The Biofinity Project: An Extensible Semantic Bridge between Biodiversity and Genomics

SCOTT, S. D.; SOH, L-K; MORIYAMA, E; OCAMPO, F. C.; JAMESON. M.L; HARRIS, S; COTTINGHAM, I; BADEN, S.; ECK, A.; LAM, DERRIK; ANDERSON, C.; MO, Y.; CLARK, D.; MOORE, M.

Montpelier, Francia

Congreso; Taxonomic Databases Working Group Annual Meeting; 2009

Biodiversity Informatic Standars, TDWG

Despite the enormous amounts of biological data available, researchers are often hard-pressed to fully exploit it due to heterogeneity, large scale, and decentralization.  We present the first release of The Biofinity Project, part of the Semantic Cyberinfrastructure for Investigation and Discovery (SCID) Project, as our answer to research roadblocks raised by decentralized, large-scale, heterogeneous datasets.Our current version of the Biofinity Project is at http://biofinity.unl.edu.  It unifies genomics and biodiversity data, thereby empowering investigation and discovery in both fields.  The current release of the Biofinity Project has the following features:1. It unifies two biodiversity databases (on scarab beetles) and one fungal genomics database, all from the project´s PIs.The databases are both browsable and searchable. 2. It offers a Google Maps-based mapping tool, which allows for study of densities of collected specimens, and the climate and topological conditions of the regions where these specimens were collected. 3. It offers the BLAST sequence similarity search tool, which runs in parallel on a 516-core computer cluster called PrairieFire. 4. It offers our new “My Lab” feature, which allows research groups to create an online laboratory database and set up its own user accounts.  Using My Lab, research groups can manage its users´ access to data, upload and modify existing datasets, and publish private lab data to the Biofinity Project ontologies—all from a single, easy-to-use web interface.  5. All the aforementioned tools and datasets are integrated under a single user interface.All functionality is accessible via a web browser.  An interface to search and browse the data is also available for the iPhone and iPod Touch.In the next few months, we will add the following features: 1. Full access to the large, publicly-available datasets at NCBI and GBIF. 2. More data sets from other Biofinity Project users, including messenger RNA data. 3. Additional bioinformatics tools, such as GARP for population modeling and CLUSTALW for multiple sequence alignment. 4. A users-only wiki for concisely describing knowledge gleaned from a user´s scientific studies, which can be made available to other Biofinity Project users at the same time that the user´s paper is published.In addition to adding even more bioinformatics databases and tools, in the long term we plan to add:  1. More intelligence in the Biofinity Project user interface to track each user´s use of the Biofinity Project, and offer suggestions as to what other tools and data sets may be useful to that user´s work. 2. Automated support for new users to quickly integrate their new data sets into the Biofinity Project and federate it with the existing data.