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January 31, 2011, at 12:26 PM by 149.155.3.120 -
Changed line 42 from:
(:includeurl http://www.sgtp.net/AndreaSplendiani/RDFScapecounter.php :)
to:
August 25, 2010, at 12:32 PM by 149.155.3.247 -
Changed lines 4-5 from:
!! Check the [[News]] section for up2date information on RDFScape !!!
to:
!! %center% %red% Check the [[News]] section for up2date information on RDFScape !!!
August 25, 2010, at 12:32 PM by 149.155.3.247 -
Added lines 3-5:

!! Check the [[News]] section for up2date information on RDFScape !!!
February 08, 2008, at 03:44 AM by 129.20.167.23 -
Changed lines 31-34 from:
This project is primarily funded by [[http://www.leafbioscience.com | Leaf Bioscience s.r.l.]] as an activity in the context of the [[http://www.dc-thera.org | EU DC-THERA]] Network of Excellence.

The conception and initial development of this project took place at the [[www.systemsbiology.fr | Systems Biology Unit of the Institut Pasteur]] and was partially funded by ESF.
to:
This project is primarily funded by [[http://www.leafbioscience.com | Leaf Bioscience s.r.l.]] as an activity in the context of the EU [[http://www.dc-thera.org | DC-THERA]] Network of Excellence.

The conception and initial development of this project took place at the [[http://www.systemsbiology.fr | Systems Biology Unit of the Institut Pasteur]] and was partially funded by [[http://www.esf.org |ESF]].
February 08, 2008, at 03:41 AM by 129.20.167.23 -
Changed lines 33-34 from:
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.
to:
The conception and initial development of this project took place at the [[www.systemsbiology.fr | Systems Biology Unit of the Institut Pasteur]] and was partially funded by ESF.
February 08, 2008, at 03:35 AM by 129.20.167.23 -
Changed line 12 from:
Current version of RDFScape is '''0.4''' and offers a rich set of features to query, visualize and overlay ontologies on other Cytoscape networks.
to:
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.
February 07, 2008, at 01:39 PM by 129.20.167.23 -
Changed lines 15-16 from:
RDFScape is released as LGPL. %green% [++Follow the link to [[Releases]] to download it++] i %black%. It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.
to:
RDFScape is released as LGPL. %green% [++Follow the link to [[Releases]] to download it++] %black%. It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.
February 07, 2008, at 01:38 PM by 129.20.167.23 -
Changed lines 15-16 from:
RDFScape is released as LGPL. %green% ++larger++ Follow the link to [[Releases]] to download it %black%. It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.
to:
RDFScape is released as LGPL. %green% [++Follow the link to [[Releases]] to download it++] i %black%. It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.
February 07, 2008, at 01:36 PM by 129.20.167.23 -
Changed lines 15-16 from:
RDFScape is released as LGPL. %green% Follow the link to [[Releases]] to download it %black%. It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.
to:
RDFScape is released as LGPL. %green% ++larger++ Follow the link to [[Releases]] to download it %black%. It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.
February 07, 2008, at 01:34 PM by 129.20.167.23 -
Changed lines 5-6 from:
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 [[http://www.biopax.org/ | 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.
to:
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 [[http://www.biopax.org/ | 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.
February 07, 2008, at 01:23 PM by 129.20.167.23 -
Changed lines 3-6 from:
RDFScape is a project that brings '''semantic web''' "features" to the popular '''systems biology''' software [[http://www.cytoscape.org | 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.
to:
RDFScape is a project that brings '''Semantic Web''' "features" to the popular '''Systems Biology''' software [[http://www.cytoscape.org | 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 [[http://www.biopax.org/ | 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.
Changed line 12 from:
Current version of RDFScape is '''0.4''' and offers a rich set of feature to query, visualize and overlay ontologies on other Cytoscape networks.
to:
Current version of RDFScape is '''0.4''' and offers a rich set of features to query, visualize and overlay ontologies on other Cytoscape networks.
Changed lines 15-16 from:
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.
to:
RDFScape is released as LGPL. %green% Follow the link to [[Releases]] to download it %black%. It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.
Changed lines 27-29 from:
X/X/2008

to:
7/2/2008
Changed lines 31-33 from:

