https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Software&feed=atom&action=history
Software - Revision history
2024-03-28T23:50:29Z
Revision history for this page on the wiki
MediaWiki 1.31.10
https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Software&diff=12088&oldid=prev
Wasila at 00:04, 10 December 2019
2019-12-10T00:04:52Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 00:04, 10 December 2019</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/owlery owlery]—web service interface for OWL API reasoner queries. In addition to direct DL queries, Owlery provides a SPARQL endpoint powered by Owlet. Written in Scala using Spray web services.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/owlery owlery]—web service interface for OWL API reasoner queries. In addition to direct DL queries, Owlery provides a SPARQL endpoint powered by Owlet. Written in Scala using Spray web services.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/scowl scowl]—a Scala library allowing a declarative approach to composing OWL expressions and axioms using the [http://owlapi.sourceforge.net/ OWL API]. Written in Scala.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/scowl scowl]—a Scala library allowing a declarative approach to composing OWL expressions and axioms using the [http://owlapi.sourceforge.net/ OWL API]. Written in Scala.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">==Software tools to access and analyze KB data==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [http://rphenoscape.phenoscape.org/ RPhenoscape]— R package that facilitates interfacing with the Phenoscape Knowledgebase for searching ontology terms, querying data matrices, obtaining dependency matrices, and computing semantic similarity metrics.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [http://beta.phenoscape.org/#/ontotrace OntoTrace] — tool used to query the KB for a synthetic character matrix of asserted and inferred presence/absence characters for anatomical structures. OntoTrace is also accessible by using [http://rphenoscape.phenoscape.org/ RPhenoscape] to query the web services API. </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Data curation tools==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Data curation tools==</div></td></tr>
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Wasila
https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Software&diff=11644&oldid=prev
Jim Balhoff: /* Phenoscape Knowledgebase */
2015-07-27T18:07:24Z
<p><span dir="auto"><span class="autocomment">Phenoscape Knowledgebase</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:07, 27 July 2015</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l6" >Line 6:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The live KB can be accessed at http://kb.phenoscape.org/. For more information on the Phenoscape Knowledgebase see these wiki pages:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The live KB can be accessed at http://kb.phenoscape.org/. For more information on the Phenoscape Knowledgebase see these wiki pages:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Phenoscape KB]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Phenoscape KB]]</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*  </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* <ins class="diffchange diffchange-inline">[[KB build process]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Software components:</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-owl-tools phenoscape-owl-tools]—build application for generating the RDF content for the Phenoscape KB, including utilities for converting datasets to OWL and running reasoning tasks. Written in Scala using the OWL API.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-owl-tools phenoscape-owl-tools]—build application for generating the RDF content for the Phenoscape KB, including utilities for converting datasets to OWL and running reasoning tasks. Written in Scala using the OWL API.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-services phenoscape-kb-services]—updated web services API for the Knowledgebase. Written in Scala using [http://spray.io Spray] web services.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-services phenoscape-kb-services]—updated web services API for the Knowledgebase. Written in Scala using [http://spray.io Spray] web services.</div></td></tr>
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Jim Balhoff
https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Software&diff=11643&oldid=prev
Jim Balhoff: /* Phenoscape Knowledgebase */
2015-07-27T18:06:49Z
<p><span dir="auto"><span class="autocomment">Phenoscape Knowledgebase</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:06, 27 July 2015</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3" >Line 3:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Phenoscape Knowledgebase==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Phenoscape Knowledgebase==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>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, web services  which provide a query API for the data, a web application user interface allowing exploration of the Knowledgebase, and accessory tools for loading data. To meet requirements for scalability, reasoning expressivity, and support for linked data standards, we are developing a our Knowledgebase infrastructure using the RDF and OWL semantic web standards.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>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, web services  which provide a query API for the data, a web application user interface allowing exploration of the Knowledgebase, and accessory tools for loading data. To meet requirements for scalability, reasoning expressivity, and support for linked data standards, we are developing a our Knowledgebase infrastructure using the RDF and OWL semantic web standards.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">The live KB can be accessed at http://kb.phenoscape.org/. For more information on the Phenoscape Knowledgebase see these wiki pages:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [[Phenoscape KB]]</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-owl-tools phenoscape-owl-tools]—build application for generating the RDF content for the Phenoscape KB, including utilities for converting datasets to OWL and running reasoning tasks. Written in Scala using the OWL API.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-owl-tools phenoscape-owl-tools]—build application for generating the RDF content for the Phenoscape KB, including utilities for converting datasets to OWL and running reasoning tasks. Written in Scala using the OWL API.</div></td></tr>
</table>
Jim Balhoff
https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Software&diff=11641&oldid=prev
