Re: [Psidev-ms-dev] Update from the PSI meeting

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Just to add an additional thought, and the potential for even more 
harmony between PSI work groups: The Molecular interactions schema has

term 	
	required 			
documentation 	

The kind of parameter, e.g. "dissociation constant".

termAc 	
	optional 			
documentation 	

Accession number of the term in the associated controlled vocabulary.

unit 	
	optional 			
documentation 	

The unit of the term, e.g. "kiloDalton".

unitAc 	
	optional 			
documentation 	

Accession number of the unit in the associated controlled vocabulary.

base 	xs:short 	optional 	10 		
documentation 	

Base of the parameter expression. Defaults to 10.

exponent 	xs:short 	optional 	0 		
documentation 	

Exponent of the value.

factor 	xs:decimal 	required 			
documentation 	

The "main" value of the parameter.

see
http://psidev.sourceforge.net/mi/rel25/doc/#complexType_parameterType_Link03B1FB80

Best regards,

Henning

Randy Julian wrote:
>
> Good catch Andy,
>
> I don’t see why the value is a required attribute. The idea of 
> userParam is that it is just like cvParam, expect the names and values 
> are uncontrolled.
>
> I think we need the units in the userParam too. This raises the 
> question of data type in both elements.
>
> In userParam we have a data type field explicitly:
>
> <xs:complexType name="UserParamType">
>
> <xs:attribute name="name" type="xs:string" use="required"/>
>
> <xs:attribute name="type" type="xs:string" />
>
> <xs:attribute name="value" type="xs:string" />
>
> <xs:attribute name="unitName" type="xs:string" />
>
> </xs:complexType>
>
> Is everyone OK with adding unitName to the userParam as an optional 
> attribute, and changing the other attributes (except name) to optional?
>
> Also, I must have missed the data type discussion – are we adding 
> something somewhere for data type validation?
>
> Thanks,
>
> Randy
>
> *From:* psi...@li... 
> [mailto:psi...@li...] *On Behalf Of 
> *Jones, Andy
> *Sent:* Monday, April 28, 2008 10:01 AM
> *To:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] Update from the PSI meeting
>
> Y it is this one that I have a problem with...
>
> <xs:complexType name="UserParamType">
>
> <xs:annotation>
>
> <xs:documentation>Uncontrolled user parameters (essentially allowing 
> free text). Before using these, one should verify whether there is an 
> appropriate CV term available, and if so, use the CV term 
> instead</xs:documentation>
>
> </xs:annotation>
>
> <xs:attribute name="name" type="xs:string" use="required">
>
> <xs:annotation>
>
> <xs:documentation>The name for the parameter.</xs:documentation>
>
> </xs:annotation>
>
> </xs:attribute>
>
> <xs:attribute name="type" type="xs:string" use="required">
>
> <xs:annotation>
>
> <xs:documentation>The type of the parameter, where 
> appropriate.</xs:documentation>
>
> </xs:annotation>
>
> </xs:attribute>
>
> <xs:attribute name="value" type="xs:string" use="required">
>
> <xs:annotation>
>
> <xs:documentation>The value for the parameter, where 
> appropriate.</xs:documentation>
>
> </xs:annotation>
>
> </xs:attribute>
>
> </xs:complexType>
>
> *From:* psi...@li... 
> [mailto:psi...@li...] *On Behalf Of 
> *Randy Julian
> *Sent:* 28 April 2008 14:54
> *To:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] Update from the PSI meeting
>
> Andy,
>
> In the schema I have, the element looks like this:
>
> <xs:complexType name="CVParamType">
>
> <xs:attribute name="cvRef" type="xs:IDREF" use="required"/>
>
> <xs:attribute name="accession" type="xs:string" use="required"/>
>
> <xs:attribute name="value" type="xs:string" use="optional"/>
>
> <xs:attribute name="name" type="xs:string" use="required"/>
>
> <xs:attribute name="unitAccession" type="xs:string" use="optional"/>
>
> <xs:attribute name="unitName" type="xs:string" use="optional"/>
>
> </xs:complexType>
>
> This is version 0.99.9 (attached). Let me know if this makes sense.
>
> Thanks,
>
> Randy
>
> *From:* psi...@li... 
> [mailto:psi...@li...] *On Behalf Of 
> *Jones, Andy
> *Sent:* Monday, April 28, 2008 9:14 AM
> *To:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] Update from the PSI meeting
>
> Hi all,
>
> I’m incorporating the mzML cvParam part (working from 0.99.9) into the 
> analysisXML draft, to see how this works with the current schema.
>
> I noticed that userParam has attributes name, value and type, and all 
> are required attributes. I would have expected value and type to be 
> optional (as suggested by the documentation) – is this an error?
>
> Cheers
>
> Andy
>
> *From:* psi...@li... 
> [mailto:psi...@li...] *On Behalf Of 
> *Eric Deutsch
> *Sent:* 28 April 2008 07:16
> *To:* Mass spectrometry standard development
> *Cc:* Eric Deutsch
> *Subject:* [Psidev-ms-dev] Update from the PSI meeting
>
> Hi everyone, we had a productive track at the PSI spring meeting. The 
> highlights are:
>
> - All suggested and needed schema revisions were completed and schema 
> version 0.99.9 is available
>
> - Most documentation updates were written. Revised full spec doc and 
> html doc still to be released.
>
> - MIAPE-MS example document almost completed
>
> - ASMS poster features planned
>
> - Journal article plans discussed
>
> - Some CV updates and future update procedure planned. Still much to do
>
> - Additional example documents are needed
>
> - Web site updated with completed work
>
> Many thanks to those who did the work at the workshop: Lennart Martens 
> (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim Shofstahl 
> (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi-Palazzi (EBI), 
> Randy Julian (Indigo), Lars Nilse (Manchester), Benito Cañas (Madrid), 
> Lola Gutierrez (Madrid), Matt Chambers (Vanderbilt), Alberto Medina 
> (Madrid)
>
> Moving forward, we have an aggressive schedule to release mzML 1.0.0 
> one month from now. Your participation is needed!
>
> We will have weekly teleconferences for the next month to try to keep 
> the focus strong. The next teleconference will be this Tuesday at 9am 
> PDT at the usual place.
>
> We have the following list of action items set at the end of the meeting:
>
> - Eric will finish documentation items (incl reviewer reply)
>
> - Pierre-Alain will finish MIAPE-MS example
>
> - Eric will do the CV to do items
>
> - Lennart will get validator finished and working
>
> - Eric will put together poster with various assistance
>
> - Lennart will write draft of manuscript
>
> - Darren and Matt and Jim will work on example files
>
> - Luisa will create the Excel sheets, one for each vendor. Eric will 
> send. Luisa will reintegrate.
>
> If you have an interest in mzML, we need your help to get it finished. 
> One of the important things we still need is more example files. If 
> you are willing to create from example files, especially by parts of 
> the schema that have not been well tested, please help. Create an 
> example file and post it. Or contact me for ideas.
>
> Thank you!
>
> Eric
>
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