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Saturday, October 8, 2011

SED-ML Web Tools & KISAO

SED-ML uses KISAO to annotate simulation algorithms with information of what kind of simulation should be performed. Until today the SED-ML Web Tools only displayed the term identifier. This has changed, now the terms will be resolved and displayed:

SED-ML-Web

To make this work I’ve modified LibSedML to resolve all KISAO terms found. This is now part of the Algorithm object, and can be accessed through the Term property.

Unfortunately KISAO is now only available in OWL format. This means people have to ‘reason’ over the document in order to find out even the most basic things. While the EBI provides a ‘libKISAO’, this library is only available for Java. 

In the end I’ve decided to convert the OWL file periodically in a more readable format:

 <term id='KISAO:0000377' 
name='one-step method'>
<definition> <![CDATA[A numerical method
for differential equations which uses one
starting value at each step.]]>
</definition>

<similarTo>KISAO:0000020</similarTo>
...
<similarTo>KISAO:0000031</similarTo>




<ancestor>KISAO:0000000</ancestor>

<descendent>KISAO:0000261</descendent>
<descendent>KISAO:0000380</descendent>
<descendent>KISAO:0000064</descendent>
<descendent>KISAO:0000286</descendent>
</term>


I will update that file periodically and have it compiled into libSedML, if you would like to have a look at it, you can access it here:



kisao.xml

1 comment:

MLB2k11 said...

Lot of useful points are there. Its really keeps me updated.
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