userguide:pride_export_properties
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userguide:pride_export_properties [2011/03/04 18:15] 132.168.74.230 |
userguide:pride_export_properties [2011/03/08 14:31] 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"> | ||
| Line 68: | Line 68: | ||
| <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> | ||
| Line 102: | Line 102: | ||
| <Database>Sp_Trembl</Database> | <Database>Sp_Trembl</Database> | ||
| </GelFreeIdentification> | </GelFreeIdentification> | ||
| + | ... | ||
| </Experiment> | </Experiment> | ||
| </ExperimentCollection> | </ExperimentCollection> | ||
| Line 111: | Line 111: | ||
| - | ===== 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]] | ||
| + | * **PRIDE Controlled Vocabulary [PRIDE]** [[http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PRIDE|Browse ontology]] | ||
| + | * **Protein Modifications (PSI-MOD) [MOD]** [[http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD|Browse ontology]] | ||
| ==== PSI CV Ontology ==== | ==== PSI CV Ontology ==== | ||
userguide/pride_export_properties.txt · Last modified: 2011/03/08 14:37 by 132.168.74.230
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