userguide:pride_export_properties
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
|
userguide:pride_export_properties [2011/03/04 18:14] 132.168.74.230 |
userguide:pride_export_properties [2011/03/08 14:31] 132.168.74.230 |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ====== 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.\\ | ||
| Line 5: | Line 5: | ||
| 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. |
| Line 25: | Line 25: | ||
| * Each property is mapped to a simple XML tag or a specific CV Param. When the property is mapped to a CV Param, **the user will have to manually provide accession and cvLabel for the cvParam, after PRIDE XML creation**. | * Each property is mapped to a simple XML tag or a specific CV Param. When the property is mapped to a CV Param, **the user will have to manually provide accession and cvLabel for the cvParam, after PRIDE XML creation**. | ||
| - | First, see **[[http://www.ebi.ac.uk/pride/ontologyHelp.do|what is a CV Param and how to use it]]**.\\ | + | **First, see [[http://www.ebi.ac.uk/pride/ontologyHelp.do|what is a CV Param and how to use it]].**\\ |
| - | Then, you will need to **[[http://www.ebi.ac.uk/ontology-lookup/|browse ontologies to find the appropriate CV Params]]** (Ontology Lookup Service). | + | **Then, you will need to [[http://www.ebi.ac.uk/ontology-lookup/|browse ontologies to find the appropriate CV Params]] (Ontology Lookup Service).** |
| - | **Notes** | + | **Notes**\\ |
| - | + | - Missing properties will have a default value in order to create the required XML tags, but their values will have to be changed by user. These default values are surrounded by three exclamation points '!!!' in order to highlight them. They are not all required (see list bellow)\\ | |
| - | - Missing properties will have a default value in order to create the required XML tags, but their values will have to be changed by user. These default values are surrounded by three exclamation points '!!!' in order to highlight them. They are not all required (see list bellow) | + | - The CV given below are examples, they are not exclusive and may change with PRIDE Format.\\ |
| - | - The CV given below are examples, they are not exclusive and may change with PRIDE Format. | + | |
| * **contact.name=**NAME: contact person name (first and last names), or role name ''(required)'' | * **contact.name=**NAME: contact person name (first and last names), or role name ''(required)'' | ||
| Line 58: | Line 57: | ||
| - | ==== 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 69: | 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 103: | Line 102: | ||
| <Database>Sp_Trembl</Database> | <Database>Sp_Trembl</Database> | ||
| </GelFreeIdentification> | </GelFreeIdentification> | ||
| + | ... | ||
| </Experiment> | </Experiment> | ||
| </ExperimentCollection> | </ExperimentCollection> | ||
| Line 112: | 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
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 4.0 International
