psidev-pi-dev — General Development List for Proteomics Informatics

[Psidev-pi-dev] Issue 49 in psi-pi: Issues / schema updates prior to version 1 release

[<cod...@go...>]

Comment #4 on issue 49 by andrewrobertjones: Issues / schema updates prior  
to version 1 release
http://code.google.com/p/psi-pi/issues/detail?id=49

The Peptide element still has an optional attribute calculatedPI but we  
have no
examples of its use.

I think this should go - Peptides have no connection with a particular  
software
package so these values are fairly meaningless.

Does anyone remember a use case for this being present?

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[Psidev-pi-dev] Issue 49 in psi-pi: Issues / schema updates prior to version 1 release

[<cod...@go...>]

Comment #3 on issue 49 by andrewrobertjones: Issues / schema updates prior  
to version 1 release
http://code.google.com/p/psi-pi/issues/detail?id=49

I think the passThreshold part of the schema is still a bit ambiguous (a  
comment
about FDR thresholds was also made by a reviewer).

I suggest we add an optional schema element to  
SpectrumIdentificationProtocol and
ProteinDetectionProtocol specifically for this purpose:

<SpectrumIdentificationProtocol id="SIP"  
AnalysisSoftware_ref="AS_mascot_server">
    <Threshold>
        <pf:cvParam accession="MS:1001316" name="mascot:SigThreshold"  
cvRef="PSI-MS"
value="0.05"/>

OR
         <pf:cvParam accession="MS:TODO" name="global FDR" cvRef="PSI-MS"  
value="0.05"/>


and the same for protein detection.

I realise there are cases where this cannot be given or it might be  
difficult to
report which peptides passed the threshold but several example files have
passThreshold set but do not specify what the threshold is.



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[Psidev-pi-dev] Issue 49 in psi-pi: Issues / schema updates prior to version 1 release

[<cod...@go...>]

Comment #2 on issue 49 by andrewrobertjones: Issues / schema updates prior  
to version 1 release
http://code.google.com/p/psi-pi/issues/detail?id=49

There are three elements I would like to remove from the schema:  
AnalysisResultList,
AnalysisResult, AnalysisResultItem. These were place holders so that any  
quant
extensions would extend from the same points in the hierarchy as
SpectrumIdentificationList, SpectrumIdentificationResult and
SpectrumIdentificationItem (same for proteins). Now that quant is going to  
be
developed independently, I can see no reason to keep them in?

Unless anyone can see some benefits, I'll remove these from the hierarchy.





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[Psidev-pi-dev] Minutes from Phone conference (May 15)

[Juan A. V. <ju...@eb...>]

Hi all,

Minutes from yesterday's phone conference can be found here:

http://www.psidev.info/index.php?q=node/415

Cheers,

Juan Antonio


Juan Antonio Vizcaíno, Ph.D.
EMBL European Bioinformatics Institute
Proteomics Services Team, PANDA Group
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD
Tel: +44 (0) 1223 492 686
Fax: +44 (0) 1223 494 468
Skype: javizca

[Psidev-pi-dev] Issue 48 in psi-pi: calculatedMassToCharge and sequenceMass have the same information

[<cod...@go...>]

Updates:
	Status: Fixed

Comment #4 on issue 48 by andrewrobertjones: calculatedMassToCharge and  
sequenceMass have the same information
http://code.google.com/p/psi-pi/issues/detail?id=48

(No comment was entered for this change.)

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[Psidev-pi-dev] Issue 48 in psi-pi: calculatedMassToCharge and sequenceMass have the same information

[<cod...@go...>]

Comment #3 on issue 48 by dcreasy: calculatedMassToCharge and sequenceMass  
have the same information
http://code.google.com/p/psi-pi/issues/detail?id=48

At the telecon on 2009-05-07 16:00  
(http://psidev.info/index.php?q=node/412) we
agreed to try removing sequenceLength, sequenceMass and MassTable_ref from  
the
<Peptide> element. Added MassTable_ref to <SpectrumIdentificationItem>

The updated Mascot N15 example shows an example of using MassTable_ref

http://code.google.com/p/psi-pi/source/browse/trunk/examples/Mascot_N15_example.mzid

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[Psidev-pi-dev] Issue 49 in psi-pi: Issues / schema updates prior to version 1 release

[<cod...@go...>]

Comment #1 on issue 49 by andrewrobertjones: Issues / schema updates prior  
to version 1 release
http://code.google.com/p/psi-pi/issues/detail?id=49

Schema update:

Removed SequenceMass, sequenceLength and MassTable_ref from Peptide

Added MassTable_ref to SpectrumIdentificationItem

Added Keys and KeyRefs for this

Some minor changes to FuGElight that shouldn't affect anything in mzIdentML

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[Psidev-pi-dev] introduction

[Darren K. <da...@pr...>]

Hi all,

I just wanted to introduce Rob Burke, who has recently joined the mail
list and will be joining on the mzIndentML conference calls.  He will
be working on the ProteoWizard implementation of mzIndentML.

