psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

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

Hi everyone, it appears that we have near consensus for Thursday at the
earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.



Agenda:

- Review what remains to be done

- Discuss (CTRL+A) header delimiter

- Discuss degree of sequence variant complexity to support

- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation

- Time slot for future calls



We may not get through this all, but let’s tackle as much as we can and
continue at the next call. I’m presenting at the top of the next hour, so
I’d like to limit this call to 55 mins.



I will send out dial-in information and reminder as we get closer.



Thanks,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Friday, May 15, 2015 10:05 AM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; Eric Deutsch; ju...@eb...; Ger...@gm...
*Cc:* Mass spectrometry standard development;
psi...@li...
*Subject:* PEFF progress and call next week and beyond



Hi everyone, we would like to set up some regular calls to carry PEFF over
the finish line. We had a good discussion at the PSI meeting, so we just
need to keep some momentum to get it finished.



I would like to set up a time next week to have conference call to discuss
some of the open issues. If you are interested in working to help complete
and resubmit PEFF, please complete the Doodle poll below (even if you
cannot attend at the suggested times next week) and I will keep you in the
loop for continuing development on this. I have sent this to the list of
coauthors on the specification and other vocal participants at the workshop
that I recall. Anyone else is welcome to join the effort even if I forgot
to add you to the list above.



http://doodle.com/but4z7ihv75byyp7



Attached are the latest document and the notes I took during the PSI
workshop.



Please respond to the doodle poll and I will email some specific agenda
point in advance of the meeting.



We should probably paste some more information here:

http://www.psidev.info/peff



Please email me if you have specific agenda items or other questions or
comments.



thanks,

Eric

[Psidev-ms-dev] PEFF progress and call next week and beyond

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

Hi everyone, we would like to set up some regular calls to carry PEFF over
the finish line. We had a good discussion at the PSI meeting, so we just
need to keep some momentum to get it finished.



I would like to set up a time next week to have conference call to discuss
some of the open issues. If you are interested in working to help complete
and resubmit PEFF, please complete the Doodle poll below (even if you
cannot attend at the suggested times next week) and I will keep you in the
loop for continuing development on this. I have sent this to the list of
coauthors on the specification and other vocal participants at the workshop
that I recall. Anyone else is welcome to join the effort even if I forgot
to add you to the list above.



http://doodle.com/but4z7ihv75byyp7



Attached are the latest document and the notes I took during the PSI
workshop.



Please respond to the doodle poll and I will email some specific agenda
point in advance of the meeting.



We should probably paste some more information here:

http://www.psidev.info/peff



Please email me if you have specific agenda items or other questions or
comments.



thanks,

Eric

[Psidev-ms-dev] Fwd: Impact assessment of EMBL-EBI: Your help requested.

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

Dear all,

If you have time to contribute to this survey on use of EMBL-EBI resources, please do so, your help would be highly appreciated. In addition, you could also win one Raspberry Pi 2 with Pibow Cases!

The online questionnaire is accessible at: https://www.surveymonkey.com/s/EBI_Impact <https://www.surveymonkey.com/s/EBI_Impact>

Thanks a lot in advance,

Juan Antonio



> Begin forwarded message:
> 
> 
> Subject: Impact assessment of EMBL-EBI: Your help requested.
> Date: 7 May 2015 12:37:29 BST
> 
> 
> 
> 
> Dear Colleague,
> 
> We are writing to you as Associate Directors of the EMBL European 
> Bioinformatics Institute to request your support and involvement in an 
> independent survey commissioned as part of a study to assess the value 
> and impact of EMBL- EBI services on the communities we serve. This is an 
> important study in a number of ways, but in particular, it will be 
> extremely useful to be able to demonstrate to funding bodies and others 
> the economic benefits of having freely accessible services and resources 
> for research in the life sciences.
> 
> Within the survey a range of methods and approaches are used including 
> the hypothetical question of willingness to pay or accept payment to be 
> without EMBL-EBI services.  We would like to highlight that this 
> question is being presented as a purely hypothetical one but necessary 
> to feed into a well known economic model of assessing services that are 
> without charge (contingent valuation).  If any questions or concerns 
> arise due to the survey please feel free to respond to this email address.
> 
> We are hopeful we can draw on the cooperation and goodwill of our user 
> community to get as large a response as possible.
> 
> Charles Beagrie Ltd is conducting the assessment and the online 
> questionnaire  is accessible at: https://www.surveymonkey.com/s/EBI_Impact <https://www.surveymonkey.com/s/EBI_Impact>
> 
> It is estimated that the survey will take around 15 minutes to complete 
> and it will close on Friday  8th May 2015.
> 
> The results of the survey will be anonymised and disseminated in 
> aggregate only and all personal data treated as confidential.
> 
> Thank you in advance for your and your colleagues participation and 
> input. We recognise there are many demands on your time. As a token of 
> appreciation for contributing, all participants who complete the survey 
> are also given the opportunity to enter a draw to win one of five 
> Raspberry Pi 2 with Pibow Cases.
> 
> Kind regards
> 
> Ewan Birney and Rolf Apweiler
> Joint Associate Directors, EMBL-EBI
> 
> 
> 
> 
> 

Re: [Psidev-ms-dev] [proteowizard-developer] mzML output and the mzML specification: problem, maybe?

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

Thanks, Bryson, I think I understand now. As we've seen, the situation is
complex. I think the intent when we designed it is that if the precursors
are present in the file they must be referenced (although this is not
enforced in XML schema because we couldn't). If there are known precursors
in the raw file that are not msconverted by choice, they really should
have proper external references, but I am not surprised if they don't. And
yes, there are reasonably use cases where you legitimately have neither.
And the schema as designed allows this.

So, I think there's not much to be done. The design is okay and flexible,
but the enforcement is such that available information may be left out
because it is sometimes truly not available.

If you have very specific examples that you can provide that show that a
raw file does have links between precursor and product spectra that are
not being written to mzML, then we might be able to find someone motivated
to fix the problem. But otherwise, I think the current state is the best
we can do. I imagine that msconvert should not be guessing which is the
precursor spectrum if the information is not available in the raw files.

Regards,
Eric


-----Original Message-----
From: Gibbons, Bryson C [mailto:bry...@pn...]
Sent: Tuesday, May 5, 2015 10:21 AM
To: pro...@li...
Cc: psi...@li...
Subject: Re: [proteowizard-developer] mzML output and the mzML
specification: problem, maybe?

I do mean that when I use msconvert to read a non-Thermo raw binary file
(in this case, a Bruker .d folder) and write mzML, the resulting mzML does
not have precursor spectrumRefs. The reason I referenced "ProteoWizard
readers", is that the responsibility for adding that information should be
with the vendor dll interface code, or "vendor readers". The code that
adds the spectrumRef to the Thermo files is part of the code that reads
the spectra using the Thermo dlls.

