psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] FW: [Psi-sc] Dates for your diaries

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

See below for announcement of next PSI meeting

> -----Original Message-----
> From: psi...@eb... [mailto:psi...@eb...] On Behalf Of
> Sandra Orchard
> Sent: 16 August 2011 09:59
> To: ps...@eb...; ps...@eb...; psi...@eb...;
> ps...@eb...
> Subject: [Psi-sc] Dates for your diaries
> 
> Dear All
> 
> The 2012 (10th anniversary) meeting of the HUPO-PSI will be held March
> 12-14th at UCSD, San Diego, CA, USA. The PSIMEx/ProteomeXchange meetings
> will then follow on the 15-16th. We will obviously not be opening
> registration until much closer to the time, but please mark off these
> dates and leave yourselves free.
> 
> Many thanks to Michael Gilson and George Nicolas for offering to act as
> local hosts.
> 
> Please can someone send this announcement to the MS and Gel lists, in
> case it holds any people who are not on PSI-announce. Also feel free to
> extend the invitation to anyone you feel may be interested in attending.
> 
> best wishes
> Sandra
> 
> --
> Sandra Orchard
> Proteomics Services Team Coordinator
> European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton,
> Cambridgeshire
> CB10 1SD
> UK
> phone: 01223 494675
> fax: 01223 494468
> email: or...@eb...
> 
> _______________________________________________
> Psi-sc mailing list
> Ps...@eb...
> http://listserver.ebi.ac.uk/mailman/listinfo/psi-sc

[Psidev-ms-dev] Dates for your diaries

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

Dear all,

I am resending this e-mail confirming the dates and place of the next  
PSI meeting.

Cheers,

Juan




Dear All

The 2012 (10th anniversary) meeting of the HUPO-PSI will be held March
12-14th at UCSD, San Diego, CA, USA. The PSIMEx/ProteomeXchange meetings
will then follow on the 15-16th. We will obviously not be opening
registration until much closer to the time, but please mark off these
dates and leave yourselves free.

Many thanks to Michael Gilson and George Nicolas for offering to act as
local hosts.

Please can someone send this announcement to the MS and Gel lists, in
case it holds any people who are not on PSI-announce. Also feel free to
extend the invitation to anyone you feel may be interested in attending.

best wishes
Sandra

-- 
Sandra Orchard
Proteomics Services Team Coordinator
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton,
Cambridgeshire
CB10 1SD
UK
phone: 01223 494675
fax: 01223 494468
email: or...@eb...

[Psidev-ms-dev] MS controlled vocabulary has disappeared, but it will come back

[David O. <do...@eb...>]

Dear PSI community,

The PSI-MS cv is not online. This is due to a problem in Sourceforge 
that has lost all the information in the CVS repositories.
The short explanation for that is "On 2011-07-16, one of our several CVS 
servers suffered a catastrophic multiple disk failure, resulting in full 
loss of the server.". More info :
https://sourceforge.net/blog/further-update-on-cvs-outage/

They are working on the problem, and say that all information will be 
again there in some days....

Let's pray then for the Sourceforge-CVS fast recovery.

Best,

David

Re: [Psidev-ms-dev] [Psidev-pi-dev] MIAPE Quant v0.5

[Alex C. <ac...@pc...>]

I pretty much agree with John's comments. Just a couple things here:

4.5 Description of the transformation
I recall that this topic raised some discussion whether it should be broken down as John proposes. The final 'consensus' was that it should a 'catch-all' field.

5. Resulting data
I think it somehow nails the discussion whether MIAPE Quant should require all three file levels (features, peptides and proteins) or only one of them. In most data analysis workflows that use features for quantitation, peptides are mapped back to features and as John mentioned only mapped features are used for quantitation (as far as I know). This 'intermediate file' will be readily available in many software tools, and from a MIAPE standpoint, it should be the most useful.
As a scientist submitting data in the MIAPE Quant format, it would not be a big deal to provide the protein (after peptide/feature summarization) file that I use for quantitation as well. 

In summary, I believe that MIAPE Quant should require a "Feature-Peptide quantitation file" containing only features and their mapped peptides that were used for quantitation analysis. Whereas, the "Protein quantitation file" should be optional.

Cheers,
Alex

Alex Campos
Proteomics Platform
Barcelona Science Park
c/ Baldiri Reixac, 10 - 12
08028 Barcelona
+34 934 034 653
ac...@pc...



On Jul 15, 2011, at 10:17 AM, John Cottrell wrote:

> Suggestions for 'glossary of required items'
> 
> These cannot all be required terms. Many should be tagged 'optional' or 'if applicable'.
> 
> 1.5. Quantitative approach
> Does 'pattern based' mean feature driven? If so, this isn't limited to label free. 
> 
> 2.2.2.2.Sample labelling with assay definition ...
> '...  the isotope-labeled element (e.g. 14N/15N)' should be  '... the isotope-labelled element (e.g. 15N)'
> 
> 2.2.3. Isotopic correction coefficients 
> Add 'In the case of other isotopic labels, percent enrichment, such as 98% 15N'
> 
> 4.1. Quantification software name, version and manufacturer
> Make it clear that this may cover multiple software programs
> 
> 4.2.Parameters used for the quantitative process
> Don't really want to refer to normalization here, because covered in 4.5. Or, if some other sort of normalization, need to clarify.
> 
> 4.5.Description of the transformation ...
> This is too much of a catch-all and needs to be sub-divided
> - ratio determination
> - peptide to protein aggregation
> - replicate aggregation
> - outlier removal
> - normalization
> - handling of shared peptides
> - specialised, protocol specific corrections, e.g. for Arg-Pro conversion
> 
> Statistical measures belong in 4.6?
> 
> 'If a protein normalization factor is used, provide the list of normalization coefficients for each protein.' is too constrained and may create unnecessary work. Better to ask for a description of any normalization procedure, e.g. 'median peptide ratio for all measurements forced to 1' or 'each sample spiked with equal amount of peptide X or protein Y, as per 2.2.4'
> 
> 5. Resulting data —5.1 Quantification values at feature level ...
> Confusing. Ignoring the typo in the numbering, do we really want features and peptides and proteins? Feature is usually an abstract term for a spot on a gel or a peak in a chromatogram but by the time we have identified and quantified peptides it has become either a peptide or a protein. Surely, no-one will report quantitation of unidentified 'features'?
> 
> John Cottrell
> Matrix Science Ltd.
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 20 7486 1050
> Fax: +44 20 7224 1344
> jco...@ma...
> http://www.matrixscience.com
> 
> Matrix Science Ltd. is registered in England and Wales
> Company number 3533898
> 
> 
> Salvador Martínez de Bartolomé wrote:
>> 
>> Hi all:
>>                 As I said in my last e-mail, my plan was to prepare the MIAPE Quant document for PSI submission next week, so tomorrow is the last day for receiving your feedback. Andy (see e-mail below) wrote the last comments in the document, but nobody else has participated since last 23 of June.
>>                 So, is there any other comment about the document? (This question is also meant for ProteoRed people that started to define the document some months ago).
>>                 I think that further discussion is still needed about the data part (section 5) in which we have to decide to include both feature, peptide and protein level results (as Martin Eisenacher suggested), to include only peptide and protein levels (as the document was defined in Heidelberg) or maybe to ask for at least one of these three levels (as suggested Andy Jones in the last e-mail). Any other opinion about it?
>>                 Thank you in advance for your participation.
>>                 Regards,
>>  
>> Salvador Martínez de Bartolomé Izquierdo
>> Bioinformatics Support - ProteoRed
>> Lab- B1, National Center for Biotechnology
>> C/ Darwin, 3 Universidad Autónoma de Madrid Cantoblanco,
>> 28049 Madrid Spain
>> Phone: +34 91 585 4613
>> Fax: +34 91 585 4506
>>  
>> http://www.proteored.org
>> http://proteo.cnb.csic.es/trac
>> https://sites.google.com/site/bioinformaticaproteomica/
>>  
>>  
>> De: Jones, Andy [mailto:And...@li...] 
>> Enviado el: 23 June 2011 12:38
>> Para: 'Salvador Martínez de Bartolomé'; 'PSI PI Dev'; 'psi...@li...'
>> CC: 'mia...@pr...'
>> Asunto: RE: [Psidev-pi-dev] MIAPE Quant v0.5
>>  
>> Hi all,
>>  
>> Apologies for not commenting on previous versions, overall I think you’ve done an excellent job with this.
>>  
>> Mainly I think the metadata parts are fine with a bit of tweaking here and there. The data part (section 5) needs a bit of wider discussion I think, since the current draft appears to ask for quantitative data for features, peptides AND proteins. I wonder if it might be appropriate to ask for at least one of these three but not all. Some labs may argue that if they are providing the raw MS data, the method they used for data analysis and a final list of proteins, someone else could recreate the “intermediate files” i.e. features if they wanted to. My preference would be to request only the data that the lab wants to report i.e. if they are reporting a peptide experiment, then Features/peptides is the resulting data, for other discovery based approaches, the final protein list may be sufficient.
>>  
>> What do others think?
>>  
>> Cheers
>> Andy
>>  
>>  
>>  
>>  
>> From: Salvador Martínez de Bartolomé [mailto:sma...@pr...] 
>> Sent: 22 June 2011 07:39
>> To: 'PSI PI Dev'; psi...@li...
>> Cc: mia...@pr...
>> Subject: [Psidev-pi-dev] MIAPE Quant v0.5
>>  
>> Hi all:
>>                 Attached you will find the MIAPE Quant guidelines (v0.5). This document describe the minimum information required to report the use of quantification techniques in a proteomics experiment. Note that the document is scope includes a wide range of quantification approaches, such as  labelled and label-free approaches as well as targeted approaches such as Selected Reaction Monitoring (SRM).
>> This document was firstly developed by ProteoRed people and then it was presented in the last HUPO-PSI spring meeting in Heidelberg. After some fruitful discussions in that meeting, the document was sent to a reduced group of people involved in current PSI developments.
>> Finally, as we planned, we have this document ready to send to the PSI mailing lists. The idea is to receive your feedback about the document and then, to submit it to the PSI document process. So, please, feel free to add, comment, delete anything that you consider. We will try to compile all comments before 15th July, and then, submit to the doc process.
>> Best regards,
>>                
>>  
>> Salvador Martínez de Bartolomé Izquierdo
>> Bioinformatics Support - ProteoRed
>> Lab- B1, National Center for Biotechnology
>> C/ Darwin, 3 Universidad Autónoma de Madrid Cantoblanco,
>> 28049 Madrid Spain
>> Phone: +34 91 585 4613
>> Fax: +34 91 585 4506
>>  
>> http://www.proteored.org
>> http://proteo.cnb.csic.es/trac
>> https://sites.google.com/site/bioinformaticaproteomica/
>>  
>>  
>> 
>> ------------------------------------------------------------------------------
>> AppSumo Presents a FREE Video for the SourceForge Community by Eric 
>> Ries, the creator of the Lean Startup Methodology on "Lean Startup 
>> Secrets Revealed." This video shows you how to validate your ideas, 
>> optimize your ideas and identify your business strategy.
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>> 
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>   

Re: [Psidev-ms-dev] [Psidev-pi-dev] MIAPE Quant v0.5

[John C. <jco...@ma...>]

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Suggestions for 'glossary of required items'<br>
<br>
These cannot all be required terms. Many should be tagged 'optional' or
'if applicable'.<br>
<br>
1.5. Quantitative approach<br>
Does 'pattern based' mean feature driven? If so, this isn't limited to
label free. <br>
<br>
2.2.2.2.Sample labelling with assay definition ...<br>
'...&nbsp; the isotope-labeled element (e.g. 14N/15N)' should be&nbsp; '... the
isotope-labelled element (e.g. 15N)'<br>
<br>
2.2.3. Isotopic correction coefficients <br>
Add 'In the case of other isotopic labels, percent enrichment, such as
98% 15N'<br>
<br>
4.1. Quantification software name, version and manufacturer<br>
Make it clear that this may cover multiple software programs<br>
<br>
4.2.Parameters used for the quantitative process<br>
Don't really want to refer to normalization here, because covered in
4.5. Or, if some other sort of normalization, need to clarify.<br>
<br>
4.5.Description of the transformation ...<br>
This is too much of a catch-all and needs to be sub-divided<br>
- ratio determination<br>
- peptide to protein aggregation<br>
- replicate aggregation<br>
- outlier removal<br>
- normalization<br>
- handling of shared peptides<br>
- specialised, protocol specific corrections, e.g. for Arg-Pro
conversion<br>
<br>
Statistical measures belong in 4.6?<br>
<br>
'If a protein normalization factor is used, provide the list of
normalization coefficients for each protein.' is too constrained and
may create unnecessary work. Better to ask for a description of any
normalization procedure, e.g. 'median peptide ratio for all
measurements forced to 1' or 'each sample spiked with equal amount of
peptide X or protein Y, as per 2.2.4'<br>
<br>
5. Resulting data &#8212;5.1 Quantification values at feature level ...<br>
Confusing. Ignoring the typo in the numbering, do we really want
features and peptides and proteins? Feature is usually an abstract term
for a spot on a gel or a peak in a chromatogram but by the time we have
identified and quantified peptides it has become either a peptide or a
protein. Surely, no-one will report quantitation of unidentified
'features'?<br>
<br>
<pre class="moz-signature" cols="72">John Cottrell
Matrix Science Ltd.
64 Baker Street
London W1U 7GB, UK
Tel: +44 20 7486 1050
Fax: +44 20 7224 1344
<a class="moz-txt-link-abbreviated" href="mailto:jco...@ma...">jco...@ma...</a>
<a class="moz-txt-link-freetext" href="http://www.matrixscience.com">http://www.matrixscience.com</a>

Matrix Science Ltd. is registered in England and Wales
Company number 3533898
</pre>
<br>
<br>
Salvador Mart&iacute;nez de Bartolom&eacute; wrote:
<blockquote cite="mid:003401cc4206$c168f560$443ae020$@proteored.org"
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  <div class="WordSection1">
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi all:<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
As I said in my last e-mail, my plan was to prepare the MIAPE Quant
document for PSI submission next week, so tomorrow is the last day for
receiving your feedback. Andy (see e-mail below) wrote the last
comments in the document, but nobody else has participated since last
23 of June. <o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
So, is there any other comment about the document? (This question is
also meant for ProteoRed people that started to define the document
some months ago).<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
I think that further discussion is still needed about the data part
(section 5) in which we have to decide to include both feature, peptide
and protein level results (as Martin Eisenacher suggested), to include
only peptide and protein levels (as the document was defined in
Heidelberg) or maybe to ask for at least one of these three levels (as
suggested Andy Jones in the last e-mail). Any other opinion about it?<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Thank you in advance for your participation.<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Regards,<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  <div>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);" lang="ES">Salvador
Mart&iacute;nez de Bartolom&eacute; Izquierdo <o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);" lang="ES">Bioinformatics
Support - ProteoRed<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Lab- B1,
National Center for Biotechnology <o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);" lang="ES">C/
Darwin, 3 Universidad Aut&oacute;noma de Madrid Cantoblanco, <o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">28049
Madrid Spain<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Phone:
+34 91 585 4613<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Fax: +34
91 585 4506<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);" lang="ES"><a
 moz-do-not-send="true" href="http://www.proteored.org"><span
 style="color: blue;" lang="EN-GB">http://www.proteored.org</span></a></span><span
 style="color: rgb(31, 73, 125);"><o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);" lang="ES"><a
 moz-do-not-send="true" href="http://proteo.cnb.csic.es/trac"><span
 style="color: blue;" lang="EN-GB">http://proteo.cnb.csic.es/trac</span></a></span><span
 style="color: rgb(31, 73, 125);"><o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);" lang="ES"><a
 moz-do-not-send="true"
 href="https://sites.google.com/site/bioinformaticaproteomica/"><span
 style="color: blue;" lang="EN-GB">https://sites.google.com/site/bioinformaticaproteomica/</span></a></span><span
 style="color: rgb(31, 73, 125);"><o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  </div>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  <div>
  <div
 style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;" lang="ES">De:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;" lang="ES">
Jones, Andy [<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
  <b>Enviado el:</b> 23 June 2011 12:38<br>
  <b>Para:</b> 'Salvador Mart&iacute;nez de Bartolom&eacute;'; 'PSI PI Dev';
'<a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a>'<br>
  <b>CC:</b> '<a class="moz-txt-link-abbreviated" href="mailto:mia...@pr...">mia...@pr...</a>'<br>
  <b>Asunto:</b> RE: [Psidev-pi-dev] MIAPE Quant v0.5<o:p></o:p></span></p>
  </div>
  </div>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi all,<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Apologies
for not commenting on previous versions, overall I think you&#8217;ve done an
excellent job with this. <o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Mainly I
think the metadata parts are fine with a bit of tweaking here and
there. The data part (section 5) needs a bit of wider discussion I
think, since the current draft appears to ask for quantitative data for
features, peptides AND proteins. I wonder if it might be appropriate to
ask for at least one of these three but not all. Some labs may argue
that if they are providing the raw MS data, the method they used for
data analysis and a final list of proteins, someone else could recreate
the &#8220;intermediate files&#8221; i.e. features if they wanted to. My preference
would be to request only the data that the lab wants to report i.e. if
they are reporting a peptide experiment, then Features/peptides is the
resulting data, for other discovery based approaches, the final protein
list may be sufficient.<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">What do
others think?<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p>&nbsp;</o:p></span></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div
 style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Salvador Mart&iacute;nez de Bartolom&eacute; <a moz-do-not-send="true"
 href="mailto:%5Bmailto:sma...@pr...%5D">[mailto:sma...@pr...]</a>
  <br>
  <b>Sent:</b> 22 June 2011 07:39<br>
  <b>To:</b> 'PSI PI Dev'; <a moz-do-not-send="true"
 href="mailto:psi...@li...">psi...@li...</a><br>
  <b>Cc:</b> <a moz-do-not-send="true"
 href="mailto:mia...@pr...">mia...@pr...</a><br>
  <b>Subject:</b> [Psidev-pi-dev] MIAPE Quant v0.5<o:p></o:p></span></p>
  </div>
  </div>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal">Hi all:<o:p></o:p></p>
  <p class="MsoNormal">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Attached you will find the MIAPE
Quant guidelines (v0.5). This document describe the minimum information
required to report the use of quantification techniques in a proteomics
experiment. Note that the document is scope includes a wide range of
quantification approaches, such as &nbsp;labelled and label-free approaches
as well as targeted approaches such as Selected Reaction Monitoring
(SRM).<o:p></o:p></p>
  <p class="MsoNormal" style="text-indent: 36pt;">This document was
firstly developed by ProteoRed people and then it was presented in the
last HUPO-PSI spring meeting in Heidelberg. After some fruitful
discussions in that meeting, the document was sent to a reduced group
of people involved in current PSI developments.<o:p></o:p></p>
  <p class="MsoNormal" style="text-indent: 36pt;">Finally, as we
planned, we have this document ready to send to the PSI mailing lists.
The idea is to receive your feedback about the document and then, to
submit it to the PSI document process. So, please, feel free to add,
comment, delete anything that you consider. We will try to compile all
comments before 15<sup>th</sup> July, and then, submit to the doc
process.<o:p></o:p></p>
  <p class="MsoNormal" style="text-indent: 36pt;">Best regards,<o:p></o:p></p>
  <p class="MsoNormal">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <o:p></o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal"><span lang="ES">Salvador Mart&iacute;nez de Bartolom&eacute;
Izquierdo <o:p></o:p></span></p>
  <p class="MsoNormal"><span lang="ES">Bioinformatics Support -
ProteoRed<o:p></o:p></span></p>
  <p class="MsoNormal">Lab- B1, National Center for Biotechnology <o:p></o:p></p>
  <p class="MsoNormal"><span lang="ES">C/ Darwin, 3 Universidad
Aut&oacute;noma de Madrid Cantoblanco, <o:p></o:p></span></p>
  <p class="MsoNormal">28049 Madrid Spain<o:p></o:p></p>
  <p class="MsoNormal">Phone: +34 91 585 4613<o:p></o:p></p>
  <p class="MsoNormal">Fax: +34 91 585 4506<o:p></o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal"><span lang="ES"><a moz-do-not-send="true"
 href="http://www.proteored.org"><span lang="EN-GB">http://www.proteored.org</span></a></span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="ES"><a moz-do-not-send="true"
 href="http://proteo.cnb.csic.es/trac"><span lang="EN-GB">http://proteo.cnb.csic.es/trac</span></a></span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="ES"><a moz-do-not-send="true"
 href="https://sites.google.com/site/bioinformaticaproteomica/"><span
 lang="EN-GB">https://sites.google.com/site/bioinformaticaproteomica/</span></a></span><o:p></o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  </div>
  </div>
  <pre wrap="">
<hr size="4" width="90%">
------------------------------------------------------------------------------
AppSumo Presents a FREE Video for the SourceForge Community by Eric 
Ries, the creator of the Lean Startup Methodology on "Lean Startup 
Secrets Revealed." This video shows you how to validate your ideas, 
optimize your ideas and identify your business strategy.
<a class="moz-txt-link-freetext" href="http://p.sf.net/sfu/appsumosfdev2dev">http://p.sf.net/sfu/appsumosfdev2dev</a></pre>
  <pre wrap="">
<hr size="4" width="90%">
_______________________________________________
Psidev-ms-dev mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Psi...@li...">Psi...@li...</a>
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  </pre>
</blockquote>
</body>
</html>

Re: [Psidev-ms-dev] TraML - Multiple locations for RetentionTimeType and ConfigurationType

[Karl C. <cl...@br...>]

Kenny,

Since a peptide retention time is the mean/median of it's transition
times, all should be slightly different. I can't think of a reason why
there should be more than 1 place where a transition retention time
should be allowed to be specified.

