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, and we work with existing open-source projects whenever possible.  Development plans can be found at our [[software roadmap]].  
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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, and we work with existing open-source projects whenever possible.  Development plans can be found at our [[software roadmap]].
  
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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.
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One of the chief objectives of the Phenoscape project is to present a centralized repository to store annotations entered by curators. 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==
 
==Phenoscape software components==
  
 
===Phenex curation tool===
 
===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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[[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 [http://oboedit.org/ OBO-Edit] and [http://www.phenote.org/ 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.
  
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===OBD Phenoscape data repository===
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===Phenoscape data repository===
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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. The ontological definitions of all the terms used in the annotation stage (on Phenex) and the annotations themselves are stored in the OBD Phenoscape database. 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 [http://zfin.org ZFIN] and [http://phenoscape.svn.sourceforge.net Phenoscape], post composed and stored in the database. An outline of these two stages is described in the [[Phenoscape data loader]] section. Lastly, 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.  
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We are adopting [http://berkeleybop.org/obd/ 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. 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 [http://zfin.org ZFIN] and [http://phenoscape.svn.sourceforge.net 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===
 
===Data services built on OBD===
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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]. The specifications of these services are detailed in [[Data Services]]
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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 [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===
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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.
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The [[Phenoscape web UI|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.
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===Synchronization Tool===
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The [[Synchronization Tool]] is a plug-in for [http://oboedit.org/ OBO-Edit] which aided in keeping the Teleost Anatomy Ontology (no longer in development) and the Zebrafish Anatomy Ontology consistent with each other.
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== Source code ==
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Phenoscape-created source code is primarily hosted at Github within the [http://github.com/phenoscape Phenoscape organization]. Some legacy projects and data are still hosted in [http://phenoscape.svn.sourceforge.net/viewvc/phenoscape our Sourceforge repository].
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Some code is being contributed back directly to a variety of existing projects we build upon, such as the [http://obo.svn.sourceforge.net/viewvc/obo/ OBO Subversion repository] on SourceForge.
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* Phenex:
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** [http://github.com/phenoscape/Phenex Github home]
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* Database and database loading:
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** [http://obo.svn.sourceforge.net/viewvc/obo/OBDAPI/trunk/scripts Browse source]
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** Code check out: <code>svn co http://obo.svn.sourceforge.net/svnroot/obo/OBDAPI/trunk</code>
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* Data services and middleware:
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** Data model and database access API (OBD-API):
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*** [http://obo.svn.sourceforge.net/viewvc/obo/OBDAPI/trunk Browse source]
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*** Code check out: <code>svn co http://obo.svn.sourceforge.net/svnroot/obo/OBDAPI/trunk</code>
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** Web-services (OBD-WS):
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*** [http://github.com/phenoscape/PhenoscapeOBD-WS Github home]
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* Web-based user interface ([http://kb.phenoscape.org Knowledge Base]):
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** [http://github.com/phenoscape/PhenoscapeWeb Github home]
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* Ontology conversion and management:
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** TTOUpdate
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*** [http://obo.svn.sourceforge.net/viewvc/phenoscape/trunk/tools/TTOUpdate Browse source]
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*** Code checkout: <code>svn co http://obo.svn.sourceforge.net/svnroot/phenoscape/trunk/tools/TTOUpdate</code>
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** Synchronization Tool
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*** [http://github.com/phenoscape/synctool-oboedit Github home]
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* Other scripts and small tools:
  
 
==Affiliated projects==
 
==Affiliated projects==
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===OBO-Edit===
 
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We are using the [http://oboedit.org/ OBO-Edit] ontology editor to develop and maintain our [[ontologies]] such as the Teleost Anatomy Ontology and the Teleost Taxonomy Ontology.
 
  
 
===NeXML===
 
===NeXML===
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Phenex saves character matrix data using the new evolutionary data standard [http://www.nexml.org/ 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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Phenex saves character matrix data using the evolutionary data standard [http://www.nexml.org/ 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.
  
 
[[Category:Informatics]]
 
[[Category:Informatics]]

Latest revision as of 22:14, 10 November 2012

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 curators. 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 aided in keeping the Teleost Anatomy Ontology (no longer in development) and the Zebrafish Anatomy Ontology consistent with each other.

Source code

Phenoscape-created source code is primarily hosted at Github within the Phenoscape organization. Some legacy projects and data are still hosted in our Sourceforge repository. Some code is being contributed back directly to a variety of existing projects we build upon, such as the OBO Subversion repository on SourceForge.

Affiliated projects

NeXML

Phenex saves character matrix data using the 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.

Retrieved from "https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Informatics&oldid=10332"