Informatics
This page provides a broad overview of our informatics activities. Phenoscape supports open development processes and collaboration. All source code we create is available from open source repositories such as Sourceforge, we work with existing open-source projects whenever possible.
Contents
Phenoscape Software Components
Phenex curation tool
Phenex is an application for annotating character matrix files with ontology terms to describe phenotypes and identify taxa. Phenex is a Java application based on code from the OBO-Edit and Phenote projects. While still under development, Phenex is ready for use and enables our ongoing data curation activities.
Data services built on OBD
We are adopting OBD as the ontology-driven datastore for our phenotype annotations. We are collaborating with the Berkeley Bioinformatics Open-source Projects group in driving future development of OBD. We are also developing a suite of web services on top of OBD to serve as a data access API and foundation for our user-oriented Phenoscape web application. These web services make use of the OBD Java API and present a RESTful service interface using Restlet.
Phenoscape web UI
The Phenoscape web application will allow scientists to browse and query the phenotype annotations as well as the supporting ontologies. Initially, the query capabilities will concentrate on implementing a select set of "use-cases", research questions that show the utility of the approach. Ultimately, we will build interfaces that allow researchers to ask open-ended questions of the data. The web application is being developed using Ruby on Rails and accesses phenotype data and ontology information via our OBD web services.
View our Software Roadmap for more development plans and progress.
- An editor to create, maintain, and manage the taxonomy of Ostariophysi. We will focus on a reference taxonomy derived from the Catalog of Fishes.
A taxonomy is a hypothesis about the phylogeny of clades of organisms, and as such we need to allow ultimately for different taxonomies that a user can choose from. - An editor to create, maintain, and manage the anatomical ontology for Ostariophysi (TAO).