--Karl

On Thursday, July 14, 2011, Kenny Helsens <ken...@ug...> wrote:
> Dear community,
>
> While working with the TraML format, I observed that there are multiple locations to place a RetentionTimeType or ConfigurationType fields.
>
> For instance, the retention time can be described both on the PeptideType and the TransitionType. So what happens when the user specifies two different values for a single transition? And anyone help me with a use case where the TransitionType is expected to occur at a different time then the PeptideType?
>
> Similarly, the ConfigurationTypes can be placed on the TargetType, ProductType and IntermediateProductType. When is it possible for the ProductType and the IntermediateProductType to have (e.g.) different collision energy values?
>
> Many thanks in advance,
>
>
>
> Kenny Helsens, PhD
>
> Computational Omics and Systems Biology Group
> Department of Medical Protein Research
> Universiteit Gent - VIB
>
> A. Baertsoenkaai 3
> B9000 Gent
> Belgium
>
> Tel: +32-92649359
> Fax: +32-92649484
>
> Skype: kennyhelsens
>
>
> ------------------------------------------------------------------------------
> AppSumo Presents a FREE Video for the SourceForge Community by Eric
> Ries, the creator of the Lean Startup Methodology on "Lean Startup
> Secrets Revealed." This video shows you how to validate your ideas,
> optimize your ideas and identify your business strategy.
> http://p.sf.net/sfu/appsumosfdev2dev
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

[Psidev-ms-dev] TraML - Multiple locations for RetentionTimeType and ConfigurationType

[Kenny H. <ken...@ug...>]

Dear community,

While working with the TraML format, I observed that there are multiple locations to place a RetentionTimeType or ConfigurationType fields.

For instance, the retention time can be described both on the PeptideType and the TransitionType. So what happens when the user specifies two different values for a single transition? And anyone help me with a use case where the TransitionType is expected to occur at a different time then the PeptideType?

Similarly, the ConfigurationTypes can be placed on the TargetType, ProductType and IntermediateProductType. When is it possible for the ProductType and the IntermediateProductType to have (e.g.) different collision energy values?

Many thanks in advance,



Kenny Helsens, PhD
 
Computational Omics and Systems Biology Group
Department of Medical Protein Research
Universiteit Gent - VIB
 
A. Baertsoenkaai 3
B9000 Gent
Belgium
 
Tel: +32-92649359
Fax: +32-92649484

Skype: kennyhelsens

Re: [Psidev-ms-dev] new instrument CV terms

[David O. <do...@eb...>]

Hi all again,

New version of the controlled vocabulary: 3.7.3
"MassLynx"(MS:1000534) linked to "Waters software" (Waters software) and 
cv terms sorted in the obo file.

Best,
David

On 12/07/2011 16:49, David Ovelleiro wrote:
> Hi Matt and community,
>
> In first place, thank you Matt for deleting the duplicated software,
> MassLynx. I did a quick check and it wasn't inside Waters software (in
> the next update, I'll quickly add the connection to Waters).
>
> Under "mass spectrometer" we have a mix of mass spectrometry
> techniques/methods and instruments... even something called "mass
> spectrometry/mass spectrometry".  But, again, if someone is planning to
> use the "mass spectrometer" terms (and people from Waters seem to be
> doing so), I think is reasonable to re-locate this.
>
> Matt, please: don't touch the sorting of the file: I'm trying to
> reproduce the way Obo-Edit works. I've posted this afternoon an email in
> their email list about the way the application works for new IDs (the
> lastID variable doesn't seem to work any more). I'll keep you all
> informed. Anyway, I'm reporting in every new update the terms added
> (MS:1001797 the last one).
>
> Best,
> David
>
> On 12/07/2011 15:57, Matthew Chambers wrote:
>> I deleted the MassLynx term, it was a duplicate. I call it a "speedy delete"...it never happened! :P
>>
>> I was preparing an email to send yesterday including that tidbit but didn't finish it. Another thing
>> I was going to mention is that "TWIMS" should be "travelling wave ion mobility spectrometer" and
>> that it's awkward for IMS to be under "mass spectrometer" as you've mentioned below. Incidentally,
>> there is no mapping in the PSI formats for the "mass spectrometer" terms and its children. A lot of
>> the terms are still in purgatory simply because there isn't a need for them in the files. If we
>> wanted to go more in the direction of an ontology, we could associate each instrument with its
>> supported spectrometry methods. But that would require considerable discussion and work for little gain.
>>
>> Also I'm not sure about this inserting new terms into the middle of the OBO. It may be valid OBO but
>> it's rather confusing. I tend to make small additions with a text editor (after running them by the
>> list) so having new terms in the middle would make it easy to choose a duplicate accession. Is it
>> alright if I move the new terms to the bottom? I wouldn't expect it to need a version bump since it
>> doesn't change anything.
>>
>> -Matt
>>
>>
>> On 7/12/2011 5:16 AM, David Ovelleiro wrote:
>>> Dear Hans, Matt, Eric and PSI community,
>>>
>>> Empower, MassLynx and Unify and TWIMS have been included in the v.3.7.2 release of the psi-ms. (
>>> v.3.7.1 had a small typo... sorry....)
>>> I think that with this, we've finished the list of terms proposed by Hans. I expect everything is
>>> fine.... if it's not... please, send an email.
>>>
>>> Dear Eric: thanks for the explanation. I was aware of the motivations for including some terms
>>> inside "purgatory". My concern is related to the fact that, if people is suggesting terms inside
>>> this "purgatory", maybe they are planning to use them. An xpath containing the word "purgatory" is,
>>> in my opinion, not very self-explanatory.
>>> To organize this, I'd propose changing the name of MS:1000293 (mass spectrometer) to "mass
>>> spectrometry methods" (I'm not sure this is the perfect name, but I suggest it because some of the
>>> patents related to them are named as "methods", e.g. http://www.freepatentsonline.com/7071465.html).
>>> We could then re-map MS:1000293 as son of "instrument" (MS:1000463). Only a suggestion... please,
>>> I'd like to hear some opinions.
>>>
>>> Best,
>>> David
>>>
>>>
>>>
>>>
>>>
>>> On 11/07/2011 17:25, Eric Deutsch wrote:
>>>> Hi David, thanks, these new terms look good to me.
>>>>
>>>> Regarding “mass spectrometry” and “purgatory”, please recall that “purgatory” is a ratty box of
>>>> terms that we just haven’t made a decision on yet. We don’t **want** and terms in “purgatory”, but
>>>> in a world of limited time, there they lie. In the CV, we are currently using “instrument” in lieu
>>>> of “mass spectrometer”. Why the term “mass spectrometer” is in purgatory I’m not quite certain. I
>>>> suppose it should just be obsoleted and make it a synonym of “instrument”. But I have a vague
>>>> recollection that we decided on “instrument” because some of these instruments have additional
>>>> components that are not strictly mass spectrometers (e.g. UV detection components). In which case,
>>>> there may be no role for a pure mass spectrometer. But maybe we couldn’t all agree on what to do,
>>>> so it lies in “purgatory” until the day that someone comes to decide and save the day.
>>>>
>>>> Regards,
>>>>
>>>> Eric
>>>>
>>>> *From:*David Ovelleiro [mailto:do...@eb...<mailto:do...@eb...>]
>>>> *Sent:* Monday, July 11, 2011 9:02 AM
>>>> *To:* Han...@wa...<mailto:Han...@wa...>
>>>> *Cc:* Mass spectrometry standard development
>>>> *Subject:* Re: [Psidev-ms-dev] new instrument CV terms
>>>>
>>>> Dear Hans, Matt and PSI community,
>>>>
>>>> I've updated the psi-ms c.v. with the 32 new Waters instruments list.
>>>> I'll also add, in a couple of days, the next 4 c.v. terms. Please, check them and if you see
>>>> anything wrong, write an email....
>>>>
>>>> [Term]
>>>> id: MS:XXXXXXX
>>>> name: MassLynx
>>>> def: "Waters software for Mass spectrometry acquisition, processing and data analysis." [PSI:MS]
>>>> is_a: MS:1000694 ! Waters software
>>>> is_a: MS:1001456 ! analysis software
>>>> is_a: MS:1001457 ! data processing software
>>>>
>>>> [Term]
>>>> id: MS:XXXXXXX
>>>> name: Empower
>>>> def: "Waters software for liquid chromatography acquisition, processing, data analysis and data
>>>> management." [PSI:MS]
>>>> is_a: MS:1000694 ! Waters software
>>>> is_a: MS:1001456 ! analysis software
>>>> is_a: MS:1001457 ! data processing software
>>>>
>>>> [Term]
>>>> id: MS:XXXXXXX
>>>> name: Unify
>>>> def: "Waters software for liquid chromatography and mass spectrometry acquisition, processing,
>>>> data analysis and data management." [PSI:MS]
>>>> is_a: MS:1000694 ! Waters software
>>>> is_a: MS:1001456 ! analysis software
>>>> is_a: MS:1001457 ! data processing software
>>>>
>>>>
>>>> ********************************** New type of mass spectrometer, TWIMS ,son of IMS
>>>>
>>>>
>>>> id: MS:XXXXXXX
>>>> name: Travelling wave ion mobility mass spectrometer
>>>> def: "An ion mobility mass spectrometry technique based on the superimposition of travelling
>>>> voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide." [PSI:MS]
>>>> synonym: "TWIMS" EXACT []
>>>> is_a: MS:1000261 ! ion mobility spectrometry
>>>>
>>>>
>>>> By the way... the "mass spectrometer" term (MS:1000293), is inside the purgatory... Do you
>>>> (community) really think this is the place for this term? Maybe is not used in the cv mappings for
>>>> mzML, but, anyway.... is strange, at least for me, finding the "mass spectrometer" in the purgatory...
>>>>
>>>> Best,
>>>> David
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 11/07/2011 07:28, Han...@wa...<mailto:Han...@wa...>   wrote:
>>>>
>>>> Dear David and Matt,
>>>>
>>>> I have provided answers 'in line' in red.
>>>>
>>>> I will try to find out, with regard to Matt's question, if the instrument type can be retrieved
>>>> from the header.txt file. The serial number, i.e. JAA143, refers to a specific type and
>>>> configuration so this may be the easiest way forward. If an overview 'lookup type' table exists, I
>>>> will forward it.
>>>>
>>>> Would you happen to know who could be contacted for column liquid chromatography and sample
>>>> preparation CV terms? We are trying to integrate those as well into sample forms and a repository
>>>> like system, but finding them is not that straightforward.
>>>>
>>>> Thanks and best regards,
>>>> Hans
>>>>
>>>>
>>>>
>>>>
>>>> Inactive hide details for "David Ovelleiro" ---08/07/2011 16:45:04---Dear Hans, Thanks for sending
>>>> us that intensive list of te"David Ovelleiro" ---08/07/2011 16:45:04---Dear Hans, Thanks for
>>>> sending us that intensive list of terms.
>>>>
>>>> From: "David Ovelleiro"<do...@eb...>   <mailto:do...@eb...>
>>>> To: "Mass spectrometry standard development"<psi...@li...>
>>>> <mailto:psi...@li...>
>>>> Cc: Han...@wa...<mailto:Han...@wa...>
>>>> Date: 08/07/2011 16:45
>>>> Subject: Re: [Psidev-ms-dev] new instrument CV terms
>>>>
>>>> ----------------------------------------------------------------------------------------------------
>>>>
>>>>
>>>>
>>>>
>>>> Dear Hans,
>>>>
>>>> Thanks for sending us that intensive list of terms.
>>>>
>>>> Some comments addressed to you and the rest of the community:
>>>>
>>>> 1. Instrument list
>>>> ===============
>>>> You’ve provided a list of 32 new instruments to be added.
>>>> a/ I’ll ad them under “Waters instrument model” (MS:1000126). Every new term will be like:
>>>> id: MS:XXXXXXX
>>>> name: Xevo TQ-S
>>>> def: "Waters quadrupole based instrument." [PSI:MS]
>>>> is_a: MS:1000126 ! Waters instrument model
>>>>
>>>> The terms “quadrupole”, “oa-ToF” and “LC-systems” will be applied correctly in each case. Is this OK?
>>>>
>>>> b/ Some of the new proposed instruments maybe overlap with some of the old ones. I list below the
>>>> four “suspects” (old terms below “Waters instrument model” MS:1000126):
>>>> Acquity UPLC FLR
>>>> Acquity UPLC PDA
>>>> GCT
>>>> quattro micro
>>>> Please Hans, check if your new terms can safely be included without repeating some of the four
>>>> previous members.
>>>>
>>>> [HV]:
>>>>
>>>> 'Acquity UPLC FLR' and 'Acquity UPLC PDA' are respectively a fluorescence and PDA detector for
>>>> 'ACQUITY UPLC' liquid chromatography systems.
>>>>
>>>> 'GCT' and 'quattro micro' have superseded by 'GCT premier' and 'Xevo TQD' mass spectrometers
>>>>
>>>> I therefore do not believe that there is CR term overlap/conflicts
>>>>
>>>>
>>>>
>>>> 2. Mass spectrometer
>>>> ==================
>>>> You propose a new “mass spectrometer type” called “Travelling wave mobility separator”.
>>>> a/ Can this be correctly included under “mass spectrometer” (MS:1000293)?
>>>> b/ Is not more appropriate to use “Travelling wave ion mobility mass spectrometer” as the name of
>>>> the new cv term?
>>>> c/ Can we use Synonym: TWIMS?
>>>> d/ We would need a short description of the new kind of mass spectrometer. I’ve found this: “An
>>>> ion mobilitymass spectrometry technique based on the superimposition of travelling voltage waves
>>>> on a radially-confining RF voltage in agas-filled,stacked-ring ion guide”. Any better suggestion?
>>>>
>>>> [HV]:
>>>>
>>>> a/b/c/ - please see Matt's reply (TWIMS is an IMS variant)
>>>> d/ see suggestion above
>>>>
>>>>
>>>> 3. Software
>>>> ===========
>>>> Three new “software” terms to be included: MassLynx, Empower and Unify. All three under “Waters
>>>> software” (MS:1000694).
>>>> a/ Please, Hans, we would need a short description of what these software do (one line each is
>>>> enough).
>>>>
>>>> [HV]:
>>>>
>>>> MassLynx:
>>>> "Mass spectrometry acquisition, processing and data analysis software"
>>>>
>>>>
>>>> Empower:
>>>> "Liquid chromatography acquisition, processing, data analysis and data management software"
>>>>
>>>> If believe that most vendors would call this CDS (chromatography data software). Would there be a
>>>> specific PSI-MS CV term for this?
>>>>
>>>>
>>>> Unify:
>>>> "Liquid chromatography and mass spectrometry acquisition, processing, data analysis and data
>>>> management software"
>>>>
>>>>
>>>>
>>>> I’ll be waiting for your comments, suggestions, changes, corrections…
>>>>
>>>> Best
>>>> david ovelleiro
>>>>
>>>>
>>>>
>>>> On 07/07/2011 09:05, Han...@wa...<mailto:Han...@wa...>wrote:
>>>>
>>>>
>>>> Dear all,
>>>>
>>>> Can the following instruments be added to the CV:
>>>>
>>>> quadrupole based:
>>>>
>>>> Xevo TQ-S
>>>> Xevo TQ MS
>>>> Xevo TQD
>>>> Acquity TQD
>>>> Acquity SQD
>>>> 3100
>>>> Quattro micro GC
>>>>
>>>> oa-ToF based:
>>>>
>>>> Synapt G2-S HDMS
>>>> Synapt G2 HDMS
>>>> Synapt HDMS
>>>> Synapt G2-S MS
>>>> Synapt G2 MS
>>>> Synapt MS
>>>> MALDI Synapt G2-S HDMS
>>>> MALDI Synapt G2 HDMS
>>>> MALDI Synapt HDMS
>>>> MALDI Synapt G2-S MS
>>>> MALDI Synapt G2 MS
>>>> MALDI Synapt MS
>>>> Xevo G2 Q-Tof
>>>> Xevo Q-Tof
>>>> Xevo G2 Tof
>>>> GCT Premier
>>>>
>>>> LC-systems:
>>>>
>>>> ACQUITY UPLC I-Class
>>>> ACQUITY UPLC
>>>> ACQUITY UPLC H-Class
>>>> ACQUITY UPLC H-Class Bio
>>>> ACQUITY UPLC Systems with 2D Technology
>>>> nanoACQUITY UPLC
>>>> nanoACQUITY UPLC System with Technology
>>>> nanoACQUITY UPLC with HDX Technology
>>>> TRIZAIC UPLC nanoTile
>>>>
>>>> software:
>>>>
>>>> MassLynx
>>>> Empower
>>>> Unify
>>>>
>>>> mass spectrometer type:
>>>>
>>>> travelling wave mobility separator
>>>>
>>>>
>>>> The vendor or brand should be listed as "Waters Corporation". Would any more information be required?
>>>>
>>>> Thanks and best regards,
>>>>
>>>> Hans
>>>>
>>>> ===========================================================
>>>> The information in this email is confidential, and is intended solely for the addressee(s).
>>>> Access to this email by anyone else is unauthorized and therefore prohibited. If you are
>>>> not the intended recipient you are notified that disclosing, copying, distributing or taking
>>>> any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
>>>> ===========================================================
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> All of the data generated in your IT infrastructure is seriously valuable.
>>>> Why? It contains a definitive record of application performance, security
>>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>>> sense of it. IT sense. And common sense.
>>>> http://p.sf.net/sfu/splunk-d2d-c2
>>>>
>>>>
>>>> _______________________________________________
>>>> Psidev-ms-dev mailing list
>>>> Psi...@li...<mailto:Psi...@li...>
>>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>>
>>>>
>>>>
>>>> --
>>>> David Ovelleiro
>>>> Bioinformatician
>>>> PRIDE Group
>>>> Proteomics Services Team, PANDA Group
>>>> EMBL European Bioinformatics Institute
>>>> Wellcome Trust Genome Campus
>>>> Hinxton, Cambridge, UK
>>>> CB10 1SD
>>>>
>>>> ===========================================================
>>>> The information in this email is confidential, and is intended solely for the addressee(s).
>>>> Access to this email by anyone else is unauthorized and therefore prohibited.    If you are
>>>> not the intended recipient you are notified that disclosing, copying, distributing or taking
>>>> any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> David Ovelleiro
>>>> Bioinformatician
>>>> PRIDE Group
>>>> Proteomics Services Team, PANDA Group
>>>> EMBL European Bioinformatics Institute
>>>> Wellcome Trust Genome Campus
>>>> Hinxton, Cambridge, UK
>>>> CB10 1SD
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> All of the data generated in your IT infrastructure is seriously valuable.
>>>> Why? It contains a definitive record of application performance, security
>>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>>> sense of it. IT sense. And common sense.
>>>> http://p.sf.net/sfu/splunk-d2d-c2
>>>>
>>>>
>>>> _______________________________________________
>>>> Psidev-ms-dev mailing list
>>>> Psi...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>> --
>>> David Ovelleiro
>>> Bioinformatician
>>> PRIDE Group
>>> Proteomics Services Team, PANDA Group
>>> EMBL European Bioinformatics Institute
>>> Wellcome Trust Genome Campus
>>> Hinxton, Cambridge, UK
>>> CB10 1SD
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> All of the data generated in your IT infrastructure is seriously valuable.
>>> Why? It contains a definitive record of application performance, security
>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>> sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-d2d-c2
>>>
>>>
>>>
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>> ------------------------------------------------------------------------------
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>


