Difference between revisions of "Software"
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The live Phenoscape Knowledgebase is available at http://kb.phenoscape.org/. It makes use of the following software projects: | The live Phenoscape Knowledgebase is available at http://kb.phenoscape.org/. It makes use of the following software projects: | ||
* [http://berkeleybop.org/obd/ OBD] - an ontology-driven datastore developed by the [http://www.berkeleybop.org/ 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 [http://obo.svn.sourceforge.net/svnroot/obo/OBDAPI/trunk OBD source code]. | * [http://berkeleybop.org/obd/ OBD] - an ontology-driven datastore developed by the [http://www.berkeleybop.org/ 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 [http://obo.svn.sourceforge.net/svnroot/obo/OBDAPI/trunk OBD source code]. | ||
| − | * Phenoscape OBD data services | + | * [https://github.com/phenoscape/PhenoscapeOBD-WS 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 make use of mostly standard SQL queries and present a [http://en.wikipedia.org/wiki/Representational_State_Transfer RESTful] service interface using [http://www.restlet.org/ Restlet]. The specifications of these services are detailed in [[Data Services]]. |
* Phenoscape web UI | * Phenoscape web UI | ||
* Phenoscape data loader | * Phenoscape data loader | ||
===RDF-OWL version (in development)=== | ===RDF-OWL version (in development)=== | ||
Revision as of 20:20, 16 April 2012
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 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
- Phenoscape data loader