Jim Balhoff: /* Repositories no longer being used/maintained */
2015-07-27T18:02:30Z
<p><span dir="auto"><span class="autocomment">Repositories no longer being used/maintained</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:02, 27 July 2015</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l31" >Line 31:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Repositories no longer being used/maintained==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Repositories no longer being used/maintained==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Classic Phenoscape KB===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Classic Phenoscape KB===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The first edition of the Phenoscape Knowledgebase is still live at http://<del class="diffchange diffchange-inline">kb</del>.phenoscape.org/. It makes use of the following software projects:</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The first edition of the Phenoscape Knowledgebase is still live at http://<ins class="diffchange diffchange-inline">fish</ins>.phenoscape.org/. It makes use of the following software projects:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [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].</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [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].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/PhenoscapeOBD-WS PhenoscapeOBD-WS] - 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 present a [http://en.wikipedia.org/wiki/Representational_State_Transfer RESTful] service interface using the [http://www.restlet.org/ Restlet] Java API. The specifications of these services are detailed in [[Data Services]].</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/PhenoscapeOBD-WS PhenoscapeOBD-WS] - 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 present a [http://en.wikipedia.org/wiki/Representational_State_Transfer RESTful] service interface using the [http://www.restlet.org/ Restlet] Java API. The specifications of these services are detailed in [[Data Services]].</div></td></tr>
</table>
Jim Balhoff
https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Software&diff=11640&oldid=prev
Jim Balhoff: /* Phenoscape Knowledgebase */
2015-07-27T18:02:14Z
<p><span dir="auto"><span class="autocomment">Phenoscape Knowledgebase</span></span></p>
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<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:02, 27 July 2015</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5" >Line 5:</td>
<td colspan="2" class="diff-lineno">Line 5:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-owl-tools phenoscape-owl-tools]—build application for generating the RDF content for the Phenoscape KB, including utilities for converting datasets to OWL and running reasoning tasks. Written in Scala using the OWL API.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-owl-tools phenoscape-owl-tools]—build application for generating the RDF content for the Phenoscape KB, including utilities for converting datasets to OWL and running reasoning tasks. Written in Scala using the OWL API.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-services phenoscape-kb-services]—updated web services API for the Knowledgebase. Written in Scala using Spray web services.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-services phenoscape-kb-services]—updated web services API for the Knowledgebase. Written in Scala using <ins class="diffchange diffchange-inline">[http://spray.io </ins>Spray<ins class="diffchange diffchange-inline">] </ins>web services.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-ui phenoscape-kb-ui]—Phenoscape KB web user interface. A client-side web application using AngularJS.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-ui phenoscape-kb-ui]—Phenoscape KB web user interface. A client-side web application using AngularJS.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-data phenoscape-data]—document store for semantically annotated character matrix files. This is the evolutionary data content for the Phenoscape KB. NeXML.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-data phenoscape-data]—document store for semantically annotated character matrix files. This is the evolutionary data content for the Phenoscape KB. NeXML.</div></td></tr>
</table>
Jim Balhoff
https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Software&diff=11639&oldid=prev
Jim Balhoff: /* Phenoscape Knowledgebase */
2015-07-27T18:01:51Z
<p><span dir="auto"><span class="autocomment">Phenoscape Knowledgebase</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:01, 27 July 2015</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5" >Line 5:</td>
<td colspan="2" class="diff-lineno">Line 5:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-owl-tools phenoscape-owl-tools]—build application for generating the RDF content for the Phenoscape KB, including utilities for converting datasets to OWL and running reasoning tasks. Written in Scala using the OWL API.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-owl-tools phenoscape-owl-tools]—build application for generating the RDF content for the Phenoscape KB, including utilities for converting datasets to OWL and running reasoning tasks. Written in Scala using the OWL API.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-services phenoscape-kb-services]—updated web services API for the Knowledgebase<del class="diffchange diffchange-inline">. Very early in development so far</del>. Written in Scala using <del class="diffchange diffchange-inline">Jersey </del>web services.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-services phenoscape-kb-services]—updated web services API for the Knowledgebase. Written in Scala using <ins class="diffchange diffchange-inline">Spray </ins>web services.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-ui phenoscape-kb-ui]—Phenoscape KB web user interface. A client-side web application using AngularJS.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-ui phenoscape-kb-ui]—Phenoscape KB web user interface. A client-side web application using AngularJS.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-data phenoscape-data]—document store for semantically annotated character matrix files. This is the evolutionary data content for the Phenoscape KB. NeXML.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-data phenoscape-data]—document store for semantically annotated character matrix files. This is the evolutionary data content for the Phenoscape KB. NeXML.</div></td></tr>
</table>
Jim Balhoff
https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Software&diff=11354&oldid=prev
Jim Balhoff: /* Other active projects */
2014-08-07T14:49:11Z
<p><span dir="auto"><span class="autocomment">Other active projects</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 14:49, 7 August 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l22" >Line 22:</td>
