Any object (Compounds, Proteins, Genes, Reaction, Pathway ...) or set of objects can be exported into CycloneML, all the way to an entire PGDB.
/**
* Example 2
* Extract a Pathway Genome DataBase (PGDB - a Cyc) into a CycloneML file as ./Cyclone_Core/Data/Pgdb/CycloneML/
* Pathway Tools is required
*/
public static String TutorialEx2(String myOrganism,int max) {
return Biocyc2Xml.createXml(myOrganism,max);
}
TutorialEx2("Ecoli",10000);
Below is an example of the CycloneML output file of a PGDB 10.5 (You can download the whole file for Pseudomonas a. CycloneML or an extract file for Escherichia coli extract ).
<?xml version="1.0" encoding="UTF-8"?>
<BioCyc xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="http://nemo-cyclone.sourceforge.net/CycloneBC96.xsd">
<!-- CycloneXSD . This file may be freely distributed and modified under the terms of the CeCILL Licence.
It should be distributed with the file. If you do not have a copy, see: http://www.cecill.info/index.en.html -->
<!-- For more information on the Cyclone project and its aims, or to join the cyclone mailing list, visit the home page at:
http://www.genoscope.cns.fr/bioinfo/nemo . Cyclone is a java project created at Genoscope, French National Sequencing Center - CNRS UMR 8030. -->
<!-- Director: Jean WEISSENBACH -->
<!-- Bioinformatic Director: Vincent SCHACHTER -->
<!-- Copyright for this file is held jointly by the individual creators. -->
<!-- Francois LE FEVRE (flefevre@genoscope.cns.fr) - Network Modeling team (NeMo), http://www.genoscope.cns.fr/bioinfo/nemo -->
<!-- Serge SMIDTAS (sergi@sergi5.com) - Network Modeling team (NeMo) - http://www.genoscope.cns.fr/bioinfo/nemo -->
<!-- and by the individual following authors. -->
<PgdbId>Ecoli1142257131369</PgdbId>
<Level>1</Level>
<Version>1</Version>
<AnatomicalStructures>
<FrameId>|Compartments|</FrameId>
<Organism>Ecoli</Organism>
<FrameType>class</FrameType>
<Comment>
<Value>"This class describes cellular compartments such as the cytoplasm. A given
compartment can be a component of a membrane, e.g., the cytoplasm is a component of the cytoplasmic membrane in the
sense that it is bounded by the cytoplasmic membrane."</Value>
</Comment>
<CreationDate>
<Value>3243104644</Value>
</CreationDate>
<Creator>
<Value>|pkarp|</Value>
</Creator>
<Instances>
<Value>|Anatomical-Structures|</Value>
<Parents>false</Parents>
</Instances>
<Schema>
<Value>T</Value>
</Schema>
</AnatomicalStructures>
<AnatomicalStructures>
<FrameId>|Membranes|</FrameId>
<Organism>Ecoli</Organism>
<FrameType>class</FrameType>
<Comment>
<Value>"This class describes cellular membranes such as the cytoplasmic membrane.
A membrane can be a Component-Of a compartment that contains it, for example, in bacteria, the cytoplasmic membrane
would be a Component-Of the periplasm."</Value>
</Comment>
<CreationDate>
<Value>3243104644</Value>
</CreationDate>
<Creator>
<Value>|pkarp|</Value>
</Creator>
<Instances>
<Value>|Anatomical-Structures|</Value>
<Parents>false</Parents>
</Instances>
<Schema>
<Value>T</Value>
</Schema>
</AnatomicalStructures>
<Cco>
<FrameId>CCO-CELLWALL</FrameId>
<Organism>Ecoli</Organism>
<FrameType>class</FrameType>
<CommonName>
<Value>"cell wall"</Value>
</CommonName>
<CreationDate>
<Value>3330884039</Value>
</CreationDate>
<Creator>
<Value>|paley|</Value>
</Creator>
<Definition>
<Value>"The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and
most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and,
often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan."</Value>
</Definition>
<DefinitionReference>
<Value>"Gene Ontology Consortium"</Value>
</DefinitionReference>
<Goid>
<Value>"GO:0005618"</Value>
</Goid>
<Instances>
<Value>CCO</Value>
<Parents>true</Parents>
</Instances>
<Instances>
<Value>CCO-SURFACE-MAT</Value>
<Parents>false</Parents>
</Instances>
<Schema>
<Value>T</Value>
</Schema>
<Sensu>
<Value>|Organisms|</Value>
</Sensu>
</Cco>
This file (Package explorer > samples/ can be browsed using Eclipse as shown below:
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