Links

  • Semantic Web languages

  • RDF triple stores
  • Related projects
    • W3C Semantic Web Health Care and Life Sciences Interest Group
    • The W3C SIG dedicated to "develop, advocate for, and support the use of Semantic Web technologies for health care and life science, with focus on biological science and translational medicine."
    • The Neurocommons
    • An open-source knowledge management research for biological research (part of the Science Commons Project).
    • Health Commons
    • "A coalition of parties interested in changing the way basic science is translated into the understanding and improvement of human health", by sharing knowledge, data and services among coalition members (part of the Science Commons Project).
    • PFAAT (Protein Family Alignment Annotation Tool
    • "Pfaat is a Java application that allows one to edit, analyze, and annotate multiple sequence alignments. The annotation features are a key component as they provide a framework to for further sequence, structure and statistical analysis."

  • Distributed Processing
    • MapReduce
    • A software framework from Google for distributed processing of very large data sets (terabytes to petabytes) using commodity-grade hardware.
    • Hadoop
    • An open-source implementation of the MapReduce distributed processing framework in Java.
    • Yahoo Pig
    • An open-source platform for analyzing large data sets using a high-level language (Pig Latin) on top of Hadoop.
    • HBase
    • An open-source implementation of the Bigtable architecture from Google.
    • Lucene
    • An open-source full-text indexing and searching software.

  • Ontologies & databasets
      • ChEBI (Chemical Entities of Biological Interest)
      • A "dictionary" of molecular entities focused on small chemical compounds.
      • Drug interaction
        • ToxNet
        • A number of databases on toxicology, hazardous chemicals, environmental health, and toxic releases.
        • MATADOR (Manually Annotated Targets and Drugs Online Resource
      • Protein ontologies & datasets
        • UniProt (The Universal Protein Resource )
        • A comprehensive resource for protein sequence and annotation data in various formats (PSI-MI, FASTA, RDF, etc.).
        • DIP (Database of Interacting Proteins)
        • IntAct
        • IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.
        • MPact
        • Contains yeast protein-protein interaction data in the PSI-MI format.
        • MINT
        • The Molecular INTeraction database -- "experimentally verified protein-protein interactions mined from the scientific literature by expert curators".
        • Cerep
        • A company providing in vitro pharmacology data & services.
      • BioPax
      • An OWL ontology as a data exchange format for biological pathway data.
      • The Gene Ontology
      • A comprehensive, structured, controlled vocabulary describing genes, gene products and sequences (cellular component, biological process and molecular function).
      • The NCBI Taxonomy
      • A comprehensive taxonomy of living organisms.
      • The Open Biomedical Ontologies
      • A collaborative repository of ontologies of biomedical interests.

  • Relevant documents/papers

  • Related conferences
    • CSB'08
    • 7th Annual International Conference on Computational Systems Bioinformatics
    • CCGrid'08
    • 8th IEEE International Symposium on Cluster Computing and the Grid
    • CIDR
    • Conference on Innovative Data Systems Research
    • CIKM
    • Conference on Information and Knowledge Management
    • C-SHALS'08
    • Conference on Semantics in Healthcare & Life Sciences
    • DASFAA'09
    • Database Systems for Advanced Applications
    • DILS'08
    • Conference on Data Integration in the Life Sciences 2008
    • EKAW'08
    • 16th International Conference on Knowledge Engineering and Knowledge Management
    • e-Science'08
    • 4th IEEE International Conference on e-Science
    • ESWC'08
    • 5th European Semantic Web Conference
    • ICDE'09
    • 25th International Conference on Data Engineering
    • Grid'08
    • 9th IEEE/ACM International Conference on Grid Computing
    • IDA'09
    • 8th International Symposium on Intelligent Data Analysis
    • ISMB'09
    • 17th Annual International Conference on Intelligent Systems for Molecular Biology
    • ISWC'08
    • 7th International Semantic Web Conference
    • InfoVis
    • IEEE Information Visualization Conference
    • KR'08
    • 11th International Conference on Principles of Knowledge Representation and Reasoning
    • PAKDD'08
    • Pacific-Asia Conference on Knowledge Discovery and Data Mining
    • SIGMOD/PODS'09
    • ACM Symposium on Principles of Database Systems
    • RECOMB'08
    • 12th Annual International Conference on Research in Computational Molecular Biology
    • SIGKDD
    • ACM International Conference on Knowledge Discovery and Data Mining
    • SIGMOD'09
    • ACM Special Interrest group on Management of Data Conference
    • SMBM'08
    • Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008)
    • SSDBM'08
    • 20th International Conference on Scientific and Statistical Database Management
    • VIS'08
    • IEEE Visualization
    • VLDB'09
    • 35th International Conference on Very Large Databases
    • WISE
    • International Conference on Web Information Systems Engineering
    • WWW'09
    • 18th International World Wide Web Conference