ProDBWiki/DeveloperDocumentation/MzDataImportSpecification - Revision history

Admin: 10 revisions

2011-10-26T06:16:39Z

10 revisions

← Older revision	Revision as of 08:16, 26 October 2011
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imported>JomunaChoudhuri at 08:53, 24 August 2005

2005-08-24T08:53:53Z

← Older revision		Revision as of 10:53, 24 August 2005
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	The importer needs to have access to the ontology and also some mapping information to see which parameter type triggers the generation of an object (e.g. name="[[IonizationType]]") and how other parameters are map into an object's attributes.		The importer needs to have access to the ontology and also some mapping information to see which parameter type triggers the generation of an object (e.g. name="[[IonizationType]]") and how other parameters are map into an object's attributes.

	The ontology doesn't exist as an OWL file yet, only as tab-delimited list at [http://psidev.sourceforge.net/ontology/PSI_ontology_mzData_v0.0.htm]. As such, it cannot define parameter dependencies (e.g. if <cvParam name="[[AnalyzerType]]" ../> exists, there must be also a <cvParam name="Resolution" .../> element). Hopefully, the first proper release of the ontology as OWL version contains this kind of information. Otherwise we have to include this information in our mapping configuration(s).		The ontology doesn't exist as an OWL file yet, only as tab-delimited list at [http://psidev.sourceforge.net/ontology/PSI_ontology_mzData_v0.0.htm]. As such, it cannot define parameter dependencies (e.g. if <cvParam name="AnalyzerType" ../> exists, there must be also a <cvParam name="Resolution" .../> element). Hopefully, the first proper release of the ontology as OWL version contains this kind of information. Otherwise we have to include this information in our mapping configuration(s).

	== Further reading ==		== Further reading ==

imported>KaiRunte at 13:29, 16 February 2005

2005-02-16T13:29:19Z

← Older revision		Revision as of 15:29, 16 February 2005
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	== Further reading ==		== Further reading ==

	[http://psidev.sourceforge.net/ms/ PSI-MS: Mass Spectrometry Standards Working Group]		* [http://psidev.sourceforge.net/ms/ PSI-MS: Mass Spectrometry Standards Working Group]
	[http://psidev.sourceforge.net/ms/xml/mzdata/mzdata.html mzData Schema Documentation]		* [http://psidev.sourceforge.net/ms/xml/mzdata/mzdata.html mzData Schema Documentation]
	[http://psidev.sourceforge.net/ontology/index.html The PSI Ontology]		* [http://psidev.sourceforge.net/ontology/index.html The PSI Ontology]
	[http://psidev.sourceforge.net/ontology/PSI_ontology_mzData_v0.0.htm PSI ontology mzData v0.0]		* [http://psidev.sourceforge.net/ontology/PSI_ontology_mzData_v0.0.htm PSI ontology mzData v0.0]
	[http://sourceforge.net/project/showfiles.php?group_id=65472 PSI Download Section (XML Schema and XML Examples)]		* [http://sourceforge.net/project/showfiles.php?group_id=65472 PSI Download Section (XML Schema and XML Examples)]

imported>KaiRunte at 13:28, 16 February 2005

2005-02-16T13:28:48Z

← Older revision		Revision as of 15:28, 16 February 2005
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	The ontology doesn't exist as an OWL file yet, only as tab-delimited list at [http://psidev.sourceforge.net/ontology/PSI_ontology_mzData_v0.0.htm]. As such, it cannot define parameter dependencies (e.g. if <cvParam name="[[AnalyzerType]]" ../> exists, there must be also a <cvParam name="Resolution" .../> element). Hopefully, the first proper release of the ontology as OWL version contains this kind of information. Otherwise we have to include this information in our mapping configuration(s).		The ontology doesn't exist as an OWL file yet, only as tab-delimited list at [http://psidev.sourceforge.net/ontology/PSI_ontology_mzData_v0.0.htm]. As such, it cannot define parameter dependencies (e.g. if <cvParam name="[[AnalyzerType]]" ../> exists, there must be also a <cvParam name="Resolution" .../> element). Hopefully, the first proper release of the ontology as OWL version contains this kind of information. Otherwise we have to include this information in our mapping configuration(s).