<td colspan="2" class="diff-lineno">Line 22:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape.github.com phenoscape.github.com]—source for Phenoscape public website</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape.github.com phenoscape.github.com]—source for Phenoscape public website</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-ontologies phenoscape-ontologies]—ontologies developed internally for the Phenoscape project. Currently contains only a demonstration ontology for presence/absence reasoning.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-ontologies phenoscape-ontologies]—ontologies developed internally for the Phenoscape project. Currently contains only a demonstration ontology for presence/absence reasoning.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* <del class="diffchange diffchange-inline">The VTOTool assembles </del>the VTO by starting from an initial taxonomy (NCBI) and deleting and splicing in group specific taxonomies (e.g., TTO, ATO<del class="diffchange diffchange-inline">).  It will also add taxonomy from PaleoDB and synonyms from other taxonomic source (e.g., Catalog of Life</del>).</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* <ins class="diffchange diffchange-inline">[http://github.com/NESCent/Taxonomy-Ontology-Tool Taxonomy-Ontology-Tool]—tool used to assemble </ins>the VTO by starting from an initial taxonomy (NCBI) and deleting and splicing in group specific taxonomies (e.g., TTO, ATO).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoday-reasoning-paper phenoday-reasoning-paper]—Demonstration code for [http://phenoday2014.bio-lark.org/pdf/11.pdf paper submission] to the Bio-ontologies SIG [http://phenoday2014.bio-lark.org Phenotype Day] at ISMB 2014.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoday-reasoning-paper phenoday-reasoning-paper]—Demonstration code for [http://phenoday2014.bio-lark.org/pdf/11.pdf paper submission] to the Bio-ontologies SIG [http://phenoday2014.bio-lark.org Phenotype Day] at ISMB 2014.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
</table>
Jim Balhoff
https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Software&diff=11353&oldid=prev
Jim Balhoff: /* Others */
2014-08-04T20:21:04Z
<p><span dir="auto"><span class="autocomment">Others</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:21, 4 August 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l44" >Line 44:</td>
<td colspan="2" class="diff-lineno">Line 44:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/CMAPOBO CMAPOBO]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/CMAPOBO CMAPOBO]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/synctool-oboedit synctool-oboedit]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/synctool-oboedit synctool-oboedit]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [http://github.com/phenoscape/ontophenotype-eol ontophenotype-eol]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* TTOTool...</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* TTOTool...</div></td></tr>
</table>
Jim Balhoff
https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Software&diff=11352&oldid=prev
Jim Balhoff: /* Others */
2014-08-04T20:20:43Z
<p><span dir="auto"><span class="autocomment">Others</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:20, 4 August 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l41" >Line 41:</td>
<td colspan="2" class="diff-lineno">Line 41:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/skeleton-image-annotation skeleton-image-annotation]—reference images for the vertebrate skeleton annotated with Uberon terms, using Phenote.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/skeleton-image-annotation skeleton-image-annotation]—reference images for the vertebrate skeleton annotated with Uberon terms, using Phenote.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-rdf-data phenoscape-kb-rdf-data]—some obsolete full dumps of the RDF knowledgebase. We are exploring making current data dumps available elsewhere, such as at http://datahub.io.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-rdf-data phenoscape-kb-rdf-data]—some obsolete full dumps of the RDF knowledgebase. We are exploring making current data dumps available elsewhere, such as at http://datahub.io.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [http://github.com/phenoscape/Phenotype-Matching-Queries Phenotype-Matching-Queries]</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [http://github.com/phenoscape/CMAPOBO CMAPOBO]</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [http://github.com/phenoscape/synctool-oboedit synctool-oboedit]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* TTOTool...</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* TTOTool...</div></td></tr>
</table>
Jim Balhoff
https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Software&diff=11351&oldid=prev
Jim Balhoff: /* Others */
2014-08-04T20:19:24Z
<p><span dir="auto"><span class="autocomment">Others</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:19, 4 August 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l40" >Line 40:</td>
<td colspan="2" class="diff-lineno">Line 40:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-builder phenoscape-builder]—early Ant-based tool for building the RDF-based KB. Replaced by Scala script within [http://github.com/phenoscape/phenoscape-owl-tools phenoscape-owl-tools].</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-builder phenoscape-builder]—early Ant-based tool for building the RDF-based KB. Replaced by Scala script within [http://github.com/phenoscape/phenoscape-owl-tools phenoscape-owl-tools].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/skeleton-image-annotation skeleton-image-annotation]—reference images for the vertebrate skeleton annotated with Uberon terms, using Phenote.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/skeleton-image-annotation skeleton-image-annotation]—reference images for the vertebrate skeleton annotated with Uberon terms, using Phenote.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-rdf-data phenoscape-kb-rdf-data]—some <del class="diffchange diffchange-inline">early </del>full dumps of the RDF knowledgebase. We are exploring making current data dumps available elsewhere, such as at http://datahub.io.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [http://github.com/phenoscape/phenoscape-kb-rdf-data phenoscape-kb-rdf-data]—some <ins class="diffchange diffchange-inline">obsolete </ins>full dumps of the RDF knowledgebase. We are exploring making current data dumps available elsewhere, such as at http://datahub.io.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* TTOTool...</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* TTOTool...</div></td></tr>
</table>
Jim Balhoff