Difference between revisions of "Informatics"

From phenoscape
(→‎[http://www.phenoscape.org/wiki/Informatics/Frontend Front end user interface tools])
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A summary of the front end user interface tools being developed primarily by Jim Balhoff
 
A summary of the front end user interface tools being developed primarily by Jim Balhoff
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===Phenex curation tool===
 
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[[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 [http://oboedit.org/ OBO-Edit] and [http://www.phenote.org/ Phenote] projects.  While still under development, Phenex is ready for use and enables our ongoing data curation activities.
 
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===Data services built on OBD===
 
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We are adopting [http://www.bioontology.org/wiki/index.php/OBD:Main_Page OBD] as the ontology-driven datastore for our phenotype annotations.  We are collaborating with the [http://www.berkeleybop.org/ 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 [http://en.wikipedia.org/wiki/Representational_State_Transfer RESTful] service interface using [http://www.restlet.org/ Restlet].
 
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===Phenoscape web UI===
 
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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 [http://www.rubyonrails.org/ Ruby on Rails] and accesses phenotype data and ontology information via our OBD web services.
 
  
 
==[[Data Repository and Data Services]]==
 
==[[Data Repository and Data Services]]==

Revision as of 16:47, 10 November 2008

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.

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