You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@taverna.apache.org by bu...@apache.org on 2015/02/03 15:05:13 UTC
svn commit: r938800 - in /websites/staging/taverna/trunk: cgi-bin/ content/
content/introduction/taverna-in-use/annotation.html
Author: buildbot
Date: Tue Feb 3 14:05:12 2015
New Revision: 938800
Log:
Staging update by buildbot for taverna
Modified:
websites/staging/taverna/trunk/cgi-bin/ (props changed)
websites/staging/taverna/trunk/content/ (props changed)
websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html
Propchange: websites/staging/taverna/trunk/cgi-bin/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Tue Feb 3 14:05:12 2015
@@ -1 +1 @@
-1656733
+1656734
Propchange: websites/staging/taverna/trunk/content/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Tue Feb 3 14:05:12 2015
@@ -1 +1 @@
-1656733
+1656734
Modified: websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html Tue Feb 3 14:05:12 2015
@@ -137,28 +137,28 @@ Instead it shows <a class="alert-link" h
<div id="content"><p>Taverna is used by various tools and projects for the association of metadata with data (annotation).
These include:
- - [Automatic Functional Annotation in a distributed Web service Environment]<a href="AFAWE">49</a> -
+ - <a href="#afawe">Automatic Functional Annotation in a distributed Web service Environment</a>(AFAWE) -
annotation of plant genes with their functionality
- - [Interactive genome annotation pipeline][50]</a> - automatic and manual annotation of genes
- - [TaWeka][51] - associating biological data with calculated functionality</p>
+ - <a href="#annotation-of-genomes">Interactive genome annotation pipeline</a></a> - automatic and manual annotation of genes
+ - <a href="#taweka">TaWeka</a> - associating biological data with calculated functionality</p>
<p>In addition, Taverna makes use of the semantic annotation that has been specified for the services provided by
- the [MOBY consortium][52].</p>
+ the <a href="#adoption-by-moby">MOBY consortium</a>.</p>
<p>Taverna has also been used for the identification of mismatches and possible annotations in workflows by the
- [iSPIDER][53] project.</p>
+ <a href="/introduction/related-projects.html#ispider">iSPIDER</a> project.</p>
<p><a name="afawe"></a></p>
<h2 id="afawe">AFAWE</h2>
-<p>The [Max Planck Institute for Plant Breeding Research][54] in Cologne, Germany have developed the
- Automatic Functional Annotation in a distributed Web Service Environment ([AFAWE][55]).
+<p>The <a href="http://www.mpiz-koeln.mpg.de/2169/en">Max Planck Institute for Plant Breeding Research</a> in Cologne, Germany have developed the
+ Automatic Functional Annotation in a distributed Web Service Environment (<a href="http://bioinfo.mpiz-koeln.mpg.de/afawe/">AFAWE</a>).
AFAWE is a tool for the automatic functional annotation of new genes in plants and other organisms.
-The annotation involves the running of several Web services, and also the execution of a Taverna [workflow][56].</p>
-<p>The annotation workflow is [available][57] on [myExperiment][58].</p>
+The annotation involves the running of several Web services, and also the execution of a Taverna <a href="http://bioinfo.mpiz-koeln.mpg.de/afawe/help/Tools.html#SIFTER">workflow</a>.</p>
+<p>The annotation workflow is <a href="http://www.myexperiment.org/workflows/95">available</a> on <a href="http://www.myexperiment.org/">myExperiment</a>.</p>
<h3 id="publications">Publications</h3>
-<p>The [paper][59] <em>Protein function prediction and annotation in an integrated environment powered by web services
+<p>The <a href="http://dx.doi.org/10.1093/bioinformatics/btn394">paper</a> <em>Protein function prediction and annotation in an integrated environment powered by web services
(AFAWE)</em> by Joecker et al describes the concepts and implementation of AFAWE.</p>
<p><a name="annotation-of-genomes"></a></p>
<h2 id="annotation-of-genomes">Annotation of genomes</h2>
-<p>A collaboration between [Tom Oinn][60] from the myGrid team and Anders Lanzen, Svenn Helge Grindhaug and
- Pal Puntervoll from the [University of Bergen][61], Norway, has produced an interactive genome annotation
+<p>A collaboration between <a href="http://www.mygrid.org.uk/about-us/people/previous-members/thomas-oinn/">Tom Oinn</a> from the myGrid team and Anders Lanzen, Svenn Helge Grindhaug and
+ Pal Puntervoll from the <a href="http://www.uib.no/en">University of Bergen</a>, Norway, has produced an interactive genome annotation
pipeline.</p>
<p>Sequencing, characterising and annotating a genome are the first steps to understanding its function.
