introduced a self-update feature which replaces version numbers by date of update.

In 2011, S3DB's API was published[4] 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.[5]

Assessments

The rationale, core data model, and usage in National Cancer Institute (NIH/NCI) SPORE awards are described and illustrated in a 2008 PLoS ONE manuscript[6] and a 2010 BMC Bioinformatics manuscript.[7]

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".[8]

References
  1. Almeida JS, Chen C, Gorlitsky R, et al. (September 2006). "Data integration gets 'Sloppy'". Nat. Biotechnol. 24 (9): 1070–1. doi:10.1038/nbt0906-1070. PMID 16964209. S2CID 8526134.
  2. Wang X, Gorlitsky R, Almeida JS (September 2005). "From XML to RDF: how semantic web technologies will change the design of 'omic' standards". Nat. Biotechnol. 23 (9): 1099–103. doi:10.1038/nbt1139. PMID 16151403. S2CID 23561352.
  3. S3QL API Basics
  4. Deus HF; MC Correa; R Stanislaus; M Miragaia; W Maass; H de Lencastre; R Fox; JS Almeida (2011). "S3QL: A distributed domain specific language for controlled semantic integration of life sciences data". BMC Bioinformatics. 12: 285. doi:10.1186/1471-2105-12-285. PMC 3155508. PMID 21756325.
  5. Correa MC, Deus HF, Vasconcelos AT, Hayashi Y, Ajani JA, Patnana SV, Almeida JS (2010). "AGUIA: autonomous graphical user interface assembly for clinical tirals semantic data services". BMC Medical Informatics and Decision Making. 10: 35. doi:10.1186/1472-6947-10-65. PMC 2987967. PMID 20977768.
  6. Deus HF, Stanislaus R, Veiga DF, et al. (2008). Ben-Jacob E (ed.). "A Semantic Web Management Model for Integrative Biomedical Informatics". PLOS ONE. 3 (8): e2946. Bibcode:2008PLoSO...3.2946D. doi:10.1371/journal.pone.0002946. PMC 2491554. PMID 18698353.
  7. Almeida JS, Deus HF, Maass W (2010). "S3DB core: a framework for RDF generation and management in bioinformatics infrastructures". BMC Bioinformatics. 11: 387. doi:10.1186/1471-2105-11-387. PMC 2918582. PMID 20646315.
  8. Chen H, Yu T, Chen JY (2012). "Semantic Web meets Integrative Biology: a survey". Briefings in Bioinformatics. 14 (1): 109–25. doi:10.1093/bib/bbs014. PMID 22492191.
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