-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD

Re: [Psidev-ms-dev] new instrument CV terms

[David O. <do...@eb...>]

Hi Matt and community,

In first place, thank you Matt for deleting the duplicated software, 
MassLynx. I did a quick check and it wasn't inside Waters software (in 
the next update, I'll quickly add the connection to Waters).

Under "mass spectrometer" we have a mix of mass spectrometry 
techniques/methods and instruments... even something called "mass 
spectrometry/mass spectrometry".  But, again, if someone is planning to 
use the "mass spectrometer" terms (and people from Waters seem to be 
doing so), I think is reasonable to re-locate this.

Matt, please: don't touch the sorting of the file: I'm trying to 
reproduce the way Obo-Edit works. I've posted this afternoon an email in 
their email list about the way the application works for new IDs (the 
lastID variable doesn't seem to work any more). I'll keep you all 
informed. Anyway, I'm reporting in every new update the terms added 
(MS:1001797 the last one).

Best,
David

On 12/07/2011 15:57, Matthew Chambers wrote:
> I deleted the MassLynx term, it was a duplicate. I call it a "speedy delete"...it never happened! :P
>
> I was preparing an email to send yesterday including that tidbit but didn't finish it. Another thing
> I was going to mention is that "TWIMS" should be "travelling wave ion mobility spectrometer" and
> that it's awkward for IMS to be under "mass spectrometer" as you've mentioned below. Incidentally,
> there is no mapping in the PSI formats for the "mass spectrometer" terms and its children. A lot of
> the terms are still in purgatory simply because there isn't a need for them in the files. If we
> wanted to go more in the direction of an ontology, we could associate each instrument with its
> supported spectrometry methods. But that would require considerable discussion and work for little gain.
>
> Also I'm not sure about this inserting new terms into the middle of the OBO. It may be valid OBO but
> it's rather confusing. I tend to make small additions with a text editor (after running them by the
> list) so having new terms in the middle would make it easy to choose a duplicate accession. Is it
> alright if I move the new terms to the bottom? I wouldn't expect it to need a version bump since it
> doesn't change anything.
>
> -Matt
>
>
> On 7/12/2011 5:16 AM, David Ovelleiro wrote:
>> Dear Hans, Matt, Eric and PSI community,
>>
>> Empower, MassLynx and Unify and TWIMS have been included in the v.3.7.2 release of the psi-ms. (
>> v.3.7.1 had a small typo... sorry....)
>> I think that with this, we've finished the list of terms proposed by Hans. I expect everything is
>> fine.... if it's not... please, send an email.
>>
>> Dear Eric: thanks for the explanation. I was aware of the motivations for including some terms
>> inside "purgatory". My concern is related to the fact that, if people is suggesting terms inside
>> this "purgatory", maybe they are planning to use them. An xpath containing the word "purgatory" is,
>> in my opinion, not very self-explanatory.
>> To organize this, I'd propose changing the name of MS:1000293 (mass spectrometer) to "mass
>> spectrometry methods" (I'm not sure this is the perfect name, but I suggest it because some of the
>> patents related to them are named as "methods", e.g. http://www.freepatentsonline.com/7071465.html).
>> We could then re-map MS:1000293 as son of "instrument" (MS:1000463). Only a suggestion... please,
>> I'd like to hear some opinions.
>>
>> Best,
>> David
>>
>>
>>
>>
>>
>> On 11/07/2011 17:25, Eric Deutsch wrote:
>>> Hi David, thanks, these new terms look good to me.
>>>
>>> Regarding “mass spectrometry” and “purgatory”, please recall that “purgatory” is a ratty box of
>>> terms that we just haven’t made a decision on yet. We don’t **want** and terms in “purgatory”, but
>>> in a world of limited time, there they lie. In the CV, we are currently using “instrument” in lieu
>>> of “mass spectrometer”. Why the term “mass spectrometer” is in purgatory I’m not quite certain. I
>>> suppose it should just be obsoleted and make it a synonym of “instrument”. But I have a vague
>>> recollection that we decided on “instrument” because some of these instruments have additional
>>> components that are not strictly mass spectrometers (e.g. UV detection components). In which case,
>>> there may be no role for a pure mass spectrometer. But maybe we couldn’t all agree on what to do,
>>> so it lies in “purgatory” until the day that someone comes to decide and save the day.
>>>
>>> Regards,
>>>
>>> Eric
>>>
>>> *From:*David Ovelleiro [mailto:do...@eb...<mailto:do...@eb...>]
>>> *Sent:* Monday, July 11, 2011 9:02 AM
>>> *To:* Han...@wa...<mailto:Han...@wa...>
>>> *Cc:* Mass spectrometry standard development
>>> *Subject:* Re: [Psidev-ms-dev] new instrument CV terms
>>>
>>> Dear Hans, Matt and PSI community,
>>>
>>> I've updated the psi-ms c.v. with the 32 new Waters instruments list.
>>> I'll also add, in a couple of days, the next 4 c.v. terms. Please, check them and if you see
>>> anything wrong, write an email....
>>>
>>> [Term]
>>> id: MS:XXXXXXX
>>> name: MassLynx
>>> def: "Waters software for Mass spectrometry acquisition, processing and data analysis." [PSI:MS]
>>> is_a: MS:1000694 ! Waters software
>>> is_a: MS:1001456 ! analysis software
>>> is_a: MS:1001457 ! data processing software
>>>
>>> [Term]
>>> id: MS:XXXXXXX
>>> name: Empower
>>> def: "Waters software for liquid chromatography acquisition, processing, data analysis and data
>>> management." [PSI:MS]
>>> is_a: MS:1000694 ! Waters software
>>> is_a: MS:1001456 ! analysis software
>>> is_a: MS:1001457 ! data processing software
>>>
>>> [Term]
>>> id: MS:XXXXXXX
>>> name: Unify
>>> def: "Waters software for liquid chromatography and mass spectrometry acquisition, processing,
>>> data analysis and data management." [PSI:MS]
>>> is_a: MS:1000694 ! Waters software
>>> is_a: MS:1001456 ! analysis software
>>> is_a: MS:1001457 ! data processing software
>>>
>>>
>>> ********************************** New type of mass spectrometer, TWIMS ,son of IMS
>>>
>>>
>>> id: MS:XXXXXXX
>>> name: Travelling wave ion mobility mass spectrometer
>>> def: "An ion mobility mass spectrometry technique based on the superimposition of travelling
>>> voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide." [PSI:MS]
>>> synonym: "TWIMS" EXACT []
>>> is_a: MS:1000261 ! ion mobility spectrometry
>>>
>>>
>>> By the way... the "mass spectrometer" term (MS:1000293), is inside the purgatory... Do you
>>> (community) really think this is the place for this term? Maybe is not used in the cv mappings for
>>> mzML, but, anyway.... is strange, at least for me, finding the "mass spectrometer" in the purgatory...
>>>
>>> Best,
>>> David
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 11/07/2011 07:28, Han...@wa...<mailto:Han...@wa...>  wrote:
>>>
>>> Dear David and Matt,
>>>
>>> I have provided answers 'in line' in red.
>>>
>>> I will try to find out, with regard to Matt's question, if the instrument type can be retrieved
>>> from the header.txt file. The serial number, i.e. JAA143, refers to a specific type and
>>> configuration so this may be the easiest way forward. If an overview 'lookup type' table exists, I
>>> will forward it.
>>>
>>> Would you happen to know who could be contacted for column liquid chromatography and sample
>>> preparation CV terms? We are trying to integrate those as well into sample forms and a repository
>>> like system, but finding them is not that straightforward.
>>>
>>> Thanks and best regards,
>>> Hans
>>>
>>>
>>>
>>>
>>> Inactive hide details for "David Ovelleiro" ---08/07/2011 16:45:04---Dear Hans, Thanks for sending
>>> us that intensive list of te"David Ovelleiro" ---08/07/2011 16:45:04---Dear Hans, Thanks for
>>> sending us that intensive list of terms.
>>>
>>> From: "David Ovelleiro"<do...@eb...>  <mailto:do...@eb...>
>>> To: "Mass spectrometry standard development"<psi...@li...>
>>> <mailto:psi...@li...>
>>> Cc: Han...@wa...<mailto:Han...@wa...>
>>> Date: 08/07/2011 16:45
>>> Subject: Re: [Psidev-ms-dev] new instrument CV terms
>>>
>>> ----------------------------------------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>> Dear Hans,
>>>
>>> Thanks for sending us that intensive list of terms.
>>>
>>> Some comments addressed to you and the rest of the community:
>>>
>>> 1. Instrument list
>>> ===============
>>> You’ve provided a list of 32 new instruments to be added.
>>> a/ I’ll ad them under “Waters instrument model” (MS:1000126). Every new term will be like:
>>> id: MS:XXXXXXX
>>> name: Xevo TQ-S
>>> def: "Waters quadrupole based instrument." [PSI:MS]
>>> is_a: MS:1000126 ! Waters instrument model
>>>
>>> The terms “quadrupole”, “oa-ToF” and “LC-systems” will be applied correctly in each case. Is this OK?
>>>
>>> b/ Some of the new proposed instruments maybe overlap with some of the old ones. I list below the
>>> four “suspects” (old terms below “Waters instrument model” MS:1000126):
>>> Acquity UPLC FLR
>>> Acquity UPLC PDA
>>> GCT
>>> quattro micro
>>> Please Hans, check if your new terms can safely be included without repeating some of the four
>>> previous members.
>>>
>>> [HV]:
>>>
>>> 'Acquity UPLC FLR' and 'Acquity UPLC PDA' are respectively a fluorescence and PDA detector for
>>> 'ACQUITY UPLC' liquid chromatography systems.
>>>
>>> 'GCT' and 'quattro micro' have superseded by 'GCT premier' and 'Xevo TQD' mass spectrometers
>>>
>>> I therefore do not believe that there is CR term overlap/conflicts
>>>
>>>
>>>
>>> 2. Mass spectrometer
>>> ==================
>>> You propose a new “mass spectrometer type” called “Travelling wave mobility separator”.
>>> a/ Can this be correctly included under “mass spectrometer” (MS:1000293)?
>>> b/ Is not more appropriate to use “Travelling wave ion mobility mass spectrometer” as the name of
>>> the new cv term?
>>> c/ Can we use Synonym: TWIMS?
>>> d/ We would need a short description of the new kind of mass spectrometer. I’ve found this: “An
>>> ion mobilitymass spectrometry technique based on the superimposition of travelling voltage waves
>>> on a radially-confining RF voltage in agas-filled,stacked-ring ion guide”. Any better suggestion?
>>>
>>> [HV]:
>>>
>>> a/b/c/ - please see Matt's reply (TWIMS is an IMS variant)
>>> d/ see suggestion above
>>>
>>>
>>> 3. Software
>>> ===========
>>> Three new “software” terms to be included: MassLynx, Empower and Unify. All three under “Waters
>>> software” (MS:1000694).
>>> a/ Please, Hans, we would need a short description of what these software do (one line each is
>>> enough).
>>>
>>> [HV]:
>>>
>>> MassLynx:
>>> "Mass spectrometry acquisition, processing and data analysis software"
>>>
>>>
>>> Empower:
>>> "Liquid chromatography acquisition, processing, data analysis and data management software"
>>>
>>> If believe that most vendors would call this CDS (chromatography data software). Would there be a
>>> specific PSI-MS CV term for this?
>>>
>>>
>>> Unify:
>>> "Liquid chromatography and mass spectrometry acquisition, processing, data analysis and data
>>> management software"
>>>
>>>
>>>
>>> I’ll be waiting for your comments, suggestions, changes, corrections…
>>>
>>> Best
>>> david ovelleiro
>>>
>>>
>>>
>>> On 07/07/2011 09:05, Han...@wa...<mailto:Han...@wa...>wrote:
>>>
>>>
>>> Dear all,
>>>
>>> Can the following instruments be added to the CV:
>>>
>>> quadrupole based:
>>>
>>> Xevo TQ-S
>>> Xevo TQ MS
>>> Xevo TQD
>>> Acquity TQD
>>> Acquity SQD
>>> 3100
>>> Quattro micro GC
>>>
>>> oa-ToF based:
>>>
>>> Synapt G2-S HDMS
>>> Synapt G2 HDMS
>>> Synapt HDMS
>>> Synapt G2-S MS
>>> Synapt G2 MS
>>> Synapt MS
>>> MALDI Synapt G2-S HDMS
>>> MALDI Synapt G2 HDMS
>>> MALDI Synapt HDMS
>>> MALDI Synapt G2-S MS
>>> MALDI Synapt G2 MS
>>> MALDI Synapt MS
>>> Xevo G2 Q-Tof
>>> Xevo Q-Tof
>>> Xevo G2 Tof
>>> GCT Premier
>>>
>>> LC-systems:
>>>
>>> ACQUITY UPLC I-Class
>>> ACQUITY UPLC
>>> ACQUITY UPLC H-Class
>>> ACQUITY UPLC H-Class Bio
>>> ACQUITY UPLC Systems with 2D Technology
>>> nanoACQUITY UPLC
>>> nanoACQUITY UPLC System with Technology
>>> nanoACQUITY UPLC with HDX Technology
>>> TRIZAIC UPLC nanoTile
>>>
>>> software:
>>>
>>> MassLynx
>>> Empower
>>> Unify
>>>
>>> mass spectrometer type:
>>>
>>> travelling wave mobility separator
>>>
>>>
>>> The vendor or brand should be listed as "Waters Corporation". Would any more information be required?
>>>
>>> Thanks and best regards,
>>>
>>> Hans
>>>
>>> ===========================================================
>>> The information in this email is confidential, and is intended solely for the addressee(s).
>>> Access to this email by anyone else is unauthorized and therefore prohibited. If you are
>>> not the intended recipient you are notified that disclosing, copying, distributing or taking
>>> any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
>>> ===========================================================
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> All of the data generated in your IT infrastructure is seriously valuable.
>>> Why? It contains a definitive record of application performance, security
>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>> sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-d2d-c2
>>>
>>>
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...<mailto:Psi...@li...>
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>
>>>
>>>
>>> --
>>> David Ovelleiro
>>> Bioinformatician
>>> PRIDE Group
>>> Proteomics Services Team, PANDA Group
>>> EMBL European Bioinformatics Institute
>>> Wellcome Trust Genome Campus
>>> Hinxton, Cambridge, UK
>>> CB10 1SD
>>>
>>> ===========================================================
>>> The information in this email is confidential, and is intended solely for the addressee(s).
>>> Access to this email by anyone else is unauthorized and therefore prohibited.    If you are
>>> not the intended recipient you are notified that disclosing, copying, distributing or taking
>>> any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
>>> ===========================================================
>>>
>>>
>>>
>>>
>>> --
>>> David Ovelleiro
>>> Bioinformatician
>>> PRIDE Group
>>> Proteomics Services Team, PANDA Group
>>> EMBL European Bioinformatics Institute
>>> Wellcome Trust Genome Campus
>>> Hinxton, Cambridge, UK
>>> CB10 1SD
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> All of the data generated in your IT infrastructure is seriously valuable.
>>> Why? It contains a definitive record of application performance, security
>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>> sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-d2d-c2
>>>
>>>
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
>> --
>> David Ovelleiro
>> Bioinformatician
>> PRIDE Group
>> Proteomics Services Team, PANDA Group
>> EMBL European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge, UK
>> CB10 1SD
>>
>>
>>
>> ------------------------------------------------------------------------------
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>>
>>
>>
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev


-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD

Re: [Psidev-ms-dev] new instrument CV terms

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

I deleted the MassLynx term, it was a duplicate. I call it a "speedy delete"...it never happened! :P

I was preparing an email to send yesterday including that tidbit but didn't finish it. Another thing 
I was going to mention is that "TWIMS" should be "travelling wave ion mobility spectrometer" and 
that it's awkward for IMS to be under "mass spectrometer" as you've mentioned below. Incidentally, 
there is no mapping in the PSI formats for the "mass spectrometer" terms and its children. A lot of 
the terms are still in purgatory simply because there isn't a need for them in the files. If we 
wanted to go more in the direction of an ontology, we could associate each instrument with its 
supported spectrometry methods. But that would require considerable discussion and work for little gain.

