Working Group
The continuing growth of bioinformatics and genomics presents an opportunity for expanding the application of evolutionary methods, with respect to both the amount and the variety of systematic comparative data. Though evolutionary biologists have developed powerful tools for inferring phylogenies, detecting selection, and so on, integrating evolutionary methodology into workflows in bioinformatics does not depend so much on the power of analysis tools as it does on a well developed informatics infrastructure: software and standards for data exchange, visualization, input-and-output, editing, control, and storage-and-retrieval. We propose a working group to facilitate (directly and indirectly) the development of this infrastructure. Through a series of four meetings, each with presentations, discussion, and actual software development, the working group will build on the foundation provided by current analysis tools and available standards. The working group will gather data sets that represent canonical use-cases; remedy inconsistencies in current NEXUS implementations, and resolve ambiguities; develop translators between NEXUS and other data formats; develop a back-end storage schema; and translate actual content from existing databases of sequence family data into a standard form. The working group will develop and implement revisions to the NEXUS standard (perhaps including an XML replacement), and will lay the ground-work for a new generation of standards by identifying different data models used in different types of evolutionary analyses, and by documenting use-cases that fall beyond the reach of current standards.
Evolutionary informatics: supporting interoperability in evolutionary analysis
| PI(s): | Arlin Stoltzfus (National Institute of Standards and Technology) Rutger Vos (University of British Columbia) |
| Start Date: | 1-Sep-2006 |
| End Date: | 31-Aug-2008 |
| Keywords: | database, genomics, phylogenetics, software, comparative methods |
The continuing growth of bioinformatics and genomics presents an opportunity for expanding the application of evolutionary methods, with respect to both the amount and the variety of systematic comparative data. Though evolutionary biologists have developed powerful tools for inferring phylogenies, detecting selection, and so on, integrating evolutionary methodology into workflows in bioinformatics does not depend so much on the power of analysis tools as it does on a well developed informatics infrastructure: software and standards for data exchange, visualization, input-and-output, editing, control, and storage-and-retrieval. We propose a working group to facilitate (directly and indirectly) the development of this infrastructure. Through a series of four meetings, each with presentations, discussion, and actual software development, the working group will build on the foundation provided by current analysis tools and available standards. The working group will gather data sets that represent canonical use-cases; remedy inconsistencies in current NEXUS implementations, and resolve ambiguities; develop translators between NEXUS and other data formats; develop a back-end storage schema; and translate actual content from existing databases of sequence family data into a standard form. The working group will develop and implement revisions to the NEXUS standard (perhaps including an XML replacement), and will lay the ground-work for a new generation of standards by identifying different data models used in different types of evolutionary analyses, and by documenting use-cases that fall beyond the reach of current standards.
Related products
Software and Datasets- Qiu, WG. 2007. A collection of data sets for phylogenetic analysis.
- Qiu, WG. 2008. A new BioPerl module for reading nexml file. Bio::TreeIO:nexml
- Prosdocimi, F., B. Chisham, E. Pontelli, J.D. Thompson, and A. Stoltzfus. 2008. Comparative Data Analysis Ontology (CDAO), an OWL-DL ontology for evolutionary comparative analysis.
- Stoltzfus, A. 2008. MIAPA annotation tool (proof-of-concept software). To demonstrate the potential for users to construct their own ontology-based MIAPA annotations, as in the knowledge capture experiment below, we have created a proof-of-concept application by adapting Phenote. The result is an interactive graphical tool for user-generated, ontology-bound MIAPA annotations.
- Lapp, H., Vos R. (2008) PhyloWS: A standard web service-interface for phylogenetic data and service providers.
- NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata R. A. Vos, J. P. Balhoff, J. A. Caravas, M. T. Holder, H. Lapp, W. P. Maddison, P. E. Midford, A. Priyam, J. Sukumaran, X. Xia and A. Stoltzfus. 2012. NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata, Systematic Biology, volume 61, issue 4, pp. 675-689
- CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis Brandon Chisham, Ben Wright, Trung Le, Tran Son and Enrico Pontelli. 2011, CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis, BMC Bioinformatics, volume 12, issue 1, pp. 98
- Initial Implementation of a Comparative Data Analysis Ontology Prosdocimi, F., B. Chisham, E. Pontelli, J.D. Thompson, and A. Stoltzfu (2009). Initial Implementation of a Comparative Data Analysis Ontology. Evolutionary Bioinformatics 5: 47-56.
- The 2006 NESCent Phyloinformatics Hackathon: A Field Report Lapp, H., S. Bala, J.P. Balhoff, et al. (2007). The 2006 NESCent phyloinformatics hackathon: A field report. Evolutionary Bioinformatics 3: 287�296.