			== Further reading ==

			[http://psidev.sourceforge.net/ms/ PSI-MS: Mass Spectrometry Standards Working Group]
			[http://psidev.sourceforge.net/ms/xml/mzdata/mzdata.html mzData Schema Documentation]
			[http://psidev.sourceforge.net/ontology/index.html The PSI Ontology]
			[http://psidev.sourceforge.net/ontology/PSI_ontology_mzData_v0.0.htm PSI ontology mzData v0.0]
			[http://sourceforge.net/project/showfiles.php?group_id=65472 PSI Download Section (XML Schema and XML Examples)]

imported>KaiRunte at 12:47, 16 February 2005

2005-02-16T12:47:44Z

← Older revision		Revision as of 14:47, 16 February 2005
Line 40:		Line 40:
	The importer needs to have access to the ontology and also some mapping information to see which parameter type triggers the generation of an object (e.g. name="[[IonizationType]]") and how other parameters are map into an object's attributes.		The importer needs to have access to the ontology and also some mapping information to see which parameter type triggers the generation of an object (e.g. name="[[IonizationType]]") and how other parameters are map into an object's attributes.

	The ontology doesn't exist as an OWL file yet, only as tab-delimited list at [http://psidev.sourceforge.net/ontology/PSI_ontology_mzData_v0.0.htm]. As such, it cannot define parameter dependencies (e.g. if <cvParam name="[[AnalyzerType]]" ../> exists, there must be also a <cvParam name="Resolution" .../> element). Hopefully, the first proper release of the ontology as OWL version contains this kind of information. Otherwise we have to include this information ~~into~~ our mapping configuration(s).		The ontology doesn't exist as an OWL file yet, only as tab-delimited list at [http://psidev.sourceforge.net/ontology/PSI_ontology_mzData_v0.0.htm]. As such, it cannot define parameter dependencies (e.g. if <cvParam name="[[AnalyzerType]]" ../> exists, there must be also a <cvParam name="Resolution" .../> element). Hopefully, the first proper release of the ontology as OWL version contains this kind of information. Otherwise we have to include this information in our mapping configuration(s).

imported>KaiRunte at 12:46, 16 February 2005

2005-02-16T12:46:33Z

← Older revision		Revision as of 14:46, 16 February 2005
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	An mzData format importer for ProDB needs to consider two different mapping problems. The first one is a relatively simple one: XML elements/attributes need to be mapped onto ProDB object attributes. The second kind of mapping is a little bit more difficult: we need to map ontology-controlled cvParam elements onto ProDB object attributes. An example:		An mzData format importer for ProDB needs to consider two different mapping problems. The first one is a relatively simple one: XML elements/attributes need to be mapped onto ProDB object attributes. The second kind of mapping is a little bit more difficult: we need to map ontology-controlled cvParam elements onto ProDB object attributes. An example:

	ProDB models the kind of ionisation directly as classes, for example DB::Ionisation::Electrospray or DB::Ionisation::Maldi. In mzData, however, this information is stored in a list of cvParam elements in mzData/description/instrument/source, for example		ProDB models the kind of ionisation directly as classes, for example DB::Ionisation::Electrospray or DB::Ionisation::Maldi. In mzData, however, this information is stored in a list of cvParam elements in mzData/description/instrument/source, for example:

	<pre><nowiki>		<pre><nowiki>
			<mzData version="1.04" accessionNumber="psi-ms:12345" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
	<description>		<description>
	<admin>		<admin>
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	</detector>		</detector>
	</instrument>		</instrument>
			...
			<description>
			...
			</mzData>
			</nowiki></pre>

			The importer needs to have access to the ontology and also some mapping information to see which parameter type triggers the generation of an object (e.g. name="[[IonizationType]]") and how other parameters are map into an object's attributes.

	</~~nowiki~~></~~pre~~>		The ontology doesn't exist as an OWL file yet, only as tab-delimited list at [http://psidev.sourceforge.net/ontology/PSI_ontology_mzData_v0.0.htm]. As such, it cannot define parameter dependencies (e.g. if <cvParam name="[[AnalyzerType]]" ../> exists, there must be also a <cvParam name="Resolution" .../> element). Hopefully, the first proper release of the ontology as OWL version contains this kind of information. Otherwise we have to include this information into our mapping configuration(s).

imported>KaiRunte at 12:31, 16 February 2005

2005-02-16T12:31:17Z

← Older revision		Revision as of 14:31, 16 February 2005
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	</analyzerList>		</analyzerList>
	<detector>		<detector>
	<cvParam cvLabel="psi" accession="" name="~~type~~" value="EM"/>		<cvParam cvLabel="psi" accession="PSI:1000021" name="DetectorType" value="ElectronMultiplier"/>
	</detector>		</detector>
	</instrument>		</instrument>

	</nowiki></pre>		</nowiki></pre>

imported>KaiRunte at 12:29, 16 February 2005

2005-02-16T12:29:41Z

@@ Line 1: / Line 1: @@
 __NOTOC__
- = mzData Import Specification =
+= mzData Import Specification =
- == Introduction ==
+== Introduction ==
 mzData is an XML exchange format for mass-spectrometry data and is created and maintained by the [http://psidev.sourceforge.net Proteomics Standards Initiative]. The format is defined by an XML schema and an ontology. The ontology defines legal values for so-called cvParam elements to provide flexibility concerning new mass-spectrometers and their componentry.
@@ Line 8: / Line 8: @@
 An mzData format importer for ProDB needs to consider two different mapping problems. The first one is a relatively simple one: XML elements/attributes need to be mapped onto ProDB object attributes. The second kind of mapping is a little bit more difficult: we need to map ontology-controlled cvParam elements onto ProDB object attributes. An example:
 ProDB models the kind of ionisation directly as classes, for example DB::Ionisation::Electrospray or DB::Ionisation::Maldi. In mzData, however, this information is stored in a list of cvParam elements in mzData/description/instrument/source, for example

imported>KaiRunte at 12:22, 16 February 2005

2005-02-16T12:22:56Z

← Older revision		Revision as of 14:22, 16 February 2005
Line 7:		Line 7:

	An mzData format importer for ProDB needs to consider two different mapping problems. The first one is a relatively simple one: XML elements/attributes need to be mapped onto ProDB object attributes. The second kind of mapping is a little bit more difficult: we need to map ontology-controlled cvParam elements onto ProDB object attributes. An example:		An mzData format importer for ProDB needs to consider two different mapping problems. The first one is a relatively simple one: XML elements/attributes need to be mapped onto ProDB object attributes. The second kind of mapping is a little bit more difficult: we need to map ontology-controlled cvParam elements onto ProDB object attributes. An example:

			ProDB models the kind of ionisation directly as classes, for example DB::Ionisation::Electrospray or DB::Ionisation::Maldi. In mzData, however, this information is stored in a list of cvParam elements in mzData/description/instrument/source, for example

imported>KaiRunte at 11:26, 16 February 2005

2005-02-16T11:26:57Z

← Older revision		Revision as of 13:26, 16 February 2005
Line 6:		Line 6:
	mzData is an XML exchange format for mass-spectrometry data and is created and maintained by the [http://psidev.sourceforge.net Proteomics Standards Initiative]. The format is defined by an XML schema and an ontology. The ontology defines legal values for so-called cvParam elements to provide flexibility concerning new mass-spectrometers and their componentry.		mzData is an XML exchange format for mass-spectrometry data and is created and maintained by the [http://psidev.sourceforge.net Proteomics Standards Initiative]. The format is defined by an XML schema and an ontology. The ontology defines legal values for so-called cvParam elements to provide flexibility concerning new mass-spectrometers and their componentry.

	An mzData format importer for !ProDB needs to consider two different mapping problems. The first one is a relatively simple one: XML elements/attributes need to be mapped onto ProDB object attributes. The second kind of mapping is a little bit more difficult: we need to map ontology-controlled cvParam elements onto ProDB object attributes. An example:		An mzData format importer for ProDB needs to consider two different mapping problems. The first one is a relatively simple one: XML elements/attributes need to be mapped onto ProDB object attributes. The second kind of mapping is a little bit more difficult: we need to map ontology-controlled cvParam elements onto ProDB object attributes. An example: