Software

This page provides a broad overview of our software development activities. Phenoscape supports open development processes and collaboration. All source code we create is available from open source repositories such as Github and Sourceforge, and we work with existing open-source projects whenever possible.

Phenoscape Knowledgebase

One of the chief objectives of the Phenoscape project is to present a centralized repository to store evolutionary phenotype annotations entered by curators and also integrate relevant data imported from partner projects. The Knowledgebase consists of a back-end semantic data store, a web service application which provides a query API for the data, a web application user interface allowing exploration of the Knowledgebase, and accessory tools for loading data.

Production version

The live Phenoscape Knowledgebase is available at http://kb.phenoscape.org/. It makes use of the following software projects:

• OBD - an ontology-driven datastore developed by the Berkeley Bioinformatics Open-source Projects group. It provides a generic schema for storing ontologies and semantic data expressed with those ontologies. It also includes an automated reasoner used to materialize inferred knowledge into the datastore. The master build script for loading the Phenoscape Knowledgebase is included within the OBD source code.
• Phenoscape OBD data services - 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 present a RESTful service interface using the Restlet Java API. The specifications of these services are detailed in Data Services.
• Phenoscape web UI - a web application providing user-friendly interfaces for browsing and querying data and ontologies within the Knowledgebase.
• Phenoscape data loader - a Java library providing translations of various data inputs into the OBD model, used within the OBD build script.

RDF-OWL version (in development)

To meet new requirements for scalability, reasoning expressivity, and support for linked data standards, we are developing a new Knowledgebase infrastructure based on RDF and OWL reasoning. Some in-progress components:

• Phenoscape content in RDF (rapidly evolving)
• Reasoning strategy overview

Phenex

Phenex is ontology annotation software tailored for phenotype annotation of evolutionary character matrices. It saves ontology annotations alongside traditional character matrix data using the new NeXML format standard for evolutionary data.

Ontology tools

Synchronization Tool

The Synchronization Tool is a plug-in for OBO-Edit which aids in keeping the Teleost Anatomy Ontology and the Zebrafish Anatomy Ontology consistent with each other.