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, and we work with existing open-source projects whenever possible. Development plans can be found at our software roadmap.

Phenoscape software components

Phenoscape comprises a front end user interface where biologists enter annotations of curated publications. This data is stored in a backend relational database for subsequent retrieval and processing

Front end user interface tools

A summary of the front end user interface tools being developed primarily by Jim Balhoff

Data Repository and Data Services

A summary of the backend database and the data services being implemented primarily by Cartik Kothari

Affiliated projects

OBO-Edit

We are using the OBO-Edit ontology editor to develop and maintain our ontologies such as the Teleost Anatomy Ontology and the Teleost Taxonomy Ontology.

NeXML

Phenex saves character matrix data using the new evolutionary data standard NeXML. NeXML is an XML Schema and has robust facilities for embedding additional data, such as our phenotype annotations, within a traditional character-by-taxon matrix.