userguide:pride_export_properties
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userguide:pride_export_properties [2011/03/04 17:05] 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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| :!: **Current limitations about using the //runDescriptor.properties// file** :!: | :!: **Current limitations about using the //runDescriptor.properties// file** :!: | ||
| - | * **The list of available properties is not not enough to create a detailled header for the PRIDE XML file**: information regarding protocol steps, sample description, additionnal information, etc. can not be provided as properties (only manually after PRIDE XML file creation) | + | * **The list of available properties is not enough to create a full detailled header for the PRIDE XML file**: information regarding protocol steps, sample description, additionnal information, etc. can not be provided as properties (specify them manually after PRIDE XML file 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**. For example, if you want to specify one analyser in the runDescriptor.properties file, the first step is to find the appropriate : | + | * 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**. |
| - | ''analyzer.1.key.1=LTQ Orbitrap'' | + | **First, see [[http://www.ebi.ac.uk/pride/ontologyHelp.do|what is a CV Param and how to use it]].**\\ |
| - | ''analyzer.1.value.1=Discovery'' | + | **Then, you will need to [[http://www.ebi.ac.uk/ontology-lookup/|browse ontologies to find the appropriate CV Params]] (Ontology Lookup Service).** |
| - | In the in the PRIDE XML, you will see: | ||
| - | ''<cvParam accession="1" cvLabel="psi" name="LTQ Orbitrap" value="Discovery"/>'' | + | **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)\\ | ||
| + | - The CV given below are examples, they are not exclusive and may change with PRIDE Format.\\ | ||
| - | You will need to change it into: | + | * **contact.name=**NAME: contact person name (first and last names), or role name ''(required)'' |
| - | + | * **contact.institute=**INSTITUTION: organisation with which the contact person or role is associated ''(required)'' | |
| - | ''<cvParam cvLabel="PSI" accession="PSI:1000449" name="LTQ Orbitrap" value="Discovery" />'' | + | * **contact.info=**INFO: information about contact (Phone number, email, postal address, etc.) ''(optional)'' |
| - | + | * **sample.name=**SPLNAME: name of the sample used to generate the data set ''(required)'' | |
| - | + | * **accession=**ACC: the accession number assigned arbitrarily to a particular mzData instance (i.e. data) file, by the generator of that file. ''(required, default to context name)'' | |
| - | cvParam example:\\ | + | * **instrument.model=**MODEL: descriptive name of the instrument (make, model, significant customizations). ''(required)'' |
| - | cvParam cvLabel="PSI" accession="PSI:1000008" name="IonizationType" value="ESI"/>\\ | + | * **instrument.source=**SRCE: one of ''(required)'' |
| - | See **[[http://www.ebi.ac.uk/pride/ontologyHelp.do|here]]** for help for using CV Param. \\ | + | * APCI: Atmospheric Pressure Chemical Ionization (PSI:1000070) |
| - | + | * CI: Chemical Ionization (PSI:1000071) | |
| - | The CV given below are examples, they are not exclusive and may change with PRIDE Format. See Pride site for more details. | + | * EI: Electronic Ionization (PSI:1000072) |
| - | + | * ESI: Electrospray Ionization (PSI:1000073) | |
| - | **__Note__:** | + | * FAB: Fast Atom Bombardment Ionization (PSI:1000074) |
| - | 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) | + | * MALDI: Matrix-assisted Laser Desorption Ionization (PSI:1000075) |
| - | + | ||
| - | * contact.name=NAME : Contact person name, or role name ''(require)'' | + | |
| - | * contact.institute=INSTITUTION: Organisation with which the contact person or role is associated ''(require)'' | + | |
| - | * contact.info=INFO : Information about contact : Phone number, email, postal address or other appropriate means of contact ''(optional)'' | + | |
| - | * sample.name=SPLNAME : Name of the sample used to generate the data set ''(require)'' | + | |
| - | * accession=ACC : The accession number assigned arbitrarily to a particular mzData instance (i.e. data) file, by the generator of that file. ''(require, default to context name)'' | + | |
| - | * instrument.model=MODEL : Descriptive name of the instrument (make, model, significant customisations). ''(require)'' | + | |
| - | * instrument.source=SRCE : One of ''(require)'' | + | |
| - | * APCI : Atmospheric Pressure Chemical Ionization (PSI:1000070) | + | |
| - | * CI : Chemical Ionization (PSI:1000071) | + | |
| - | * EI : Electronic Ionization (PSI:1000072) | + | |
| - | * ESI : Electrospray Ionization (PSI:1000073) | + | |
| - | * FAB : Fast Atom Bombardment Ionization (PSI:1000074) | + | |
| - | * MALDI : Matrix-assisted Laser Desorption Ionization (PSI:1000075) | + | |
| * Mass analyser component list (e.g. quadrupole, collision cell); ordered so as to reflect the physical order of the described components in the mass spectrometer. For each analyser (number replaced in {0}), defines as many key-value pairs as necessary (replace pair number in {1}) ''(require at least one, even if no CV in generated XML...)'' | * Mass analyser component list (e.g. quadrupole, collision cell); ordered so as to reflect the physical order of the described components in the mass spectrometer. For each analyser (number replaced in {0}), defines as many key-value pairs as necessary (replace pair number in {1}) ''(require at least one, even if no CV in generated XML...)'' | ||
| - | * analyzer.{0}.key.{1} : Keys examples. See Ontology here after for other examples Analyzer Descoriptio (PSI:1000010 to PSI:1000025) and Analyzer type (PSI:1000078 to PSI:1000084) | + | * **analyzer.{0}.key.{1}=** Keys examples. See Ontology here after for other examples Analyzer Descoriptio (PSI:1000010 to PSI:1000025) and Analyzer type (PSI:1000078 to PSI:1000084) |
| - | * analyzer.{0}.value.{1} : Value associated to specified key (AnalyzerType=PaulIonTrap; Resolution=2000; ResolutionMethod=FWHM; ResolutionType=Constant; ...) if necessary | + | * **analyzer.{0}.value.{1}=** Value associated to specified key (AnalyzerType=PaulIonTrap; Resolution=2000; ResolutionMethod=FWHM; ResolutionType=Constant; ...) if necessary |
| - | * dectector.key : Key value = Terms that describe the detector (example: Detector Type (PSI:1000026); Detector Acquisition Mode(PSI:1000027), ... to PSI:1000029 and all CV where is_a = PSI:1000026 to 29) ) ''(require even if no CV in generated XML ...)'' | + | * **dectector.key** : Key value = Terms that describe the detector (example: Detector Type (PSI:1000026); Detector Acquisition Mode(PSI:1000027), ... to PSI:1000029 and all CV where is_a = PSI:1000026 to 29) ) ''(required even if no CV in generated XML ...)'' |
| - | * dectector.value : Associated value if necessary | + | * **detector.value=**associated value if necessary |
| - | * processing.software.name : The official name for the software package used. ''(require)'' | + | * **processing.software.name** : The official name for the software package used. ''(require)'' |
| - | * processing.software.version : The version number of the software package. ''(require)'' | + | * **processing.software.version** : The version number of the software package. ''(require)'' |
| - | * processing.method.{0}.key : Description of the default peak processing method. (Deisotoping PSI:1000033; Charge Deconvolution PSI:1000034; Peak Processing PSI:1000035 ) ''(optional)'' | + | * **processing.method.{0}.key** : Description of the default peak processing method. (Deisotoping PSI:1000033; Charge Deconvolution PSI:1000034; Peak Processing PSI:1000035 ) ''(optional)'' |
| - | * processing.method.{0}.value : associated value (true/false, CentroidMassSpectrum...) ''(optional)'' | + | * **processing.method.{0}.value** : associated value (true/false, CentroidMassSpectrum...) ''(optional)'' |
| - | ==== 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 81: | 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 115: | Line 102: | ||
| <Database>Sp_Trembl</Database> | <Database>Sp_Trembl</Database> | ||
| </GelFreeIdentification> | </GelFreeIdentification> | ||
| + | ... | ||
| </Experiment> | </Experiment> | ||
| </ExperimentCollection> | </ExperimentCollection> | ||
| Line 124: | 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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