Also I'm not sure about this inserting new terms into the middle of the OBO. It may be valid OBO but 
it's rather confusing. I tend to make small additions with a text editor (after running them by the 
list) so having new terms in the middle would make it easy to choose a duplicate accession. Is it 
alright if I move the new terms to the bottom? I wouldn't expect it to need a version bump since it 
doesn't change anything.

-Matt


On 7/12/2011 5:16 AM, David Ovelleiro wrote:
> Dear Hans, Matt, Eric and PSI community,
>
> Empower, MassLynx and Unify and TWIMS have been included in the v.3.7.2 release of the psi-ms. (
> v.3.7.1 had a small typo... sorry....)
> I think that with this, we've finished the list of terms proposed by Hans. I expect everything is
> fine.... if it's not... please, send an email.
>
> Dear Eric: thanks for the explanation. I was aware of the motivations for including some terms
> inside "purgatory". My concern is related to the fact that, if people is suggesting terms inside
> this "purgatory", maybe they are planning to use them. An xpath containing the word "purgatory" is,
> in my opinion, not very self-explanatory.
> To organize this, I'd propose changing the name of MS:1000293 (mass spectrometer) to "mass
> spectrometry methods" (I'm not sure this is the perfect name, but I suggest it because some of the
> patents related to them are named as "methods", e.g. http://www.freepatentsonline.com/7071465.html).
> We could then re-map MS:1000293 as son of "instrument" (MS:1000463). Only a suggestion... please,
> I'd like to hear some opinions.
>
> Best,
> David
>
>
>
>
>
> On 11/07/2011 17:25, Eric Deutsch wrote:
>>
>> Hi David, thanks, these new terms look good to me.
>>
>> Regarding “mass spectrometry” and “purgatory”, please recall that “purgatory” is a ratty box of
>> terms that we just haven’t made a decision on yet. We don’t **want** and terms in “purgatory”, but
>> in a world of limited time, there they lie. In the CV, we are currently using “instrument” in lieu
>> of “mass spectrometer”. Why the term “mass spectrometer” is in purgatory I’m not quite certain. I
>> suppose it should just be obsoleted and make it a synonym of “instrument”. But I have a vague
>> recollection that we decided on “instrument” because some of these instruments have additional
>> components that are not strictly mass spectrometers (e.g. UV detection components). In which case,
>> there may be no role for a pure mass spectrometer. But maybe we couldn’t all agree on what to do,
>> so it lies in “purgatory” until the day that someone comes to decide and save the day.
>>
>> Regards,
>>
>> Eric
>>
>> *From:*David Ovelleiro [mailto:do...@eb... <mailto:do...@eb...>]
>> *Sent:* Monday, July 11, 2011 9:02 AM
>> *To:* Han...@wa... <mailto:Han...@wa...>
>> *Cc:* Mass spectrometry standard development
>> *Subject:* Re: [Psidev-ms-dev] new instrument CV terms
>>
>> Dear Hans, Matt and PSI community,
>>
>> I've updated the psi-ms c.v. with the 32 new Waters instruments list.
>> I'll also add, in a couple of days, the next 4 c.v. terms. Please, check them and if you see
>> anything wrong, write an email....
>>
>> [Term]
>> id: MS:XXXXXXX
>> name: MassLynx
>> def: "Waters software for Mass spectrometry acquisition, processing and data analysis." [PSI:MS]
>> is_a: MS:1000694 ! Waters software
>> is_a: MS:1001456 ! analysis software
>> is_a: MS:1001457 ! data processing software
>>
>> [Term]
>> id: MS:XXXXXXX
>> name: Empower
>> def: "Waters software for liquid chromatography acquisition, processing, data analysis and data
>> management." [PSI:MS]
>> is_a: MS:1000694 ! Waters software
>> is_a: MS:1001456 ! analysis software
>> is_a: MS:1001457 ! data processing software
>>
>> [Term]
>> id: MS:XXXXXXX
>> name: Unify
>> def: "Waters software for liquid chromatography and mass spectrometry acquisition, processing,
>> data analysis and data management." [PSI:MS]
>> is_a: MS:1000694 ! Waters software
>> is_a: MS:1001456 ! analysis software
>> is_a: MS:1001457 ! data processing software
>>
>>
>> ********************************** New type of mass spectrometer, TWIMS ,son of IMS
>>
>>
>> id: MS:XXXXXXX
>> name: Travelling wave ion mobility mass spectrometer
>> def: "An ion mobility mass spectrometry technique based on the superimposition of travelling
>> voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide." [PSI:MS]
>> synonym: "TWIMS" EXACT []
>> is_a: MS:1000261 ! ion mobility spectrometry
>>
>>
>> By the way... the "mass spectrometer" term (MS:1000293), is inside the purgatory... Do you
>> (community) really think this is the place for this term? Maybe is not used in the cv mappings for
>> mzML, but, anyway.... is strange, at least for me, finding the "mass spectrometer" in the purgatory...
>>
>> Best,
>> David
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 11/07/2011 07:28, Han...@wa... <mailto:Han...@wa...> wrote:
>>
>> Dear David and Matt,
>>
>> I have provided answers 'in line' in red.
>>
>> I will try to find out, with regard to Matt's question, if the instrument type can be retrieved
>> from the header.txt file. The serial number, i.e. JAA143, refers to a specific type and
>> configuration so this may be the easiest way forward. If an overview 'lookup type' table exists, I
>> will forward it.
>>
>> Would you happen to know who could be contacted for column liquid chromatography and sample
>> preparation CV terms? We are trying to integrate those as well into sample forms and a repository
>> like system, but finding them is not that straightforward.
>>
>> Thanks and best regards,
>> Hans
>>
>>
>>
>>
>> Inactive hide details for "David Ovelleiro" ---08/07/2011 16:45:04---Dear Hans, Thanks for sending
>> us that intensive list of te"David Ovelleiro" ---08/07/2011 16:45:04---Dear Hans, Thanks for
>> sending us that intensive list of terms.
>>
>> From: "David Ovelleiro" <do...@eb...> <mailto:do...@eb...>
>> To: "Mass spectrometry standard development" <psi...@li...>
>> <mailto:psi...@li...>
>> Cc: Han...@wa... <mailto:Han...@wa...>
>> Date: 08/07/2011 16:45
>> Subject: Re: [Psidev-ms-dev] new instrument CV terms
>>
>> ----------------------------------------------------------------------------------------------------
>>
>>
>>
>>
>> Dear Hans,
>>
>> Thanks for sending us that intensive list of terms.
>>
>> Some comments addressed to you and the rest of the community:
>>
>> 1. Instrument list
>> ===============
>> You’ve provided a list of 32 new instruments to be added.
>> a/ I’ll ad them under “Waters instrument model” (MS:1000126). Every new term will be like:
>> id: MS:XXXXXXX
>> name: Xevo TQ-S
>> def: "Waters quadrupole based instrument." [PSI:MS]
>> is_a: MS:1000126 ! Waters instrument model
>>
>> The terms “quadrupole”, “oa-ToF” and “LC-systems” will be applied correctly in each case. Is this OK?
>>
>> b/ Some of the new proposed instruments maybe overlap with some of the old ones. I list below the
>> four “suspects” (old terms below “Waters instrument model” MS:1000126):
>> Acquity UPLC FLR
>> Acquity UPLC PDA
>> GCT
>> quattro micro
>> Please Hans, check if your new terms can safely be included without repeating some of the four
>> previous members.
>>
>> [HV]:
>>
>> 'Acquity UPLC FLR' and 'Acquity UPLC PDA' are respectively a fluorescence and PDA detector for
>> 'ACQUITY UPLC' liquid chromatography systems.
>>
>> 'GCT' and 'quattro micro' have superseded by 'GCT premier' and 'Xevo TQD' mass spectrometers
>>
>> I therefore do not believe that there is CR term overlap/conflicts
>>
>>
>>
>> 2. Mass spectrometer
>> ==================
>> You propose a new “mass spectrometer type” called “Travelling wave mobility separator”.
>> a/ Can this be correctly included under “mass spectrometer” (MS:1000293)?
>> b/ Is not more appropriate to use “Travelling wave ion mobility mass spectrometer” as the name of
>> the new cv term?
>> c/ Can we use Synonym: TWIMS?
>> d/ We would need a short description of the new kind of mass spectrometer. I’ve found this: “An
>> ion mobilitymass spectrometry technique based on the superimposition of travelling voltage waves
>> on a radially-confining RF voltage in agas-filled,stacked-ring ion guide”. Any better suggestion?
>>
>> [HV]:
>>
>> a/b/c/ - please see Matt's reply (TWIMS is an IMS variant)
>> d/ see suggestion above
>>
>>
>> 3. Software
>> ===========
>> Three new “software” terms to be included: MassLynx, Empower and Unify. All three under “Waters
>> software” (MS:1000694).
>> a/ Please, Hans, we would need a short description of what these software do (one line each is
>> enough).
>>
>> [HV]:
>>
>> MassLynx:
>> "Mass spectrometry acquisition, processing and data analysis software"
>>
>>
>> Empower:
>> "Liquid chromatography acquisition, processing, data analysis and data management software"
>>
>> If believe that most vendors would call this CDS (chromatography data software). Would there be a
>> specific PSI-MS CV term for this?
>>
>>
>> Unify:
>> "Liquid chromatography and mass spectrometry acquisition, processing, data analysis and data
>> management software"
>>
>>
>>
>> I’ll be waiting for your comments, suggestions, changes, corrections…
>>
>> Best
>> david ovelleiro
>>
>>
>>
>> On 07/07/2011 09:05, Han...@wa... <mailto:Han...@wa...>wrote:
>>
>>
>> Dear all,
>>
>> Can the following instruments be added to the CV:
>>
>> quadrupole based:
>>
>> Xevo TQ-S
>> Xevo TQ MS
>> Xevo TQD
>> Acquity TQD
>> Acquity SQD
>> 3100
>> Quattro micro GC
>>
>> oa-ToF based:
>>
>> Synapt G2-S HDMS
>> Synapt G2 HDMS
>> Synapt HDMS
>> Synapt G2-S MS
>> Synapt G2 MS
>> Synapt MS
>> MALDI Synapt G2-S HDMS
>> MALDI Synapt G2 HDMS
>> MALDI Synapt HDMS
>> MALDI Synapt G2-S MS
>> MALDI Synapt G2 MS
>> MALDI Synapt MS
>> Xevo G2 Q-Tof
>> Xevo Q-Tof
>> Xevo G2 Tof
>> GCT Premier
>>
>> LC-systems:
>>
>> ACQUITY UPLC I-Class
>> ACQUITY UPLC
>> ACQUITY UPLC H-Class
>> ACQUITY UPLC H-Class Bio
>> ACQUITY UPLC Systems with 2D Technology
>> nanoACQUITY UPLC
>> nanoACQUITY UPLC System with Technology
>> nanoACQUITY UPLC with HDX Technology
>> TRIZAIC UPLC nanoTile
>>
>> software:
>>
>> MassLynx
>> Empower
>> Unify
>>
>> mass spectrometer type:
>>
>> travelling wave mobility separator
>>
>>
>> The vendor or brand should be listed as "Waters Corporation". Would any more information be required?
>>
>> Thanks and best regards,
>>
>> Hans
>>
>> ===========================================================
>> The information in this email is confidential, and is intended solely for the addressee(s).
>> Access to this email by anyone else is unauthorized and therefore prohibited. If you are
>> not the intended recipient you are notified that disclosing, copying, distributing or taking
>> any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
>> ===========================================================
>>
>>
>> ------------------------------------------------------------------------------
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>>
>>
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li... <mailto:Psi...@li...>
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
>>
>>
>> --
>> David Ovelleiro
>> Bioinformatician
>> PRIDE Group
>> Proteomics Services Team, PANDA Group
>> EMBL European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge, UK
>> CB10 1SD
>>
>> ===========================================================
>> The information in this email is confidential, and is intended solely for the addressee(s).
>> Access to this email by anyone else is unauthorized and therefore prohibited.    If you are
>> not the intended recipient you are notified that disclosing, copying, distributing or taking
>> any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
>> ===========================================================
>>
>>
>>
>>
>> --
>> David Ovelleiro
>> Bioinformatician
>> PRIDE Group
>> Proteomics Services Team, PANDA Group
>> EMBL European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge, UK
>> CB10 1SD
>>
>>
>> ------------------------------------------------------------------------------
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>>
>>
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>
> --
> David Ovelleiro
> Bioinformatician
> PRIDE Group
> Proteomics Services Team, PANDA Group
> EMBL European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, UK
> CB10 1SD
>
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
>
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] new instrument CV terms

[David O. <do...@eb...>]

Dear Hans, Matt, Eric and PSI community,

Empower, MassLynx and Unify and TWIMS have been included in the v.3.7.2 
release of the psi-ms. ( v.3.7.1 had a small typo... sorry....)
I think that with this, we've finished the list of terms proposed by 
Hans. I expect everything is fine.... if it's not... please, send an email.

Dear Eric: thanks for the explanation. I was aware of the motivations 
for including some terms inside "purgatory". My concern is related to 
the fact that, if people is suggesting terms inside this "purgatory", 
maybe they are planning to use them. An xpath containing the word 
"purgatory" is, in my opinion, not very self-explanatory.
To organize this, I'd propose changing the name of MS:1000293 (mass 
spectrometer) to "mass spectrometry methods" (I'm not sure this is the 
perfect name, but I suggest it because some of the patents related to 
them are named as "methods", e.g. 
http://www.freepatentsonline.com/7071465.html). We could then re-map 
MS:1000293 as son of "instrument" (MS:1000463). Only a suggestion... 
please, I'd like to hear some opinions.

Best,
David





On 11/07/2011 17:25, Eric Deutsch wrote:
>
> Hi David, thanks, these new terms look good to me.
>
> Regarding "mass spectrometry" and "purgatory", please recall that 
> "purgatory" is a ratty box of terms that we just haven't made a 
> decision on yet. We don't **want** and terms in "purgatory", but in a 
> world of limited time, there they lie. In the CV, we are currently 
> using "instrument" in lieu of "mass spectrometer". Why the term "mass 
> spectrometer" is in purgatory I'm not quite certain. I suppose it 
> should just be obsoleted and make it a synonym of "instrument". But I 
> have a vague recollection that we decided on "instrument" because some 
> of these instruments have additional components that are not strictly 
> mass spectrometers (e.g. UV detection components). In which case, 
> there may be no role for a pure mass spectrometer. But maybe we 
> couldn't all agree on what to do, so it lies in "purgatory" until the 
> day that someone comes to decide and save the day.
>
> Regards,
>
> Eric
>
> *From:*David Ovelleiro [mailto:do...@eb... <mailto:do...@eb...>]
> *Sent:* Monday, July 11, 2011 9:02 AM
> *To:* Han...@wa... <mailto:Han...@wa...>
> *Cc:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] new instrument CV terms
>
> Dear Hans, Matt and PSI community,
>
> I've updated the psi-ms c.v. with the 32 new Waters instruments list.
> I'll also add, in a couple of days, the next 4 c.v. terms. Please, 
> check them and if you see anything wrong, write an email....
>
> [Term]
> id: MS:XXXXXXX
> name: MassLynx
> def: "Waters software for Mass spectrometry acquisition, processing 
> and data analysis." [PSI:MS]
> is_a: MS:1000694 ! Waters software
> is_a: MS:1001456 ! analysis software
> is_a: MS:1001457 ! data processing software
>
> [Term]
> id: MS:XXXXXXX
> name: Empower
> def: "Waters software for liquid chromatography acquisition, 
> processing, data analysis and data management." [PSI:MS]
> is_a: MS:1000694 ! Waters software
> is_a: MS:1001456 ! analysis software
> is_a: MS:1001457 ! data processing software
>
> [Term]
> id: MS:XXXXXXX
> name: Unify
> def: "Waters software for liquid chromatography and mass spectrometry 
> acquisition, processing, data analysis and data management." [PSI:MS]
> is_a: MS:1000694 ! Waters software
> is_a: MS:1001456 ! analysis software
> is_a: MS:1001457 ! data processing software
>
>
> ********************************** New type of mass spectrometer, 
> TWIMS ,son of IMS
>
>
> id: MS:XXXXXXX
> name: Travelling wave ion mobility mass spectrometer
> def: "An ion mobility mass spectrometry technique based on the 
> superimposition of travelling voltage waves on a radially-confining RF 
> voltage in a gas-filled, stacked-ring ion guide." [PSI:MS]
> synonym: "TWIMS" EXACT []
> is_a: MS:1000261 ! ion mobility spectrometry
>
>
> By the way... the "mass spectrometer" term (MS:1000293), is inside the 
> purgatory...  Do you (community) really think this is the place for 
> this term? Maybe is not used in the cv mappings for mzML, but, 
> anyway.... is strange, at least for me, finding the "mass 
> spectrometer" in the purgatory...
>
> Best,
> David
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On 11/07/2011 07:28, Han...@wa... 
> <mailto:Han...@wa...> wrote:
>
> Dear David and Matt,
>
> I have provided answers 'in line' in red.
>
> I will try to find out, with regard to Matt's question, if the 
> instrument type can be retrieved from the header.txt file. The serial 
> number, i.e. JAA143, refers to a specific type and configuration so 
> this may be the easiest way forward. If an overview 'lookup type' 
> table exists, I will forward it.
>
> Would you happen to know who could be contacted for column liquid 
> chromatography and sample preparation CV terms? We are trying to 
> integrate those as well into sample forms and a repository like 
> system, but finding them is not that straightforward.
>
> Thanks and best regards,
> Hans
>
>
>
>
> Inactive hide details for "David Ovelleiro" ---08/07/2011 
> 16:45:04---Dear Hans, Thanks for sending us that intensive list of 
> te"David Ovelleiro" ---08/07/2011 16:45:04---Dear Hans, Thanks for 
> sending us that intensive list of terms.
>
> From: "David Ovelleiro" <do...@eb...> <mailto:do...@eb...>
> To: "Mass spectrometry standard development" 
> <psi...@li...> 
> <mailto:psi...@li...>
> Cc: Han...@wa... <mailto:Han...@wa...>
> Date: 08/07/2011 16:45
> Subject: Re: [Psidev-ms-dev] new instrument CV terms
>
> ------------------------------------------------------------------------
>
>
>
>
> Dear Hans,
>
> Thanks for sending us that intensive list of terms.
>
> Some comments addressed to you and the rest of the community:
>
> 1. Instrument list
> ===============
> You've provided a list of 32 new instruments to be added.
> a/ I'll ad them under "Waters instrument model" (MS:1000126). Every 
> new term will be like:
> id: MS:XXXXXXX
> name: Xevo TQ-S
> def: "Waters quadrupole based instrument." [PSI:MS]
> is_a: MS:1000126 ! Waters instrument model
>
> The terms "quadrupole", "oa-ToF" and "LC-systems" will be applied 
> correctly in each case. Is this OK?
>
> b/ Some of the new proposed instruments maybe overlap with some of the 
> old ones. I list below the four "suspects" (old terms below "Waters 
> instrument model" MS:1000126):
> Acquity UPLC FLR
> Acquity UPLC PDA
> GCT
> quattro micro
> Please Hans, check if your new terms can safely be included without 
> repeating some of the four previous members.
>
> [HV]:
>
> 'Acquity UPLC FLR' and 'Acquity UPLC PDA' are respectively a 
> fluorescence and PDA detector for 'ACQUITY UPLC' liquid chromatography 
> systems.
>
> 'GCT' and 'quattro micro' have superseded by 'GCT premier' and 'Xevo 
> TQD' mass spectrometers
>
> I therefore do not believe that there is CR term overlap/conflicts
>
>
>
> 2. Mass spectrometer
> ==================
> You propose a new "mass spectrometer type" called "Travelling wave 
> mobility separator".
> a/ Can this be correctly included under "mass spectrometer" (MS:1000293)?
> b/ Is not more appropriate to use "Travelling wave ion mobility mass 
> spectrometer" as the name of the new cv term?
> c/ Can we use Synonym: TWIMS?
> d/ We would need a short description of the new kind of mass 
> spectrometer. I've found this: "An ion mobilitymass spectrometry 
> technique based on the superimposition of travelling voltage waves on 
> a radially-confining RF voltage in agas-filled,stacked-ring ion 
> guide". Any better suggestion?
>
> [HV]:
>
> a/b/c/ - please see Matt's reply (TWIMS is an IMS variant)
> d/ see suggestion above
>
>
> 3. Software
> ===========
> Three new "software" terms to be included: MassLynx, Empower and 
> Unify. All three under "Waters software" (MS:1000694).
> a/ Please, Hans, we would need a short description of what these 
> software do (one line each is enough).
>
> [HV]:
>
> MassLynx:
> "Mass spectrometry acquisition, processing and data analysis software"
>
>
> Empower:
> "Liquid chromatography acquisition, processing, data analysis and data 
> management software"
>
> If believe that most vendors would call this CDS (chromatography data 
> software). Would there be a specific PSI-MS CV term for this?
>
>
> Unify:
> "Liquid chromatography and mass spectrometry acquisition, processing, 
> data analysis and data management software"
>
>
>
> I'll be waiting for your comments, suggestions, changes, corrections...
>
> Best
> david ovelleiro
>
>
>
> On 07/07/2011 09:05, Han...@wa... 
> <mailto:Han...@wa...>wrote:
>
>
> Dear all,
>
> Can the following instruments be added to the CV:
>
> quadrupole based:
>
> Xevo TQ-S
> Xevo TQ MS
> Xevo TQD
> Acquity TQD
> Acquity SQD
> 3100
> Quattro micro GC
>
> oa-ToF based:
>
> Synapt G2-S HDMS
> Synapt G2 HDMS
> Synapt HDMS
> Synapt G2-S MS
> Synapt G2 MS
> Synapt MS
> MALDI Synapt G2-S HDMS
> MALDI Synapt G2 HDMS
> MALDI Synapt HDMS
> MALDI Synapt G2-S MS
> MALDI Synapt G2 MS
> MALDI Synapt MS
> Xevo G2 Q-Tof
> Xevo Q-Tof
> Xevo G2 Tof
> GCT Premier
>
> LC-systems:
>
> ACQUITY UPLC I-Class
> ACQUITY UPLC
> ACQUITY UPLC H-Class
> ACQUITY UPLC H-Class Bio
> ACQUITY UPLC Systems with 2D Technology
> nanoACQUITY UPLC
> nanoACQUITY UPLC System with Technology
> nanoACQUITY UPLC with HDX Technology
> TRIZAIC UPLC nanoTile
>
> software:
>
> MassLynx
> Empower
> Unify
>
> mass spectrometer type:
>
> travelling wave mobility separator
>
>
> The vendor or brand should be listed as "Waters Corporation". Would 
> any more information be required?
>
> Thanks and best regards,
>
> Hans
>
> ===========================================================
> The information in this email is confidential, and is intended solely 
> for the addressee(s).
> Access to this email by anyone else is unauthorized and therefore 
> prohibited. If you are
> not the intended recipient you are notified that disclosing, copying, 
> distributing or taking
> any action in reliance on the contents of this information is strictly 
> prohibited and may be unlawful.
> ===========================================================
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li... 
> <mailto:Psi...@li...>
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>
>
> -- 
> David Ovelleiro
> Bioinformatician
> PRIDE Group
> Proteomics Services Team, PANDA Group
> EMBL European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, UK
> CB10 1SD
>
> ===========================================================
> The information in this email is confidential, and is intended solely for the addressee(s).
> Access to this email by anyone else is unauthorized and therefore prohibited.  If you are
> not the intended recipient you are notified that disclosing, copying, distributing or taking
> any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
> ===========================================================
>
>
>
>
> -- 
> David Ovelleiro
> Bioinformatician
> PRIDE Group
> Proteomics Services Team, PANDA Group
> EMBL European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, UK
> CB10 1SD
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev


-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD

Re: [Psidev-ms-dev] new instrument CV terms

[David O. <do...@eb...>]

Dear Hans, Matt and PSI community,

I've updated the psi-ms c.v. with the 32 new Waters instruments list.
I'll also add, in a couple of days, the next 4 c.v. terms. Please, check 
them and if you see anything wrong, write an email....

[Term]
id: MS:XXXXXXX
name: MassLynx
def: "Waters software for Mass spectrometry acquisition, processing and 
data analysis." [PSI:MS]
is_a: MS:1000694 ! Waters software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:XXXXXXX
name: Empower
def: "Waters software for liquid chromatography acquisition, processing, 
data analysis and data management." [PSI:MS]
is_a: MS:1000694 ! Waters software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:XXXXXXX
name: Unify
def: "Waters software for liquid chromatography and mass spectrometry 
acquisition, processing, data analysis and data management." [PSI:MS]
is_a: MS:1000694 ! Waters software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software


********************************** New type of mass spectrometer, TWIMS 
,son of IMS


id: MS:XXXXXXX
name: Travelling wave ion mobility mass spectrometer
def: "An ion mobility mass spectrometry technique based on the 
superimposition of travelling voltage waves on a radially-confining RF 
voltage in a gas-filled, stacked-ring ion guide." [PSI:MS]
synonym: "TWIMS" EXACT []
is_a: MS:1000261 ! ion mobility spectrometry


By the way... the "mass spectrometer" term (MS:1000293), is inside the 
purgatory...  Do you (community) really think this is the place for this 
term? Maybe is not used in the cv mappings for mzML, but, anyway.... is 
strange, at least for me, finding the "mass spectrometer" in the 
purgatory...

Best,
David















On 11/07/2011 07:28, Han...@wa... wrote:
>
> Dear David and Matt,
>
> I have provided answers 'in line' in red.
>
> I will try to find out, with regard to Matt's question, if the 
> instrument type can be retrieved from the header.txt file. The serial 
> number, i.e. JAA143, refers to a specific type and configuration so 
> this may be the easiest way forward. If an overview 'lookup type' 
> table exists, I will forward it.
>
> Would you happen to know who could be contacted for column liquid 
> chromatography and sample preparation CV terms? We are trying to 
> integrate those as well into sample forms and a repository like 
> system, but finding them is not that straightforward.
>
> Thanks and best regards,
> Hans
>
>
>
>
> Inactive hide details for "David Ovelleiro" ---08/07/2011 
> 16:45:04---Dear Hans, Thanks for sending us that intensive list of 
> te"David Ovelleiro" ---08/07/2011 16:45:04---Dear Hans, Thanks for 
> sending us that intensive list of terms.
>
> From: "David Ovelleiro" <do...@eb...>
> To: "Mass spectrometry standard development" 
> <psi...@li...>
> Cc: Han...@wa...
> Date: 08/07/2011 16:45
> Subject: Re: [Psidev-ms-dev] new instrument CV terms
>
> ------------------------------------------------------------------------
>
>
>
> Dear Hans,
>
> Thanks for sending us that intensive list of terms.
>
> Some comments addressed to you and the rest of the community:
>
> 1. Instrument list
> ===============
> You’ve provided a list of 32 new instruments to be added.
> a/ I’ll ad them under “Waters instrument model” (MS:1000126). Every 
> new term will be like:
> id: MS:XXXXXXX
> name: Xevo TQ-S
> def: "Waters quadrupole based instrument." [PSI:MS]
> is_a: MS:1000126 ! Waters instrument model
>
> The terms “quadrupole”, “oa-ToF” and “LC-systems” will be applied 
> correctly in each case. Is this OK?
>
> b/ Some of the new proposed instruments maybe overlap with some of the 
> old ones. I list below the four “suspects” (old terms below “Waters 
> instrument model” MS:1000126):
> Acquity UPLC FLR
> Acquity UPLC PDA
> GCT
> quattro micro
> Please Hans, check if your new terms can safely be included without 
> repeating some of the four previous members.
>
> [HV]:
>
> 'Acquity UPLC FLR' and 'Acquity UPLC PDA' are respectively a 
> fluorescence and PDA detector for 'ACQUITY UPLC' liquid chromatography 
> systems.
>
> 'GCT' and 'quattro micro' have superseded by 'GCT premier' and 'Xevo 
> TQD' mass spectrometers
>
> I therefore do not believe that there is CR term overlap/conflicts
>
>
>
> 2. Mass spectrometer
> ==================
> You propose a new “mass spectrometer type” called “Travelling wave 
> mobility separator”.
> a/ Can this be correctly included under “mass spectrometer” (MS:1000293)?
> b/ Is not more appropriate to use “Travelling wave ion mobility mass 
> spectrometer” as the name of the new cv term?
> c/ Can we use Synonym: TWIMS?
> d/ We would need a short description of the new kind of mass 
> spectrometer. I’ve found this: “An ion mobilitymass spectrometry 
> technique based on the superimposition of travelling voltage waves on 
> a radially-confining RF voltage in agas-filled,stacked-ring ion 
> guide”. Any better suggestion?
>
> [HV]:
>
> a/b/c/ - please see Matt's reply (TWIMS is an IMS variant)
> d/ see suggestion above
>
>
> 3. Software
> ===========
> Three new “software” terms to be included: MassLynx, Empower and 
> Unify. All three under “Waters software” (MS:1000694).
> a/ Please, Hans, we would need a short description of what these 
> software do (one line each is enough).
>
> [HV]:
>
> MassLynx:
> "Mass spectrometry acquisition, processing and data analysis software"
>
>
> Empower:
> "Liquid chromatography acquisition, processing, data analysis and data 
> management software"
>
> If believe that most vendors would call this CDS (chromatography data 
> software). Would there be a specific PSI-MS CV term for this?
>
>
> Unify:
> "Liquid chromatography and mass spectrometry acquisition, processing, 
> data analysis and data management software"
>
>
>
> I’ll be waiting for your comments, suggestions, changes, corrections…
>
> Best
> david ovelleiro
>
>
>
> On 07/07/2011 09:05, _Ha...@wa..._ 
> <mailto:Han...@wa...>wrote:
>
>
>     Dear all,
>
>     Can the following instruments be added to the CV:
>
>     quadrupole based:
>
>     Xevo TQ-S
>     Xevo TQ MS
>     Xevo TQD
>     Acquity TQD
>     Acquity SQD
>     3100
>     Quattro micro GC
>
>     oa-ToF based:
>
>     Synapt G2-S HDMS
>     Synapt G2 HDMS
>     Synapt HDMS
>     Synapt G2-S MS
>     Synapt G2 MS
>     Synapt MS
>     MALDI Synapt G2-S HDMS
>     MALDI Synapt G2 HDMS
>     MALDI Synapt HDMS
>     MALDI Synapt G2-S MS
>     MALDI Synapt G2 MS
>     MALDI Synapt MS
>     Xevo G2 Q-Tof
>     Xevo Q-Tof
>     Xevo G2 Tof
>     GCT Premier
>
>     LC-systems:
>
>     ACQUITY UPLC I-Class
>     ACQUITY UPLC
>     ACQUITY UPLC H-Class
>     ACQUITY UPLC H-Class Bio
>     ACQUITY UPLC Systems with 2D Technology
>     nanoACQUITY UPLC
>     nanoACQUITY UPLC System with Technology
>     nanoACQUITY UPLC with HDX Technology
>     TRIZAIC UPLC nanoTile
>
>     software:
>
>     MassLynx
>     Empower
>     Unify
>
>     mass spectrometer type:
>
>     travelling wave mobility separator
>
>
>     The vendor or brand should be listed as "Waters Corporation".
>     Would any more information be required?
>
>     Thanks and best regards,
>
>     Hans
>
>     ===========================================================
>     The information in this email is confidential, and is intended
>     solely for the addressee(s).
>     Access to this email by anyone else is unauthorized and therefore
>     prohibited. If you are
>     not the intended recipient you are notified that disclosing,
>     copying, distributing or taking
>     any action in reliance on the contents of this information is
>     strictly prohibited and may be unlawful.
>     ===========================================================
>
>
>     ------------------------------------------------------------------------------
>     All of the data generated in your IT infrastructure is seriously
>     valuable.
>     Why? It contains a definitive record of application performance,
>     security
>     threats, fraudulent activity, and more. Splunk takes this data and
>     makes
>     sense of it. IT sense. And common sense.
>     _http://p.sf.net/sfu/splunk-d2d-c2_
>
>
>     _______________________________________________
>     Psidev-ms-dev mailing list
>     _Ps...@li..._
>     <mailto:Psi...@li...>
>     _https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev_
>
>
>
> -- 
> David Ovelleiro
> Bioinformatician
> PRIDE Group
> Proteomics Services Team, PANDA Group
> EMBL European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, UK
> CB10 1SD
> ===========================================================
> The information in this email is confidential, and is intended solely for the addressee(s).
> Access to this email by anyone else is unauthorized and therefore prohibited.  If you are
> not the intended recipient you are notified that disclosing, copying, distributing or taking
> any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
> ===========================================================


-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD

Re: [Psidev-ms-dev] new instrument CV terms

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

Sounds great. I don't see any overlap in the instrument terms (they're all qualified differently). 
We do need the "TWIMS" clarification. If it's IMS, then it can go under "IMS" (which in turn is a 
child of mass spectrometer).

I'd also love to hear from Waters how to tell exactly what instrument was used for a .raw 
acquisition! All I've ever been able to get was the "class" of instrument, and sometimes not even 
that. If it's always supposed to be like this in the _HEADER.TXT, then what is the list of possible 
values?
$$ Instrument: JAA143 Synapt MS

-Matt


On 7/8/2011 9:44 AM, David Ovelleiro wrote:
> Dear Hans,
>
> Thanks for sending us that intensive list of terms.
>
> Some comments addressed to you and the rest of the community:
>
> 1. Instrument list
> ===============
> You’ve provided a list of 32 new instruments to be added.
> a/ I’ll ad them under “Waters instrument model” (MS:1000126). Every new term will be like:
> id: MS:XXXXXXX
> name: Xevo TQ-S
> def: "Waters quadrupole based instrument." [PSI:MS]
> is_a: MS:1000126 ! Waters instrument model
>
> The terms “quadrupole”, “oa-ToF” and “LC-systems” will be applied correctly in each case. Is this OK?
>
> b/ Some of the new proposed instruments maybe overlap with some of the old ones. I list below the
> four “suspects” (old terms below “Waters instrument model” MS:1000126):
> Acquity UPLC FLR
> Acquity UPLC PDA
> GCT
> quattro micro
> Please Hans, check if your new terms can safely be included without repeating some of the four
> previous members.
>
> 2. Mass spectrometer
> ==================
> You propose a new “mass spectrometer type” called “Travelling wave mobility separator”.
> a/ Can this be correctly included under “mass spectrometer” (MS:1000293)?
> b/ Is not more appropriate to use “Travelling wave ion mobility mass spectrometer” as the name of
> the new cv term?
> c/ Can we use Synonym: TWIMS ?
> d/ We would need a short description of the new kind of mass spectrometer. I’ve found this: “A mass
> spectrometry technique based in the superimposition of travelling voltage waves on a
> radially-confining RF voltage in the gas-filled , stacked-ring ion guide”. Any better suggestion?
>
>
> 3. Software
> ===========
> Three new “software” terms to be included: MassLynx, Empower and Unify. All three under “Waters
> software” (MS:1000694).
> a/ Please, Hans, we would need a short description of what these software do (one line each is enough).
>
>
>
> I’ll be waiting for your comments, suggestions, changes, corrections…
>
> Best
> david ovelleiro
>
>
>
> On 07/07/2011 09:05, Han...@wa... wrote:
>>
>> Dear all,
>>
>> Can the following instruments be added to the CV:
>>
>> quadrupole based:
>>
>> Xevo TQ-S
>> Xevo TQ MS
>> Xevo TQD
>> Acquity TQD
>> Acquity SQD
>> 3100
>> Quattro micro GC
>>
>> oa-ToF based:
>>
>> Synapt G2-S HDMS
>> Synapt G2 HDMS
>> Synapt HDMS
>> Synapt G2-S MS
>> Synapt G2 MS
>> Synapt MS
>> MALDI Synapt G2-S HDMS
>> MALDI Synapt G2 HDMS
>> MALDI Synapt HDMS
>> MALDI Synapt G2-S MS
>> MALDI Synapt G2 MS
>> MALDI Synapt MS
>> Xevo G2 Q-Tof
>> Xevo Q-Tof
>> Xevo G2 Tof
>> GCT Premier
>>
>> LC-systems:
>>
>> ACQUITY UPLC I-Class
>> ACQUITY UPLC
>> ACQUITY UPLC H-Class
>> ACQUITY UPLC H-Class Bio
>> ACQUITY UPLC Systems with 2D Technology
>> nanoACQUITY UPLC
>> nanoACQUITY UPLC System with Technology
>> nanoACQUITY UPLC with HDX Technology
>> TRIZAIC UPLC nanoTile
>>
>> software:
>>
>> MassLynx
>> Empower
>> Unify
>>
>> mass spectrometer type:
>>
>> travelling wave mobility separator
>>
>>
>> The vendor or brand should be listed as "Waters Corporation". Would any more information be required?
>>
>> Thanks and best regards,
>>
>> Hans

Re: [Psidev-ms-dev] new instrument CV terms

[David O. <do...@eb...>]

Dear Hans,

Thanks for sending us that intensive list of terms.

Some comments addressed to you and the rest of the community:

1. Instrument list
===============
You've provided a list of 32 new instruments to be added.
a/ I'll ad them under "Waters instrument model" (MS:1000126). Every new 
term will be like:
id: MS:XXXXXXX
name: Xevo TQ-S
def: "Waters quadrupole based instrument." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

The terms "quadrupole", "oa-ToF" and "LC-systems" will be applied 
correctly in each case. Is this OK?

b/ Some of the new proposed instruments maybe overlap with some of the 
old ones. I list below the four "suspects" (old terms below "Waters 
instrument model" MS:1000126):
Acquity UPLC FLR
Acquity UPLC PDA
GCT
quattro micro
Please Hans, check if your new terms can safely be included without 
repeating some of the four previous members.

2. Mass spectrometer
==================
You propose a new "mass spectrometer type" called "Travelling wave 
mobility separator".
a/ Can this be correctly included under "mass spectrometer" (MS:1000293)?
b/ Is not more appropriate to use "Travelling wave ion mobility mass 
spectrometer" as the name of the new cv term?
c/ Can we use Synonym: TWIMS ?
d/ We would need a short description of the new kind of mass 
spectrometer. I've found this: "A mass spectrometry technique based in 
the superimposition of travelling voltage waves on a radially-confining 
RF voltage in the gas-filled , stacked-ring ion guide". Any better 
suggestion?


3. Software
===========
Three new "software" terms to be included: MassLynx, Empower and Unify. 
All three under "Waters software" (MS:1000694).
a/ Please, Hans, we would need a short description of what these 
software do (one line each is enough).



I'll be waiting for your comments, suggestions, changes, corrections...

Best
david ovelleiro



On 07/07/2011 09:05, Han...@wa... wrote:
>
> Dear all,
>
> Can the following instruments be added to the CV:
>
> quadrupole based:
>
> Xevo TQ-S
> Xevo TQ MS
> Xevo TQD
> Acquity TQD
> Acquity SQD
> 3100
> Quattro micro GC
>
> oa-ToF based:
>
> Synapt G2-S HDMS
> Synapt G2 HDMS
> Synapt HDMS
> Synapt G2-S MS
> Synapt G2 MS
> Synapt MS
> MALDI Synapt G2-S HDMS
> MALDI Synapt G2 HDMS
> MALDI Synapt HDMS
> MALDI Synapt G2-S MS
> MALDI Synapt G2 MS
> MALDI Synapt MS
> Xevo G2 Q-Tof
> Xevo Q-Tof
> Xevo G2 Tof
> GCT Premier
>
> LC-systems:
>
> ACQUITY UPLC I-Class
> ACQUITY UPLC
> ACQUITY UPLC H-Class
> ACQUITY UPLC H-Class Bio
> ACQUITY UPLC Systems with 2D Technology
> nanoACQUITY UPLC
> nanoACQUITY UPLC System with Technology
> nanoACQUITY UPLC with HDX Technology
> TRIZAIC UPLC nanoTile
>
> software:
>
> MassLynx
> Empower
> Unify
>
> mass spectrometer type:
>
> travelling wave mobility separator
>
>
> The vendor or brand should be listed as "Waters Corporation". Would 
> any more information be required?
>
> Thanks and best regards,
>
> Hans
>
> ===========================================================
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-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD

[Psidev-ms-dev] new instrument CV terms

[<Han...@wa...>]

Dear all,

Can the following instruments be added to the CV:

quadrupole based:

 Xevo TQ-S
 Xevo TQ MS
 Xevo TQD
 Acquity TQD
 Acquity SQD
 3100
 Quattro micro GC

oa-ToF based:

 Synapt G2-S HDMS
 Synapt G2 HDMS
 Synapt HDMS
 Synapt G2-S MS
 Synapt G2 MS
 Synapt MS
 MALDI Synapt G2-S HDMS
 MALDI Synapt G2 HDMS
 MALDI Synapt HDMS
 MALDI Synapt G2-S MS
 MALDI Synapt G2 MS
 MALDI Synapt MS
 Xevo G2 Q-Tof
 Xevo Q-Tof
 Xevo G2 Tof
 GCT Premier

LC-systems:

 ACQUITY UPLC I-Class
 ACQUITY UPLC
 ACQUITY UPLC H-Class
 ACQUITY UPLC H-Class Bio
 ACQUITY UPLC Systems with 2D Technology
 nanoACQUITY UPLC
 nanoACQUITY UPLC System with Technology
 nanoACQUITY UPLC with HDX Technology
 TRIZAIC UPLC nanoTile

software:

MassLynx
Empower
Unify

mass spectrometer type:

travelling wave mobility separator


The vendor or brand should be listed as "Waters Corporation". Would any more information be required?

Thanks and best regards,

Hans
===========================================================
The information in this email is confidential, and is intended solely for the addressee(s). 
Access to this email by anyone else is unauthorized and therefore prohibited.  If you are 
not the intended recipient you are notified that disclosing, copying, distributing or taking 
any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
===========================================================

Re: [Psidev-ms-dev] [Psidev-pi-dev] PSI controlled vocabularies maintenance

[Trish W. <plw...@gm...>]

Hi Eric,

Sorry for the delay, I was out of town. Anytime in the next two weeks works
for me.

For loading ontologies, there is a nightly pull process and we are pulling
PSI-MS from:
http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obofor
PSI-MS. There was a small interruption in the regular process due to
some needed code updates a few weeks back, but the nightly update process is
running again.

Trish

2011/6/7 Eric Deutsch <Eri...@sy...>

> Hi Trish, I don’t know if you got a response off list, but I’ll assume not.
> We haven’t really had a lot of work on the CV beyond dumping in terms of
> late, but maybe now that David is going to put a lot of work into the CV,
> this make sense. David is away right now, but maybe once he returns, we can
> schedule a demo to see if it might work for him and us. So this would be in
> about a week or two.
>
>
>
> I was browsing out CV at BioPortal today after failing to get OBO-Edit
> working on my desktop. BioPortal really is quite nice, I like it! Our CV was
> a little out of date, not very, but just a few weeks. Can you remind me what
> the mechanism is for updating the CV? Can you pull it out of CVS nightly or
> something like that?
>
>
>
> Regards,
>
> Eric
>
>
>
>
>
> *From:* Trish Whetzel [mailto:plw...@gm...]
> *Sent:* Tuesday, May 31, 2011 3:17 PM
> *To:* Steffen Neumann
> *Cc:* psi...@li...; Mass spectrometry standard
> development
> *Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] PSI controlled vocabularies
> maintenance
>
>
>
> Hi all,
>
>
>
> I'm the Outreach Coordinator with the National Center for Biomedical
> Ontology (NCBO) and have worked on psi-ms in the past. At NCBO we have a
> system for proposing new terms and adding comments for the ontology
> maintainers to review and discuss with the submitter along with other
> features for ontology curation. I'd love to demo the system to your group.
> Does this sound of interest?
>
>
>
> Best regards,
>
> Trish
>
>
> Sent from my iPhone
>
>
> On May 31, 2011, at 3:21 PM, Steffen Neumann <sne...@ip...>
> wrote:
>
> Hi,
>
> On Tue, 2011-05-31 at 17:04 +0100, David Ovelleiro wrote:
>
> Maybe it makes not much sense for people who is registered in the
>
> mailing lists to use it, and it also seems that is not a prodigy of
>
> performance....
>
>
> So the form for CV terms doesn't really work,
>
> On Tue, 2011-05-31 at 12:55 +0100, David Ovelleiro wrote:
> ...
>
> The proposals/changes/.... will be included also in the googleDoc
>
> located there (starting in some hours):
>
>
> https://spreadsheets.google.com/pub?hl=en_US&hl=en_US&key=0Av19CsTVDoOQdENWSmJDS3ZfN2tPdEhaaldzcWVNY3c&output=html
>
>
> but I think the spreadsheet is hardly maintainable
> in the long run. What about the approach to use a (bug) tracker,
> as shown (mostly by the psi-pi folks) for several of the mz* formats ?
>
> There could be types for reparenting, definition editing, adding,
> deleting, ... Updates would go the the (which ?) list etc.
> Commits could include which issue was fixed etc.
>
> Yours,
> Steffen
>
> --
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                  +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
>
>
>
>
> ------------------------------------------------------------------------------
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>
>

Re: [Psidev-ms-dev] Authentication

[Steffen N. <sne...@ip...>]

Hi,

On Wed, 2011-06-08 at 22:23 -0700, Eric Deutsch wrote:
> 2)      This seems like an awful lot of terms, I wonder if really all
> of these are necessary.
Indeed, they break down the cert information into individual terms.

So software has to break down a cert into these parts to put them into 
the cvParams, and then for validation another software will have 
to collect them back together for verification. An alternative might be 
to leave the cert intact in some form of formatted ASCII (x509, PEM, whatever*)
which is readable/parsable for the authentication libraries used.

Yours,
Steffen

(*) Not sure whether these formats are applicable or the right choice, 
    just given as examples.

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

Re: [Psidev-ms-dev] Authentication

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

 Alfs_Signaturtext

Hi Alfons, thank you for putting this together. I have a couple thoughts:



1)      Have you checked to see if there are already other ontologies that
include this information?

2)      This seems like an awful lot of terms, I wonder if really all of
these are necessary. The more terms we have, the more complicated it is for
software to use them. We might be better off coming up with a minimal set of
terms and recommend how to use them.

3)      Terms like “E” seem somewhat poorly named. I guess that this is the
way it can appear in the certificates, but it seems weak for the CV term.
Maybe it’s fine.

4)      The really useful part will be to get some example files that
implement the terms and perhaps more importantly some software that can
write and read the authentication information and do something sensible with
it. Starting out with add all this to the mzML wrapper schema for indexing
seems like the best place to start.



Regards,

Eric





*From:* Alf. Hester [mailto:Alf...@an...]
*Sent:* Wednesday, June 08, 2011 2:03 AM
*To:* psi...@li...
*Cc:* Eric Deutsch; psi...@li...
*Subject:* Authentication



Dear all,

here are the cv params which are available for authentication "addon" to our
XML-formats.
I derived the names of the parameter from "Certificate Viewer" of Firefox
(English Version)

If you want to have a look at this in Firefox,
you can find your installed certificates and the terms they use there in
Firefox (Version 4.0.1) as follows:
Tools/Options
then in the Options window
Advanced - Encryption
Button "View Certificates"
"Authorities" contains some pre-installed certificates, just select one and
press button "View"

Please let me know your ideas, comments, ...

Best regards
Alfons :-)


format-version: 1.2
date: 13:12:2010 10:00
saved-by: Alf. Hester
auto-generated-by: OBO-Edit 2.1-beta6
default-namespace: default_namespace


[Term]
id: AUTH:0000000
name: public key method
namespace: Authentication
def: "Refers to the public key method or methods." [COMPUTIS:AUTH
"Authentication also used in Computis"]
created_by: ahester
creation_date: 2010-10-05T09:19:14Z

[Term]
id: AUTH:0000001
name: checksums
namespace: Authentication
def: "Checksums which are created by different checksum algorithms. (A
synonym for checksum is hash value and sometimes thumbprint)."
[COMPUTIS:AUTH "Authentication also used in Computis"]
created_by: Alf. Hester
creation_date: 2010-10-05T09:47:11Z

[Term]
id: AUTH:0000002
name: certificate
namespace: Authentication
def: "Contains parameters which belongs to a certificate." [COMPUTIS:AUTH
"Authentication also used in Computis"]
created_by: Alf. Hester
creation_date: 2010-10-05T09:52:03Z

[Term]
id: AUTH:0000003
name: version
namespace: Authentication
def: "Version of the certificate." [COMPUTIS:AUTH "Authentication also used
in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T09:55:38Z

[Term]
id: AUTH:0000004
name: serial_number
namespace: Authentication
def: "Serial number of the certificate." [COMPUTIS:AUTH "Authentication also
used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T09:56:17Z

[Term]
id: AUTH:0000005
name: certificate_signature_algorithm
namespace: Authentication
def: "The algorithms used to sign the certificate (e.g. PKCS #1 SHA-1 With
RSA Encryption)." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T09:57:04Z

[Term]
id: AUTH:0000006
name: issuer
namespace: Authentication
def: "Data about issuer of the certificate." [COMPUTIS:AUTH "Authentication
also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T10:05:58Z

[Term]
id: AUTH:0000007
name: E
namespace: Authentication
def: "Email address of issuer." [COMPUTIS:AUTH "Authentication also used in
Computis"]
is_a: AUTH:0000006 ! issuer
created_by: Alf. Hester
creation_date: 2010-10-05T10:06:46Z

[Term]
id: AUTH:0000008
name: CN
namespace: Authentication
def: "Name of the issuer of the certificate." [COMPUTIS:AUTH "Authentication
also used in Computis"]
is_a: AUTH:0000006 ! issuer
created_by: Alf. Hester
creation_date: 2010-10-05T10:07:28Z

[Term]
id: AUTH:0000009
name: OU
namespace: Authentication
def: "URL of the issuer of the certificate." [COMPUTIS:AUTH "Authentication
also used in Computis"]
is_a: AUTH:0000006 ! issuer
created_by: Alf. Hester
creation_date: 2010-10-05T10:08:03Z

[Term]
id: AUTH:0000010
name: O
namespace: Authentication
def: "Level of authority of the issuer. (e.g. The level \"Root CA\" means
the issuer is authorised to emit root certificates)." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000006 ! issuer
created_by: Alf. Hester
creation_date: 2010-10-05T10:08:32Z

[Term]
id: AUTH:0000011
name: validity
namespace: Authentication
def: "Contains information about the time frame a certificate is allowed to
be used for signing." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T10:14:54Z

[Term]
id: AUTH:0000012
name: not_before
namespace: Authentication
def: "The point of time the usability of the certificate begins."
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000011 ! validity
created_by: Alf. Hester
creation_date: 2010-10-05T10:17:12Z

[Term]
id: AUTH:0000013
name: not_after
namespace: Authentication
def: "The point of time the usability of the certificate ends."
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000011 ! validity
created_by: Alf. Hester
creation_date: 2010-10-05T10:18:29Z

[Term]
id: AUTH:0000014
name: subject
namespace: Authentication
def: "The person (or institution, machine, ... ) which is the owner of the
certificate." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T10:19:32Z

[Term]
id: AUTH:0000015
name: SE
namespace: Authentication
def: "Email address of the certificate owner." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000014 ! subject
created_by: Alf. Hester
creation_date: 2010-10-05T10:21:34Z

[Term]
id: AUTH:0000016
name: SCN
namespace: Authentication
def: "Name of the certificate." [COMPUTIS:AUTH "Authentication also used in
Computis"]
is_a: AUTH:0000014 ! subject
created_by: Alf. Hester
creation_date: 2010-10-05T10:22:29Z

[Term]
id: AUTH:0000017
name: subject_public_key_info
namespace: Authentication
def: "Information of the public key of the certificate owner."
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T10:23:33Z

[Term]
id: AUTH:0000018
name: subject_public_key_algorithm
namespace: Authentication
def: "Algorithm used to create the public key of certificate owner."
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000017 ! subject_public_key_info
created_by: Alf. Hester
creation_date: 2010-10-05T10:24:18Z

[Term]
id: AUTH:0000019
name: subjects_public_key
namespace: Authentication
def: "The public key of the owner of the certificate itself." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000017 ! subject_public_key_info
created_by: Alf. Hester
creation_date: 2010-10-05T10:25:15Z

[Term]
id: AUTH:0000020
name: extensions
namespace: Authentication
def: "Extensions of the certificate." [COMPUTIS:AUTH "Authentication also
used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T10:26:12Z

[Term]
id: AUTH:0000021
name: certificate_base_constraints
namespace: Authentication
def: "This value contains constraints for the certificate." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000020 ! extensions
created_by: Alf. Hester
creation_date: 2010-10-05T10:26:51Z

[Term]
id: AUTH:0000022
name: netscape_certificate_comment
namespace: Authentication
def: "Comment on the certificate provided e.g. by Seemonkey and
Thunderbird." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000020 ! extensions
created_by: Alf. Hester
creation_date: 2010-10-05T11:15:58Z

[Term]
id: AUTH:0000023
name: extended_key_usage
namespace: Authentication
def: "Information about usage of the extended usage of the key."
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000020 ! extensions
created_by: Alf. Hester
creation_date: 2010-10-05T11:17:40Z

[Term]
id: AUTH:0000024
name: authority_information_access
namespace: Authentication
def: "URI address where certificate can be verified." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000020 ! extensions
created_by: Alf. Hester
creation_date: 2010-10-05T11:22:18Z

[Term]
id: AUTH:0000025
name: certificate_subject_alt_name
namespace: Authentication
def: "Alternative name of the owner of the certificate." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000020 ! extensions
created_by: Alf. Hester
creation_date: 2010-10-05T11:24:36Z

[Term]
id: AUTH:0000026
name: certificate_signature_value
namespace: Authentication
def: "Usually a part of the signature of the certificate." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T11:28:20Z

[Term]
id: AUTH:0000027
name: checksums_plain
namespace: Authentication
def: "Plain checksums derived directly from the checksum calculation
algorithm." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000001 ! checksums
created_by: Alf. Hester
creation_date: 2010-10-05T11:36:55Z

[Term]
id: AUTH:0000028
name: checksums_ciphered
namespace: Authentication
def: "The ciphered versions of the corresponding plain checksums from
checksums_plain." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000001 ! checksums
created_by: Alf. Hester
creation_date: 2010-10-05T11:45:20Z

[Term]
id: AUTH:0000029
name: c_Haval_256
namespace: Authentication
def: "A ciphered checksum derived from Haval 256 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:46:18Z

[Term]
id: AUTH:0000030
name: c_MD4
namespace: Authentication
def: "A ciphered checksum derived from MD 4 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:47:09Z

[Term]
id: AUTH:0000031
name: c_MD5
namespace: Authentication
def: "The ciphered checksum derived from MD5 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:47:34Z

[Term]
id: AUTH:0000032
name: c_RipeMD_128
namespace: Authentication
def: "The ciphered checksum derived from RipeMD-128 algorithm."
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:49:34Z

[Term]
id: AUTH:0000033
name: c_RipeMD_160
namespace: Authentication
def: "The ciphered checksum derived from RipeMD-160 algorithm."
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:50:13Z

[Term]
id: AUTH:0000034
name: c_SHA1
namespace: Authentication
def: "The ciphered checksum derived from SHA-1 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:50:46Z

[Term]
id: AUTH:0000035
name: c_SHA256
namespace: Authentication
def: "The ciphered checksum derived from SHA-256 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:51:12Z

[Term]
id: AUTH:0000036
name: c_SHA384
namespace: Authentication
def: "The ciphered checksum derived from SHA-384 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:51:41Z

[Term]
id: AUTH:0000037
name: c_SHA512
namespace: Authentication
def: "The ciphered checksum derived from SHA-512 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:52:30Z

[Term]
id: AUTH:0000038
name: c_Tiger
namespace: Authentication
def: "The ciphered checksum derived from Tiger algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:52:58Z

[Term]
id: AUTH:0000039
name: p_Haval_256
namespace: Authentication
def: "The checksum derived from algorithm." [COMPUTIS:AUTH "Authentication
also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:53:21Z

[Term]
id: AUTH:0000040
name: p_MD4
namespace: Authentication
def: "The checksum derived from MD4 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:53:50Z

[Term]
id: AUTH:0000041
name: p_MD5
namespace: Authentication
def: "The checksum derived from MD5 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:54:15Z

[Term]
id: AUTH:0000042
name: p_RipeMD_128
namespace: Authentication
def: "The checksum derived from RipeMD-128 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:54:36Z

