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.

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.

Phenoscape web UI

• 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).
• A database and web-application to store the taxonomies, ontologies, and phenotype data. The web-application will allow scientists to browse and query the ontologies as well as the phenotype data.
  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.

APIs

Proposals

• Ontology Data Service API Description