Difference between revisions of "Informatics"
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| − | 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. | + | 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== | ==Phenoscape Software Components== | ||
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* An editor to create, maintain, and manage the taxonomy of Ostariophysi. We will focus on a reference taxonomy derived from the [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes].<br/>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 taxonomy of Ostariophysi. We will focus on a reference taxonomy derived from the [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes].<br/>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). | * An editor to create, maintain, and manage the anatomical ontology for Ostariophysi (TAO). | ||
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* 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.<br/>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. | * 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.<br/>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. | ||
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==[[Software roadmap]]== | ==[[Software roadmap]]== | ||
Revision as of 17:03, 5 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, we work with existing open-source projects whenever possible.
Contents
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
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.