[Term]
id: AUTH:0000043
name: p_RipeMD_160
namespace: Authentication
def: "The checksum derived from RipeMD-160 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:55:01Z

[Term]
id: AUTH:0000044
name: p_SHA1
namespace: Authentication
def: "The checksum derived from SHA-1 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:55:35Z

[Term]
id: AUTH:0000045
name: p_SHA256
namespace: Authentication
def: "The checksum derived from SHA-256 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:55:58Z

[Term]
id: AUTH:0000046
name: p_SHA384
namespace: Authentication
def: "The checksum derived from SHA-384 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:56:23Z

[Term]
id: AUTH:0000047
name: p_SHA512
namespace: Authentication
def: "The checksum derived from SHA-512 algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:56:46Z

[Term]
id: AUTH:0000048
name: p_Tiger
namespace: Authentication
def: "The checksum derived from Tiger algorithm." [COMPUTIS:AUTH
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:57:13Z

[Term]
id: AUTH:0000049
name: key_open
namespace: Authentication
def: "This specifies the open key, also referred to as the public key."
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-18T10:06:50Z

[Term]
id: AUTH:0000050
name: key_RSA
namespace: Authentication
def: "This item is the open (public) key acquired by RSA algorithm."
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000000 ! public key method
created_by: Alf. Hester
creation_date: 2010-10-18T10:19:00Z

[Term]
id: AUTH:0000051
name: key_ElGamal
namespace: Authentication
def: "This item refers to the open (public) key calculated by ElGamal
algorithm." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000000 ! public key method
created_by: Alf. Hester
creation_date: 2010-10-18T10:21:35Z

-- 

*Alfons Hester*

*(Dipl-Math.)***



Institut für anorganische und analytische Chemie

Justus-Liebig-Universität Giessen

Schubertstraße 60 / Haus 16



35392 Gießen

*Alfons Hester*

*(Dipl-Math.)***



Institute of Inorganic and Analytical Chemistry

Justus-Liebig-University Giessen (Germany)

Schubertstraße 60 / Building 16



35392 Giessen



e-mail: Alf...@an...
<MailTo:Alf...@an...>

Tel:    +49 641 99 34821

Fax:    +49 641 99 34809

Skype:  Sophoklos





 \ <{
  \| /7                   I+I+I=II /\
 __|/__                              \ c")
 \    /                              ;-/\>
  \__/                                 ||

[Psidev-ms-dev] Authentication

[Alf. H. <Alf...@an...>]

Dear all,

here are the cv params which are available for authentication "addon" to 
our XML-formats.
I derived the names of the parameter from "Certificate Viewer" of 
Firefox (English Version)

If you want to have a look at this in Firefox,
you can find your installed certificates and the terms they use there in 
Firefox (Version 4.0.1) as follows:
Tools/Options
then in the Options window
Advanced - Encryption
Button "View Certificates"
"Authorities" contains some pre-installed certificates, just select one 
and press button "View"

Please let me know your ideas, comments, ...

Best regards
Alfons :-)


format-version: 1.2
date: 13:12:2010 10:00
saved-by: Alf. Hester
auto-generated-by: OBO-Edit 2.1-beta6
default-namespace: default_namespace


[Term]
id: AUTH:0000000
name: public key method
namespace: Authentication
def: "Refers to the public key method or methods." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
created_by: ahester
creation_date: 2010-10-05T09:19:14Z

[Term]
id: AUTH:0000001
name: checksums
namespace: Authentication
def: "Checksums which are created by different checksum algorithms. (A 
synonym for checksum is hash value and sometimes thumbprint)." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
created_by: Alf. Hester
creation_date: 2010-10-05T09:47:11Z

[Term]
id: AUTH:0000002
name: certificate
namespace: Authentication
def: "Contains parameters which belongs to a certificate." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
created_by: Alf. Hester
creation_date: 2010-10-05T09:52:03Z

[Term]
id: AUTH:0000003
name: version
namespace: Authentication
def: "Version of the certificate." [COMPUTIS:AUTH "Authentication also 
used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T09:55:38Z

[Term]
id: AUTH:0000004
name: serial_number
namespace: Authentication
def: "Serial number of the certificate." [COMPUTIS:AUTH "Authentication 
also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T09:56:17Z

[Term]
id: AUTH:0000005
name: certificate_signature_algorithm
namespace: Authentication
def: "The algorithms used to sign the certificate (e.g. PKCS #1 SHA-1 
With RSA Encryption)." [COMPUTIS:AUTH "Authentication also used in 
Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T09:57:04Z

[Term]
id: AUTH:0000006
name: issuer
namespace: Authentication
def: "Data about issuer of the certificate." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T10:05:58Z

[Term]
id: AUTH:0000007
name: E
namespace: Authentication
def: "Email address of issuer." [COMPUTIS:AUTH "Authentication also used 
in Computis"]
is_a: AUTH:0000006 ! issuer
created_by: Alf. Hester
creation_date: 2010-10-05T10:06:46Z

[Term]
id: AUTH:0000008
name: CN
namespace: Authentication
def: "Name of the issuer of the certificate." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000006 ! issuer
created_by: Alf. Hester
creation_date: 2010-10-05T10:07:28Z

[Term]
id: AUTH:0000009
name: OU
namespace: Authentication
def: "URL of the issuer of the certificate." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000006 ! issuer
created_by: Alf. Hester
creation_date: 2010-10-05T10:08:03Z

[Term]
id: AUTH:0000010
name: O
namespace: Authentication
def: "Level of authority of the issuer. (e.g. The level \"Root CA\" 
means the issuer is authorised to emit root certificates)." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000006 ! issuer
created_by: Alf. Hester
creation_date: 2010-10-05T10:08:32Z

[Term]
id: AUTH:0000011
name: validity
namespace: Authentication
def: "Contains information about the time frame a certificate is allowed 
to be used for signing." [COMPUTIS:AUTH "Authentication also used in 
Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T10:14:54Z

[Term]
id: AUTH:0000012
name: not_before
namespace: Authentication
def: "The point of time the usability of the certificate begins." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000011 ! validity
created_by: Alf. Hester
creation_date: 2010-10-05T10:17:12Z

[Term]
id: AUTH:0000013
name: not_after
namespace: Authentication
def: "The point of time the usability of the certificate ends." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000011 ! validity
created_by: Alf. Hester
creation_date: 2010-10-05T10:18:29Z

[Term]
id: AUTH:0000014
name: subject
namespace: Authentication
def: "The person (or institution, machine, ... ) which is the owner of 
the certificate." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T10:19:32Z

[Term]
id: AUTH:0000015
name: SE
namespace: Authentication
def: "Email address of the certificate owner." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000014 ! subject
created_by: Alf. Hester
creation_date: 2010-10-05T10:21:34Z

[Term]
id: AUTH:0000016
name: SCN
namespace: Authentication
def: "Name of the certificate." [COMPUTIS:AUTH "Authentication also used 
in Computis"]
is_a: AUTH:0000014 ! subject
created_by: Alf. Hester
creation_date: 2010-10-05T10:22:29Z

[Term]
id: AUTH:0000017
name: subject_public_key_info
namespace: Authentication
def: "Information of the public key of the certificate owner." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T10:23:33Z

[Term]
id: AUTH:0000018
name: subject_public_key_algorithm
namespace: Authentication
def: "Algorithm used to create the public key of certificate owner." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000017 ! subject_public_key_info
created_by: Alf. Hester
creation_date: 2010-10-05T10:24:18Z

[Term]
id: AUTH:0000019
name: subjects_public_key
namespace: Authentication
def: "The public key of the owner of the certificate itself." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000017 ! subject_public_key_info
created_by: Alf. Hester
creation_date: 2010-10-05T10:25:15Z

[Term]
id: AUTH:0000020
name: extensions
namespace: Authentication
def: "Extensions of the certificate." [COMPUTIS:AUTH "Authentication 
also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T10:26:12Z

[Term]
id: AUTH:0000021
name: certificate_base_constraints
namespace: Authentication
def: "This value contains constraints for the certificate." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000020 ! extensions
created_by: Alf. Hester
creation_date: 2010-10-05T10:26:51Z

[Term]
id: AUTH:0000022
name: netscape_certificate_comment
namespace: Authentication
def: "Comment on the certificate provided e.g. by Seemonkey and 
Thunderbird." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000020 ! extensions
created_by: Alf. Hester
creation_date: 2010-10-05T11:15:58Z

[Term]
id: AUTH:0000023
name: extended_key_usage
namespace: Authentication
def: "Information about usage of the extended usage of the key." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000020 ! extensions
created_by: Alf. Hester
creation_date: 2010-10-05T11:17:40Z

[Term]
id: AUTH:0000024
name: authority_information_access
namespace: Authentication
def: "URI address where certificate can be verified." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000020 ! extensions
created_by: Alf. Hester
creation_date: 2010-10-05T11:22:18Z

[Term]
id: AUTH:0000025
name: certificate_subject_alt_name
namespace: Authentication
def: "Alternative name of the owner of the certificate." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000020 ! extensions
created_by: Alf. Hester
creation_date: 2010-10-05T11:24:36Z

[Term]
id: AUTH:0000026
name: certificate_signature_value
namespace: Authentication
def: "Usually a part of the signature of the certificate." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-05T11:28:20Z

[Term]
id: AUTH:0000027
name: checksums_plain
namespace: Authentication
def: "Plain checksums derived directly from the checksum calculation 
algorithm." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000001 ! checksums
created_by: Alf. Hester
creation_date: 2010-10-05T11:36:55Z

[Term]
id: AUTH:0000028
name: checksums_ciphered
namespace: Authentication
def: "The ciphered versions of the corresponding plain checksums from 
checksums_plain." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000001 ! checksums
created_by: Alf. Hester
creation_date: 2010-10-05T11:45:20Z

[Term]
id: AUTH:0000029
name: c_Haval_256
namespace: Authentication
def: "A ciphered checksum derived from Haval 256 algorithm." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:46:18Z

[Term]
id: AUTH:0000030
name: c_MD4
namespace: Authentication
def: "A ciphered checksum derived from MD 4 algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:47:09Z

[Term]
id: AUTH:0000031
name: c_MD5
namespace: Authentication
def: "The ciphered checksum derived from MD5 algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:47:34Z

[Term]
id: AUTH:0000032
name: c_RipeMD_128
namespace: Authentication
def: "The ciphered checksum derived from RipeMD-128 algorithm." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:49:34Z

[Term]
id: AUTH:0000033
name: c_RipeMD_160
namespace: Authentication
def: "The ciphered checksum derived from RipeMD-160 algorithm." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:50:13Z

[Term]
id: AUTH:0000034
name: c_SHA1
namespace: Authentication
def: "The ciphered checksum derived from SHA-1 algorithm." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:50:46Z

[Term]
id: AUTH:0000035
name: c_SHA256
namespace: Authentication
def: "The ciphered checksum derived from SHA-256 algorithm." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:51:12Z

[Term]
id: AUTH:0000036
name: c_SHA384
namespace: Authentication
def: "The ciphered checksum derived from SHA-384 algorithm." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:51:41Z

[Term]
id: AUTH:0000037
name: c_SHA512
namespace: Authentication
def: "The ciphered checksum derived from SHA-512 algorithm." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:52:30Z

[Term]
id: AUTH:0000038
name: c_Tiger
namespace: Authentication
def: "The ciphered checksum derived from Tiger algorithm." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000028 ! checksums_ciphered
created_by: Alf. Hester
creation_date: 2010-10-05T11:52:58Z

[Term]
id: AUTH:0000039
name: p_Haval_256
namespace: Authentication
def: "The checksum derived from algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:53:21Z

[Term]
id: AUTH:0000040
name: p_MD4
namespace: Authentication
def: "The checksum derived from MD4 algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:53:50Z

[Term]
id: AUTH:0000041
name: p_MD5
namespace: Authentication
def: "The checksum derived from MD5 algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:54:15Z

[Term]
id: AUTH:0000042
name: p_RipeMD_128
namespace: Authentication
def: "The checksum derived from RipeMD-128 algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:54:36Z

[Term]
id: AUTH:0000043
name: p_RipeMD_160
namespace: Authentication
def: "The checksum derived from RipeMD-160 algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:55:01Z

[Term]
id: AUTH:0000044
name: p_SHA1
namespace: Authentication
def: "The checksum derived from SHA-1 algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:55:35Z

[Term]
id: AUTH:0000045
name: p_SHA256
namespace: Authentication
def: "The checksum derived from SHA-256 algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:55:58Z

[Term]
id: AUTH:0000046
name: p_SHA384
namespace: Authentication
def: "The checksum derived from SHA-384 algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:56:23Z

[Term]
id: AUTH:0000047
name: p_SHA512
namespace: Authentication
def: "The checksum derived from SHA-512 algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:56:46Z

[Term]
id: AUTH:0000048
name: p_Tiger
namespace: Authentication
def: "The checksum derived from Tiger algorithm." [COMPUTIS:AUTH 
"Authentication also used in Computis"]
is_a: AUTH:0000027 ! checksums_plain
created_by: Alf. Hester
creation_date: 2010-10-05T11:57:13Z

[Term]
id: AUTH:0000049
name: key_open
namespace: Authentication
def: "This specifies the open key, also referred to as the public key." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000002 ! certificate
created_by: Alf. Hester
creation_date: 2010-10-18T10:06:50Z

[Term]
id: AUTH:0000050
name: key_RSA
namespace: Authentication
def: "This item is the open (public) key acquired by RSA algorithm." 
[COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000000 ! public key method
created_by: Alf. Hester
creation_date: 2010-10-18T10:19:00Z

[Term]
id: AUTH:0000051
name: key_ElGamal
namespace: Authentication
def: "This item refers to the open (public) key calculated by ElGamal 
algorithm." [COMPUTIS:AUTH "Authentication also used in Computis"]
is_a: AUTH:0000000 ! public key method
created_by: Alf. Hester
creation_date: 2010-10-18T10:21:35Z


-- 

Alfons Hester
(Dipl-Math.)

Institut für anorganische und analytische Chemie	
Justus-Liebig-Universität Giessen
Schubertstraße 60 / Haus 16

35392 Gießen

	

Alfons Hester
(Dipl-Math.)

Institute of Inorganic and Analytical Chemistry
Justus-Liebig-University Giessen (Germany)
Schubertstraße 60 / Building 16

35392 Giessen
       

e-mail:Alf...@an...  <MailTo:Alf...@an...>
Tel:    +49 641 99 34821
Fax:    +49 641 99 34809
Skype:  Sophoklos

       

	 \ <{
   \| /7                   I+I+I=II /\
  __|/__                              \ c")
  \    /                              ;-/\>
   \__/                                 ||

Re: [Psidev-ms-dev] [Psidev-pi-dev] PSI controlled vocabularies maintenance

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

Hi Trish, I don’t know if you got a response off list, but I’ll assume not.
We haven’t really had a lot of work on the CV beyond dumping in terms of
late, but maybe now that David is going to put a lot of work into the CV,
this make sense. David is away right now, but maybe once he returns, we can
schedule a demo to see if it might work for him and us. So this would be in
about a week or two.



I was browsing out CV at BioPortal today after failing to get OBO-Edit
working on my desktop. BioPortal really is quite nice, I like it! Our CV was
a little out of date, not very, but just a few weeks. Can you remind me what
the mechanism is for updating the CV? Can you pull it out of CVS nightly or
something like that?



Regards,

Eric





*From:* Trish Whetzel [mailto:plw...@gm...]
*Sent:* Tuesday, May 31, 2011 3:17 PM
*To:* Steffen Neumann
*Cc:* psi...@li...; Mass spectrometry standard
development
*Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] PSI controlled vocabularies
maintenance



Hi all,



I'm the Outreach Coordinator with the National Center for Biomedical
Ontology (NCBO) and have worked on psi-ms in the past. At NCBO we have a
system for proposing new terms and adding comments for the ontology
maintainers to review and discuss with the submitter along with other
features for ontology curation. I'd love to demo the system to your group.
Does this sound of interest?



Best regards,

Trish


Sent from my iPhone


On May 31, 2011, at 3:21 PM, Steffen Neumann <sne...@ip...> wrote:

Hi,

On Tue, 2011-05-31 at 17:04 +0100, David Ovelleiro wrote:

Maybe it makes not much sense for people who is registered in the

mailing lists to use it, and it also seems that is not a prodigy of

performance....


So the form for CV terms doesn't really work,

On Tue, 2011-05-31 at 12:55 +0100, David Ovelleiro wrote:
...

The proposals/changes/.... will be included also in the googleDoc

located there (starting in some hours):

https://spreadsheets.google.com/pub?hl=en_US&hl=en_US&key=0Av19CsTVDoOQdENWSmJDS3ZfN2tPdEhaaldzcWVNY3c&output=html


but I think the spreadsheet is hardly maintainable
in the long run. What about the approach to use a (bug) tracker,
as shown (mostly by the psi-pi folks) for several of the mz* formats ?

There could be types for reparenting, definition editing, adding,
deleting, ... Updates would go the the (which ?) list etc.
Commits could include which issue was fixed etc.

Yours,
Steffen

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                 +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409



------------------------------------------------------------------------------
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Installation's a snap, and flexible recovery options mean your data is safe,
secure and there when you need it. Data protection magic?
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Re: [Psidev-ms-dev] PSI-MS updates today and SOP for commit with OBO-Edit

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

Sorry for the slow catchup, but this is excellent, David, many thanks for
tidying this all up! All these changes and suggestions are great.