I can definitely understand the problem when the mzML file is MS2 only,
which you can create using msconvert. Two options could be to still have
the spectrumRef there (if msconvert created it) even though the precursor
spectrum is not in the mzML file (which unfortunately could break
something that assumes that if it is present, it is in the same file); or
the external id could be used, which presents the same set of issues, in
addition to the external reference requirements. It could also not have
the spectrumRef, as it currently is. If you create a MS2-only mzML file
from Thermo data it still contains the spectrumRef (as well as saying the
file still includes MS1 spectra, which is a different problem).

Bryson

-----Original Message-----
From: Steffen Neumann [mailto:sne...@ip...]
Sent: Tuesday, May 05, 2015 4:49 AM
To: pro...@li...
Cc: psi...@li...
Subject: Re: [proteowizard-developer] mzML output and the mzML
specification: problem, maybe?

Hi,

On Mo, 2015-05-04 at 21:08 -0700, Eric Deutsch wrote:
...
> So is your question: is the fact that some writers like Bruker
> software do not write spectrumRefs (or the alternative) a problem?

we're using Bruker QqTOF as well, and the issue might lay deeper than just
the writer. We have some mzML files which are MS2 *only*, so the *is no*
precursor spectrum at all. I am unsure if you can do MS2 or MSn only
measurements in Orbitraps, but it might be that there are cases where
spectrumRef must be left out.

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] [proteowizard-developer] mzML output and the mzML specification: problem, maybe?

[Gibbons, B. C <bry...@pn...>]

I do mean that when I use msconvert to read a non-Thermo raw binary file (in this case, a Bruker .d folder) and write mzML, the resulting mzML does not have precursor spectrumRefs. The reason I referenced "ProteoWizard readers", is that the responsibility for adding that information should be with the vendor dll interface code, or "vendor readers". The code that adds the spectrumRef to the Thermo files is part of the code that reads the spectra using the Thermo dlls.

I can definitely understand the problem when the mzML file is MS2 only, which you can create using msconvert. Two options could be to still have the spectrumRef there (if msconvert created it) even though the precursor spectrum is not in the mzML file (which unfortunately could break something that assumes that if it is present, it is in the same file); or the external id could be used, which presents the same set of issues, in addition to the external reference requirements. It could also not have the spectrumRef, as it currently is. If you create a MS2-only mzML file from Thermo data it still contains the spectrumRef (as well as saying the file still includes MS1 spectra, which is a different problem).

Bryson

-----Original Message-----
From: Steffen Neumann [mailto:sne...@ip...] 
Sent: Tuesday, May 05, 2015 4:49 AM
To: pro...@li...
Cc: psi...@li...
Subject: Re: [proteowizard-developer] mzML output and the mzML specification: problem, maybe?

Hi,

On Mo, 2015-05-04 at 21:08 -0700, Eric Deutsch wrote:
...
> So is your question: is the fact that some writers like Bruker 
> software do not write spectrumRefs (or the alternative) a problem?

we're using Bruker QqTOF as well, and the issue might lay deeper than just the writer. We have some mzML files which are MS2 *only*, so the *is no* precursor spectrum at all. I am unsure if you can do MS2 or MSn only measurements in Orbitraps, but it might be that there are cases where spectrumRef must be left out.

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

Re: [Psidev-ms-dev] [proteowizard-developer] mzML output and the mzML specification: problem, maybe?

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

Hi,

On Mo, 2015-05-04 at 21:08 -0700, Eric Deutsch wrote:
...
> So is your question: is the fact that some writers like Bruker
> software do not write spectrumRefs (or the alternative) a problem?

we're using Bruker QqTOF as well, and the issue might lay deeper 
than just the writer. We have some mzML files which are MS2 *only*,
so the *is no* precursor spectrum at all. I am unsure if you can 
do MS2 or MSn only measurements in Orbitraps, but it might be 
that there are cases where spectrumRef must be left out.

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

Re: [Psidev-ms-dev] [proteowizard-developer] mzML output and the mzML specification: problem, maybe?

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

Hi Bryson, I believe that your impression is correct. In practice, most
documents use the spectrumRef. The alternate use of (sourceFileRef and
externalSpectrumID) is rare, but supported. My very vague recollection is
that it is not possible in XML schema to enforce mandatory attribute (A and
B) or C. So our solution is to make them all optional. Originally we had
only spectrumRefs. But then someone what the ability to refer to spectra
external to the document. There is a semantic validator software that is
supposed to flag incorrect use of this as an error, but I am not certain
that it does. And it is not universally used. This is a good lesson in “any
disagreeable shortcut left unblocked will be taken!”.



So is your question: is the fact that some writers like Bruker software do
not write spectrumRefs (or the alternative) a problem?



Regards

Eric





*From:* Gibbons, Bryson C [mailto:bry...@pn...]
*Sent:* Monday, May 4, 2015 3:19 PM
*To:* pro...@li...
*Subject:* [proteowizard-developer] mzML output and the mzML specification:
problem, maybe?



In some of my improvements to the mzRefinery filter (in particular for
adjusting precursor metadata using the scan start time from the precursor
itself) I ended up breaking part of its functionality: updating precursor
metadata for MSn scans. I hadn’t noticed this previously because I was
primarily using it on mzML files produced from Thermo instruments, but when
I tried it again recently on some Bruker QqTOF I found that precursor
metadata was not being updated. After some testing to determine why this
was happening, I found that while the Thermo reader populates precursor
element spectrumRef attribute, the Bruker reader (and apparently most of
the other vendor readers as well) do not, instead leaving no attributes on
the precursor element. I’m assuming that a good part of this is probably
because the vendor files/dlls don’t provide a good process to determine
which scan is the precursor.



The mzML 1.1.0 specification for the <precursor> element states: (
http://www.peptideatlas.org/tmp/mzML1.1.0.html#precursor)

*Attribute Name*

*Data Type*

*Use*

*Definition*

externalSpectrumID

xs:string

optional

For precursor spectra that are external to this document, this string MUST
correspond to the 'id' attribute of a spectrum in the external document
indicated by 'sourceFileRef'.

sourceFileRef

xs:IDREF

optional

For precursor spectra that are external to this document, this attribute
MUST reference the 'id' attribute of a sourceFile representing that
external document.

spectrumRef

xs:string

optional

For precursor spectra that are local to this document, this attribute MUST
be used to reference the 'id' attribute of the spectrum corresponding to
the precursor spectrum.



Though all are listed as optional attributes, the descriptions leave the
impression of “you must either use externalSpectrumID and sourceFileRef, or
use spectrumRef”. I don’t know if that is what it is supposed to mean,
because the mzML 1.0.0 specification left the “spectrumRef” attribute
optional with the definition of “Reference to the id attribute of the
spectrum from which the precursor was selected.”



Is this a problem, or am I misreading the mzML specification?



Thank you,



Bryson Gibbons

[Psidev-ms-dev] Summary of PSI meeting 2015 in Seattle

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

Dear all,

I am providing here a summary of the sessions where I was directly involved, related mainly with the activities of the PSI-PI working group and ProteomeXchange. I am not covering here the developments related to compression and mzML, and to PEFF.

Of course, additions and edits are wellcome. 

	
1) mzIdentML 1.2

There was no session devoted to mzIdentML in the meeting. Juan Antonio presented the current status of things using slides from Andy. During the meeting, it was suggested to add guidelines in the new version 1.2 about how to report:

- Identification results coming from chimeric spectra.
- ProteoGenomics searches using (incrementally larger) databases, ideally reporting in more detail how the FDR calculation was performed.

The format does not need to change at all, only extra instructions need to be added indicating how to do it.


2) mzQuantML

There was no session devoted to mzQuantML in the meeting.  Simon Perkins (Liverpool University) presented the current status of things. The guidelines for reporting SRM results in mzQuantML have been recently finished and published (http://www.ncbi.nlm.nih.gov/pubmed/25884107 <http://www.ncbi.nlm.nih.gov/pubmed/25884107>). 

Parag asked whether mzQuantML could support the combination of SILAC and iTRAQ in the same dataset. People are now starting to do this. This is currently not supported.

It was mentioned several times in the ProteomeXchange session (e.g. by Brendan) the need to trace back to the original features, to ensure that researches can take informed decissions about the reliability of the reported quantitative results. This is supported in mzQuantML.


3) mzTab

Ongoing extensions for metabolomics (COSMOS Consortium) and glycomics (MIRAGE Consortium) data. There was a remote meeting and there is an agreement in how to proceeed. The specification will need to be modified slightly to have:

- A core part: Metadata information that is common to all techniques. Common framework.
- Extensions for the different techniques: at the moment proteomics, metabolomics and glycomics. There could be more in the future. 
- Juan Antonio and Timo to help and advice, but not to lead.
- Proposed face to face meeting between people from MIRAGE and S. Neumann on June in Postdam.
- Juan Antonio to send MIRAGE document to everyone involved in the session.


4) ProteoGenomics approaches

The first day there were talks by X. Wang (Vanderbilt University, “proBAM") and Gerben Menschaert (Ghent University, “Proteogenomics in need for integration standards”).

The proBAM format, presented by X. Wang  was very well received. She is interested in getting the format through the PSI document process. The file format:
- includes the exact positions of the origin of the peptide ID in the genome.
- Detailed information about the PSM (like scores).
- Serving as a well defined interface between PSM identification and downstream analyses.
- The big advantage is that the current software that can read BAM files can also read proBAM files.
- Junction peptides are encoded in the CIDAR string section of proBAM.

In addition:

- A much simpler standard format for reporting peptides in BED format was also reported by Juan Antonio (“pepBED”). It is complementary to the proBAM format. Being developed by Andy Jones/EBI in the context of a BBSRC grant.
- Inter-conversion between those formats (proBAM, peptBED) and mzTab should be be possible.
- Do a MIAPE MSI extension for ProteoGenomics approaches? Eric to contact Alexey Nesvizhskii to see if he would be interested (follow up on what he published in the Proteogenomics review in Nature Methods, PMID: 25357241).

Gerben stressed several times the need to report in detail the analysis workflow used in ProteoGenomics pipelines.


5) New format for spectral library files?

Simon Perkins (Liverpool University) summarized the situation of the current available formats:

splib/spectLib
NIST formats
BiblioSpec/blib
hlf
ms2/ssl
For small molecules: MassBank, mzCloud, not peptide specific collections.

The main piece of the information lacking there is the lack of metadata about e.g. the origin of spectra that constitute the spectral library. Since it does not make sense to develop a format from scratch it was proposed to develop a format for the metadata associated to spectral libraries, that could be used together with any of the existing formats.

- Eric and Nuno to discuss and draft the first list of requirements.

Other points mentioned in the session:

- Brendan: Important to differentiate between primary information and derived information.
- Nuno -> Secretomes -> mixed peptides and metabolites in the same sample. 


6) ProteomeXchange session

There were talks by Henning, Juan Antonio, Nuno and Eric about the overall status and the current resources: PRIDE, MassIVE and PeptideAtlas/PASSEL.
- The grant we applied for (BBSRC/NSF joint funding) was well reviewed but not successful.
- We should try again this year (deadline for the initial letter of intent is May 31st).
- Number of citations to PRIDE and reuse of data has increased a lot in 2014.
- Ongoing: development of PROXI and extension of the ProteomeCentral concept to include other omics data types (e.g. metabolomics) in the context of BD2K initiatives.

There were also talks from Shin (JPOST) and Brendan (Panorama).
- The Japanese database JPOST will definitely go forward since they have been successful in the grant application. It will contain original results and reprocessed data.
- Panorama:
	- Repository for Skyline documents
	- Does not store raw data at present (one of the requirement of ProteomeXchange).
	- Raw data should be in other resources: PASSEL and/or Chorus.

- Robert Chalkley reported the status of things in MCP:
	- MCP guidelines for authors are being updated. At the moment, quantification related guidelines are not going to change significantly. Not many details are provided in those.
	- it was discussed the need to have these guidelines much more “tightened up”.
	- Mandatory deposition of raw data is happening in practise although the guidelines of the journal have not been changed yet. It is supposed to happen soon.

Discussion:

- Need to have a unique identified for spectra. This could be transformed into a unique URL for spectra that would be very useful for journals.
- This is only possible for open peak list files. PRIDE has developed an approach that is happy to report to others.
- However this is not possible for raw files (e.g. “Partial” submissions), since conversion using ProteoWizard will result in different files depending on the version of the PW software and/or the vendor libraries.
- Nuno highlighted during the session to have better sample related metadata annotation.
	- Initially we put the emphasis in making the submission process easy.
	- Maybe it is now the point of tighten things, especially in the case of "partial" submissions.


7) PROXI (ProteomeXchange query interface)

- Remote presentation of Yasset to describe the current status. Consensus with MassIVE in how to proceed:
	- Focus in identification first (v1.0).
	- API REST interface to be developed.

- Concentrate in the interface and “forget” for now about general limitations on reporting (e.g. mapping of protein identifiers, update protein sequences) since these are independent problems. Guidelines will need to drafted about this.
- Skype call to be scheduled to continue with this work.


8) GitHub migration

- Mathias has created an organisation in GitHub called “HUPO-PSI”.
- He will migrate the current PSI-DEV Google SVN repository under that organisation. He will send an e-mail to the mailing list once this is done.
	- Owners and other roles need to be decided.

- The PRIDE team will migrate the mzTab Google SVN asap.
- For now only the formats, example files, etc will be included, not the libraries (e.g. jmzIdentML, jmzML, etc etc), although this can be changed if there is consensus.
-At the moment the PSI-MI group has created a different GitHub repository.