* At the time being, this project is partially founded by ESF foundation and [[http://www.leafbioscience.com | Leaf Bioscience s.r.l.]] (through [[http://www.dc-thera.org | 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.
to:
This project is primarily funded by [[http://www.leafbioscience.com | Leaf Bioscience s.r.l.]] as an activity in the context of the [[http://www.dc-thera.org | 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.
February 07, 2008, at 01:16 PM by 129.20.167.23 -
Changed lines 17-18 from:
RDFScape depends on the following softawre and libraries:
to:
RDFScape depends on the following software and libraries:
February 07, 2008, at 01:15 PM by 129.20.167.23 -
Changed lines 5-6 from:
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.
to:
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.
Changed lines 9-16 from:
Beside this, RDFScape offers reach query capabilities on ontologies (SPARQL,RDQL,Strings, interactive browsing) and a customizable visualization features.



Current version of RDFScape is available on svn.

%red% '''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'''.
to:
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.
February 07, 2008, at 01:10 PM by 129.20.167.23 -
Deleted lines 6-8:


Changed lines 8-18 from:
Features include:

* SPARQL/RDQL/Class based queries
* Graphical quey interface (users can draw patterns of graphs with "variables").
* Interactive browsing of ontologies
* Selection/Color by namespace
* 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) (under development)''
* ''Inference of statements from data (under development)''
to:

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


February 07, 2008, at 01:08 PM by 129.20.167.23 -
Changed lines 3-4 from:
RDFScape is a project that brings '''semantic web''' "features" to the popular '''systems biology''' software [[http://www.cytoscape.org | Cytoscape]].
to:
RDFScape is a project that brings '''semantic web''' "features" to the popular '''systems biology''' software [[http://www.cytoscape.org | 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.



February 07, 2008, at 01:03 PM by 129.20.167.23 -
Changed lines 3-5 from:
RDFScape is a project that brings semantic web "features" to the popular systems biology software [[http://www.cytoscape.org | Cytoscape]].

to:
RDFScape is a project that brings '''semantic web''' "features" to the popular '''systems biology''' software [[http://www.cytoscape.org | Cytoscape]].

http://www.sgtp.net/AndreaSplendiani/ext/rdfscape/newRDFScapeScreenshot.png
February 05, 2008, at 10:05 AM by 129.20.167.23 -
Changed lines 1-2 from:
(:keywords semantic web, systems biology, ontology, OWL, RDF, biopax, pathways :)
to:
(:keywords semantic web, systems biology, ontology, OWL, RDF, biopax, pathways, Andrea Splendiani, bioinformatics :)
January 28, 2008, at 11:57 AM by 129.20.167.23 -
Changed lines 23-26 from:
* The Systems Biology analysis and visualization software [[http://www.cytoscape.org | Cytoscape]]
* The RDF / Semantic web library[[http://jena.sourceforge.net | Jena]]
* The OWL reasoner [[http://pellet.owldl.com |Pellet]]
to:
* The Systems Biology analysis and visualization software [[http://www.cytoscape.org | Cytoscape]]
* The RDF / Semantic web library [[http://jena.sourceforge.net | Jena]]
* The OWL reasoner [[http://pellet.owldl.com |Pellet]]
January 28, 2008, at 11:56 AM by 129.20.167.23 -
Changed lines 21-33 from:
It relies on:

* [[http://www.cytoscape.org | Cytoscape 2.5.1]] [[notes on cytoscape version]]
* [[http://jena.sourceforge.net | Jena 2.5.4]] [[notes on Jena version]]
* [[http://pellet.owldl.com |Pellet 1.5.1]] [4notes 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

to:
RDFScape depends on the following softawre and libraries:

* The Systems Biology analysis and visualization software [[http://www.cytoscape.org | Cytoscape]]
* The RDF / Semantic web library[[http://jena.sourceforge.net | Jena]]
* The OWL reasoner [[http://pellet.owldl.com |Pellet]]

For a description of version requirements refer to [[Dependencies]]



X/X/2008

January 28, 2008, at 11:38 AM by 129.20.167.23 -
Changed lines 3-5 from:
RDFScape (is this the final name ?) is a project that brings semantic web "features" to the popular systems biology software [[http://www.cytoscape.org | Cytoscape]].

to:
RDFScape is a project that brings semantic web "features" to the popular systems biology software [[http://www.cytoscape.org | Cytoscape]].

January 24, 2008, at 08:04 AM by 129.20.167.23 -
Added lines 1-2:
(:keywords semantic web, systems biology, ontology, OWL, RDF, biopax, pathways :)
January 23, 2008, at 04:01 PM by 129.20.167.23 -
Changed line 22 from:
* [[http://jena.sourceforge.net | Jena 2.5.2]] [[notes on Jena version]]
to:
* [[http://jena.sourceforge.net | Jena 2.5.4]] [[notes on Jena version]]
January 23, 2008, at 03:49 PM by 129.20.167.23 -
Changed lines 17-18 from:
%red% '''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 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'''.
to:
%red% '''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'''.
Changed line 21 from:
* [[http://www.cytoscape.org | Cytoscape 2.4.1]] [[notes on cytoscape version]]
to:
* [[http://www.cytoscape.org | Cytoscape 2.5.1]] [[notes on cytoscape version]]
Changed lines 23-24 from:
* [[http://pellet.owldl.com |Pellet 1.5]] [[notes on Pellet version]]
to:
* [[http://pellet.owldl.com |Pellet 1.5.1]] [4notes on Pellet version]]
January 18, 2008, at 03:48 PM by 82.236.175.137 -
Changed line 6 from:
* SPAQRL/RDQL/Class based queries
to:
* SPARQL/RDQL/Class based queries
January 18, 2008, at 01:02 PM by 129.20.167.27 -
Changed lines 4-5 from:
Features include!:
to:
Features include:
January 18, 2008, at 01:02 PM by 129.20.167.27 -
Changed lines 4-5 from:
Features include:
to:
Features include!:
July 23, 2007, at 06:39 PM by 86.59.104.195 -
Changed lines 17-19 from:
%red% ''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 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.
to:
%red% '''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'''.
July 23, 2007, at 06:38 PM by 86.59.104.195 -
Added lines 16-19:

%red% ''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.
June 07, 2007, at 08:27 PM by 129.20.167.21 -
Changed lines 34-35 from:
For more informations mail andrea -> sgtp dot net.
to:
For more informations mail andrea.splendiani -> univ-rennes1.fr dot net.
June 07, 2007, at 08:26 PM by 129.20.167.21 -
Changed lines 18-21 from:
* Cytoscape 2.4.1 [[notes on cytoscape version]]
* Jena 2.5.2 [[notes on Jena version]]
* Pellet 1.5 [[notes on Pellet version]]
to:
* [[http://www.cytoscape.org | Cytoscape 2.4.1]] [[notes on cytoscape version]]
* [[http://jena.sourceforge.net | Jena 2.5.2]] [[notes on Jena version]]
* [[http://pellet.owldl.com |Pellet 1.5]] [[notes on Pellet version]]
Deleted line 25:
Changed lines 32-33 from:
* 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.
to:
* At the time being, this project is partially founded by ESF foundation and [[http://www.leafbioscience.com | Leaf Bioscience s.r.l.]] (through [[http://www.dc-thera.org | 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.
June 07, 2007, at 07:59 PM by 129.20.167.21 -
Changed line 18 from:
* Cytoscape 2.4 [[notes on cytoscape version]]
to:
* Cytoscape 2.4.1 [[notes on cytoscape version]]
June 07, 2007, at 07:58 PM by 129.20.167.21 -
Changed lines 20-21 from:
* Pellet svn [[notes on Pellet version]]
to:
* Pellet 1.5 [[notes on Pellet version]]
June 07, 2007, at 07:16 AM by 129.20.167.21 -
Changed lines 15-28 from:



