Check the News section for up2date information on RDFScape !!!

Check the News section for up2date information on RDFScape !!!

This project is primarily funded by Leaf Bioscience s.r.l. as an activity in the context of the EU DC-THERA Network of Excellence.

The conception and initial development of this project took place at the Systems Biology Unit of the Institut Pasteur and was partially funded by ESF.

The conception and initial development of this project took place at the Systems Biology Unit of the Institut Pasteur? and was partially funded by ESF.

Current version of RDFScape is 0.4.1 and offers a rich set of features to query, visualize and overlay ontologies on other Cytoscape networks.

RDFScape is released as LGPL. Follow the link to Releases to download it . It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.

RDFScape is released as LGPL. Follow the link to Releases to download it i . It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.

RDFScape is released as LGPL. ++larger++ Follow the link to Releases to download it . It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.

Unlike other ontology-based features in Cytoscape, RDFScape doesn't consider ontologies as annotation, but as a knowledge-base that can be interpreted through standard inference processes and through custom inference rules. The result is that ontologies can be interpreted for specific analysis needs. For instance, a pathway ontology such as biopax can be easily abstracted to an interaction network. Or as a causal network, once of notion on causal effect is defined on the ontology.

RDFScape is a project that brings Semantic Web "features" to the popular Systems Biology software Cytoscape. It allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape. A full list of features is reporte in Features.

Unlike other ontology-based features in Cytoscape, RDFScape doesn't consider ontologies as annotation, but as a knowledge-base that can be interpreted through standard inference processes and through custom inference rules. The result is that ontologies can be interpreted for specific analysis needs. For instance, a pathway ontology such as biopaxcan be easily abstracted to an interaction network. Or as a causal network, once of notion on causal effect is defined on the ontology.

Current version of RDFScape is 0.4 and offers a rich set of features to query, visualize and overlay ontologies on other Cytoscape networks.

RDFScape is released as LGPL. Follow the link to Releases to download it . It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.

7/2/2008

This project is primarily funded by Leaf Bioscience s.r.l. as an activity in the context of the EU DC-THERA Network of Excellence.

The conception and initial debvelopment of this project took place at the Systems Biology Unit of the Institut Pasteur and was partially funded by ESF.

RDFScape depends on the following software and libraries:

Unlike other ontology-based features in Cytoscape, RDFScape doesn't condider ontologies as annotation, but as a knowledge-base that can be interpreted through standard inference processes and through custom inference rules. The result is that ontologies can be interpreted for specific analysis needs. For instance, a pathway ontology such as biopax can be easily abstracted to an interaction network. Or as a causal network, once of notion on causal effect is defined on the ontology.

Beside this, RDFScape offers reach query capabilities on ontologies (SPARQL,RDQL,Strings, interactive browsing) and a customizable visualization features.

Current version of RDFScape is 0.4 and offers a rich set of feature to query, visualize and overlay ontologies on other Cytoscape networks. Future versions of RDFScape will address the interpretation of experimental data given ontological a-priori information.

RDFScape is released as LGPL. Follow the link to Releases to download it. It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.

Beside this, RDFScape offers reach query capabilities on ontologies (SPARQL,RDQL,Strings, interactive browsing) and a customizable visualization features.

RDFScape is a project that brings semantic web "features" to the popular systems biology software Cytoscape. It allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape. A full list of featurtes is reporte in Features.

Unlike other ontology-based features in Cytoscape, RDFScape doesn't condider ontologies as annotation, but as a knowledge-base that can be interpreted through standard inference processes and through custom inference rules. The result is that ontologies can be interpreted for specific analysis needs. For instance, a pathway ontology such as biopax can be easily abstracted to an interaction network. Or as a causal network, once of notion on causal effect is defined on the ontology.

RDFScape is a project that brings semantic web "features" to the popular systems biology software Cytoscape.

http://www.sgtp.net/AndreaSplendiani/ext/rdfscape/newRDFScapeScreenshot.png

(:keywords semantic web, systems biology, ontology, OWL, RDF, biopax, pathways, Andrea Splendiani, bioinformatics :)

• The Systems Biology analysis and visualization software Cytoscape
• The RDF / Semantic web library Jena
• The OWL reasoner Pellet

RDFScape depends on the following softawre and libraries:

 * The Systems Biology analysis and visualization software Cytoscape 
 * The RDF / Semantic web libraryJena 
 * The OWL reasoner Pellet 

For a description of version requirements refer to Dependencies

X/X/2008

RDFScape is a project that brings semantic web "features" to the popular systems biology software Cytoscape.

(:keywords semantic web, systems biology, ontology, OWL, RDF, biopax, pathways :)

 * Jena 2.5.4 notes on Jena version

NOTE: RDFScape is a project in continous development. It is intended for knowledgable people interested in exploring new applications of semantic web technologies in the life science area. At least at this stage it is not easy to use for the general public. Interested people are invited to contact the author to build a small focused user base.

 * Cytoscape 2.5.1 notes on cytoscape version

 * Pellet 1.5.1 [4notes on Pellet version]] 

• SPARQL/RDQL/Class based queries

Features include:

Features include!:

NOTE: RDFScape is a project in continous development. It is intended for knowledgable users interested in exploring new applications of semantic web technologies in the life science area. At least at this stage there is not easy to use for the general public. Interested people are invited to contact the author to build a small focused user base.