Best regards,

Juan Antonio

Re: [Psidev-ms-dev] [Psidev-pi-dev] Bidding farewell to Google Code -- Migrate your projects !

[Gorka P. <gor...@eh...>]

On 09/04/15 16:56, Mathias Walzer wrote:
> I already checked the repository structure of psi-pi (as I was at it anyways) and the files that would have to go (from all revisions) are:
> PAnalyzer-v1.1b6_Rosetta-take2.tar

Hi Mathias, sorry I missed this notice. There is no problem with 
removing PAnalyzer-v1.1b6_Rosetta-take2.tar from all revisions. It is an 
intermediate file which I suppose was committed accidentally, the 
desired mzid files are already committed out of the tar.

Best wishes,
Gorka

-- 

Gorka Prieto Agujeta, PhD
Senior Lecturer
gor...@eh...
(+34) 94 601 3994

DEPARTMENT OF COMMUNICATIONS ENGINEERING
UNIVERSITY OF THE BASQUE COUNTRY (UPV/EHU)
Alda. Urquijo, s/n | 48013 BILBAO (Spain)
T.: +34 946014036|F.: +34 946014259
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Re: [Psidev-ms-dev] [Psidev-pi-dev] Bidding farewell to Google Code -- Migrate your projects !

[Mathias W. <wa...@in...>]

Dear all,

I had another project on google code and opted for the migration to github.
So I can shed some light on the up- and downsides of the migration to github which hopefully aids you in evaluating alternatives so we can have a productive discussion in Seattle.

Upside: 
*they adopted the concept of organizations (as meta-account, which can hold several projects/repositories, e.g. PSI-PI/MS containing mzml, mzidentml, mzquantml, cv(!))
*free for open source projects
*using git as repository management software (forking and merging helps maintaining an overview and keeps the master repo clean)
*clean web UI where you can do as much as in google code and more 
 -discussion boards for each merge from a fork('pull request')
 -diff views are very helpful
 -nice issue management, also with integrated discussion board
*quite seamless migration ( without that much effort, once you did it first time ;) )

Downside:
*committers need a github account
*hard file size limitation (<100mb ^§, each repository <1GB)
*wiki-migration does not quite work (psi-pi wiki on gcode is marginal)
*using git as repository management software (needs some getting used to)

hope this helps.
cheers,
 Mathias


§:
I already checked the repository structure of psi-pi (as I was at it anyways) and the files that would have to go (from all revisions) are:
PAnalyzer-v1.1b6_Rosetta-take2.tar
mouse_dataset_-_combination.pia.1.2.mzid
and hard at the limit: MSGFplus_tandem.pia.1.2.mzid

----- Original Message -----
From: "Steffen Neumann" <sne...@ip...>
To: psi...@li...
Cc: "psidev-pi-dev" <psi...@li...>
Sent: Thursday, 19 March, 2015 5:11:12 PM
Subject: [Psidev-pi-dev] Bidding farewell to Google Code -- Migrate your	projects !

Hi,

I would like to bring the following (sad) news to you:

	"Google code will be shutting down the service 
	about 10 months from now on January 25th, 2016"

Please check the following post for the full story:
http://google-opensource.blogspot.de/2015/03/farewell-to-google-code.html

There are several projects in Proteomics I am aware of 
that make heavy use of google code platform. 

	PLEASE START THINKING ABOUT THE UNAVOIDABLE MIGRATION NOW !

Sorry for the shouting, but migration is a big task 
and should not be rushed, so please start to think 
about it now, and/or at the HUPO-PSI meeting in Seattle 
next month. 

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] HUPO PSI 2015 spring workshop in Seattle April 13, 14, 15

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

Hi everyone, here is your final reminder for the PSI Spring 2015 workshop.
I need to get the final numbers for the caterer in a few days, so please
register now if you have not done so yet.



If you are unable to join in person, you may be able to join remotely. I am
intending to try to have a live GoToMeeting session open for at least some
parts of the workshop. If you are interested in joining the meeting
remotely, please email me directly which parts you hope to join, and I will
keep you informed about the status of the session. I will email everyone
who expresses interest the GoToMeeting URL and updates on what is planned.



I look forward to seeing many of you in Seattle!



Regards,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Wednesday, March 25, 2015 10:05 AM
*To:* psi...@eb...; psi...@li...;
psi...@li...
*Cc:* Eric Deutsch
*Subject:* RE: HUPO PSI 2015 spring workshop in Seattle April 13, 14, 15



Hi everyone, this is the penultimate reminder to register for the PSI
conference if you plan to participate. We welcome everyone’s participation,
and this year’s workshop will feature some good discussions about spectra
library formats, mzML 2.0, ProteomeXchange & PROXI, PSI-MI XML 3.0 & JAMI,
metabolomics, and more! I need to give final numbers to the catering people
next week, so please register this week if you will join us. An updated
agenda and registration forms are available at:



http://www.psidev.info/content/hupo-psi-meeting-2015



Regards,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Thursday, March 12, 2015 10:48 AM
*To:* psi...@eb...; psi...@li...;
psi...@li...
*Cc:* Eric Deutsch
*Subject:* RE: HUPO PSI 2015 spring workshop in Seattle April 13, 14, 15



Hi everyone, we are about a month away from the beginning of the PSI
workshop in Seattle. Thank you to everyone who has already registered and
made arrangements. For everyone else who is intending to come or is still
thinking about it, now is the perfect time to register your intent to
participate in the workshop. Work will continue on mzML, mzTab, PROXI, and
PEFF, as well as aligned metabolomics efforts, and efforts to integrate
proteomics and genomics data. Wide participation is what makes the work of
the PSI successful.



Registration and logistical information may be found here:



http://www.psidev.info/content/hupo-psi-meeting-2015



Please do register soon so that I can have accurate participant numbers for
catering.



Please let me know if you have any questions. I look forward to seeing you
in Seattle!



Regards,

Eric







*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Wednesday, December 10, 2014 7:02 AM
*To:* psi...@eb...; psi...@li...;
psi...@li...
*Cc:* Eric Deutsch
*Subject:* HUPO PSI 2015 spring workshop in Seattle April 13, 14, 15



Hi everyone, I am pleased to announce that the 2015 HUPO PSI spring
workshop will be hosted in Seattle at the Institute for Systems Biology on
April 13, 14, 15. Our registration page will open in January, but please
mark your calendars now for full-day sessions all 3 days and plan on
joining us in Seattle to continue important work on standards.



Regards,

Eric

[Psidev-ms-dev] FW: Abstract Submission Deadline Extension

[<eri...@sy...>]

Hi everyone, it’s quite possible that some or all of the email to you from
HUPO 2015 Vancouver has been trapped in your spam filters. If you have not
been receiving emails from HUPO2015, please see attachment for the latest
email  and deadlines.



Regards,

Eric





Dear Members of the Scientific Organizing Committee,



We wanted to send you a quick update to let you know that the *Abstract and
Travel Grant Submission Deadline for HUPO 2015 has been extended to April
10, 2015 (23:59 PST). *Unfortunately our submission numbers are very low at
this point. We are experiencing some challenges getting our emails through
to people, so would appreciate if we could count on your support to spread
the word about HUPO 2015 in Vancouver and the extended submission deadline
Friday, April 10.



*If you could help us and send personal invitations to your network of
friends and colleagues about HUPO and the abstract submission deadline that
would be greatly appreciated. Please feel free to use the below or attached
email.*



Further information on the Congress can be found on the Congress website at
www.hupo2015.com. I am also here to answer any questions you may have.



Thank you very much in advance for any support you may be able to provide
in promoting the HUPO 2015 World Congress, Vancouver, Canada, September 27
– 30, 2015. Your support is greatly appreciated.



Best Regards,

Grit







Grit Schoenherr

HUPO 2015 Senior Conference Manager

*www.hupo2015.com* <www.hupo2015.com>



c/o International Conference Services Ltd.

www.icsevents.com

2101 – 1177 West Hastings Street

Vancouver, BC, Canada V6E 2K3

*Direct Line [+1] 604 638 3864*

P [+1] 604 681 2153 ext. 116

F [+1] 604 681 1049

E *hup...@ic...* <hup...@ic...>



Please - only print this email if necessary!



*www.icsevents.com* <http://www.icsevents.com/>
*LinkedIn* <http://www.linkedin.com/pub/grit-schoenherr/11/a82/874>
 *Twitter
<http://twitter.com/#!/ICS_Events>*

*Locations:* *Vancouver* <http://www.icsevents.com/meet_the_team.html>,
*Toronto* <http://www.icsevents.com/meet_the_team_toronto.html>, *Vienna*
<http://www.icsevents.com/meet_the_team_vienna.html>, *Denver*
<http://www.icsevents.com/meet_the_team_denver.html>
*International Accreditations:* *IAPCO* <http://www.iapco.org/>, *ICCA*
<http://www.iccaworld.com/index.cfm>





*From:* HUPO 2015 Congress Secretariat [mailto:hup...@ic...
<hup...@ic...>]
*Sent:* Tuesday, March 24, 2015 8:33 AM
*To:* HUPO2015
*Subject:* Abstract Submission Deadline Extension



[image: HUPO 2015 Banner]
ABSTRACT SUBMISSION DEADLINE EXTENSION Abstract Submission Deadline Has
Been Extended To: April 10, 2015 (23:59 PST)

The extended deadline for abstract submission for the 14th Human Proteome
Organization World Congress is Friday, April 10, 2015 (23:59 PST)!

To review submission guidelines and submission categories, please click
here >>
<https://www.eiseverywhere.com/emarketing/go.php?i=currentblast&e=subscriberemailec&l=http://hupo2015.com/program/call-for-abstracts/>

*Extended Abstract Submission Deadline is April 10, 2015.*

*Submit an Abstract >>
<https://www.eiseverywhere.com/emarketing/go.php?i=currentblast&e=subscriberemailec&l=http://hupo2015.com/program/call-for-abstracts/>*


 Late Breaking Abstract Submission

The Congress offers *Late Breaking Abstract Submission* *by Monday, June 8,
2015*; however, *priority for oral abstract presentations* will be *given
to authors submitting their abstract before* the extended submission
deadline coming up *Friday, April 10, 2015*.



*IMPORTANT DATES*

*OPEN
<https://www.eiseverywhere.com/emarketing/go.php?i=currentblast&e=subscriberemailec&l=http://hupo2015.com/program/call-for-abstracts/>*

Abstract Submission

*April 10, 2015*

Registration and Housing Opens

*April 10, 2015 *(23:59 PST)

Extended Abstract Submission Deadline

*May 11, 2015*

Abstract Acceptance Notification

*June 8, 2015 *(23:59 PST)

Late Breaking Abstract Submission Deadline

*June 12, 2015*

Early Registration Deadline

*August 14, 2015*

Regular Registration Deadline

*September 27 - 30, 2015*

Congress Dates











*HUPO 2015 NEWSLETTER:*

Join the mailing list to receive regular updates about the HUPO 2015
Congress in Vancouver.



*Click Here to Join*
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*STAY UP TO DATE*: WWW.HUPO2015.COM
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You have received this message because you have an existing relationship
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[Psidev-ms-dev] New version 3.75.0 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached you find the new version 3.75.0 of the psi-ms.obo file.


Changed CV terms in version 3.75.0 of psi-ms.obo:
=================================================
************ Changed is_a from 'p-value for peptides'
************ --> 'distinct peptide-level p-value'
[Term]
id: MS:1001396
name: Phenyx:PepPvalue
def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001870 ! distinct peptide-level p-value

************ Added is_a: MS:1002358 !
************ search engine specific score for distinct peptides
[Term]
id: MS:1002468
name: PeptideShaker peptide score
def: "The probability based PeptideShaker peptide score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002358 ! search engine specific score for distinct peptides
relationship: has_order MS:1002108 ! higher score better

************ Added is_a: MS:1002368 !
************ search engine specific score for protein groups
[Term]
id: MS:1002470
name: PeptideShaker protein group score
def: "The probability based PeptideShaker protein group score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] minor update 1.0.1 to recommendation document (adding SRM to file format mzQuantML), 14-days public comment

[Martin E. <mar...@ru...>]

Dear colleague,
dear member of the Proteomics community,
 
please forward this message to potentially interested colleagues!
 
A modified specification of the mzQuantML recommendation document was
submitted to the PSI document process 
including the encoding of SRM quantification results. After careful
consideration and discussion with the submitters I
think it is minor and therefore version 1.0.1 (if you disagree, especially
if existing software is made incompatible,
please give me a note).
 
Please review the updated specification document below WITHIN TWO WEEKS and
send any corrections or
comments until April 12th to the handling editor mar...@ru....
 
The original version 1.0.0 (incl. SRM rule file and example under
development for 1.0.1) can be found HERE
<https://code.google.com/p/mzquantml/source/browse/#svn%2Ftrunk> .
 
The 1.0.1 draft specification document together with a DIFF doc to 1.0.0 can
be found HERE <http://www.psidev.info/mzquantml-101-in-docproc> .
 
The public comment period enables the wider community to provide feedback
on a proposed standard before it is formally accepted, and thus is an
important step in the standardisation process.
 
   Many thanks for your valuable time and participation
     Martin Eisenacher (PSI Editor)
 
--
PD Dr. Martin Eisenacher
Forschungsbereich Medizinische Bioinformatik
Medizinisches Proteom-Center (MPC)
Ruhr-Universität Bochum
 
Tel.: +49 / 234 / 32 - 29288
Fax: +49 / 234 / 32 - 14554
http://www.ruhr-uni-bochum.de/mpc/medical_bioinformatics/index.html.de
 
 

Re: [Psidev-ms-dev] HUPO PSI 2015 spring workshop in Seattle April 13, 14, 15

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

Hi everyone, this is the penultimate reminder to register for the PSI
conference if you plan to participate. We welcome everyone’s participation,
and this year’s workshop will feature some good discussions about spectra
library formats, mzML 2.0, ProteomeXchange & PROXI, PSI-MI XML 3.0 & JAMI,
metabolomics, and more! I need to give final numbers to the catering people
next week, so please register this week if you will join us. An updated
agenda and registration forms are available at:



http://www.psidev.info/content/hupo-psi-meeting-2015



Regards,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Thursday, March 12, 2015 10:48 AM
*To:* psi...@eb...; psi...@li...;
psi...@li...
*Cc:* Eric Deutsch
*Subject:* RE: HUPO PSI 2015 spring workshop in Seattle April 13, 14, 15



Hi everyone, we are about a month away from the beginning of the PSI
workshop in Seattle. Thank you to everyone who has already registered and
made arrangements. For everyone else who is intending to come or is still
thinking about it, now is the perfect time to register your intent to
participate in the workshop. Work will continue on mzML, mzTab, PROXI, and
PEFF, as well as aligned metabolomics efforts, and efforts to integrate
proteomics and genomics data. Wide participation is what makes the work of
the PSI successful.



Registration and logistical information may be found here:



http://www.psidev.info/content/hupo-psi-meeting-2015



Please do register soon so that I can have accurate participant numbers for
catering.



Please let me know if you have any questions. I look forward to seeing you
in Seattle!



Regards,

Eric







*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Wednesday, December 10, 2014 7:02 AM
*To:* psi...@eb...; psi...@li...;
psi...@li...
*Cc:* Eric Deutsch
*Subject:* HUPO PSI 2015 spring workshop in Seattle April 13, 14, 15



Hi everyone, I am pleased to announce that the 2015 HUPO PSI spring
workshop will be hosted in Seattle at the Institute for Systems Biology on
April 13, 14, 15. Our registration page will open in January, but please
mark your calendars now for full-day sessions all 3 days and plan on
joining us in Seattle to continue important work on standards.



Regards,

Eric

[Psidev-ms-dev] Release candidate 3.75.0_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached you the release candidate 3.75.0_rc1 of the psi-ms.obo file.


Changed CV terms in version 3.75.0_rc1 of psi-ms.obo:
=====================================================
************ Changed is_a from 'p-value for peptides'
************ --> 'distinct peptide-level p-value'
[Term]
id: MS:1001396
name: Phenyx:PepPvalue
def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001870 ! distinct peptide-level p-value

************ Added is_a: MS:1002358 !
************ search engine specific score for distinct peptides
[Term]
id: MS:1002468
name: PeptideShaker peptide score
def: "The probability based PeptideShaker peptide score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002358 ! search engine specific score for distinct peptides
relationship: has_order MS:1002108 ! higher score better

************ Added is_a: MS:1002368 !
************ search engine specific score for protein groups
[Term]
id: MS:1002470
name: PeptideShaker protein group score
def: "The probability based PeptideShaker protein group score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Bidding farewell to Google Code -- Migrate your projects !

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

Hi,

I would like to bring the following (sad) news to you:

	"Google code will be shutting down the service 
	about 10 months from now on January 25th, 2016"

Please check the following post for the full story:
http://google-opensource.blogspot.de/2015/03/farewell-to-google-code.html

There are several projects in Proteomics I am aware of 
that make heavy use of google code platform. 

	PLEASE START THINKING ABOUT THE UNAVOIDABLE MIGRATION NOW !

Sorry for the shouting, but migration is a big task 
and should not be rushed, so please start to think 
about it now, and/or at the HUPO-PSI meeting in Seattle 
next month. 

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

[Psidev-ms-dev] save-the-date OpenMS-User Meeting 2015

[Martin E. <mar...@ru...>]

Dear friends of OpenMS,
 
we are happy to announce the 8th OpenMS User Meeting from 
September 16th-18th 2015 (first day optional hands-on day)
at the Medizinisches Proteom-Center in Bochum.
 
During the meeting we will present the capabilities of OpenMS, and discuss
your needs and future directions in mass spectrometry. This year’s meeting
will include an optional OpenMS tutorial session on the first day
(Wednesday)
with the general conference starting on Thursday, September 17.
Traditionally,
the schedule of our meetings is very flexible, allowing discussions and
contributions from the participants.
 
You can bring your data, an OpenMS wish list, ideas for collaboration
projects,
and also give a talk about your project. This may include suggestions in
areas
where currently available software solutions were unsatisfactory. We would
be very happy to welcome you in Bochum this year.
 
Fees
The exact fees will be announced soon.
 
Social event
A dinner at the  <http://www.bergbaumuseum.de/> Deutsches
Bergbau-Museum-Museum (German Mining Museum)
with a tour through the visitor mine and up the headframe.
 
More information
 <http://open-ms.sourceforge.net/um2015/>
http://open-ms.sourceforge.net/um2015/ 
 
See you in Bochum
   The OpenMS Team and the local hosts
 
 
--
PD Dr. Martin Eisenacher
Research Area Medical Bioinformatics
Medizinisches Proteom-Center (MPC)
Ruhr-Universität Bochum
 
phone: +49 / 234 / 32 - 29288
fax: +49 / 234 / 32 - 14554
 <http://www.medizinisches-proteom-center.de/Bioinfo>
http://www.medizinisches-proteom-center.de/Bioinfo
 
 

Re: [Psidev-ms-dev] HUPO PSI 2015 spring workshop in Seattle April 13, 14, 15

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

Hi everyone, we are about a month away from the beginning of the PSI
workshop in Seattle. Thank you to everyone who has already registered and
made arrangements. For everyone else who is intending to come or is still
thinking about it, now is the perfect time to register your intent to
participate in the workshop. Work will continue on mzML, mzTab, PROXI, and
PEFF, as well as aligned metabolomics efforts, and efforts to integrate
proteomics and genomics data. Wide participation is what makes the work of
the PSI successful.



Registration and logistical information may be found here:



http://www.psidev.info/content/hupo-psi-meeting-2015



Please do register soon so that I can have accurate participant numbers for
catering.



Please let me know if you have any questions. I look forward to seeing you
in Seattle!



Regards,

Eric







*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Wednesday, December 10, 2014 7:02 AM
*To:* psi...@eb...; psi...@li...;
psi...@li...
*Cc:* Eric Deutsch
*Subject:* HUPO PSI 2015 spring workshop in Seattle April 13, 14, 15



Hi everyone, I am pleased to announce that the 2015 HUPO PSI spring
workshop will be hosted in Seattle at the Institute for Systems Biology on
April 13, 14, 15. Our registration page will open in January, but please
mark your calendars now for full-day sessions all 3 days and plan on
joining us in Seattle to continue important work on standards.



Regards,

Eric

[Psidev-ms-dev] New version 3.74.0 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached you find new version 3.74.0 of the psi-ms.obo file.


Changed CV terms in version 3.74.0 of psi-ms.obo:
=================================================
************ Changed is_a relationship from 'quality estimation method 
details'
************ --> 'statistical threshold'
[Term]
id: MS:1001494
name: no threshold
def: "In case no threshold was used." [PSI:PI]
is_a: MS:1002482 ! statistical threshold

************ Added links to the paper in the definition
[Term]
id: MS:1002406
name: count of identified clusters
def: "The number of protein clusters that have been identified, which 
must match the number of clusters that pass the threshold in the file." 
[DOI:10.1002/pmic.201400080, PMID:25092112]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002405 ! protein cluster details

************ Removed the suffix UNDER DISCUSSION from the following two 
terms
[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is the final set of identifications to be interpreted by 
consuming software. Amongst the set of SpectrumIdentificationList(s) 
that are flagged with the term, each spectrum must not be referenced 
from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is not the final set of identifications to be interpreted by 
consuming software. This term should be used when results are provided 
from multiple search engines for the results from each search engine 
before they are combined to give consensus identifications. Amongst the 
set of SpectrumIdentificationList(s) that are flagged with the term, 
each spectrum may be referenced from more than one 
SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details


New CV terms in version 3.74.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002569
name: ProteomeDiscoverer:Number of Spectra Processed At Once
def: "Number of spectra processed at once in a ProteomeDiscoverer 
search." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002570
name: sequence multiply subsumable protein
def: "A protein for which the matched peptide sequences are the same, or 
a subset of, the matched peptide sequences for two or more other 
proteins combined. These other proteins need not all be in the same 
group." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002571
name: spectrum multiply subsumable protein
def: "A protein for which the matched spectra are the same, or a subset 
of, the matched spectra for two or more other proteins combined. These 
other proteins need not all be in the same group." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship

************ Two new terms for finer granulated distinction between the 
diffe-
************ rent statistical threshold types, needed for mapping file rules
[Term]
id: MS:1002572
name: protein detection statistical threshold
def: "Estimated statistical threshold used for protein detection." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002573
name: spectrum identification statistical threshold
def: "Estimated statistical threshold used for spectrum identification." 
[PSI:MS]
is_a: MS:1002482 ! statistical threshold

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.74.0_rc1 of psi-ms.obo

[Daniel S. <dsc...@ip...>]

Dear all.

I tend agree with Andy here. For DL ontologies where the is_a needs to 
be logically correct at all times for automated reasoning, the OBO 
Foundry naming conventions won't allow errant classifications like
/ no/ /threshold is_a statistical threshold/
But for PSI, where we have a simple taxonomic CV driving an intuitive 
user friendly parameter annotation, I  guess its fine in the pragmatic 
sense. You could read the terms
as being linguistic ellipses, where the implicit postfix " /indicating 
parameter/" is left out, e.g. a better but longer name would be
/no/ /threshold indicating  parameter is_a statistical threshold/ 
indicating /parameter/

How this would be represented in OWL DL is dependent on the type of 
reasoning you envision, which is impacted by closed vs. open world 
assumption / the expressivity regime of your choice. That is why I 
always fought for defining best-practice patterns for a particular 
regime (use case in mind), i.e. as an ontology design pattern in a 
corresponding pattern repository, e.g.
http://ontologydesignpatterns.org/wiki/Submissions:*Parameter*

In formal ontologies one could allow such indicators under an 
appropriate information artefact/parameter/threshold 
parameter/parameter_indicating_no_threashold
in case of a simple taxonomy, or for the case of axiomatic class 
definitions,  one of the many possibilities using BFO and a lacks object 
property is mentioned in
http://ontology.buffalo.edu/medo/negative_findings.pdf
But all this is a bit remote for our scope ;-)

Best regards,
     Daniel.

Am 09.03.2015 um 12:14 schrieb Jones, Andy:
> Hi Steffen,
>
> We need to put this term into data formats so it is clear that the user is saying - I did not use a threshold on my data. If there is a blank, we cannot distinguish between a badly formatted file (i.e. I used a threshold but forgot to tell you) or the no threshold case. The PSI-MS CV is generally a pragmatic collection of terms rather than an ontology, but I agree it is sensible for us to be aware of good practice in ontologies. Under good practice ontology guidelines, how is it expected that one can distinguish the "null" case from the "zero" case - as in this example?
>
> Best wishes
> Andy
>
>
>
>
> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: 09 March 2015 11:07
> To: Mass spectrometry standard development
> Cc: psi...@li...; Daniel Schober; psi...@li...
> Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Release candidate 3.74.0_rc1 of psi-ms.obo
>
> Hi,
>
> On Fr, 2015-03-06 at 17:03 +0100, mayerg97 wrote:
> ...
>> Changed CV terms in version 3.74.0_rc1 of psi-ms.obo:
>> =====================================================
>> ************ Changed is_a relationship from 'quality estimation method
>> details'
>> ************ --> 'statistical threshold'
>> [Term]
>> id: MS:1001494
>> name: no threshold
>> def: "In case no threshold was used." [PSI:PI]
>> is_a: MS:1002482 ! statistical threshold
> There are some ontology guidelines, which strongly discourage the uses of negative Terms "no xxx" . In practice, they are sometimes added for pragmatic reasons, but why not leaving blank if no threshold is used ? Since this is a "Changed term", it must have been present before, but I just wanted to mention for the future.
>
> Yours,
> Steffen
>
>
>
>

-- 

Dr. Daniel Schober
Leibniz Institute of Plant Biochemistry, http://www.IPB-Halle.de
Dept. for Stress and Developmental Biology Bioinformatics & Mass Spectrometry
Weinberg 3 Tel. +49 (0) 345 5582 - 1476
06120 Halle

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.74.0_rc1 of psi-ms.obo

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

Hi Steffen,

We need to put this term into data formats so it is clear that the user is saying - I did not use a threshold on my data. If there is a blank, we cannot distinguish between a badly formatted file (i.e. I used a threshold but forgot to tell you) or the no threshold case. The PSI-MS CV is generally a pragmatic collection of terms rather than an ontology, but I agree it is sensible for us to be aware of good practice in ontologies. Under good practice ontology guidelines, how is it expected that one can distinguish the "null" case from the "zero" case - as in this example?

Best wishes
Andy 




-----Original Message-----
From: Steffen Neumann [mailto:sne...@ip...] 
Sent: 09 March 2015 11:07
To: Mass spectrometry standard development
Cc: psi...@li...; Daniel Schober; psi...@li...
Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Release candidate 3.74.0_rc1 of psi-ms.obo

Hi,

On Fr, 2015-03-06 at 17:03 +0100, mayerg97 wrote:
...
> Changed CV terms in version 3.74.0_rc1 of psi-ms.obo:
> =====================================================
> ************ Changed is_a relationship from 'quality estimation method 
> details'
> ************ --> 'statistical threshold'
> [Term]
> id: MS:1001494
> name: no threshold
> def: "In case no threshold was used." [PSI:PI]
> is_a: MS:1002482 ! statistical threshold

There are some ontology guidelines, which strongly discourage the uses of negative Terms "no xxx" . In practice, they are sometimes added for pragmatic reasons, but why not leaving blank if no threshold is used ? Since this is a "Changed term", it must have been present before, but I just wanted to mention for the future.

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

Re: [Psidev-ms-dev] Release candidate 3.74.0_rc1 of psi-ms.obo

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

Hi,

On Fr, 2015-03-06 at 17:03 +0100, mayerg97 wrote:
...
> Changed CV terms in version 3.74.0_rc1 of psi-ms.obo:
> =====================================================
> ************ Changed is_a relationship from 'quality estimation method 
> details'
> ************ --> 'statistical threshold'
> [Term]
> id: MS:1001494
> name: no threshold
> def: "In case no threshold was used." [PSI:PI]
> is_a: MS:1002482 ! statistical threshold

There are some ontology guidelines, which strongly discourage 
the uses of negative Terms "no xxx" . In practice, they are 
sometimes added for pragmatic reasons, but why not 
leaving blank if no threshold is used ? Since this is a "Changed term",
it must have been present before, but I just wanted to mention 
for the future.

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

[Psidev-ms-dev] Release candidate 3.74.0_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.74.0_rc1 of the psi-ms.obo file.


Changed CV terms in version 3.74.0_rc1 of psi-ms.obo:
=====================================================
************ Changed is_a relationship from 'quality estimation method 
details'
************ --> 'statistical threshold'
[Term]
id: MS:1001494
name: no threshold
def: "In case no threshold was used." [PSI:PI]
is_a: MS:1002482 ! statistical threshold

************ Added links to the paper in the definition
[Term]
id: MS:1002406
name: count of identified clusters
def: "The number of protein clusters that have been identified, which 
must match the number of clusters that pass the threshold in the file." 
[DOI:10.1002/pmic.201400080, PMID:25092112]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002405 ! protein cluster details

************ Removed the suffix UNDER DISCUSSION from the following two 
terms
[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is the final set of identifications to be interpreted by 
consuming software. Amongst the set of SpectrumIdentificationList(s) 
that are flagged with the term, each spectrum must not be referenced 
from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is not the final set of identifications to be interpreted by 
consuming software. This term should be used when results are provided 
from multiple search engines for the results from each search engine 
before they are combined to give consensus identifications. Amongst the 
set of SpectrumIdentificationList(s) that are flagged with the term, 
each spectrum may be referenced from more than one 
SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details


New CV terms in version 3.74.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002569
name: ProteomeDiscoverer:Number of Spectra Processed At Once
def: "Number of spectra processed at once in a ProteomeDiscoverer 
search." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002570
name: sequence multiply subsumable protein
def: "A protein for which the matched peptide sequences are the same, or 
a subset of, the matched peptide sequences for two or more other 
proteins combined. These other proteins need not all be in the same 
group." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002571
name: spectrum multiply subsumable protein
def: "A protein for which the matched spectra are the same, or a subset 
of, the matched spectra for two or more other proteins combined. These 
other proteins need not all be in the same group." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship

************ Two new terms for finer granulated distinction between the 
diffe-
************ rent statistical threshold types, needed for mapping file rules
[Term]
id: MS:1002572
name: protein detection statistical threshold
def: "Estimated statistical threshold used for protein detection." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002573
name: spectrum identification statistical threshold
def: "Estimated statistical threshold used for spectrum identification." 
[PSI:MS]
is_a: MS:1002482 ! statistical threshold

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 3.73.0 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached you find the new version 3.73.0 of the psi-ms.obo file.

It contains new terms for localization score thresholds, added string 
value-types
for PTM location scores, and some updated definitions for PTM site 
location terms.


Changed CV terms in version 3.73.0 of psi-ms.obo:
==================================================
************ Updated the definitions of the following terms:
[Term]
id: MS:1001969
name: phosphoRS score
def: "phosphoRS score for PTM site location at the PSM-level." 
[DOI:10.1021/pr200611n, PMID:22073976]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1001985
name: Ascore
def: "A-score for PTM site location at the PSM-level." 
[DOI:10.1038/nbt1240, PMID:16964243]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002536
name: D-Score
def: "D-Score for PTM site location at the PSM-level." 
[DOI:10.1002/pmic.201200408, PMID:23307401]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002537
name: MD-Score
def: "MD-Score for PTM site location at the PSM-level." 
[DOI:10.1074/mcp.M110.003830–1, PMID:21057138]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002550
name: peptide:phosphoRS score
def: "phosphoRS score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002551
name: peptide:Ascore
def: "A-score score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002553
name: peptide:D-Score
def: "D-Score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002554
name: peptide:MD-Score
def: "MD-Score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

************ Renamed from 'order' --> 'modification index'
[Term]
id: MS:1002504
name: modification index
def: "The order of modifications to be referenced elsewhere in the 
document." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters

************ Added string value-type\:string and
************ relationship: has_regexp MS:10012505 ! regular expression 
for modification localization scoring
************ to all PSM-level PTM localization score's and
************ to all peptide-level PTM localization score's, e.g.
[Term]
id: MS:1002551
name: peptide:Ascore
def: "A-score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring



New CV terms in version 3.73.0 of psi-ms.obo:
=============================================
************ New terms for PTM localization score thresholds.
[Term]
id: MS:1002555
name: PTM localization score threshold
def: "Threshold for PTM site location score." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1002556
name: Ascore threshold
def: "Threshold for Ascore PTM site location score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002557
name: D-Score threshold
def: "Threshold for D-score PTM site location score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002558
name: MD-Score threshold
def: "Threshold for MD-score PTM site location score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002559
name: H-Score threshold
def: "Threshold for H-score PTM site location score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:10025560
name: DeBunker:score threshold
def: "Threshold for DeBunker PTM site location score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002561
name: Mascot:PTM site assignment confidence threshold
def: "Threshold for Mascot PTM site assignment confidence." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002562
name: MSQuant:PTM-score threshold
def: "Threshold for MSQuant:PTM-score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002563
name: MaxQuant:PTM Score threshold
def: "Threshold for MaxQuant:PTM Score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002564
name: MaxQuant:P-site localization probability threshold
def: "Threshold for MaxQuant:P-site localization probability." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002565
name: MaxQuant:PTM Delta Score threshold
def: "Threshold for MaxQuant:PTM Delta Score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002566
name: MaxQuant:Phospho (STY) Probabilities threshold
def: "Threshold for MaxQuant:Phospho (STY) Probabilities." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002567
name: phosphoRS score threshold
def: "Threshold for phosphoRS score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002568
name: phosphoRS site probability threshold
def: "Threshold for phosphoRS site probability." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de