Important stages in this include gene prediction, comparative genomics and function prediction of genes and
@@ -166,24 +166,24 @@ Important stages in this include gene pr
With workflows all of these stages can be automate, requiring little human interaction.
However, manual inspection can be required at certain points in the process.</p>
<h3 id="publications_1">Publications</h3>
-<p>[Articles and papers][62] about the success of Taverna for genome annotation are available on-line.</p>
+<p><a href="http://www.mygrid.org.uk/bibsearch-results/?bibliography_subject=genome-annotation">Articles and papers</a> about the success of Taverna for genome annotation are available on-line.</p>
<p><a name="taweka"></a></p>
<h2 id="taweka">TaWeka</h2>
-<p>[Luna De Ferrari][63] from the Computational Systems Biology &
- [Bioinformatics group at the University of Edinburgh][64] has developed [TaWeka][65],</p>
+<p><a href="http://homepages.inf.ed.ac.uk/ldeferra/">Luna De Ferrari</a> from the Computational Systems Biology &
+ <a href="http://www.bioinformatics.ed.ac.uk/">Bioinformatics group at the University of Edinburgh</a> has developed <a href="http://mook.inf.ed.ac.uk/twiki/bin/view.cgi/PublicCSB/TaWeka">TaWeka</a>,</p>
<blockquote>
<p>a rapid prototyping tool for biological classifiers.</p>
</blockquote>
<p>TaWeka uses Taverna workflows to store data retrieved from webservices, e.g. queries of biological data,
into a database.
-[Weka][66] is then used to run machine learning experiments on the data in order to evaluate and improve
+<a href="http://www.cs.waikato.ac.nz/ml/weka/">Weka</a> is then used to run machine learning experiments on the data in order to evaluate and improve
biological classification functions.</p>
<h3 id="publications_2">Publications</h3>
-<p>A poster [<em>TaWeka: from biological web services to data mining</em>][67] by De Ferrara and Goryanin describes the
+<p>A poster <a href="http://mook.inf.ed.ac.uk/twiki/pub/PublicCSB/TaWekaPosters/colourA4_16.pdf"><em>TaWeka: from biological web services to data mining</em></a> by De Ferrara and Goryanin describes the
purpose and implementation of TaWeka.</p>
<p><a name="adoption-by-moby"></a></p>
<h2 id="adoption-by-the-moby-consortium">Adoption by the Moby consortium</h2>
-<p>The [Moby][68] project develops a system for interoperability between biological data hosts and
+<p>The <a href="http://biomoby.open-bio.org/">Moby</a> project develops a system for interoperability between biological data hosts and
analytical services.
Their relationship with Taverna is multiple:</p>
<ul>
@@ -195,7 +195,7 @@ Their relationship with Taverna is multi
<li>Specific support for Moby services is available within Taverna.</li>
</ul>
<h3 id="publications_3">Publications</h3>
-<p>The [paper][69] <em>Interoperability with Moby 1.0âItâs better than sharing your toothbrush!</em> by the
+<p>The <a href="http://dx.doi.org/10.1093/bib/bbn003">paper</a> <em>Interoperability with Moby 1.0âItâs better than sharing your toothbrush!</em> by the
Moby consortium gives an overview of Moby and their activities.</p></div>
</div>