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userguide:pride_export_properties [2011/03/04 18:15] 132.168.74.230 |
userguide:pride_export_properties [2011/03/08 14:28] 132.168.74.230 |
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- | ====== More about PRIDE XML format & runDescriptor.properties ====== | + | ====== More details about PRIDE XML format & runDescriptor.properties ====== |
[[http://www.ebi.ac.uk/pride/|PRIDE]] (PRoteomics IDEntifications database) is a public data repository for proteomics data.\\ | [[http://www.ebi.ac.uk/pride/|PRIDE]] (PRoteomics IDEntifications database) is a public data repository for proteomics data.\\ | ||
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The PRIDE XML schema documentation is available [[http://www.ebi.ac.uk/pride/schemaDocumentation.do|here]].\\ | The PRIDE XML schema documentation is available [[http://www.ebi.ac.uk/pride/schemaDocumentation.do|here]].\\ | ||
- | To provide meta info about your experiment for the PRIDE XML file, it's possible either to use PRIDE Converter (recommended at present) or to use the //runDescriptor.properties// file in hEIDI. | + | To provide meta info about your experiment for the PRIDE XML file, it's possible either to use PRIDE Converter (recommended) or to use the //runDescriptor.properties// file in hEIDI. |
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- | ==== Minimum XML File ==== | + | ==== Default PRIDE XML file (i.e. obtained if runDescriptor.properties is empty) ==== |
<code> | <code> | ||
<ExperimentCollection version="2.1"> | <ExperimentCollection version="2.1"> | ||
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<mzData xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="1.05" xsi:noNamespaceSchemaLocation="http://psidev.sourceforge.net/ms/xml/mzdata/mzdata.xsd" accessionNumber="Context_2"> | <mzData xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="1.05" xsi:noNamespaceSchemaLocation="http://psidev.sourceforge.net/ms/xml/mzdata/mzdata.xsd" accessionNumber="Context_2"> | ||
<description> | <description> | ||
- | <admin> | + | <admin> |
- | <sampleName>!!! SAMPLE NAME !!!</sampleName> | + | <sampleName>!!! SAMPLE NAME !!!</sampleName> |
<contact> | <contact> | ||
- | <name>!!! USER NAME !!!</name> | + | <name>!!! USER NAME !!!</name> |
- | <institution>!!! USER INSTITUTION !!!</institution> | + | <institution>!!! USER INSTITUTION !!!</institution> |
- | <contactInfo>!!! USER INFOS / TEL ... !!!</contactInfo> | + | <contactInfo>!!! USER INFOS / TEL ... !!!</contactInfo> |
</contact> | </contact> | ||
</admin> | </admin> | ||
<instrument> | <instrument> | ||
- | <instrumentName>!!! INSTRUMENT MODEL !!!</instrumentName> | + | <instrumentName>!!! INSTRUMENT MODEL !!!</instrumentName> |
<source> | <source> | ||
- | <cvParam accession="1" cvLabel="psi" name="type" value="!!! INSTRUMENT SOURCE!!!"/> | + | <cvParam accession="1" cvLabel="psi" name="type" value="!!! INSTRUMENT SOURCE!!!"/> |
</source> | </source> | ||
<analyzerList count="1"> | <analyzerList count="1"> | ||
- | <analyzer> | + | <analyzer> |
- | </analyzer> | + | </analyzer> |
</analyzerList> | </analyzerList> | ||
<detector> | <detector> | ||
- | </detector> | + | </detector> |
</instrument> | </instrument> | ||
<dataProcessing> | <dataProcessing> | ||
- | <software> | + | <software> |
- | <name>!!! PROCESSING SOFTWARE NAME !!!</name> | + | <name>!!! PROCESSING SOFTWARE NAME !!!</name> |
- | <version>!!! PROCESSING SOFTWARE NAME !!!</version> | + | <version>!!! PROCESSING SOFTWARE NAME !!!</version> |
</software> | </software> | ||
</dataProcessing> | </dataProcessing> | ||
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<Database>Sp_Trembl</Database> | <Database>Sp_Trembl</Database> | ||
</GelFreeIdentification> | </GelFreeIdentification> | ||
+ | ... | ||
</Experiment> | </Experiment> | ||
</ExperimentCollection> | </ExperimentCollection> | ||
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- | ===== Pride Controlled Vocabulary (CV) ===== | + | ===== PRIDE Controlled Vocabulary (CV) ===== |
+ | |||
+ | There are several CV, coming from several ontologies, used in a PRIDE XML file.\\ | ||
+ | You can find more details about CV on PRIDE website at [[http://www.ebi.ac.uk/pride/ontologyHelp.do|help for using CV]]. | ||
- | There is several CV used in PRIDE XML. You can find on PRIDE site a [[http://www.ebi.ac.uk/pride/ontologyHelp.do|help for using CV]]. | + | Here are some examples of Ontologies/CV: |
+ | * **Mass Spectroscopy Cv (PSI-MS) [PSI]** [[http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PSI|Browse ontology]] | ||
==== PSI CV Ontology ==== | ==== PSI CV Ontology ==== |