NOTE: RDFScape is a project in continous development. It is intended for knowledgable users interested in exploring new applications of semantic web technologies in the life science area. At least at this stage there is not easy to use for the general public. Interested people are invited to contact the author to build a small focused user base.

For more informations mail andrea.splendiani -> univ-rennes1.fr dot net.

 * Cytoscape 2.4.1 notes on cytoscape version
 * Jena 2.5.2 notes on Jena version
 * Pellet 1.5 notes on Pellet version 

• At the time being, this project is partially founded by ESF foundation and Leaf Bioscience s.r.l. (through EU DC-THERA project) (the total does not account for more than a part-time position). It is developed within the Systems Biology Unit of the Institut Pasteur.

 * Cytoscape 2.4.1 notes on cytoscape version

 * Pellet 1.5 notes on Pellet version 

Current version of RDFScape is available on svn. It relies on:

 * Pellet svn notes on Pellet version 

while the basic stable functionalities are present, a set of minor improvements are underway, refers to binaries 0.2.x for the last uptodate binary available.

7/6/2007

• SPAQRL/RDQL/Class based queries

• Extension of term scoring function (From terms enrichment to ontology patterns enrichment) (under development)
• Inference of statements from data (under development)

• SPQRL/RDQL/Class based queries

• Reasoning (RDFS/OWL) + custom rules (Jena rule reasoner + Pellet)
• Cytoscape graph annotation with ontologies (including inferred statements)
• Extension of term scoring function (From terms enrichment to ontology patterns enrichment)

The first version of RDFScape was released in mid2006, with a set of the above functionalities disabled (it has been used in its entierity as proof of concept only). Following this release, a set of improvements was made, but changes in the technologies RDFSCape relies to have made the project undelirvrable.

Last released version depends on:

 * Cytoscape 2.2
 * Jena 2.4
 * Pellet 1.3

Work is underway to port RDFScape to the current version of the required technologies:

 * Cytoscape 2.4 notes on cytoscape version
 * Jena 2.5.2 notes on Jena version
 * Pellet 1.4 notes on Pellet version

Next release will be announced here. People interested in the project and willing to contribute to testing are encouraged to contact the author via email.

25/4/2007

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Note on RDFScape code availability / project status.

We first developed an early prototype with all functionalities implemented as a proof-of-concept (including functionalities stated as "future" above). The code-base for this version is currently not available on this website.

In a second time we started refactoring. A subset of the original project was released as v. 0.1(1) and on revisions on the branch cytoscape-2.2.

From the on we have targeted the rest of the functionalities (including improvements and bug-fix) to Cytoscape v. 2.4 (Java 1.5, due in december). This development is on the main trunk of subversion.

Version 0.1.1 is the last version working on Cytoscape 2.2.

Cytoscape v. 2.3 is not supported.

For more informations mail andrea -> sgtp dot net.

• v.0.1 First version available to use
• v.0.2- Revised versions after testing/refactoring
• v.0.5 Integration of new features
• v.0.6- Revised version after testing/refactoring

• The software is in eary alpha. Although usuable, is not well tested and some bugs make it not easily usable to non-experienced users.
• Being very research oriented, the numbering of versions doesn't follow srict rules. Tentatively:

 * v.0.1  First version available to use
 * v.0.2- Revised versions after testing/refactoring
 * v.0.5  Integration of new features
 * v.0.6- Revised version after testing/refactoring

• Target of the first public "quality" release is the set of functionalities in v.0.1, expected to be of acceptable quality by v.0.3

(:counter:)

(:counter:)

(:includeurl http://www.sgtp.net/AndreaSplendiani/RDFScapecounter.php :)

• At the time being, this project is partially founded by ESF foundation and Leaf Bioscience s.r.l. (through EU DC-THERA project) (the total does not account for more than a part-time position). It is developed within the Systems Biology Unit of the Institut Pasteur.

(:includeurl http://www.sgtp.net/AndreaSplendiani/RDFScapecounter.php :)

RDFScape (is this the final name ?) is a project that brings semantic web "features" to the popular systems biology software Cytoscape.

Features include:

• SPQRL/RDQL/Custom queries
• Graphical quey interface (users can draw patterns of graphs with "variables").
• Interactive browsing of ontologies
• Selection/Color by namespace
• Reasoning + custom rules
• 1-n correspondence between URIs and elements in the graph (useful for currency metabolites)
• Merging of information in ontologies with information in a generic graph

A future release will include:

• Extension of term scoring function
• Inference of statements from data

This is a first summary, more to come.

Some notes:

• The software is in eary alpha. Although usuable, is not well tested and some bugs present make quite unusable to non-experienced users. Hence, it is not released yet in binary or source code. It is anyway available to interested people who my provide feedback (ask via mail). Expect a first release (GPL) within 2-3 months, and no activity in the next month (this is dated 31st March, 2006).
• There is not a complete explanation of the project at the time, some screenshots may help to get a better idea (not posted yet).
• At the time being, this project is partially founded by ESF foundation and Leaf Bioscience s.r.l. (through EU DC-THERA project) (the total does not account for more than a part-time position).

For more informations mail andrea -> pasteur dot fr.