Diversity and Phenotypes
GMOD's capabilities in managing phenotype and natural diversity data is scattered across partially redundant and outdated modules, does not support modern ontology-based entity-quality data, and lacks a web-interface. The sophisticated phenotype annotation tools that do exist cannot interface with Chado, GMOD's central relational data model. Yet, phenotypic and genetic diversity data are central to many evolutionary research questions.
A Natural Diversity Module initiative to address at least the deficiencies within Chado has already formed earlier this year. Several key developers (one of the original developers of the module, and the developer of Phenex, a phenotype curation tool) are already local to NESCent, and so the hackathon provides a unique opportunity to review and refine the natural diversity data model face-to-face, and to integrate it with an updated and reconciled phenotype module. A recently reported prototype of a Chado data adapter for Phenote, GMODs phenotype annotation tool, could be generalized to become the data persistence interface for such data.
Aside from the data model deficiencies, the ANISEED project has started efforts to generalize its sophisticated atlas/image-based web interface for phenotype data, and to make it operate on top of Chado. The hackathon could harness this synergy to help this effort leap forward, which could ultimately provide GMOD with the currently missing web-interface for such data.
Participants are encouraged to make any test datasets you have available for the hackathon. NESCent has created an FTP repository:
with Objectives subdirectories for these files. Directions on how to upload files was sent to the mailing list on 2010/10/28.
Please describe on this web page any datasets you have shared that are related to this objective.
- Describe your dataset here.
Please add your name below.
- Seth Redmond
- Vladimir Gapeyev
- Matt Yoder
- Jim Balhoff
- Yuri Bendana
- Maren Friesen
- Terry Casstevens
- Delphine Dauga
- Data display by geolocation via google maps
- Data display of phenotypes via google motion charts
- Data display of phenotypes via protovis
- Web app for creating data sheets/entering data into database
- GBrowse GWAS tracks -> phenotype visualizations
- Whole-genome plots for GWAS/pop gen -> GBrowse
- Genomic locations of a statistic -> select cutoff and get all genes within X Kb (.csv) -> GO enrichment tests, expression pattern enrichment
- Improvement: For a given visualization, have a stable weblink to share with collaborators with annotation (like "Star" with comments)
- Front end for Chado Natural Diversity