For those of you who I haven't met via the mzML working group, we work
in Parag Mallick's lab at University of Southern California.  The
ProteoWizard project page is here:
http://proteowizard.sourceforge.net

Cheers!


Darren

[Psidev-pi-dev] Issue 50 in psi-pi: Taxonomy for each protein (DBSequence)

[<cod...@go...>]

Comment #1 on issue 50 by pierrealainbinz: Taxonomy for each protein  
(DBSequence)
http://code.google.com/p/psi-pi/issues/detail?id=50

I vote for the option with different CV terms, all with a is_a: MS:1001089  
relationship.

But I would prefer to see the latter be renamed molecule taxonomy, as it  
can be a
result from a search in a nucleotide sequence database and not a protein  
sequence
database (some tools do on-the-fly translation of nucleotide sequences)



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Re: [Psidev-pi-dev] [Psidev-ms-dev] Merged CV

[Matthew C. <mat...@va...>]

I found some redundant names after the merge that causes problems with pwiz.

id: MS:1000336
name: neutral loss
def: "The loss of an uncharged species during a rearrangement process." [PSI:MS]
is_a: MS:1000445 ! sequential m/z separation method ?


id: MS:1001061

name: neutral loss
def: "Leave this to PSI-MOD?" [PSI:PI]
is_a: MS:1001055 ! modification parameters


and


id: MS:1000796
name: spectrum title
def: "A free-form text title describing a spectrum." [PSI:MS]
comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list. This term corresponds to Protein Informatics CV term PI:00416
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute


id: MS:1001416
name: spectrum title
def: "Holds the spectrum title from different input file formats, e.g. MGF TITLE." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details


I'm pretty sure one of each duplicate pair should be obsoleted, which will render it more or less invisible to pwiz. Thoughts?

-Matt



Pierre-Alain Binz wrote:
> Fine with me.
> Yes, the ms-vocab list should be used for this. Request for changes 
> can be done on other lists, but the actual changes should be 
> documented there (not a perfect tracking system, but easy to search). 
> The CV editors must be in the list, and only those in the list are 
> allowed to edit.
>
> If the changes are quick, there is probably no need to "lock" the file 
> via a short announce on the vocab list. But if the work to be done is 
> longer (a few hours), it should be mentioned (I start, it's done) on 
> the list
>
> Does that sounds ok?
> If yes, Eric can summarise the process (pragmatism is key here)
>
> Pierre-Alain
>
> Eric Deutsch wrote:
>>
>> Hi everyone, with the merging of the CV, we should probably review 
>> the versioning rules and, assuming we still like them, try to stick 
>> to them.
>>
>> According to our spec doc:
>>
>> A new psi-ms.obo should then be released by updating the file on the 
>> CVS server without changing the name of the file (this would alter 
>> the propagation of the file to the OBO website and to other ontology 
>> services that rely on file stable URI). For this reason an internal 
>> version number with two decimals (x.y.z) should be increased:
>>
>> • x should be increased when a first level term are renamed added 
>> deleted or rearranged in the structure. Such rearrangement is suppose 
>> to be rare and is very likely to have repercussion on the mapping.
>>
>> • y should be increased when any other term except the first level 
>> one is altered.
>>
>> • z should be increased when there is no term addition or deletion 
>> but just editing on the definitions or other minor changes.
>>
>> Are we all still on board with this?
>>
>> I made the new merged CV version 2.0.0.
>>
>> Since we have more people editing now, it is probably more important 
>> than ever to follow the edit protocol:
>>
>> - Grab the latest CV from CVS
>>
>> - Edit as necessary relatively quickly
>>
>> - Update the internal version number according to the rules above
>>
>> - Update the “lastID.txt” file in CVS too
>>
>> - Commit changes
>>
>> We have a psidev-ms-vocab email list which is rather disused. I 
>> suggest we make sure all the main editors are on it and update things 
>> so that the CVS commit messages go to that list to help us keep 
>> up-to-date. Does this seem good?
>>
>> Thanks,
>>
>> Erric
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------
>> The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
>> production scanning environment may not be a perfect world - but thanks to
>> Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
>> Series Scanner you'll get full speed at 300 dpi even with all image 
>> processing features enabled. http://p.sf.net/sfu/kodak-com
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>   

[Psidev-pi-dev] Issue 50 in psi-pi: Taxonomy for each protein (DBSequence)

[<cod...@go...>]

Status: Accepted
Owner: dcreasy
Labels: Type-Defect Priority-Medium

New issue 50 by dcreasy: Taxonomy for each protein (DBSequence)
http://code.google.com/p/psi-pi/issues/detail?id=50

We don't currently have an example for MS:1001089 and MS:1001090 and they
are not well defined.

[Term]
id: MS:1001089
name: protein taxonomy
def: "The taxonomy of the resultant protein from the search." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1001090
name: taxonomy nomenclature
def: "The system used to indicate taxonomy. There should be an enumerated
list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID
(ex. RABIT from the full protein ID ALBU_RABIT)." [PSI:PI]
is_a: MS:1001089 ! protein taxonomy

This seems a little unwieldy to me. How about just having different CV for
each type of ID. For example


<DBSequence id="x" length="449" SearchDatabase_ref="y" accession="z" >
   <seq>MGKEKFHINIVVIGHVDSGKSTTTGHLIY...</seq>
   <pf:cvParam accession="MS:1001088" name="protein description"
cvRef="PSI-MS" value="Elongation factor..." />
   <pf:cvParam accession="MS:xxxxxx1" name="taxonomy: NCBI TaxID"
cvRef="PSI-MS" value="9606" />
   <pf:cvParam accession="MS:xxxxxx2" name="taxonomy: common name"
cvRef="PSI-MS" value="human" />
   <pf:cvParam accession="MS:xxxxxx3" name="taxonomy: scientific name"
cvRef="PSI-MS" value="Homo sapiens" />
   <pf:cvParam accession="MS:xxxxxx4" name="taxonomy: Swiss-Prot ID"
cvRef="PSI-MS" value="HUMAN" />
</DBSequence>

It should be possible to have 0..many taxonomy definitions for each  
sequence.

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[Psidev-pi-dev] Issue 31 in psi-pi: Specifying the Search Database(s) Unambiguously - MIRIAM?

[<cod...@go...>]

Comment #10 on issue 31 by dcreasy: Specifying the Search Database(s)  
Unambiguously - MIRIAM?
http://code.google.com/p/psi-pi/issues/detail?id=31

Thanks for finding this out. I guess the most commonly used 'database' in  
the mass
spec world is the NCBI 'nr' database. Be interesting to know if this is not  
included
because of '1' or '2'.

Also, how about MSIPI. http://www.pil.sdu.dk/msipi.htm
Would they include this as a separate database?

Please let us know what they decide about '3'

Thanks,
David

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[Psidev-pi-dev] Changes to the PI group structure.

[David C. <dc...@ma...>]

Hi,

At the recent meeting in Turku, we made three changes to those in the 
'official roles' in the PSI-PI group:

Jenny Siepen is having to step down from being the secretary and 	Juan 
Antonio Vizcaíno has kindly offered to take over.

Zsuzanna Bencsath-Makkai has been unable to give much time to the PSI 
recently, so Andreas Bertsch has been coordinating much of the ontology 
work.

Angel Pizarro has also been unable to be as actively involved as in the 
past, and Andy Jones has volunteered to take over as the chair of the 
group. Hopefully Angel will continue to have some time to provide 
feedback and expertise to the process.

Many thanks to Angel, Jenny and Zsuzanna to all the input that they have 
provided in the past.

And, as always we are looking for more people to be actively involved 
through providing comments on the specifications and joining in on the 
telephone conference calls.

http://psidev.info/index.php?q=node/319#group_structure


David

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898

[Psidev-pi-dev] Mascot mzIdentML Examples

[David C. <dc...@ma...>]

Hi,

I've updated the Mascot mzIdentML examples. I've also changed the 
extension to .mzid and changed the links on the page here:

http://psidev.info/index.php?q=node/319#deliverablequicklinks

A few errors I can't explain - they are either bugs in the mapping file 
or the examples:

Mascot_MSMS_example.mzid:
No mapping rule found for element 
'/mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ModificationParams/SearchModification/SpecificityRules'


Mascot_NA_example.mzid:
Value of CV term not allowed: 'MS:1001423 - translation table 
description'...


David
-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898

[Psidev-pi-dev] PSI-PI conference call 4pm UK, Thurs 14th May

[Jones, A. <And...@li...>]

Hi everyone,



There will be an mzIdentML working group conference call on Thurs 14th May at 4:00pm UK time:



http://www.timeanddate.com/worldclock/fixedtime.html?day=14&month=5&year=2009&hour=16&min=0&sec=0&p1=136





Agenda:



-       Review minutes from last call: http://www.psidev.info/index.php?q=node/412

- Review of merged CV:

    http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-ms.obo

- Updates to the example instance docs - problems identified

- Outstanding schema issues

- Other outstanding items on the issues list.



Please send me any further items for the agenda.



Dial in details:



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

+ Generic international: +44 2083222500 (UK number)



access code: 297427

cheers
Andy

[Psidev-pi-dev] Issue 31 in psi-pi: Specifying the Search Database(s) Unambiguously - MIRIAM?

[<cod...@go...>]

Comment #9 on issue 31 by javizca74: Specifying the Search Database(s)  
Unambiguously - MIRIAM?
http://code.google.com/p/psi-pi/issues/detail?id=31

Hi,

This is what I found out after a meeting with the MIRIAM people today:

1. The only requirements for a database to be included in MIRIAM are: to be  
freely
available, accessible on-line, to have stable and unique identifiers for  
the entries
and no licence restriction for using it.
2.Apart from that, if any resource is not there yet is because noone has  
told them
yet. They are very happy to add new ones and it should be a very  
straightforward process.
3.I have told them about the fact that they have at present UniProt and  
UniParc, for
instance, but no specific entries for UniProtKB/SwissProt, TrEMBL,  
UniRef,...They are
going to think about this. Again, noone had told them before.
4.Both the MIRIAM identifier (for instance, for PRIDE MIR:00000065) or the  
MIRIAM URN
(urn:miriam:pride) could be used for referencing the database.
5.For IPI, they do not want to split it by different species, but as  
pointed out
before, to add a new CV term (taxID) would be possible.

I think it is out of the scope here, but MIRIAM is being used in MIAME  
documents to
assure that the identifiers reported match the corresponding referenced  
database.



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Re: [Psidev-pi-dev] [Psidev-ms-dev] Referencing spectra in mzML from mzIdentML documents

[Eric D. <ede...@sy...>]

Yes! Please do.

Thanks,
Eric


> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: Tuesday, May 05, 2009 11:19 AM
> To: Mass spectrometry standard development; psidev-pi-
> de...@li...
> Subject: [Psidev-ms-dev] Referencing spectra in mzML from mzIdentML
> documents
> 
> Hi,
> 
> Bringing up an old topic...
> 
> In the documentation for analysisXML (now called mzIdentML) we have:
> 
> Spectra represented in mzML (in the <Spectrum> element) have two unique
> identifiers, one newly generated for mzML stored in the ID attribute,
> and one using the system above derived from the source file, stored in
> the nativeID attribute. If the source file is mzML,
> SpectrumIdentificationResult SHOULD reference the ID in mzML since this
> value has a data type of xsd:id and is thus guaranteed to be unique.
> 
> 
> Should this be replaced with something like:
> 
> Spectra represented in mzML (in the <Spectrum> element) have two unique
> identifiers, one newly generated for mzML stored in the index attribute,
> and one using the system above derived from the source file, stored in
> the id attribute. If the source file is mzML,
> SpectrumIdentificationResult SHOULD reference the id in mzML since this
> value is more descriptive and is guaranteed to be unique.
> 
> 
> David
> 
> --
> David Creasy
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
> 
> dc...@ma...
> http://www.matrixscience.com
> 
> Matrix Science Ltd. is registered in England and Wales
> Company number 3533898
> 
> --------------------------------------------------------------------------
> ----
> The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
> production scanning environment may not be a perfect world - but thanks to
> Kodak, there's a perfect scanner to get the job done! With the NEW KODAK
> i700
> Series Scanner you'll get full speed at 300 dpi even with all image
> processing features enabled. http://p.sf.net/sfu/kodak-com
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-pi-dev] PSI-PI Working group conference call on Thursday 7th May at 4:00pm UK time

[David C. <dc...@ma...>]

Minutes available here:
http://psidev.info/index.php?q=node/412

(Thanks to Juan Antonio)

David Creasy wrote:
> Hi everyone,
> 
> There will be an mzIdentML working group conference call tomorrow 
> (Thursday) at 4:00pm UK time:
> 
> http://www.timeanddate.com/worldclock/fixedtime.html?day=7&month=5&year=2009&hour=16&min=0&sec=0&p1=136 
> 
> 
> Minutes from the spring meeting in Turku at:
> http://psidev.info/index.php?q=node/410
> 
> Agenda:
> - Review of merged CV:
>    http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-ms.obo
>   (NB. this is a temporary location...)
>   If possible, please review before the telecon.
>   This page describes where each term may appear: 
> http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/analysisXML/mapping_and_cv.html 
> 
> 
> - Timeplan for updates to the example instance docs
> - Other outstanding items on the issues list.
> 
> Dial in details:
> 
> + Germany: 08001012079
> + Switzerland: 0800000860
> + UK: 08081095644
> + USA: 1-866-314-3683
> + Generic international: +44 2083222500 (UK number)
> 
> access code: 297427
> 

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898

[Psidev-pi-dev] Issue 47 in psi-pi: The name of AnalysisXML

[<cod...@go...>]

Updates:
	Status: Fixed

Comment #5 on issue 47 by andrewrobertjones: The name of AnalysisXML
http://code.google.com/p/psi-pi/issues/detail?id=47

(No comment was entered for this change.)

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[Psidev-pi-dev] Issue 49 in psi-pi: Issues / schema updates prior to version 1 release

[<cod...@go...>]

Status: Accepted
Owner: andrewrobertjones
Labels: Type-Defect Priority-Medium

New issue 49 by andrewrobertjones: Issues / schema updates prior to version  
1 release
http://code.google.com/p/psi-pi/issues/detail?id=49

Minor schema update:

Removed mzIdentML-->DatabaseReference

This is no longer a valid element now that Database has been removed.

(i.e. this gave the ability for a file to reference a corresponding
database entry, don't think this is required)



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[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[<cod...@go...>]

Comment #67 on issue 42 by andrewrobertjones: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

"Regular expression" appears under search input details. These should  
perhaps come
under cleavage agent details and be re-named to "Cleavage agent regular  
expression"

"spectrum identification result details" looks fairly similar to "search  
result
details". It also has some child terms that look a bit strange: "MGF Raw  
Scans"

"Unknown modification" appears directly beneath "spectrum interpretation"  
is this
correct?

"role type" (contact roles) appears under "spectrum interpretation" - these  
should
probably go under contacts at the top of the CV

"taxonomy nomenclature" - I don't understand the usage of this term





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[Psidev-pi-dev] Issue 48 in psi-pi: calculatedMassToCharge and sequenceMass have the same information

[<cod...@go...>]

Comment #2 on issue 48 by andrewrobertjones: calculatedMassToCharge and  
sequenceMass have the same information
http://code.google.com/p/psi-pi/issues/detail?id=48

As far as I remember the reason why both were kept is because they fulfil  
slightly
different roles.

The Peptide element could be re-used by different  
SpectrumIdentificationItems (i.e.
different charge states would give different values). I think this is quite  
a weak
difference though and I wonder if we should get rid of some of the optional  
elements
on Peptide: sequenceMass and sequenceLength, the latter seems particularly  
pointless.
I notice that peptideSequence is optional, probably this should be  
mandatory? Are
there any use cases where a peptideSequence could not be provided?

It also appears that the sequenceMass and calculatedMassToCharge values  
don't tally
in the Sequest example! Another good reason to get rid of one or the  
other...









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[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[<cod...@go...>]

Comment #65 on issue 42 by a.bertsch0815: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

- added PEFF
- deleted MS:1001214 prot:global FDR  changed pep:global FDR (MS:1001364)  
to simply
global FDR, changed inheritence structure to fit into both locations

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[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[<cod...@go...>]

Comment #66 on issue 42 by a.bertsch0815: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

TODOs
- Compile a Software List  (Mascot and Co., only included so far, greylag  
added.
- Mapping for checksums for databases (terms contained in PSI-MS)
- Database terms? Taxonomy?
Mapping rules missing:
/mzIdentML/DataCollection/Inputs/SourceFile/
/mzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem/PeptideEvidence/
/mzIdentML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbiguityGroup/

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[Psidev-pi-dev] PSI-PI Working group conference call on Thursday 7th May at 4:00pm UK time

[David C. <dc...@ma...>]

Hi everyone,

There will be an mzIdentML working group conference call tomorrow 
(Thursday) at 4:00pm UK time:

http://www.timeanddate.com/worldclock/fixedtime.html?day=7&month=5&year=2009&hour=16&min=0&sec=0&p1=136

Minutes from the spring meeting in Turku at:
http://psidev.info/index.php?q=node/410

Agenda:
- Review of merged CV:
    http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-ms.obo
   (NB. this is a temporary location...)
   If possible, please review before the telecon.
   This page describes where each term may appear: 
http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/analysisXML/mapping_and_cv.html

- Timeplan for updates to the example instance docs
- Other outstanding items on the issues list.

Dial in details:

+ Germany: 08001012079
+ Switzerland: 0800000860
+ UK: 08081095644
+ USA: 1-866-314-3683
+ Generic international: +44 2083222500 (UK number)

access code: 297427

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Matrix Science
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dc...@ma...
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