- 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
- Distributed Processing
A software framework from Google for distributed processing of very large data sets (terabytes
to petabytes) using commodity-grade hardware.
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.
An open-source implementation of the Bigtable architecture from Google.
An open-source full-text indexing and searching software.
- Ontologies & databasets
- ChEBI (Chemical Entities of Biological
A "dictionary" of molecular entities focused on small chemical compounds.
- Drug interaction
A number of databases on toxicology, hazardous chemicals, environmental health, and
- 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 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.
Contains yeast protein-protein interaction data in the PSI-MI format.
The Molecular INTeraction database -- "experimentally verified protein-protein
interactions mined from the scientific literature by expert curators".
A company providing in vitro pharmacology data & services.
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
- M. Scott Marshall and Eric Prud'hommeaux (editors), A
Prototype Knowledge Base for the Life Sciences, W3C Interest Group Note.
- Matthias Samwald and Kei-Hoi Cheung (editors), Experiences with the conversion of
SenseLab databases to RDF/OWL, W3C Interest Group Note.
- David B. Searls,Data
Integration: Challenges for Drug Discovery, Nature Reviews Drug Discovery, 2005. 4(1): p45-58.
- Ted Slater, Christopher Bouton, and Enoch S. Huang, Beyond Data Integration, Drug Discovery Today,
- Related conferences
7th Annual International Conference on Computational Systems Bioinformatics
8th IEEE International Symposium on Cluster Computing and the Grid
Conference on Innovative Data Systems Research
Conference on Information and Knowledge Management
Conference on Semantics in Healthcare & Life Sciences
Database Systems for Advanced Applications
Conference on Data Integration in the Life Sciences 2008
16th International Conference on Knowledge Engineering and Knowledge Management
4th IEEE International Conference on e-Science
5th European Semantic Web Conference
25th International Conference on Data Engineering
9th IEEE/ACM International Conference on Grid Computing
8th International Symposium on Intelligent Data Analysis
17th Annual International Conference on Intelligent Systems for Molecular Biology
7th International Semantic Web Conference
IEEE Information Visualization Conference
11th International Conference on Principles of Knowledge Representation and Reasoning
Pacific-Asia Conference on Knowledge Discovery and Data Mining
ACM Symposium on Principles of Database Systems
12th Annual International Conference on Research in Computational Molecular Biology
ACM International Conference on Knowledge Discovery and Data Mining
ACM Special Interrest group on Management of Data Conference
Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008)
20th International Conference on Scientific and Statistical Database Management
35th International Conference on Very Large Databases
International Conference on Web Information Systems Engineering
18th International World Wide Web Conference