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.

One of the chief objectives of the Phenoscape project is to present a centralized repository to store annotations entered by ichthyologists. These annotations can be queried from a user interface and used to answer Driving Research Questions and for advanced Phenoscape use cases. The following tools which are under various stages of development, will serve to realize this objective.

Phenoscape software components

Phenex curation tool

Phenex is a platform-independent desktop application for annotating character-by-taxon matrices with ontology terms. Phenex allows a user to describe phenotypic variation among taxa (or specimens) using Entity-Quality syntax and write the data to a NeXML file. Phenex is written in Java, based on code from the OBO-Edit and Phenote project, and is being released under an open-source license. It can be configured to load user-selected ontologies, and in this way can be adapted to data curation in different taxonomic groups.

Phenoscape data repository

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. The ontological definitions of all the terms used in the annotation stage (on Phenex) and the annotations themselves are stored in the Phenoscape data repository. In sequential order, the term definitions in all the ontologies are first downloaded and stored in the database. Next, the annotations of phenotypes are downloaded from ZFIN and Phenoscape, post composed and stored in the database. An outline of these two stages is described in the Phenoscape data loader section. Then, the OBD Reasoner is used to extract inferences from the annotations and definitions in the OBD Phenoscape database. These inferences are added to the database as well.

Data services built on 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 mostly standard SQL Queries and present a RESTful service interface using Restlet. The specifications of these services are detailed in Data Services.

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.

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.

Source code

The software source code is in part being contributed back directly to a variety of existing projects we build upon, and mostly deposited in the SourceForge.net svn repository.

• Phenex:
  • Browse source
  • Code checkout: svn co https://obo.svn.sourceforge.net/svnroot/obo/phenex/trunk
• Database and database loading:
  • Browse source
  • Code check out: svn co https://obo.svn.sourceforge.net/svnroot/obo/OBDAPI/trunk/scripts
  • Some unit tests are in the process of being migrated from the old location:
    • Code checkout: svn co https://phenoscape.svn.sourceforge.net/svnroot/phenoscape/trunk/src/PhenoscapeDataLoader/test
    • Browse source
• Data services and middleware:
  • Data model and database access API (OBD-API):
    • Browse source
    • Code check out: svn co https://obo.svn.sourceforge.net/svnroot/obo/OBDAPI/trunk
  • Web-services (OBD-WS):
    • Browse source
    • Code checkout: svn co https://obo.svn.sourceforge.net/svnroot/obo/OBD-WS/trunk
• Web-based user interface (Knowledge Base):
  • Browse source
  • Code checkout: svn co https://phenoscape.svn.sourceforge.net/svnroot/phenoscape/trunk/src/PhenoscapeWeb
• Ontology conversion and management:
  • TTOUpdate
    • Browse source
    • Code checkout: svn co https://obo.svn.sourceforge.net/svnroot/phenoscape/trunk/tools/TTOUpdate
  • Synchronization Tool
    • Browse source
    • Code checkout: svn co https://phenoscape.svn.sourceforge.net/svnroot/phenoscape/trunk/src/SynchronizationTool
• Other scripts and small tools:

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.