Leveraging SADI semantic web services to exploit fish ecotoxicology data

Matthew M. Hindle*, Alexandre Riazanov, Edward S. Goudreau, Christopher J. Martyniuk, Christopher J.O. Baker

*Corresponding author for this work

Research output: Contribution to journalConference articlepeer-review

Abstract / Description of output

In order to interpret experimental Omics-data, ecotoxicologists are faced with an array of disconnected bioinformatics databases and algorithms. These include tools for microarray analysis, gene annotation, functional gene set enrichment, and network analysis. Drawing together these Web tools and resources is a frequently labour-consuming technical exercise in identifying links across database records and the connecting input and output formats of tools. Interpreting experimental Omics-data in the context of the current available knowledge and methodologies from a single query platform with explicit semantics would be a valuable asset for toxicology in the analysis of DNA, transcriptomics, proteomic, and metabolomic experimental data. Methods: We have created 30+ SADI semantic Web Services, resources and tools pertinent to the interpretation of Omics toxicological data. These services encompass a wide range of algorithms, domains and databases, including sequence alignment and protein domain finding tools (e.g. BLAST, HMMR3, and InterProScan), databases containing experimentally validated protein functions (e.g. ZFIN and MGI), and central repositories of sequence and microarray data (e.g. ArrayExpress and NCBI-RefSeq). All these services can be leveraged through SPARQL queries submitted to the SHARE query engine. This paradigm provides a single access-point on the Web for a toxicologist to submit semantically rich queries that are resolved using the relevant databases and tools. This frees the ecotoxicologist from learning unnecessary details concerning tool interfaces and the semantic idiosyncrasies of databases. Results: We present a series of example queries for ecotoxicology, which facilitate the interpretation of transcriptomics data in the context of public knowledge and current tools. These queries include common tasks, specific to a user's experimental data set, such as gene ontology annotation of probes on a custom microarray experiment for an aquatic species of interest.

Original languageEnglish
Pages (from-to)19-33
Number of pages15
JournalCEUR Workshop Proceedings
Publication statusPublished - 1 Dec 2011
Event3rd Canadian Semantic Web Symposium, CSWS 2011 - Vancouver, BC, Canada
Duration: 5 Aug 20115 Aug 2011

Keywords / Materials (for Non-textual outputs)

  • Ecotoxicology
  • Fish
  • SADI
  • Semantic Web Services
  • Toxicology


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