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:
to:
Current version of RDFScape is available on svn.
It relies on:
Changed lines 20-26 from:
* 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

to:
* 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

June 07, 2007, at 07:10 AM by 129.20.167.21 -
Changed line 6 from:
* SPQRL/RDQL/Class based queries
to:
* SPAQRL/RDQL/Class based queries
Changed lines 12-14 from:
* Extension of term scoring function (From terms enrichment to ontology patterns enrichment)
* Inference of statements from data
to:
* ''Extension of term scoring function (From terms enrichment to ontology patterns enrichment) (under development)''
* ''Inference of statements from data (under development)''



April 25, 2007, at 02:06 PM by 129.20.167.21 -
Added line 3:
Changed line 6 from:
* SPQRL/RDQL/Custom queries
to:
* SPQRL/RDQL/Class based queries
Changed lines 10-15 from:
* 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
to:
* 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)
Changed lines 15-16 from:
This is a first summary, more to come.
to:
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

Changed lines 37-53 from:
Some notes:
!!! 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.

----

to:
October 27, 2006, at 05:00 PM by 84.103.181.243 -
Changed lines 19-20 from:
===
to:
----
Changed lines 35-37 from:
___

to:
----

October 27, 2006, at 04:59 PM by 84.103.181.243 -
Changed lines 19-20 from:
___
to:
===
October 27, 2006, at 04:58 PM by 84.103.181.243 -
Changed lines 19-20 from:
---
to:
___
Changed lines 35-37 from:
---

to:
___

October 27, 2006, at 04:57 PM by 84.103.181.243 -
Added lines 19-20:
---
Changed lines 35-37 from:


to:
---

October 27, 2006, at 04:18 PM by 84.103.181.243 -
Changed lines 20-27 from:

* 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
to:
!!! 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.



Changed lines 38-39 from:
For more informations mail andrea -> pasteur dot fr.
to:
For more informations mail andrea -> sgtp dot net.
June 20, 2006, at 04:53 PM by 143.48.245.95 -
Changed lines 23-26 from:
* 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
to:
* 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
June 20, 2006, at 04:50 PM by 143.48.245.95 -
Changed lines 21-22 from:
* 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).
to:
* 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
April 12, 2006, at 09:11 AM by 157.99.164.31 -
Added line 26:
April 12, 2006, at 09:10 AM by 157.99.164.31 -
Changed lines 26-28 from:

(:counter:)
to:
%right% (:counter:)
April 12, 2006, at 08:52 AM by 157.99.164.31 -
Changed lines 27-29 from:
to:
(:counter:)

(:includeurl http://www.sgtp.net/AndreaSplendiani/RDFScapecounter.php :)
April 05, 2006, at 01:27 PM by 130.88.195.129 -
Changed line 27 from:
(:includeurl http://www.sgtp.net/AndreaSplendiani/RDFScapecounter.php :)
to:
April 05, 2006, at 11:31 AM by 130.88.195.129 -
Changed lines 23-24 from:
* 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).
to:
* 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.
March 31, 2006, at 01:05 PM by 157.99.164.31 -
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(:includeurl http://www.sgtp.net/AndreaSplendiani/RDFScapecounter.php :)
March 31, 2006, at 12:23 PM by 157.99.164.31 -
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RDFScape (is this the final name ?) is a project that brings semantic web "features" to the popular systems biology software [[http://www.cytoscape.org | 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.