KeyValueData

Specification

Here is the initial specification of a prototype SBML annotation that holds typed key:value pairs. Useful for stroring arbitrary metadata not easily encoded using the legitimate SBML annotation mechanisms. Especially big thanks to Frank Bergmann whose ParameterSets provided the inspiration for this annotation and whose extremely useful comments and suggestions helped me out tremendously.

<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
	<data id="Node0" type="sbmlId" value="1"/>
	<data id="MyDogsName" type="string" value="Woof"/>
	<data id="needvacation" type="boolean" value="true"/>
	<data id="Trustlevel" type="integer" value="-5"/>
	<data id="deltaG" type="double" value="2335066.4573"/>
</listOfKeyValueData>

where id is a case insensitive string conforming to the requirements of an SBML sid and type is one of:

If you are interesting in dicussing this annotation please contact me here [-spaces]: b g o l i [at] u s e r s [dot] s o u r c e f o r g e [dot] n e t

Practical example

This annotation was developed to enable the metatdata encoded in "old school" SBML L2V1 genome scale reconstructions that used an arbitrary block of HTML code located in the <notes/> element to be slightly more strictly encoded in SBML L3. Here is an example of the old reaction <notes/> HTML encoded as KeyValueData in an <annotation/>:

<reaction id="R_DAPE" name="diaminopimelate epimerase" reversible="true">
      <notes>
<html:p>SUBSYSTEM: Citric Acid Cycle</html:p>
<html:p>NAME: Citrate lyase#ABBREVIATION:CitDEF#</html:p>
<html:p>EC Number: 4.1.3.6</html:p>
<html:p>GENE ASSOCIATION: (b0616 and b0615 and b0617)</html:p>
<html:p>Equation: [c] : cit --&gt; ac + oaa</html:p>
<html:p>genes: </html:p>
<html:p>proteins: </html:p>
<html:p>LOCUS: b0617#ABBREVIATION:citD#ECNUMBERS:4.1.3.6#</html:p>
<html:p>Abbreviation: R_CITL</html:p>
<html:p>Synonyms: _0</html:p>
<html:p>Confidence Level: 4</html:p>
</notes>
<annotation>
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
<data id="subsystem" type="string" value="Citric Acid Cycle"/>
<data id="name" type="string" value="Citrate lyase#ABBREVIATION:CitDEF#"/>
<data id="ec_number" type="string" value="4.1.3.6"/>
<data id="gene_association" type="string" value="(b0616 and b0615 and b0617)"/>
<data id="equation" type="string" value="[c] : cit --&gt; ac + oaa"/>
<data id="genes" type="string"/>
<data id="proteins" type="string"/>
<data id="locus" type="string" value="b0617#ABBREVIATION:citD#ECNUMBERS:4.1.3.6#"/>
<data id="abbreviation" type="string" value="R_CITL"/>
<data id="synonyms" type="string" value="_0"/>
<data id="confidence_level" type="string" value="4"/>
</listOfKeyValueData>
</annotation> </reaction>
© Brett G. Olivier Amsterdam 2012