Bioinformatics - Activities
Objectives
- to support the organization, integration, and dissemination of information by providing hardware and software infrastructure to manage sequence, expression, and structural information produced by the Consortium.
- to develop WWW enabled applications to foster collaboration and share data, common and customized sequence analysis tools to identify and characterize new protein sequences, and standard relational database techniques to manage and store protein sequence and expression data.
- to build a molecule-centric knowledgebase for organizing data available on target proteins from all of the research projects.
| Activity | Status | Contact |
| Cell Migration KnowledgeBase (CMKB) | in progress | cmckb-help@virginia.edu |
| Reactome | in progress | Lisa Matthews |
| Proteomics | in progress | W. Pearson/T. Laudeman |
| Gene Expression/Microarray | in progress | W. Pearson/T. Laudeman |
Cell Migration KnowledgeBase (CMKB)
The Cell Migration Knowledgebase (CMKB) is a database of keys facts about proteins, families, and complexes involved in cell migration. The CMKB provides a large amount of automated and curated data, collected from numerous online resources that are updated monthly. These data include names, synonyms, sequence information, summaries, CMC research data, reagents, structures, as well as protein family and complex details.
Our ultimate goal is to create a comprehensive database that will enable the cell migration community to conveniently access significant information about a molecule of interest. This will also serve as a stepping stone to pathway analysis and demonstrate how these molecules coordinate with one another during cell adhesion and movement.
Please contact David Abraham if you would like to author a protein, family or complex or if you would like to suggest the addition of a protein that is absent from the CMKB.
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Reactome
Reactome is a curated database of biological processes in humans. It covers biological pathways ranging from the basic processes of metabolism to high-level processes such as hormonal signalling. While Reactome is targeted at human pathways, it also includes many individual biochemical reactions from non-human systems such as rat, mouse, fugu fish and zebra fish. This makes the database relevant to the large number of researchers who work on model organisms. All the information in Reactome is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Our ontology ensures that the various events are linked in an appropriate spatial and temporal context.
The basic information in Reactome is provided by bench biologists who are experts in that domain of biology. The information is then managed and edited by the Reactome staff at CSHL and the EBI, and entered into a relational database. They are then reviewed by other biological researchers for consistency and accuracy. Following peer-review, the information is published to the web.
Reactome supersedes an earlier project called The Genome Knowledgebase and incorporates all the information previously available in its predecessor. Reactome sports a radically redesigned user interface in which the entire set of human pathways known to the database are represented as a series of constellations in a "starry sky." The starry sky can be used to navigate through the universe of human reactions and is invaluable to visualize connections between pathways, some of which will be surprising to biologists who are not familiar with pathways outside their domain of research.
The Bioinformatics group of the Cell Migration Consortium, in collaboration with Reactome, is developing a Flash-based user-friendly interface for utilizing available figures and drawings of signaling mechanisms, complex formation, and protein-protein interactions for incorporation and annotation of cell migration pathways for incorporation into Reactome and the CMKB.
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Proteomics
The Bioinformatics group of the Cell Migration Consortium has developed tools for mass spectrometry data management, analysis, and presentation for use by the Proteomics groups of the Protein Discovery Initiative. For data management, an experiment and analysis data is entered into a relational database. MS peptide results are compared to a human protein database and peptide hits are displayed in a comparison format. In addition, new search tools for identifying experiments, post-translational modifications, and protein hits have been developed.
Protein identification software is available under the MIT Open Source license from Dr. Bill Pearson.
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Gene Expression
The Bioinformatics groups has developed tools for microarray data management, analysis, and presentation for use by the Gene Expression group of the Protein Discovery Initiative.