Regards,
Eric


> -----Original Message-----
> From: David Ovelleiro [mailto:do...@eb...]
> Sent: Thursday, June 02, 2011 7:18 AM
> To: psi...@li...; Mass spectrometry standard
> development
> Subject: [Psidev-ms-dev] PSI-MS updates today and SOP for commit with
> OBO-Edit
>
> Dear all,
>
> PSI-MS updates today
> ====================
> Maybe you've realised that five new versions of the psi-ms file have
> been released today.
> All new versions are related to several errors in the CV file that made
> impossible the normal commit workflow with OBO-Edit.
> All this new versions have been created editing manually the obo file,
> something that is fine if you know exactly what you are doing... I'll
> describe the motivations for the changes:
>
> Revision 1.161 -> Changes in ID's of two ProteomeDiscoverer terms with
> 8
> digits instead of 7 (MS:10001664 and MS:10001665).
> Problem: Taking these terms into account, OBO-Edit would have used
> MS:10001666 as the new term.
>
> Revision 1.162 -> Changes in ID's of one duplicated ProteomeDiscoverer
> term MS:1001497 instead of MS:1001597 (the original MS:1001597 was
> "spectrum sub-set protein")
> Problem: using the same ID for two terms produces an strange "merged"
> term when you save it with OBO-Edit (among other problems, I guess....)
>
> Revision 1.163 -> Replaced in definition of 3 terms [PSI-MS] by the
> correct form, [PSI:MS]
> Problem: the save with OBO-Edit was corrupted
>
> Revision 1.164 -> Substitution in three cases of the deprecated
> expression <exact_synonym: "foo" []> by <synonym: "foo" EXACT []>
> Problem: not really a problem... OBO-Edit changes automatically to new
> form
>
> Revision 1.165 -> Correction of wrong syntax in several xref
> descriptions ("32-bit integer", "64-bit integer" and "null-terminated
> ASCII string"): the comments use <"foo"> format, not <!foo>
> Problem: The comments were lost when saving with OBO-Edit
>
> These mistakes are not tragic by themselves, but produced loss of data
> in some cases and the malfunction of OBO-Edit. I'd suggest the use of
> OBO-Edit, if not for the changes in the CV, at least for checking that
> they are correctly implemented.
>
> I hope that the new version is OK for everybody.
>
>
> SOP for commit with OBO-Edit
> ============================
> I've written a new/updated version of the SOP for committing new
> versions of the CV with OBO-Edit (using the file "oboedit_notes.txt" in
> the repository). I'll attach the contents of this little manual at the
> end of this mail. If everything is OK, I'll commit the changes to the
> PSI repository. Maybe you'll want to try the "Save as" using OBO-Edit
> and check that everything is fine. In my computer, everything worked.
> The only changes that will be introduced in the CV if you follow the
> SOP
> are:
> 1/ Reordering of the lines inside every item
> 2/ Removing blank lines inside items
> 3/ Correcting wrong/incomplete/inaccurate relationships (e.g.
> MS:1000548)
> 4/ Loss of the description of the "replaced by" in obsolete terms (this
> is the only loss of information....
>    in the line "replaced_by: MS:1000336 ! neutral loss", the
> description
> "neutral loss" is lost (the ID is kept))
>
> If everything is fine for you, tomorrow,  I'll commit a new version of
> the CV "OBO-Edit-compatible" (and the submitting SOP also).
>
> Best Regards,
> David
>
> PS: the SOP
>
>
> =======================================================================
> =========
> Notes on using OBO-Edit (Updated by D.Ovelleiro June 2011, OBO-Edit
> version 2.1 beta13)
> -----------------------
>
> Saving psi-ms.obo from OBO-Edit is tricky.
>
> Before checking in psi-ms.obo, please verify the following:
> 1) contains the import statement
> 2) does not contain terms from the Unit Ontology or other ontologies
> 3) contains the MS relationships (e.g. part_of, has_units)
>
> psi-ms.obo imports the Unit Ontology (unit.obo) via an import statement
> at the top of the file:
> import: unit.obo
> We would really like to do the following:
> import:
> http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/un
> it.obo
> But OBO-Edit replaces this by "ontology: pato"
>
>
>
> We have not figured out yet how to accomplish #1 from within OBO-Edit,
> so the whole header
> must be added manually after saving with OBO-Edit.
>
> To save only the MS terms from OBO-Edit:
> 1) File/Save As
> 2) Select Advanced...
> 3) Select "OBO_1_2" for "Output Type"
> 4) + (add new "Stored adapter settings" profile)
> 5) "Save path:" (with browse button) for the output psi-ms.obo file
> 6) Check "Filter terms"
> 7) In "Object filtering" choose -> Fin terms that:"have" a:"Namespace"
> that:"contains" the value:"MS"
> 8) check "Allow dangling parents" (allows has_units UO:xxxxxxx)
> 9) check "include is_a closure for cross-referenced terms"
>    (allows the terms from unit.obo to be included
>    as relationship, e.g.: has_units UO:0000166 ! parts per notation)
> 10) Root selection algorithm :"GREEDY"
> 11) ID Rules: "Don't write ID rules"
> 12) Press Ok
> 13) Once the new obo file is generated, delete the complete header
> (everything before the first [Term])
>     and paste the Header Template (below) with the correct information
> instead of the XXXXXX
>
>
> Notes on versioning of the CV:
> -------------------------------
> Versions of the CV will be revioned: x.y.z
>    z means no new term (editing of names or definitions or other minor
> changes)
>    y means new term or obsoletion
>    x means change in root level terms (impacts mapping file)
>
>
> HEADER TEMPLATE FOR COPY-PASTE (Change the XXXXXX values!)
> -----------------------------------------------------------
> format-version: 1.2
> date: XX:XX:XXXX XX:XX
> saved-by: XXXXXXXXX
> auto-generated-by: OBO-Edit 2.1-beta 13
> default-namespace: MS
> remark: namespace: MS
> data-version: X.XX.X
> remark: version: X.XX.X
> remark: release date: XXXX-XX-X
> remark: coverage: Mass spectrometer output files and spectra
> interpretation
> remark: creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu>
> remark: creator: Andreas Bertsch <bertsch <-at->
> informatik.uni-tuebingen.de>
> remark: creator: Marius Kallhardt <Marius.Kallhardt <-at-> bdal.de>
> remark: creator: Eric Deutsch <edeutsch <-at-> systemsbiology.org>
> remark: creator: Fredrik Levander <fredrik.levander <-at->
> immun.lth.se>
> remark: creator: Gerhard Mayer <mayerg97 <-at-> rub.de>
> remark: publisher: HUPO Proteomics Standards Initiative Mass
> Spectrometry Standards Working Group and HUPO Proteomics Standards
> Initiative Proteomics Informatics Working Group
> remark: When appropriate the definition and synonyms of a term are
> reported exactly as in the chapter 12 of IUPAC orange book. See
> http://www.iupac.org/projects/2003/2003-056-2
>
> -500.html.
> import:
> http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/un
> it.obo
>
> =======================================================================
> =========
>
>
> --
> David Ovelleiro
> Bioinformatician
> PRIDE Group
> Proteomics Services Team, PANDA Group
> EMBL European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, UK
> CB10 1SD
>
>
> -----------------------------------------------------------------------
> -------
> Simplify data backup and recovery for your virtual environment with
> vRanger.
> Installation's a snap, and flexible recovery options mean your data is
> safe,
> secure and there when you need it. Data protection magic?
> Nope - It's vRanger. Get your free trial download today.
> http://p.sf.net/sfu/quest-sfdev2dev
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] New commit: Obo-Edit compliant psi-ms.obo and updated Obo-Edit edit SOP

[David O. <do...@eb...>]

Dear all,

I've just uploaded the a new version of the psi-ms CV.
Is saved using Obo-Edit (refer to my last email for more info).
I've also commited an updated version of the SOP for saving with Obo-Edit.

I'll be two weeks out of office: please, send all your proposals for new 
changes, additions,... when I'm back I'll take care of them.

-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD

[Psidev-ms-dev] PSI-MS updates today and SOP for commit with OBO-Edit

[David O. <do...@eb...>]

Dear all,

PSI-MS updates today
====================
Maybe you've realised that five new versions of the psi-ms file have 
been released today.
All new versions are related to several errors in the CV file that made 
impossible the normal commit workflow with OBO-Edit.
All this new versions have been created editing manually the obo file, 
something that is fine if you know exactly what you are doing... I'll 
describe the motivations for the changes:

Revision 1.161 -> Changes in ID's of two ProteomeDiscoverer terms with 8 
digits instead of 7 (MS:10001664 and MS:10001665).
Problem: Taking these terms into account, OBO-Edit would have used 
MS:10001666 as the new term.

Revision 1.162 -> Changes in ID's of one duplicated ProteomeDiscoverer 
term MS:1001497 instead of MS:1001597 (the original MS:1001597 was 
"spectrum sub-set protein")
Problem: using the same ID for two terms produces an strange "merged" 
term when you save it with OBO-Edit (among other problems, I guess....)

Revision 1.163 -> Replaced in definition of 3 terms [PSI-MS] by the 
correct form, [PSI:MS]
Problem: the save with OBO-Edit was corrupted

Revision 1.164 -> Substitution in three cases of the deprecated 
expression <exact_synonym: "foo" []> by <synonym: "foo" EXACT []>
Problem: not really a problem... OBO-Edit changes automatically to new form

Revision 1.165 -> Correction of wrong syntax in several xref 
descriptions ("32-bit integer", "64-bit integer" and "null-terminated 
ASCII string"): the comments use <"foo"> format, not <!foo>
Problem: The comments were lost when saving with OBO-Edit

These mistakes are not tragic by themselves, but produced loss of data 
in some cases and the malfunction of OBO-Edit. I'd suggest the use of 
OBO-Edit, if not for the changes in the CV, at least for checking that 
they are correctly implemented.

I hope that the new version is OK for everybody.


SOP for commit with OBO-Edit
============================
I've written a new/updated version of the SOP for committing new 
versions of the CV with OBO-Edit (using the file "oboedit_notes.txt" in 
the repository). I'll attach the contents of this little manual at the 
end of this mail. If everything is OK, I'll commit the changes to the 
PSI repository. Maybe you'll want to try the "Save as" using OBO-Edit 
and check that everything is fine. In my computer, everything worked. 
The only changes that will be introduced in the CV if you follow the SOP 
are:
1/ Reordering of the lines inside every item
2/ Removing blank lines inside items
3/ Correcting wrong/incomplete/inaccurate relationships (e.g. MS:1000548)
4/ Loss of the description of the "replaced by" in obsolete terms (this 
is the only loss of information....
   in the line "replaced_by: MS:1000336 ! neutral loss", the description 
"neutral loss" is lost (the ID is kept))

If everything is fine for you, tomorrow,  I'll commit a new version of 
the CV "OBO-Edit-compatible" (and the submitting SOP also).

Best Regards,
David

PS: the SOP


================================================================================
Notes on using OBO-Edit (Updated by D.Ovelleiro June 2011, OBO-Edit 
version 2.1 beta13)
-----------------------

Saving psi-ms.obo from OBO-Edit is tricky.

Before checking in psi-ms.obo, please verify the following:
1) contains the import statement
2) does not contain terms from the Unit Ontology or other ontologies
3) contains the MS relationships (e.g. part_of, has_units)

psi-ms.obo imports the Unit Ontology (unit.obo) via an import statement 
at the top of the file:
import: unit.obo
We would really like to do the following:
import: 
http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo
But OBO-Edit replaces this by "ontology: pato"



We have not figured out yet how to accomplish #1 from within OBO-Edit, 
so the whole header
must be added manually after saving with OBO-Edit.

To save only the MS terms from OBO-Edit:
1) File/Save As
2) Select Advanced...
3) Select "OBO_1_2" for "Output Type"
4) + (add new "Stored adapter settings" profile)
5) "Save path:" (with browse button) for the output psi-ms.obo file
6) Check "Filter terms"
7) In "Object filtering" choose -> Fin terms that:"have" a:"Namespace" 
that:"contains" the value:"MS"
8) check "Allow dangling parents" (allows has_units UO:xxxxxxx)
9) check "include is_a closure for cross-referenced terms"
   (allows the terms from unit.obo to be included
   as relationship, e.g.: has_units UO:0000166 ! parts per notation)
10) Root selection algorithm :"GREEDY"
11) ID Rules: "Don't write ID rules"
12) Press Ok
13) Once the new obo file is generated, delete the complete header 
(everything before the first [Term])
    and paste the Header Template (below) with the correct information 
instead of the XXXXXX


Notes on versioning of the CV:
-------------------------------
Versions of the CV will be revioned: x.y.z
   z means no new term (editing of names or definitions or other minor 
changes)
   y means new term or obsoletion
   x means change in root level terms (impacts mapping file)


HEADER TEMPLATE FOR COPY-PASTE (Change the XXXXXX values!)
-----------------------------------------------------------
format-version: 1.2
date: XX:XX:XXXX XX:XX
saved-by: XXXXXXXXX
auto-generated-by: OBO-Edit 2.1-beta 13
default-namespace: MS
remark: namespace: MS
data-version: X.XX.X
remark: version: X.XX.X
remark: release date: XXXX-XX-X
remark: coverage: Mass spectrometer output files and spectra interpretation
remark: creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu>
remark: creator: Andreas Bertsch <bertsch <-at-> 
informatik.uni-tuebingen.de>
remark: creator: Marius Kallhardt <Marius.Kallhardt <-at-> bdal.de>
remark: creator: Eric Deutsch <edeutsch <-at-> systemsbiology.org>
remark: creator: Fredrik Levander <fredrik.levander <-at-> immun.lth.se>
remark: creator: Gerhard Mayer <mayerg97 <-at-> rub.de>
remark: publisher: HUPO Proteomics Standards Initiative Mass 
Spectrometry Standards Working Group and HUPO Proteomics Standards 
Initiative Proteomics Informatics Working Group
remark: When appropriate the definition and synonyms of a term are 
reported exactly as in the chapter 12 of IUPAC orange book. See 
http://www.iupac.org/projects/2003/2003-056-2

-500.html.
import: 
http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo

================================================================================


-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD

Re: [Psidev-ms-dev] [Psidev-pi-dev] PSI controlled vocabularies maintenance

[David O. <do...@eb...>]

Hi ,

I think that Steffen is right about the limited use for the spreadsheet.
I made a test in the  Tracker: MS controlled vocabulary changes 
(http://sourceforge.net/tracker/?group_id=65472&atid=848524).
If everybody thinks this is OK, I'll list the new proposals tomorrow in 
this list.
Only one question... is anybody else receiving annoying message in 
his/her mail while updating the state of the bug??? This would be an 
argument against the use of this system... otherwise, we could give it a 
try.

Regards,
David


On 31/05/2011 20:21, Steffen Neumann wrote:
> Hi,
>
> On Tue, 2011-05-31 at 17:04 +0100, David Ovelleiro wrote:
>> Maybe it makes not much sense for people who is registered in the
>> mailing lists to use it, and it also seems that is not a prodigy of
>> performance....
> So the form for CV terms doesn't really work,
>
> On Tue, 2011-05-31 at 12:55 +0100, David Ovelleiro wrote:
> ...
>> The proposals/changes/.... will be included also in the googleDoc
>> located there (starting in some hours):
>> https://spreadsheets.google.com/pub?hl=en_US&hl=en_US&key=0Av19CsTVDoOQdENWSmJDS3ZfN2tPdEhaaldzcWVNY3c&output=html
> but I think the spreadsheet is hardly maintainable
> in the long run. What about the approach to use a (bug) tracker,
> as shown (mostly by the psi-pi folks) for several of the mz* formats ?
>
> There could be types for reparenting, definition editing, adding,
> deleting, ... Updates would go the the (which ?) list etc.
> Commits could include which issue was fixed etc.
>
> Yours,
> Steffen
>


-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD

Re: [Psidev-ms-dev] ontology hierarchy below MS:1000458 ! source

[David O. <do...@eb...>]

Dear Matt and Eric,

For me is fine the Eric's proposal (inlet properties inside the source 
properties), as far as we keep in mind that the inlet can or cannot be 
part of the source: that's why I proposed an alternate way of organizing 
this. My only concern was having some property for an inlet incompatible 
with the source but, after looking for examples, I must admit that were 
somewhat bizarre...
Matt's argument about both being under the same XML element makes sense 
to me. If nobody finds a reason to not doing this, I'll list this update 
(hopefully tomorrow) in the new additions proposal.

Best,

David

On 01/06/2011 15:51, Eric Deutsch wrote:
> It would seem to me that often the inlet is a component of a source, and
> if an attribute is clearly an attribute of an inlet, then it would be tidy
> to classify it as such. However, from a practical use in mzML, it doesn't
> matter. So I would lean to the side of keeping them separate where it
> makes sense if David is willing to organize this. However, I don't feel
> very strongly either way.
>
> David, I am fine with your proposal if that's the way you'd like to
> organize it.
>
> We should remember that this will likely require a change to the mzML
> mapping file.
>
> Thanks,
> Eric
>
>
>> -----Original Message-----
>> From: Matthew Chambers [mailto:mat...@gm...]
>> Sent: Tuesday, May 31, 2011 12:25 PM
>> To: psi...@li...
>> Subject: Re: [Psidev-ms-dev] ontology hierarchy below MS:1000458 !
>> source
>>
>> Is there a good reason to separate "inlet attributes" from "source
>> attributes?" After all, they are
>> going under the same XML element (source).
>>
>> -Matt
>>
>>
>> On 5/31/2011 12:19 PM, David Ovelleiro wrote:
>>> Dear Steffen and Eric,
>>>
>>> At this moment I'm working in the "source" members.
>>> The problem here, as discussed in the PSI meeting in Heidelberg, is
>> that
>>> the distinction between a source and and inlet is not very clear in
>> some
>>> cases.
>>> Let's have one example:
>>> MS:1000055: continuous flow fast atom bombardment (defined as an
>> inlet)
>>> ->   "Fast atom bombardment ionization in which the analyte in
>> solution is
>>> entrained in a flowing liquid matrix."
>>> MS:1000074: fast atom bombardment ionization (defined as a ionization
>>> type) ->   "The ionization of any species by the interaction of a
>> focused
>>> beam of neutral atoms having a translational energy of several
>> thousand
>>> eV with a sample that is typically dissolved in a solvent matrix. See
>>> also secondary ionization."
>>>
>>> We found this kind of ambiguities. The problem is that depending on
>> the
>>> instrument design, in some cases, inlet and source are the same, or
>>> share components.
>>>
>>> Taking this into account, I'd propose an slightly different approach:
>>>
>>> [Term]
>>> id: MS:1000XXX
>>> name: inlet attribute
>>> def: "Property of an inlet device that needs a value." [PSI:MS]
>>> is_a: MS:1000458 ! source
>>>
>>>     Here, the inlet attribute is son to source, at the same level than
>>> "source attribute". Doing this, in the cases that the inlet is
>> something
>>> completely different from the source, using an "inlet attribute"
>> outside
>>> the "source attribute" seems more correct to me....
>>>
>>> What do you think?
>>>
>>> David
>>>
>>>
>>>
>>>
>>>
>>> On 28/05/2011 13:09, Neumann, Steffen wrote:
>>>> Hi,
>>>>
>>>> yes, that's fine with me.
>>>>
>>>> Yours,
>>>> Steffen
>>>>
>>>> ________________________________________
>>>> From: Eric Deutsch [ede...@sy...]
>>>> Sent: 28 May 2011 08:05
>>>> To: Mass spectrometry standard development
>>>> Cc: Eric Deutsch
>>>> Subject: Re: [Psidev-ms-dev] ontology hierarchy below MS:1000458 !
>> source
>>>> Hi Steffen, this is a pretty messy situation. Maybe David would like
>> to
>>>> take this on sometime. For now, I think what you propose is fine,
>> except I
>>>> don't think the second relationship is useful, so just:
>>>>
>>>> [Term]
>>>> id: MS:1000XXX
>>>> name: inlet attribute
>>>> def: "Property of an inlet device that needs a value." [PSI:MS]
>>>> is_a: MS:1000482 ! source attribute
>>>>
>>>> Regards,
>>>> Eric
>>>>
>>>>
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>>>
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>> -------
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> ------------------------------------------------------------------------------
> Simplify data backup and recovery for your virtual environment with vRanger.
> Installation's a snap, and flexible recovery options mean your data is safe,
> secure and there when you need it. Data protection magic?
> Nope - It's vRanger. Get your free trial download today.
> http://p.sf.net/sfu/quest-sfdev2dev
> _______________________________________________
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-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD