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From: Chris T. <chr...@eb...> - 2012-02-22 11:08:38
|
Sorry -- didn't mean to follow on from the thread or anything... C. On 22/02/2012 10:54, Chris Taylor wrote: > Is this interesting? > > http://en.wikipedia.org/wiki/Data_Format_Description_Language > > C. > > > On 20/02/2012 15:21, Gerhard Mayer wrote: >> Dear community, >> >> attached there's the psi-ms.obo release candidate 3.20.0_rc1. >> It contains some terms used by the ProteinScape LIMS system. >> >> Comments, proposals and suggestions are as always welcome. >> >> 1. Changes to existing CV terms: >> ================================ >> ************ The following terms changed it's name from >> ProteomeDiscoverer:Mascot:Use MudPIT Scoring to the more general >> term Mascot:use MudPIT scoring >> [Term] >> id: MS:1001667 >> name: Mascot:use MudPIT scoring >> def: "Determines whether to use MudPIT instead of normal >> scoring." [PSI:MS] >> xref: value-type:xsd\:boolean "The allowed value-type for this >> CV term." >> is_a: MS:1001302 ! search engine specific input parameter >> >> >> 2. Newly added CV terms: >> ======================== >> [Term] >> id: MS:1001963 >> name: ProteinExtractor:Weighting >> def: "Weighting factor for protein list compilation by >> ProteinExtractor." [PSI:MS] >> xref: value-type:xsd\:double "The allowed value-type for this CV >> term." >> is_a: MS:1001302 ! search engine specific input parameter >> >> [Term] >> id: MS:1001964 >> name: ProteinScape:2nd round Mascot >> def: "Flag indicating a second round search with Mascot." [PSI:MS] >> xref: value-type:xsd\:boolean "The allowed value-type for this >> CV term." >> is_a: MS:1001302 ! search engine specific input parameter >> >> [Term] >> id: MS:1001965 >> name: ProteinScape:2nd round Phenyx >> def: "Flag indicating a second round search with Phenyx." [PSI:MS] >> xref: value-type:xsd\:boolean "The allowed value-type for this >> CV term." >> is_a: MS:1001302 ! search engine specific input parameter >> >> Best regards, >> Gerhard >> >> >> >> ------------------------------------------------------------------------------ >> Try before you buy = See our experts in action! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-dev2 >> >> >> >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >> >> >> >> ----- >> No virus found in this message. >> Checked by AVG - www.avg.com >> Version: 2012.0.1913 / Virus Database: 2113/4820 - Release Date: 02/19/12 > -- _______________________ chr...@eb... http://mibbi.org/ |
From: Chris T. <chr...@eb...> - 2012-02-22 10:54:30
|
Is this interesting? http://en.wikipedia.org/wiki/Data_Format_Description_Language C. On 20/02/2012 15:21, Gerhard Mayer wrote: > Dear community, > > attached there's the psi-ms.obo release candidate 3.20.0_rc1. > It contains some terms used by the ProteinScape LIMS system. > > Comments, proposals and suggestions are as always welcome. > > 1. Changes to existing CV terms: > ================================ > ************ The following terms changed it's name from > ProteomeDiscoverer:Mascot:Use MudPIT Scoring to the more general > term Mascot:use MudPIT scoring > [Term] > id: MS:1001667 > name: Mascot:use MudPIT scoring > def: "Determines whether to use MudPIT instead of normal > scoring." [PSI:MS] > xref: value-type:xsd\:boolean "The allowed value-type for this > CV term." > is_a: MS:1001302 ! search engine specific input parameter > > > 2. Newly added CV terms: > ======================== > [Term] > id: MS:1001963 > name: ProteinExtractor:Weighting > def: "Weighting factor for protein list compilation by > ProteinExtractor." [PSI:MS] > xref: value-type:xsd\:double "The allowed value-type for this CV > term." > is_a: MS:1001302 ! search engine specific input parameter > > [Term] > id: MS:1001964 > name: ProteinScape:2nd round Mascot > def: "Flag indicating a second round search with Mascot." [PSI:MS] > xref: value-type:xsd\:boolean "The allowed value-type for this > CV term." > is_a: MS:1001302 ! search engine specific input parameter > > [Term] > id: MS:1001965 > name: ProteinScape:2nd round Phenyx > def: "Flag indicating a second round search with Phenyx." [PSI:MS] > xref: value-type:xsd\:boolean "The allowed value-type for this > CV term." > is_a: MS:1001302 ! search engine specific input parameter > > Best regards, > Gerhard > > > > ------------------------------------------------------------------------------ > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > > > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > ----- > No virus found in this message. > Checked by AVG - www.avg.com > Version: 2012.0.1913 / Virus Database: 2113/4820 - Release Date: 02/19/12 -- _______________________ chr...@eb... http://mibbi.org/ |
From: Gerhard M. <Ger...@ru...> - 2012-02-20 15:21:54
|
Dear community, attached there's the psi-ms.obo release candidate 3.20.0_rc1. It contains some terms used by the ProteinScape LIMS system. Comments, proposals and suggestions are as always welcome. 1. Changes to existing CV terms: ================================ ************ The following terms changed it's name from ProteomeDiscoverer:Mascot:Use MudPIT Scoring to the more general term Mascot:use MudPIT scoring [Term] id: MS:1001667 name: Mascot:use MudPIT scoring def: "Determines whether to use MudPIT instead of normal scoring." [PSI:MS] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001302 ! search engine specific input parameter 2. Newly added CV terms: ======================== [Term] id: MS:1001963 name: ProteinExtractor:Weighting def: "Weighting factor for protein list compilation by ProteinExtractor." [PSI:MS] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1001964 name: ProteinScape:2nd round Mascot def: "Flag indicating a second round search with Mascot." [PSI:MS] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1001965 name: ProteinScape:2nd round Phenyx def: "Flag indicating a second round search with Phenyx." [PSI:MS] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001302 ! search engine specific input parameter Best regards, Gerhard -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |
From: Gerhard M. <Ger...@ru...> - 2012-02-20 08:33:47
|
Dear community, I updated the psi-ms.obo file to the version 3.19.0 in the SourceForge CVS. It contains the new term 'peptide spectrum match scoring algorithm' instead of the 'scoring model' and a term for the use of C13 peaks in peak detection. 1. Changes to existing CV terms: ================================ ************ TODOscoring model is now obsoleted (replaced by peptide spectrum match scoring algorithm) [Term] id: MS:1001065 name: TODOscoring model def: "OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms!" [PSI:PI] comment: This term was made obsolete and is replaced by the term (MS:1001961). is_a: MS:1001249 ! search input details is_obsolete: true replaced_by: MS:1001961 ************ The following terms changed it's name from ProteomeDiscoverer:Mascot:Instrument to the more general term Mascot:Instrument [Term] id: MS:1001656 name: Mascot:Instrument def: "Type of instrument used to acquire the data in the raw file." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001302 ! search engine specific input parameter 2. Newly added CV terms: ======================== [Term] id: MS:1001961 name: peptide spectrum match scoring algorithm def: "Algorithm used to score the match between a spectrum and a peptide ion." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1001962 name: Mascot:C13 counts def: "C13 peaks to use in peak detection." [PSI:MS] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1001302 ! search engine specific input parameter Best regards, Gerhard -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |
From: Eric D. <Eri...@sy...> - 2012-02-14 00:30:28
|
Hi everyone, this is a reminder about the PSI MSS WG teleconference call tomorrow, Tuesday, at the usual time. 08:00 San Francisco 11:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + Finland: 080011569 + UK: 08081095644 + USA: 1-866-832-8490 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) Plans and agenda for spring PSI workshop in San Diego March 12-14 2) mzML status 3) TraML status 4) Discuss controlled vocabulary items 5) MIAPE – MS 6) MIAPE – Quant Next meeting: - Feb 28 8am Seattle Time? |
From: Gerhard M. <Ger...@ru...> - 2012-02-13 16:06:04
|
Dear proteomics community, Dear community, attached there's a proposal for the release candidate 3.19.0_rc1 of psi-ms.obo. It contains the terms proposed by Salvador for use in the MIAPE-MSI, with the term name 'aquisition instrument type' instead of the 'scoring model'. Comments, proposals and suggestions are as always welcome. 1. Changes to existing CV terms: ================================ ************ Mascot:ProteinScoringMethod now is_a aquisition instrument type [Term] id: MS:1001318 name: Mascot:ProteinScoringMethod xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001302 ! search engine specific input parameter is_a: MS:1001961 ! aquisition instrument type ************ Phenyx:Scoring Model now is_a aquisition instrument type [Term] id: MS:1001376 name: Phenyx:Scoring Model xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001302 ! search engine specific input parameter is_a: MS:1001961 ! aquisition instrument type ************ ProteinExtractor:Methodname now is_a aquisition instrument type [Term] id: MS:1001424 name: ProteinExtractor:Methodname xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001302 ! search engine specific input parameter is_a: MS:1001961 ! aquisition instrument type ************ ProteomeDiscoverer:Mascot:Instrument is now obsoleted (replaced by Mascot:Instrument) [Term] id: MS:1001656 name: ProteomeDiscoverer:Mascot:Instrument def: "OBSOLETE: Type of instrument used to acquire the data in the raw file." [PSI:MS] comment: This term was made obsolete and is replaced by the more general term Mascot:Instrument (MS:1001962). xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001302 ! search engine specific input parameter is_obsolete: true replaced_by: MS:1001962 2. Newly added CV terms: ======================== [Term] id: MS:1001961 name: aquisition instrument type def: "Descriptor of the scoring algorithm in the search engine describing the aquisition instrument type." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1001962 name: Mascot:Instrument def: "Type of instrument used to acquire the data in the raw file." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001302 ! search engine specific input parameter is_a: MS:1001961 ! aquisition instrument type Best regards, Gerhard Am 07.02.2012 17:43, schrieb Salvador Martínez de Bartolomé: > Dear all: > Just in case you find it appropriate now, I have some suggestions to > share with you regarding the terms needed to the MIAPE MSI validation on the > mzIdentML: > - New term “scoring model”. It maps with the MIAPE MSI where we > have: "Descriptor of the scoring algorithm in the search engine (such as > ESI-TRAP in Mascot, ESI)" > - To assign the following terms as children (is_a relationship) of > the new "scoring model": > - MS:1001318 (Mascot:ProteinScoringMethod) > - MS:1001376 (Phenyx:Scoring Model) > - MS:1001424 (ProteinExtractor:Methodname ) (I'm not sure if > this term belongs to the "scoring model" category, I'm not familiar with > ProteinExtractor at all). > - MS:1001656 (ProteomeDiscoverer:Mascot:Instrument) > - New term "Mascot:Instrument" (the same as previous one, > but just for MASCOT parameters) > - Any other term? > Also, feel free to comment on the list. > Cheers, > > 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/ > > > > -----Mensaje original----- > De: Jones, Andy [mailto:And...@li...] > Enviado el: 07 February 2012 16:53 > Para: 'psi...@li...' > CC: Ghali, Fawaz; 'Terry Farrah' > Asunto: Re: [Psidev-pi-dev] Decision on the new version 1.1.0 mzIdentML > > While I remember, either in San Diego or on a conference call we should > finalise the terms for protein grouping proposed a while back by Terry > Farrah. We had a call on this issue and generally I think we were in favour > of including these suggestions but I don't think they got filtered through > to the CV. Fawaz in my group is currently working on implementing protein > inference terms in our local tools, so this has given me some impetus to get > this solved! I've re-attached the relevant spreadsheets here. > > Feel free to comment on the list with suggestions etc. > > Cheers > Andy > > > >> -----Original Message----- >> From: Jones, Andy [mailto:And...@li...] >> Sent: 15 August 2011 10:47 >> To: 'psi...@li...' >> Subject: [Psidev-pi-dev] FW: Decision on the new version 1.1.0 >> mzIdentML >> >> Hi all, >> >> The mzIdentML public comment phase has now been completed. There are >> comments from one reviewer below, which just require a bit of tidying >> up on the website and specification document. >> >> We also had some comments on the public page and powerpoints forwarded >> on the mailing list from Terry Farrah, who makes some useful points on >> CV terms for protein grouping, also see his spreadsheet here: >> https://docs.google.com/spreadsheet/ccc?authkey=CLyO_M4M&key=0Au0Yx >> TvKYBycdEF5ZkxGMXlpSDZ0S29KWXItZGJ6Z2c&authkey=CLyO_M4M#gid=0 >> >> I haven't critically reviewed these in detail but from a first look, >> it appears that these are all sensible suggestions that we should consider > taking on board. >> Can someone remind me what the process is for changing or updating CV >> terms? My preference would be to get these terms resolved outside of >> the PSI process i.e. get the v1.1 schema released this week to avoid >> further delays then spend a few weeks making sure we have a set of CV >> terms we are happy with. Does this sound reasonable? If so, I'll get >> the changes made to the specification document and website this week, >> then we can announce the completion of this process. >> Best wishes >> Andy >> >> >> >> >> >> >> >>> -----Original Message----- >>> From: Christian Stephan [mailto:chr...@ru...] >>> Sent: 15 August 2011 09:08 >>> To: Jones, Andy >>> Subject: Decision on the new version 1.1.0 mzIdentML >>> >>> Dear Andy, >>> after the public Review phase and two invited speaker I decide to >>> accept your new mzIdentML version after minor changes based on the >>> comments of >> the >>> reviewer (see below). >>> So please answer to the comments and add also the full documentation >>> to >> the >>> website. Please come back to me if this is done. After this I will >>> official announce the release of mzIdentML. >>> >>> Best regards, >>> >>> Christian >>> >>> >>> Reviewer 1: >>> My lab reviewed the previous version of this file when it was called >>> analysisXML. I was positive about it then, and I’m even more >>> positive about it now. The new name, mzIdentML is a great >>> improvement and the changes >> made >>> to the schema and to the specification document since v1.0.0 are all >>> welcome. >>> Need and Scope >>> Such a standard is very much needed. Many people, including some >>> core facilities, still only provide simple lists of proteins found >>> with no other detail so the sooner we can get people adopting >>> mzIdentML the better. It will not only improve scientists’ >>> understanding of the provenance of results, it should also make it >>> much easier for people to deposit their data in repositories such as > PRIDE. >>> In some ways this standard seems long overdue, but given the rapid >>> development of the peptide identification field in recent years it >>> would have been a mistake to rush this out earlier when techniques >>> such as decoys and spectral library searching were not mature. >>> The scope of the standard is well defined – to my mind the >>> boundaries of the use cases are drawn in the right places, e.g. no >>> support for quantitative information and no anonymous biomarker > discovery data. >>> Specification Document >>> The specification document (mzIdentML1.1.0.doc) is missing from the >>> PSI >> page >>> (http://www.psidev.info/index.php?q=node/453) so my review is based >>> on a June 13 version of the file retrieved from Google Code. >>> Obviously this omission needs fixing. >>> The specification is clearly described and materials are well >>> organised. I found the example files at Google Code particularly >>> useful to understand how things work. I don’t know if these examples >>> are an official part of the process but it might be advantageous if >>> at least some of them were accessible direct from the PSI page. >>> The specification seems easier to follow than the previous version. >>> The direct adoption of FuGE instead of FuGE-light makes things a lot >>> simpler. It seems that some of the more non-standard use cases are >>> also better >> explained >>> than before, e.g. multiple search engines. The catchall solution of >>> using multiple mzIdent files for complex workflows is facile but >>> effective for even the most exotic use cases that I could think of. >>> I only have a couple of minor comments on the detail of the document: >>> Section 4, bullet point 3 (page 6): Should it not be STRONGLY >>> RECOMMENDED that mzML is used? I understand the need to support >>> legacy formats but it really doesn’t seem sensible to encourage their > use at all. >>> Section 5.1.3 (page 9). Is the example XML code correct? I don’t see >>> how this references the third spectrum in the file. Capitalisation >>> of tags here is also not consistent with the rest of the document. >>> Conclusion >>> As I said in the previous review, a standard in this area is much >>> needed and mzIdent appears to address the need well. The authors >>> have done well to improve the standard further, clearly taking on >>> board comments from reviewers and others. I have no doubt that >>> further improvements could be made, but I see no obvious problems in >>> v1.1.0 and my recommendation would >> be >>> to get this released and adopted as soon as practicable. >>> >>> >>> >>> -- >>> Dr. Christian Stephan >>> Head of Bioinformatics >>> Medizinisches Proteom-Center >>> Zentrum Klinische Forschung (ZKF E.141) Ruhr-Universität-Bochum >>> 44870 Bochum >>> Phone: +49 234 32 29 288 >>> Fax: +49 234 32 14 554 >>> http://www.medizinisches-proteom-center.de >>> >> >> ---------------------------------------------------------------------- >> -------- uberSVN's rich system and user administration capabilities >> and model configuration take the hassle out of deploying and managing >> Subversion and the tools developers use with it. Learn more about >> uberSVN and get a free download at: >> http://p.sf.net/sfu/wandisco-dev2dev >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |
From: Eric D. <ede...@sy...> - 2012-02-07 16:34:00
|
_______________________________________________ Psi-announce mailing list Psi...@eb... http://listserver.ebi.ac.uk/mailman/listinfo/psi-announce |
From: Eric D. <ede...@sy...> - 2012-02-07 16:03:23
|
Hi Gerhard, thank you for your very efficient handling of these CV issues. All the below looks good to me except for one. I would suggest we rename" id: MS:1001955 name: NoCleavage to: name: no cleavage to follow our natural English convention, unless there is a very good reason to leave it like this? Thanks, Eric > -----Original Message----- > From: Gerhard Mayer [mailto:Ger...@ru...] > Sent: Monday, February 06, 2012 1:00 AM > To: psi...@li...; psidev-pi- > de...@li...; Mass spectrometry standard development > Subject: [Psidev-ms-vocab] Release candidate psi-ms.obo 3.18.0_rc2 > > Dear community, > > attached there's the release candidate 3.18.0_rc2 for the next > psi-ms.obo version. > Comments and suggestions are welcome. > > If there are no objections to this release candidates, > I plan to update the controlled vocabulary in about five days. > > > 1. Changes to existing CV terms: > ================================ > ************ Renamed: spectrum form database nativeID format --> > spectrum from database integer nativeID format > [Term] > id: MS:1001526 > name: spectrum from database integer nativeID format > def: "databasekey=xsd:long." [PSI:MS] > comment: A unique identifier of a spectrum stored in a database (e.g. a > PRIMARY KEY identifier). > is_a: MS:1000767 ! native spectrum identifier format > > ************ Renamed: spectrum form database nativeID format --> > spectrum from database string nativeID format > [Term] > id: MS:1001532 > name: spectrum from database string nativeID format > def: "databasekey=xsd:string." [PSI:MS] > comment: A unique identifier of a spectrum stored in a database (e.g. a > PRIMARY KEY identifier). > is_a: MS:1000767 ! native spectrum identifier format > is_a: MS:1001529 ! spectra data details > > /************ Renamed: LC-MS label-free --> LC-MS label-free > quantitation analysis > [Term] > id: MS:1001834 > name: LC-MS label-free quantitation analysis > def: "LC-MS label-free workflow (RT m/z map)." [PSI:PI] > is_a: MS:1001833 ! quantitation analysis summary > > /************ Renamed: SILAC --> SILAC quantitation analysis > [Term] > id: MS:1001835 > name: SILAC quantitation analysis > def: "SILAC workflow (heavy, light, and sometimes medium peak)." > [PSI:PI] > is_a: MS:1001833 ! quantitation analysis summary > > /************ Renamed: spectral counting --> spectral counting > quantitation analysis > [Term] > id: MS:1001836 > name: spectral counting quantitation analysis > def: "Spectral counting workflow (number of identified MS/MS spectra as > approximation of peptide / protein quant)." [PSI:PI] > is_a: MS:1001833 ! quantitation analysis summary > > /************ Renamed: iTraq --> iTraq quantitation analysis > [Term] > id: MS:1001837 > name: iTraq quantitation analysis > def: "iTraq workflow (reporter ions on MS/MS level)." [PSI:PI] > is_a: MS:1001833 ! quantitation analysis summary > > ************ Renamed: SRM --> SRM quantitation analysis > [Term] > id: MS:1001838 > name: SRM quantitation analysis > def: "Selected Reaction Monitoring workflow (XIC quant. of precursor / > fragment mass pair)." [PSI:PI] > is_a: MS:1001833 ! quantitation analysis summary > > ************ Renamed: metabolic labeling 14N / 15N --> metabolic > labeling 14N / 15N quantitation analysis > [Term] > id: MS:1001839 > name: metabolic labeling 14N / 15N quantitation analysis > def: "Metabolic labeling workflow (heavy and light versions of > peptides, > depending on number of nitrogens)." [PSI:PI] > is_a: MS:1001833 ! quantitation analysis summary > > *********** made the term NoEnzyme obsolete > [Term] > id: MS:1001091 > name: NoEnzyme > is_a: MS:1001045 ! cleavage agent name > comment: This term was made obsolete because it is ambiguous and is > replaced by NoCleavage (MS:1001955) and unspecific cleavage > (MS:1001956). > is_obsolete: true > > *********** changed the referencing regexp to MS:1001957 > [Term] > id: MS:1001915 > name: leukocyte elastase > def: "Enzyme leukocyte elastase (EC 3.4.21.37)." > [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.37 > "BRENDA"] > is_a: MS:1001045 ! cleavage agent name > relationship: has_regexp MS:1001957 ! (?<=[ALIV])(?!P) > > *********** changed the referencing regexp to MS:1001958 > [Term] > id: MS:1001916 > name: proline endopeptidase > def: "Enzyme proline endopeptidase (EC 3.4.21.26)." > [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.26 > "BRENDA"] > is_a: MS:1001045 ! cleavage agent name > relationship: has_regexp MS:1001958 ! (?<=[HKR]P)(?!P) > > *********** changed the referencing regexp to MS:1001959 > [Term] > id: MS:1001917 > name: glutamyl endopeptidase > def: "Enzyme glutamyl endopeptidase (EC 3.4.21.19)." > [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.19 > "BRENDA"] > synonym: "staphylococcal protease" EXACT [] > synonym: "Glu-C" EXACT [] > is_a: MS:1001045 ! cleavage agent name > relationship: has_regexp MS:1001959 ! (?<=[^E]E) > > *********** changed the referencing regexp to MS:1001960 > [Term] > id: MS:1001918 > name: 2-iodobenzoate > def: "Chemical iodobenzoate. Cleaves after W." > [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pccompound&term > =4739928 > "PubChem"] > is_a: MS:1001045 ! cleavage agent name > relationship: has_regexp MS:1001960 ! (?<=W) > > > > 2. Newly added CV terms: > ======================== > [Term] > id: MS:1001946 > name: PEAKS Studio > def: "PEAKS Studio software for data analysis." [PSI:MS] > is_a: MS:1001139 ! quantitation software name > is_a: MS:1001456 ! analysis software > is_a: MS:1001457 ! data processing software > > [Term] > id: MS:1001947 > name: PEAKS Online > def: "PEAKS Online software for high throughput data analysis." > [PSI:MS] > is_a: MS:1001139 ! quantitation software name > is_a: MS:1001456 ! analysis software > is_a: MS:1001457 ! data processing software > > [Term] > id: MS:1001948 > def: "PEAKS Node software for high throughput data analysis." [PSI:MS] > is_a: MS:1001139 ! quantitation software name > is_a: MS:1001456 ! analysis software > is_a: MS:1001457 ! data processing software > > [Term] > id: MS:1001949 > name: BSI software > def: "Bioinformatics Solutions Inc. Software for data processing and > analysis." [PSI:MS] > is_a: MS:1000531 ! software > > [Term] > id: MS:1001950 > name: PEAKS:peptideScore > def: "The PEAKS peptide '-10lgP Score'." [PSI:MS] > xref: value-type:xsd\:double "The allowed value-type for this CV term." > is_a: MS:1001143 ! search engine specific score for peptides > is_a: MS:1001153 ! search engine specific score > > [Term] > id: MS:1001951 > name: PEAKS:proteinScore > def: "The PEAKS protein '-10lgP Score'." [PSI:MS] > xref: value-type:xsd\:double "The allowed value-type for this CV term." > is_a: MS:1001116 ! single protein result details > is_a: MS:1001153 ! search engine specific score > > [Term] > id: MS:1001952 > name: ZCore:probScore > def: "The ZCore probability score." [PSI:MS] > xref: value-type:xsd\:double "The allowed value-type for this CV term." > is_a: MS:1001143 ! search engine specific score for peptides > is_a: MS:1001153 ! search engine specific score > > [Term] > id: MS:1001953 > name: source interface manufacturer > def: "The source interface manufacturer." [PSI:MS] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > relationship: part_of MS:1001931 ! source interface > > [Term] > id: MS:1001954 > name: acquisition parameter > def: "Parameters used in the mass spectrometry acquisition." [PSI:MS] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > relationship: part_of MS:1001458 ! spectrum generation information > > [Term] > id: MS:1001955 > name: NoCleavage > def: "No cleavage." [PSI:MS] > is_a: MS:1001045 ! cleavage agent name > > [Term] > id: MS:1001956 > name: unspecific cleavage > def: "Unspecific cleavage." [PSI:MS] > is_a: MS:1001045 ! cleavage agent name > > [Term] > id: MS:1001957 > name: (?<=[ALIV])(?!P) > is_a: MS:1001180 ! Cleavage agent regular expression > > [Term] > id: MS:1001958 > name: (?<=[HKR]P)(?!P) > is_a: MS:1001180 ! Cleavage agent regular expression > > [Term] > id: MS:1001959 > name: (?<=[^E]E) > is_a: MS:1001180 ! Cleavage agent regular expression > > [Term] > id: MS:1001960 > name: (?<=W) > is_a: MS:1001180 ! Cleavage agent regular expression > > > Best regards, > Gerhard > > -- > --- > Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer > BioInformatik > Medizinisches-Proteom-Center (MPC) > Ruhr-Universität Bochum > Zentrum für klinische Forschung I (ZKF I) > E.042 > Universitätsstrasse 150 > D-44801 Bochum > > Phone: +49(0)234/32-29836 > Fax: +49(0)234/32-14554 > Email: Ger...@ru... > Web: http://www.medizinisches-proteom-center.de |
From: Gerhard M. <Ger...@ru...> - 2012-02-06 09:00:34
|
Dear community, attached there's the release candidate 3.18.0_rc2 for the next psi-ms.obo version. Comments and suggestions are welcome. If there are no objections to this release candidates, I plan to update the controlled vocabulary in about five days. 1. Changes to existing CV terms: ================================ ************ Renamed: spectrum form database nativeID format --> spectrum from database integer nativeID format [Term] id: MS:1001526 name: spectrum from database integer nativeID format def: "databasekey=xsd:long." [PSI:MS] comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). is_a: MS:1000767 ! native spectrum identifier format ************ Renamed: spectrum form database nativeID format --> spectrum from database string nativeID format [Term] id: MS:1001532 name: spectrum from database string nativeID format def: "databasekey=xsd:string." [PSI:MS] comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). is_a: MS:1000767 ! native spectrum identifier format is_a: MS:1001529 ! spectra data details /************ Renamed: LC-MS label-free --> LC-MS label-free quantitation analysis [Term] id: MS:1001834 name: LC-MS label-free quantitation analysis def: "LC-MS label-free workflow (RT m/z map)." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary /************ Renamed: SILAC --> SILAC quantitation analysis [Term] id: MS:1001835 name: SILAC quantitation analysis def: "SILAC workflow (heavy, light, and sometimes medium peak)." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary /************ Renamed: spectral counting --> spectral counting quantitation analysis [Term] id: MS:1001836 name: spectral counting quantitation analysis def: "Spectral counting workflow (number of identified MS/MS spectra as approximation of peptide / protein quant)." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary /************ Renamed: iTraq --> iTraq quantitation analysis [Term] id: MS:1001837 name: iTraq quantitation analysis def: "iTraq workflow (reporter ions on MS/MS level)." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary ************ Renamed: SRM --> SRM quantitation analysis [Term] id: MS:1001838 name: SRM quantitation analysis def: "Selected Reaction Monitoring workflow (XIC quant. of precursor / fragment mass pair)." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary ************ Renamed: metabolic labeling 14N / 15N --> metabolic labeling 14N / 15N quantitation analysis [Term] id: MS:1001839 name: metabolic labeling 14N / 15N quantitation analysis def: "Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens)." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary *********** made the term NoEnzyme obsolete [Term] id: MS:1001091 name: NoEnzyme is_a: MS:1001045 ! cleavage agent name comment: This term was made obsolete because it is ambiguous and is replaced by NoCleavage (MS:1001955) and unspecific cleavage (MS:1001956). is_obsolete: true *********** changed the referencing regexp to MS:1001957 [Term] id: MS:1001915 name: leukocyte elastase def: "Enzyme leukocyte elastase (EC 3.4.21.37)." [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.37 "BRENDA"] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001957 ! (?<=[ALIV])(?!P) *********** changed the referencing regexp to MS:1001958 [Term] id: MS:1001916 name: proline endopeptidase def: "Enzyme proline endopeptidase (EC 3.4.21.26)." [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.26 "BRENDA"] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001958 ! (?<=[HKR]P)(?!P) *********** changed the referencing regexp to MS:1001959 [Term] id: MS:1001917 name: glutamyl endopeptidase def: "Enzyme glutamyl endopeptidase (EC 3.4.21.19)." [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.19 "BRENDA"] synonym: "staphylococcal protease" EXACT [] synonym: "Glu-C" EXACT [] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001959 ! (?<=[^E]E) *********** changed the referencing regexp to MS:1001960 [Term] id: MS:1001918 name: 2-iodobenzoate def: "Chemical iodobenzoate. Cleaves after W." [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pccompound&term=4739928 "PubChem"] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001960 ! (?<=W) 2. Newly added CV terms: ======================== [Term] id: MS:1001946 name: PEAKS Studio def: "PEAKS Studio software for data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001947 name: PEAKS Online def: "PEAKS Online software for high throughput data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001948 def: "PEAKS Node software for high throughput data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001949 name: BSI software def: "Bioinformatics Solutions Inc. Software for data processing and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1001950 name: PEAKS:peptideScore def: "The PEAKS peptide '-10lgP Score'." [PSI:MS] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001951 name: PEAKS:proteinScore def: "The PEAKS protein '-10lgP Score'." [PSI:MS] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001116 ! single protein result details is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001952 name: ZCore:probScore def: "The ZCore probability score." [PSI:MS] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001953 name: source interface manufacturer def: "The source interface manufacturer." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001931 ! source interface [Term] id: MS:1001954 name: acquisition parameter def: "Parameters used in the mass spectrometry acquisition." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1001955 name: NoCleavage def: "No cleavage." [PSI:MS] is_a: MS:1001045 ! cleavage agent name [Term] id: MS:1001956 name: unspecific cleavage def: "Unspecific cleavage." [PSI:MS] is_a: MS:1001045 ! cleavage agent name [Term] id: MS:1001957 name: (?<=[ALIV])(?!P) is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001958 name: (?<=[HKR]P)(?!P) is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001959 name: (?<=[^E]E) is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001960 name: (?<=W) is_a: MS:1001180 ! Cleavage agent regular expression Best regards, Gerhard -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |
From: Matthew C. <mat...@gm...> - 2012-02-03 23:07:12
|
According to the mapping file, any child of spectrum type is valid. Did we decide that it would be acceptable not to use the more specific terms? -Matt |
From: Salvador M. de B. <sma...@pr...> - 2012-02-02 14:26:35
|
I have just reviewed the recently added CV Terms and I would like to suggest two more terms that I had in my list of suggested terms (for MIAPE MS validation) and they have not been added. Maybe, I have missed some reason to not add them. In that case, I'm sorry. The terms are: name: source interface manufacturer def: "The source interface manufacturer." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001931 ! source interface name: acquisition parameter def: "Parameters used in the mass spectrometry acquisition" xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001458 ! spectrum generation information Thank you! 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/ -----Mensaje original----- De: Gerhard Mayer [mailto:Ger...@ru...] Enviado el: 02 February 2012 14:33 Para: psi...@li...; psi...@li...; Mass spectrometry standard development Asunto: [Psidev-pi-dev] Changes in psi-ms.obo 3.18.0 Dear community, sorry, I forgot to mention the changes in the new release candidate. 1. Open questions: ================== The following two terms have an identical name, but different data types. Maybe it would be a good idea to rename the term MS:1001532 to something other, e.g. "spectrum from database nativeID format string". Any comments on that? [Term] id: MS:1001526 name: spectrum from database nativeID format def: "databasekey=xsd:Long." [PSI:MS] comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1001532 name: spectrum from database nativeID format def: "databasekey=xsd:string." [PSI:MS] comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). is_a: MS:1000767 ! native spectrum identifier format is_a: MS:1001529 ! spectra data details 2. Newly added CV terms: ======================== [Term] id: MS:1001946 name: PEAKS Studio def: "PEAKS Studio software for data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001947 name: PEAKS Online def: "PEAKS Online software for high throughput data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001948 def: "PEAKS Node software for high throughput data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001949 name: BSI software def: "Bioinformatics Solutions Inc. Software for data processing and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1001950 name: PEAKS:peptideScore def: "The PEAKS peptide '-10lgP Score'." [PSI:MS] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001951 name: PEAKS:proteinScore def: "The PEAKS protein '-10lgP Score'." [PSI:MS] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001116 ! single protein result details is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001952 name: ZCore:probScore def: "The ZCore probability score." [PSI:MS] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score Best regards, Gerhard -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |
From: Gerhard M. <Ger...@ru...> - 2012-02-02 13:33:19
|
Dear community, sorry, I forgot to mention the changes in the new release candidate. 1. Open questions: ================== The following two terms have an identical name, but different data types. Maybe it would be a good idea to rename the term MS:1001532 to something other, e.g. "spectrum from database nativeID format string". Any comments on that? [Term] id: MS:1001526 name: spectrum from database nativeID format def: "databasekey=xsd:Long." [PSI:MS] comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1001532 name: spectrum from database nativeID format def: "databasekey=xsd:string." [PSI:MS] comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). is_a: MS:1000767 ! native spectrum identifier format is_a: MS:1001529 ! spectra data details 2. Newly added CV terms: ======================== [Term] id: MS:1001946 name: PEAKS Studio def: "PEAKS Studio software for data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001947 name: PEAKS Online def: "PEAKS Online software for high throughput data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001948 def: "PEAKS Node software for high throughput data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001949 name: BSI software def: "Bioinformatics Solutions Inc. Software for data processing and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1001950 name: PEAKS:peptideScore def: "The PEAKS peptide '-10lgP Score'." [PSI:MS] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001951 name: PEAKS:proteinScore def: "The PEAKS protein '-10lgP Score'." [PSI:MS] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001116 ! single protein result details is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001952 name: ZCore:probScore def: "The ZCore probability score." [PSI:MS] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score Best regards, Gerhard -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |
From: Gerhard M. <Ger...@ru...> - 2012-02-02 13:24:10
|
Dear community, attached there's the release candidate for the next psi-ms.obo version 3.18.0_rc1. Comments and suggestions are welcome. If there are no objections to this release candidates, I plan to update the controlled vocabulary in about five days ( next tuesday). Best regards, Gerhard -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |
From: Gerhard M. <Ger...@ru...> - 2012-02-02 12:11:19
|
Dear community, I updated the psi-ms.obo file to the version 3.17.0 in the SourceForge CVS. It contains all the new terms as discussed in the PSI MSS WG teleconference call last tuesday. The term MS:1001934 (source sprayer type) was added as a parent term (without a data type), so we can add the child terms later. Best regards, Gerhard -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |
From: Eric D. <ede...@sy...> - 2012-01-31 17:02:51
|
Hi everyone, we tweaked or approved the terms sent by Gerhard 8 hr ago. Please see call minutes for details. However, one term was not resolved. This is part of the addition of terms for MIAPE-MS. In the current proposal we have: [Term] id: MS:1001934 name: source sprayer type def: "The source sprayer type." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001933 ! source sprayer This seems like it should not be a term that supports a value, but rather a parent term for several children. But what should the children be? We were not able to make a list of suitable source sprayer types. Can someone help? Or other comments? We propose: [Term] id: MS:1001934 name: source sprayer type def: "The source sprayer type." [PSI:MS] relationship: part_of MS:1001933 ! source sprayer [Term] id: MS:100???? name: ??????? sprayer def: "???????." [PSI:MS] relationship: part_of MS:1001934 ! source sprayer type more… Thoughts? Thanks, Eric |
From: Eric D. <Eri...@sy...> - 2012-01-31 16:56:54
|
Present: Jim, Florian, Steffen, Eric, Matt 1) Plans and agenda for spring PSI workshop in San Diego March 12-14 + Likely attendance by some of the present + Please advertize this more and promote attendance. + Please register now and make hotel bookings 2) mzML status 3) TraML status We need to update the web page with implementations - jTraML - Anubis - ATAQS - Metshot R package. Steffen will send. - More. 4) Discuss controlled vocabulary items. +Here are some proposed modifications to Garhard’s latest from 8 hr ago: ************ def: field defined [Term] id: MS:1000836 name: dried droplet MALDI matrix preparation def: "Dried droplet in MALDI matrix preparation." [PSI:MS] is_a: MS:1000833 ! matrix application type ************ def: field defined [Term] id: MS:1000837 name: printed MALDI matrix preparation def: "Printed MALDI matrix preparation." [PSI:MS] is_a: MS:1000833 ! matrix application type ************ def: field defined [Term] id: MS:1000838 name: sprayed MALDI matrix preparation def: "Sprayed MALDI matrix preparation." [PSI:MS] is_a: MS:1000833 ! matrix application type ************ A new relation in "precolated plate": now also a "sample plate type"; def: field defined [Term] id: MS:1000839 name: precoated MALDI sample plate def: "Precoated MALDI sample plate." [PSI:MS] is_a: MS:1000833 ! matrix application type is_a: MS:1001938 ! sample plate type [Term] id: MS:1001915 name: leukocyte elastase def: "Enzyme leukocyte elastase (EC 3.4.21.37)." [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.37 "BRENDA"] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001176 ! (?<=[ALIV])(?!P) We note for DOI, there is a regexp that could be applied in the validator, but this is not done presently. There was concern that “source sprayer type” should be a parent term and not allow a value. But what Should the children be?? [Term] id: MS:1001934 name: source sprayer type def: "The source sprayer type." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001933 ! source sprayer Bring this topic up on the list. Remove value type in: [Term] id: MS:1001938 name: sample plate type def: "The sample plate type." [PSI:MS] relationship: part_of MS:1001937 ! sample plate - Proposed commit from Gerhard - CXP, LECO instrument - cleavage agents - others? 5) MIAPE – MS 6) MIAPE – Quant + No discussion for now. Will discuss at future call and workshop. Next meeting: - Feb 14 8am Seattle Time? +yes *From:* Eric Deutsch [mailto:Eri...@sy...] *Sent:* Monday, January 30, 2012 9:46 AM *To:* Mass spectrometry standard development *Cc:* Eric Deutsch *Subject:* PSI MSS WG call reminder Hi everyone, this is a reminder about the PSI MSS WG teleconference call tomorrow, Tuesday, at the usual time. 08:00 San Francisco 11:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + Finland: 080011569 + UK: 08081095644 + USA: 1-866-832-8490 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) Plans and agenda for spring PSI workshop in San Diego March 12-14 2) mzML status 3) TraML status 4) Discuss controlled vocabulary items: - Proposed commit from Gerhard - CXP, LECO instrument - cleavage agents - others? 5) MIAPE – MS 6) MIAPE – Quant Next meeting: - Feb 14 8am Seattle Time? |
From: Jon I. <ji...@eb...> - 2012-01-31 13:49:19
|
Dear chaps I guess using ontology definitions is a good thing if you have the resources to do it and the ontologies you want are up to scratch. Anyhow, to reiterate what Matus said, if you decide on that route, then we'll very gladly add whatever new identifiers, formats or anything else that you might need. The idea in any case is that EDAM will provide a comprehensive catalogue of all common data identifiers and formats. So, please feel free to keep in touch! Cheers Jon > Hi Steffen, > > Oliver explained the way we tried to solve it in the case of mzTab. > > There have been several e-mails and conversations in the past about the general problem here and > this is the adaptation of proteomics data format (such as traML or mzML) to work with metabolomics > data. For instance, our colleagues here at the EBI (the group headed by C. Steinbeck) are going to > use mzML and also mzTab for the MS derived data because there is not much well established in the > metabolomics field. > > So the general problem is should we really try to move this really forward? This of course would > mean a lot of extra work like, you say, working with new ontologies. But in my opinion is > something that will need to get done sooner or later. > > I would like to know your opinion on this. Anyone else's opinion is of course also welcome. Maybe, > a lot of things have already been done and I am not aware of them. > > Thanks, > > Juan > > > On 25 Jan 2012, at 15:06, Oliver Kohlbacher wrote: > >> Steffen, >> >> you might want to have a look at the mzTab specification, more precisely >> at the 'small molecule table' therein. >> The approach chosen there is rather pragmatic: a database ID and a chemical >> formula. Chemical formula is of course well specified and for most practical >> purposes database IDs like PubChem or HMDB are entirely sufficient imho. >> >> http://code.google.com/p/mztab/wiki/FileFormat#Format_Specification >> >> CHeers, >> Oliver >> >> >> On Jan 25, 2012, at 3:12 PM, Steffen Neumann wrote: >> >>> Hi, >>> >>> I am currently preparing a set of MRM Transitions >>> as showcase for TraML in Metabolomics. >>> >>> I'll need to specify for which <Compound> a transition >>> was obtained. Currently, we only have cvParams >>> for "predicted isoelectric point", "theoretical mass" >>> and children of "chemical compound formula": >>> http://www.peptideatlas.org/schemas/TraML/1.0.0/TraML1.0.0.html#Compound >>> >>> This is a) far from complete, and b) underspecified, >>> because MS:1000867 "structural formula" does not specify >>> whether the value shall be SMILES, InChI or whatever. >>> >>> Is there a way to embrace (pun intended :-) >>> the EDAM (EMBRACE Data and Methods) ontology of [...] identifiers >>> for <Compound> ? Then we'd have something like this: >>> >>> <TraML> >>> <cv URI="http://edamontology.org/ontology?format=obo" >>> fullName="EDAM (EMBRACE Data And Methods)" id="EDAM" version="unknown" /> >>> ... >>> <Compound> >>> <cvParam accession="EDAM_data:1172" cvRef="EDAM" name="PubChem CID" value="932" /> >>> </Compound> >>> >>> EDAM has entries for a gazillion different compound identifiers: >>> http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM&termId=EDAM_data:1086&termName=Compound%20identifier >>> >>> and InChI, SMILES, molecular formula: >>> http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM&termId=EDAM_format%3A2035&termName=Chemical%20formula%20format >>> >>> The only downside I can see is that the converters and validators >>> need to slurp in another ontology of respectable size. >>> >>> Thoughts ? >>> >>> 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 >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Keep Your Developer Skills Current with LearnDevNow! >>> The most comprehensive online learning library for Microsoft developers >>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >>> Metro Style Apps, more. Free future releases when you subscribe now! >>> http://p.sf.net/sfu/learndevnow-d2d >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> >> --- >> Oliver Kohlbacher (oli...@un...) >> Professor, Applied Bioinformatics, Center for Bioinformatics Tuebingen >> Dept. of Computer Science, University of Tuebingen >> phone: +49-7071-29-70457 http://abi.inf.uni-tuebingen.de >> >> vCard at: http://abi.inf.uni-tuebingen.de/People/kohlbach/vCard >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Keep Your Developer Skills Current with LearnDevNow! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-d2d >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > |
From: Gerhard M. <Ger...@ru...> - 2012-01-31 08:55:08
|
Hello all, in the attachment you'll find the obo file of the v3.17.0 release candidate 2 to be discussed at todays PSI MSS WG teleconference call (see email from Eric). It contains all requests and proposals from the the ms-vocab list since the last official release at Nov 24th, 2011 of the obo file (version 3.16.0). In addition I made sure that each definition ends with a period (full stop) according to the "Guidelines for the development of Controlled Vocabularies". Likewise I putted the [Typedef] stanzas before the [Term] stanzas and in the header tags I made sure that the 'import' tag occurs before the 'default-namespace' and that the 'remark' tags are compliant with the order rules mentioned in the "OBO Flat File Format Specification, version 1.2". Please check if the list is complete and the terms are correctly defined. Any feedback and further suggestions are appreciated. 1. Changes to already existing CV terms: ======================================== ************ Added Clostripain as synonym to "Arg-C" and the missing definition field [Term] id: MS:1001303 name: Arg-C def: "Endoproteinase Arg-C." [PSI:PI] synonym: "clostripain" EXACT [] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001272 ! (?<=R)(?!P) ************ Added the missing definition field [Term] id: MS:1001307 name: CNBr def: "Cyanogen bromide." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001333 ! (?<=M) ************ def: field defined [Term] id: MS:1000836 name: dried dropplet def: "Dried dropplet in MALDI matrix preparation." [PSI:MS] is_a: MS:1000833 ! matrix application type ************ def: field defined [Term] id: MS:1000837 name: printed def: "Printed MALDI matrix preparation." [PSI:MS] is_a: MS:1000833 ! matrix application type ************ def: field defined [Term] id: MS:1000838 name: sprayed def: "Sprayed MALDI matrix prerparation." [PSI:MS] is_a: MS:1000833 ! matrix application type ************ A new relation in "precolated plate": now also a "sample plate type"; def: field defined [Term] id: MS:1000839 name: precoated plate def: "Precoated plate." [PSI:MS] is_a: MS:1000833 ! matrix application type is_a: MS:1001938 ! sample plate type ************ "paul ion trap" is now obsolete, because redundant to quadrupole ion trap [Term] id: MS:1000297 name: paul ion trap def: "OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected." [PSI:MS] comment: This term was made obsolete because it is redundant to quadrupole ion trap synonym: "quadrupole ion trap" RELATED [] is_a: MS:1000479 ! purgatory is_obsolete: true ************ "axial ejection linear ion trap" is now a linear ion trap [Term] id: MS:1000078 name: axial ejection linear ion trap def: "A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer." [PSI:MS] is_a: MS:1000291 ! linear ion trap ************ "radial ejection linear ion trap" is now a linear ion trap [Term] id: MS:1000083 name: radial ejection linear ion trap def: "A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer." [PSI:MS] is_a: MS:1000291 ! linear ion trap 2. Open questions (please email me further informations): ========================================================= - How to represent the source (reference definitions) of the cleavage agents? 3. Newly added CV terms: ======================== [Term] id: MS:1001914 name: pymzML def: "Python module to interface mzML Data." [PSI:MS] is_a: MS:1001457 ! data processing software [Term] id: MS:1001915 name: leukocyteelastase def: "Enzyme leukocyte elastase (EC 3.4.21.37)." [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.37 "BRENDA"] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001176 ! (?<=[ALIV])(?!P) [Term] id: MS:1001916 name: proline endopeptidase def: "Enzyme proline endopeptidase (EC 3.4.21.26)." [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.26 "BRENDA"] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001176 ! (?<=[HKR]P)(?!P) [Term] id: MS:1001917 name: glutamyl endopeptidase def: "Enzyme Glutamyl endopeptidase (EC 3.4.21.19)." [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.19 "BRENDA"] synonym: "staphylococcal protease" EXACT [] synonym: "Glu-C" EXACT [] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001176 ! (?<=[^E]E) [Term] id: MS:1001918 name: 2-iodobenzoate def: "Chemical iodobenzoate. Cleaves after W." [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pccompound&term=4739928 "PubChem"] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001176 ! (?<=W) [Term] id: MS:1001919 name: ProteomeXchange accession number def: "Main identifier of a ProteomeXchange dataset." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001921 name: ProteomeXchange accession number version number def: "Version number of a ProteomeXchange accession number." [PSI:PI] xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001922 name: Digital Object Identifier (DOI) def: "DOI unique identifier." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier relationship: has_regexp MS:1001176 ! (10\.(\d)+(\.(\d)*)?/[^\*].+) [Term] id: MS:1001923 name: external reference keyword def: "Free text attribute that can enrich the information about an entity." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001924 name: journal article keyword def: "Keyword present in a scientific publication." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword [Term] id: MS:1001925 name: submitter keyword def: "Keyword assigned by the data submitter." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword [Term] id: MS:1001926 name: curator keyword def: "Keyword assigned by a data curator." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword [Term] id: MS:1001927 name: Tranche file hash def: "Hash assigned by the Tranche resource to an individual file." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001928 name: Tranche project hash def: "Hash assigned by the Tranche resource to a whole project." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001929 name: PRIDE experiment URI def: "URI that allows the access to one experiment in the PRIDE database." [PSI:PI] xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001930 name: PRIDE project URI def: "URI that allows the access to one project in the PRIDE database." [PSI:PI] xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001931 name: source interface def: "The source interface." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1001932 name: source interface model def: "The source interface model." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001931 ! source interface [Term] id: MS:1001933 name: source sprayer def: "The source sprayer." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1001934 name: source sprayer type def: "The source sprayer type." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001933 ! source sprayer [Term] id: MS:1001935 name: source sprayer manufacturer def: "The source sprayer manufacturer." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001933 ! source sprayer [Term] id: MS:1001936 name: source sprayer model def: "The source sprayer model." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001933 ! source sprayer [Term] id: MS:1001937 name: sample plate def: "Plate where the sample solution is spotted in a MALDI or similar instrument." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1001938 name: sample plate type def: "The sample plate type." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001937 ! sample plate [Term] id: MS:1001939 name: stainless steel plate def: "Stainless steel plate." [PSI:MS] is_a: MS:1001938 ! sample plate type [Term] id: MS:1001940 name: coated glass plate def: "Coated glass plate." [PSI:MS] is_a: MS:1001938 ! sample plate type [Term] id: MS:1001941 name: electrospray supply type def: "Whether the sprayer is fed or is loaded with sample once." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1001942 name: static supply electrospray def: "The sprayer is loaded with sample once." [PSI:MS] is_a: MS:1001941 ! electrospray supply type [Term] id: MS:1001943 name: fed supply electrospray def: "The sprayer is continuously fed with sample." [PSI:MS] is_a: MS:1001941 ! electrospray supply type [Term] id: MS:1001944 name: Collision cell exit potential def: "Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000218 ! volt synonym: "CXP" EXACT [] [Term] id: MS:1001945 name: Pegasus 4D def: "LECO nominal mass resolution time-of-flight GCxGC mass spectrometer." [PSI:MS] is_a: MS:1001800 ! LECO instrument model Best regards, Gerhard -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |
From: Eric D. <Eri...@sy...> - 2012-01-30 17:46:01
|
Hi everyone, this is a reminder about the PSI MSS WG teleconference call tomorrow, Tuesday, at the usual time. 08:00 San Francisco 11:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + Finland: 080011569 + UK: 08081095644 + USA: 1-866-832-8490 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) Plans and agenda for spring PSI workshop in San Diego March 12-14 2) mzML status 3) TraML status 4) Discuss controlled vocabulary items: - Proposed commit from Gerhard - CXP, LECO instrument - cleavage agents - others? 5) MIAPE – MS 6) MIAPE – Quant Next meeting: - Feb 14 8am Seattle Time? |
From: Nils H. <nil...@ce...> - 2012-01-27 11:26:24
|
Hi all, I browsed the current CVS version of the ontology at sourceforge and noticed that there are some machines already defined for the hardware vendor LECO. However, the LECO Pegasus IV GCxGC TOF-MS is missing, which is used for comprehensive two-dimensional chromatography mass-spectrometry. So I would like propose addition of the following term (derived from the existing ones for LECO machinery): [Term] id: MS:? name: Pegasus 4D def: "LECO nominal mass resolution time-of-flight GCxGC mass spectrometer." [PSI:MS] is_a: MS:1001800 ! LECO instrument model Please provide any comments if this term needs clarification or has already been provided. Yours, Nils -- Nils Hoffmann phone: +49-521-106-4342 Bielefeld University room: U10-144 Faculty of Technology, Genome Informatics P.O. Box 10 01 31 33501 Bielefeld, Germany http://www.cebitec.uni-bielefeld.de/~hoffmann |
From: Juan A. V. <ju...@eb...> - 2012-01-26 09:23:51
|
Hi all, Thanks to Eric and Pierre-Alain for their feedback. You were right about the lack of consistency in the naming. After thinking a bit more about it, I think that at least for the moment there is no need to have a 'ProteomeXchange secondary identifier". If it is finally needed, we can add it at a later stage when it is clear what it can be. -The ProteomeXchange accession number should be a string. It will have this structure: PXD00123. I have removed the 'primary' from the name and changed slightly the definition. - ProteomeXchange accession number version number is an integer and I have corrected the name of the term. PXD00123.1 - I agree with Pierre-Alain's proposal for keyword. I have added the string type for the Tranche related terms, as suggested by Eric. And yes, about the publication, we can use the PubMed ID. The other terms will be created in the PRIDE CV. Cheers, Juanan [Term] id: MS:1001919 name: ProteomeXchange accession number def: "Unique identifier of a ProteomeXchange dataset." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier PLEASE DELETE [Term] id: MS:1001920 name: ProteomeXchange secondary identifier def: "Secondary identifier of a ProteomeXchange dataset." [PSI:PI] is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001921 name: ProteomeXchange accession number version number def: "Version number of a ProteomeXchange accession number." [PSI:PI] xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001922 name: Digital Object Identifier (DOI) def: "DOI unique identifier." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier relationship: has_regexp MS:1001176 ! (10\.(\d)+(\.(\d)*)?/[^\*].+) [Term] id: MS:1001923 name: external reference keyword def: "Free text attribute that can enrich the information about an entity." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001924 name: journal article keyword def: "Keyword present in a scientific publication." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword [Term] id: MS:1001925 name: submitter keyword def: "Keyword assigned by the data submitter." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword [Term] id: MS:1001926 name: curator keyword def: "Keyword assigned by a data curator." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword [Term] id: MS:1001927 name: Tranche file hash def: "Hash assigned by the Tranche resource to an individual file." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001928 name: Tranche project hash def: "Hash assigned by the Tranche resource to a whole project." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001929 name: PRIDE experiment URI def: "URI that allows the access to one experiment in the PRIDE database." [PSI:PI] xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001930 name: PRIDE project URI def: "URI that allows the access to one project in the PRIDE database." [PSI:PI] xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier On 26 Jan 2012, at 07:49, pierre-alain binz wrote: > > Hi Eric, these PX accession change proposals came from me: > I was not comfortable with the original proposal from Juan: > > ProteomeXchange accession number > ProteomeXchange identifier > ProteomeXchange accession version number > > As there might be incoherence and lacking precision between term names > and definitions: From the proposed definitions > - the accession number, defined as "Main identifier of a ProteomeXchange > dataset.", might not be a "number", > - the identifier, defined as "Secondary identifier of a ProteomeXchange > dataset." might be a number, > - the accession version number, defined as "Version number of a > ProteomeXchange accession number" is badly termed. It should be either > an "accession number version number" and therefore force the value to be > a number or an "accession number version" and the datatype defined if > the value should be a number or not. > See also my email from monday 23. > > > Cheers > Pierre-Alain > > On 25.01.2012 18:24, Eric Deutsch wrote: >> Hi Gerhard, many thanks for agreeing to take over and for putting all this >> together. First, regarding timing. I think it would be great if you could >> collect feedback over the next few days and then put out a new proposed >> revision, and then give us a chance to discuss it at the MSSWG call on >> Tuesday (17:00 your time; please join us if you can!). Once the results >> from that discussion have taken place, then it would be best to make any >> final necessary revisions and then commit. Would that be okay? >> >> Here are some responses to your queries below: >> >>> 2. Open questions (please email me further informations): >>> ========================================================= >>> What are the datatypes for the following terms? >>> >>> MS:1001919 (ProteomeXchange primary accession number) >> This should just be "ProteomeXchange accession number" as proposed by >> Juanan, no? I don't know where "primary" came from. This should be an >> positive integer like "123". I think this is what Juanan had in mind? >> Please correct if I misunderstood this! >> >>> MS:1001920 (ProteomeXchange secondary identifier) >> This should just be "ProteomeXchange identifier" as proposed by Juanan, >> no? I don't know where "secondary" came from. This should be a string like >> "PXD000123" >> >>> MS:1001921 (ProteomeXchange primary accession version number) >> This should just be "ProteomeXchange accession version number " as >> proposed by Juanan, no? I don't know where "primary" came from. This >> should be a positive integer like "4" >> >>> MS:1001927 (Tranche file hash) >> This should be an xsd:string >> >>> MS:1001928 (Tranche project hash) >> This should be an xsd:string >> >> >> Thanks, >> Eric >> >> >>> -----Original Message----- >>> From: Gerhard Mayer [mailto:Ger...@ru...] >>> Sent: Wednesday, January 25, 2012 6:33 AM >>> To: psi...@li...; psidev-pi- >>> de...@li...; Mass spectrometry standard development >>> Subject: [Psidev-ms-vocab] Release candidate for the next release of >>> psi-ms.obo >>> >>> Hello all, >>> >>> I took over the CV maintenance of the psi-ms.obo file from David. >>> >>> David, in the name of the community I would like to thank you so much >>> for your efforts in >>> maintaining the CV during the last year. >>> >>> In the following you find a list of all requests and proposals which I >>> found in the ms-vocab list >>> since the last official release at Nov 24th, 2011 of the obo file >>> (version 3.16.0). >>> In addition I made sure that each definition ends with a period (full >>> stop) according to the >>> "Guidelines for the development of Controlled Vocabularies". >>> >>> Please check if the list is complete and the terms are correctly >>> defined. >>> At point 2.) I have also listed some open questions for added terms, >>> for >>> which I hope to get answers >>> from the community. Any feedback and further suggestions are >>> appreciated. >>> If there are no further objections and / or discussions I plan to >>> release the new version next tuesday (Jan 31th). >>> >>> In the attachment you'll find the obo file of the v3.17.0 release >>> candidate. >>> >>> >>> 1. Changes to already existing CV terms: >>> ======================================== >>> ************ Added Clostripain as synonym to "Arg-C" and the missing >>> definition field >>> [Term] >>> id: MS:1001303 >>> name: Arg-C >>> def: "Endoproteinase Arg-C." [PSI:PI] >>> synonym: "Clostripain" EXACT [] >>> is_a: MS:1001045 ! cleavage agent name >>> relationship: has_regexp MS:1001272 ! (?<=R)(?!P) >>> >>> ************ A new relation in "precolated plate": now also a "sample >>> plate type" >>> [Term] >>> id: MS:1000839 >>> name: precoated plate >>> def: "Precoated plate." [PSI:MS] >>> is_a: MS:1000833 ! matrix application type >>> is_a: MS:1001938 ! sample plate type >>> >>> ************ "paul ion trap" is now obsolete, because redundant to >>> quadrupole ion trap >>> [Term] >>> id: MS:1000297 >>> name: paul ion trap >>> def: "OBSOLETE A device that permits the trapping of ions by means of >>> an >>> alternating current voltage. The ejection of ions with a m/z less than >>> a >>> prescribed value and retention of those with higher mass depends on the >>> application of radio frequency voltages between a ring electrode and >>> two >>> end-cap electrodes to confine the ions in a circular path. The choice >>> of >>> these voltages determines the m/z below which ions are ejected." >>> [PSI:MS] >>> comment: This term was made obsolete because it is redundant to >>> quadrupole ion trap >>> synonym: "quadrupole ion trap" RELATED [] >>> is_a: MS:1000479 ! purgatory >>> is_obsolete: true >>> >>> ************ "axial ejection linear ion trap" is now a linear ion trap >>> [Term] >>> id: MS:1000078 >>> name: axial ejection linear ion trap >>> def: "A linear ion trap mass spectrometer where ions are ejected along >>> the axis of the analyzer." [PSI:MS] >>> is_a: MS:1000291 ! linear ion trap >>> >>> ************ "radial ejection linear ion trap" is now a linear ion trap >>> [Term] >>> id: MS:1000083 >>> name: radial ejection linear ion trap >>> def: "A linear ion trap mass spectrometer where ions are ejected along >>> the radius of the analyzer." [PSI:MS] >>> is_a: MS:1000291 ! linear ion trap >>> >>> >>> 2. Open questions (please email me further informations): >>> ========================================================= >>> What are the datatypes for the following terms? >>> >>> MS:1001919 (ProteomeXchange primary accession number) >>> MS:1001920 (ProteomeXchange secondary identifier) >>> MS:1001921 (ProteomeXchange primary accession version number) >>> MS:1001927 (Tranche file hash) >>> MS:1001928 (Tranche project hash) >>> >>> >>> 3. Newly added CV terms: >>> ======================== >>> [Term] >>> id: MS:1001914 >>> name: pymzML >>> def: "Python module to interface mzML Data." [PSI:MS] >>> is_a: MS:1001457 ! data processing software >>> >>> [Term] >>> id: MS:1001915 >>> name: elastase >>> def: "Enzyme elastase. Cleaves after A, L, I or V, except when P is >>> after A, L, I or V." [PSI:MS] >>> is_a: MS:1001045 ! cleavage agent name >>> relationship: has_regexp MS:1001176 ! (?<=[ALIV])(?!P) >>> >>> [Term] >>> id: MS:1001916 >>> name: proline endopeptidase >>> def: "Enzyme proline endopeptidase. Cleaves after P." [PSI:MS] >>> is_a: MS:1001045 ! cleavage agent name >>> relationship: has_regexp MS:1001176 ! (?<=P) >>> >>> [Term] >>> id: MS:1001917 >>> name: staphylococcal protease >>> def: "Staphylococcal protease. Cleaves after E." [PSI:MS] >>> is_a: MS:1001045 ! cleavage agent name >>> relationship: has_regexp MS:1001176 ! (?<=E) >>> >>> [Term] >>> id: MS:1001918 >>> name: jodobenzoate >>> def: "Chemical Jodobenzoate. Cleaves after W." [PSI:MS] >>> is_a: MS:1001045 ! cleavage agent name >>> relationship: has_regexp MS:1001176 ! (?<=W) >>> >>> [Term] >>> id: MS:1001919 >>> name: ProteomeXchange primary accession number >>> def: "Main identifier of a ProteomeXchange dataset." [PSI:PI] >>> is_a: MS:1000878 ! external reference identifier >>> >>> [Term] >>> id: MS:1001920 >>> name: ProteomeXchange secondary identifier >>> def: "Secondary identifier of a ProteomeXchange dataset." [PSI:PI] >>> is_a: MS:1000878 ! external reference identifier >>> >>> [Term] >>> id: MS:1001921 >>> name: ProteomeXchange primary accession version number >>> def: "Version number of a ProteomeXchange accession number." [PSI:PI] >>> is_a: MS:1000878 ! external reference identifier >>> >>> [Term] >>> id: MS:1001922 >>> name: Digital Object Identifier (DOI) >>> def: "DOI unique identifier." [PSI:PI] >>> xref: value-type:xsd\:string "The allowed value-type for this CV term." >>> is_a: MS:1000878 ! external reference identifier >>> relationship: has_regexp MS:1001176 ! (10\.(\d)+(\.(\d)*)?/[^\*].+) >>> >>> [Term] >>> id: MS:1001923 >>> name: external reference keyword >>> def: "Free text attribute that can enrich the information about an >>> entity." [PSI:PI] >>> xref: value-type:xsd\:string "The allowed value-type for this CV term." >>> is_a: MS:1000878 ! external reference identifier >>> >>> [Term] >>> id: MS:1001924 >>> name: journal article keyword >>> def: "Keyword present in a scientific publication." [PSI:PI] >>> xref: value-type:xsd\:string "The allowed value-type for this CV term." >>> is_a: MS:1001923 ! external reference keyword >>> >>> [Term] >>> id: MS:1001925 >>> name: submitter keyword >>> def: "Keyword assigned by the data submitter." [PSI:PI] >>> xref: value-type:xsd\:string "The allowed value-type for this CV term." >>> is_a: MS:1001923 ! external reference keyword >>> >>> [Term] >>> id: MS:1001926 >>> name: curator keyword >>> def: "Keyword assigned by a data curator." [PSI:PI] >>> xref: value-type:xsd\:string "The allowed value-type for this CV term." >>> is_a: MS:1001923 ! external reference keyword >>> >>> [Term] >>> id: MS:1001927 >>> name: Tranche file hash >>> def: "Hash assigned by the Tranche resource to an individual file." >>> [PSI:PI] >>> is_a: MS:1000878 ! external reference identifier >>> >>> [Term] >>> id: MS:1001928 >>> name: Tranche project hash >>> def: "Hash assigned by the Tranche resource to a whole project." >>> [PSI:PI] >>> is_a: MS:1000878 ! external reference identifier >>> >>> [Term] >>> id: MS:1001929 >>> name: PRIDE experiment URI >>> def: "URI that allows the access to one experiment in the PRIDE >>> database." [PSI:PI] >>> xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." >>> is_a: MS:1000878 ! external reference identifier >>> >>> [Term] >>> id: MS:1001930 >>> name: PRIDE project URI >>> def: "URI that allows the access to one project in the PRIDE database." >>> [PSI:PI] >>> xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." >>> is_a: MS:1000878 ! external reference identifier >>> >>> [Term] >>> id: MS:1001931 >>> name: source interface >>> def: "The source interface." [PSI:MS] >>> relationship: part_of MS:1000458 ! source >>> >>> [Term] >>> id: MS:1001932 >>> name: source interface model >>> def: "The source interface model." [PSI:MS] >>> xref: value-type:xsd\:string "The allowed value-type for this CV term." >>> relationship: part_of MS:1001931 ! source interface >>> >>> [Term] >>> id: MS:1001933 >>> name: source sprayer >>> def: "The source sprayer." [PSI:MS] >>> relationship: part_of MS:1000458 ! source >>> >>> [Term] >>> id: MS:1001934 >>> name: source sprayer type >>> def: "The source sprayer type." [PSI:MS] >>> xref: value-type:xsd\:string "The allowed value-type for this CV term." >>> relationship: part_of MS:1001933 ! source sprayer >>> >>> [Term] >>> id: MS:1001935 >>> name: source sprayer manufacturer >>> def: "The source sprayer manufacturer." [PSI:MS] >>> xref: value-type:xsd\:string "The allowed value-type for this CV term." >>> relationship: part_of MS:1001933 ! source sprayer >>> >>> [Term] >>> id: MS:1001936 >>> name: source sprayer model >>> def: "The source sprayer model." [PSI:MS] >>> xref: value-type:xsd\:string "The allowed value-type for this CV term." >>> relationship: part_of MS:1001933 ! source sprayer >>> >>> [Term] >>> id: MS:1001937 >>> name: sample plate >>> def: "Plate where the sample solution is spotted in a MALDI or similar >>> instrument." [PSI:MS] >>> relationship: part_of MS:1000458 ! source >>> >>> [Term] >>> id: MS:1001938 >>> name: sample plate type >>> def: "The sample plate type." [PSI:MS] >>> xref: value-type:xsd\:string "The allowed value-type for this CV term." >>> relationship: part_of MS:1001937 ! sample plate >>> >>> [Term] >>> id: MS:1001939 >>> name: stainless steel plate >>> def: "Stainless steel plate." [PSI:MS] >>> is_a: MS:1001938 ! sample plate type >>> >>> [Term] >>> id: MS:1001940 >>> name: coated glass plate >>> def: "Coated glass plate." [PSI:MS] >>> is_a: MS:1001938 ! sample plate type >>> >>> [Term] >>> id: MS:1001941 >>> name: electrospray supply type >>> def: "Whether the sprayer is fed or is loaded with sample once." >>> [PSI:MS] >>> relationship: part_of MS:1000458 ! source >>> >>> [Term] >>> id: MS:1001942 >>> name: static supply electrospray >>> def: "The sprayer is loaded with sample once." [PSI:MS] >>> is_a: MS:1001941 ! electrospray supply type >>> >>> [Term] >>> id: MS:1001943 >>> name: fed supply electrospray >>> def: "The sprayer is continuously fed with sample." [PSI:MS] >>> is_a: MS:1001941 ! electrospray supply type >>> >>> [Term] >>> id: MS:1001944 >>> name: Collision cell exit potential >>> def: "Potential difference between Q2 and Q3 in a triple quadrupole >>> instrument in volts." [PSI:MS] >>> xref: value-type:xsd\:float "The allowed value-type for this CV term." >>> is_a: MS:1000510 ! precursor activation attribute >>> relationship: has_units UO:0000218 ! volt >>> synonym: "CXP" EXACT [] >>> >>> Best regards, >>> Gerhard >>> >>> -- >>> --- >>> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer >>> BioInformatik >>> Medizinisches-Proteom-Center (MPC) >>> Ruhr-Universität Bochum >>> Zentrum für klinische Forschung I (ZKF I) >>> E.042 >>> Universitätsstrasse 150 >>> D-44801 Bochum >>> >>> Phone: +49(0)234/32-29836 >>> Fax: +49(0)234/32-14554 >>> Email: Ger...@ru... >>> Web: http://www.medizinisches-proteom-center.de >> ------------------------------------------------------------------------------ >> Keep Your Developer Skills Current with LearnDevNow! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-d2d >> _______________________________________________ >> Psidev-ms-vocab mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Psidev-ms-vocab mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab |
From: Eric D. <ede...@sy...> - 2012-01-25 17:24:06
|
Hi Gerhard, many thanks for agreeing to take over and for putting all this together. First, regarding timing. I think it would be great if you could collect feedback over the next few days and then put out a new proposed revision, and then give us a chance to discuss it at the MSSWG call on Tuesday (17:00 your time; please join us if you can!). Once the results from that discussion have taken place, then it would be best to make any final necessary revisions and then commit. Would that be okay? Here are some responses to your queries below: > 2. Open questions (please email me further informations): > ========================================================= > What are the datatypes for the following terms? > > MS:1001919 (ProteomeXchange primary accession number) This should just be "ProteomeXchange accession number" as proposed by Juanan, no? I don't know where "primary" came from. This should be an positive integer like "123". I think this is what Juanan had in mind? Please correct if I misunderstood this! > MS:1001920 (ProteomeXchange secondary identifier) This should just be "ProteomeXchange identifier" as proposed by Juanan, no? I don't know where "secondary" came from. This should be a string like "PXD000123" > MS:1001921 (ProteomeXchange primary accession version number) This should just be "ProteomeXchange accession version number " as proposed by Juanan, no? I don't know where "primary" came from. This should be a positive integer like "4" > MS:1001927 (Tranche file hash) This should be an xsd:string > MS:1001928 (Tranche project hash) This should be an xsd:string Thanks, Eric > -----Original Message----- > From: Gerhard Mayer [mailto:Ger...@ru...] > Sent: Wednesday, January 25, 2012 6:33 AM > To: psi...@li...; psidev-pi- > de...@li...; Mass spectrometry standard development > Subject: [Psidev-ms-vocab] Release candidate for the next release of > psi-ms.obo > > Hello all, > > I took over the CV maintenance of the psi-ms.obo file from David. > > David, in the name of the community I would like to thank you so much > for your efforts in > maintaining the CV during the last year. > > In the following you find a list of all requests and proposals which I > found in the ms-vocab list > since the last official release at Nov 24th, 2011 of the obo file > (version 3.16.0). > In addition I made sure that each definition ends with a period (full > stop) according to the > "Guidelines for the development of Controlled Vocabularies". > > Please check if the list is complete and the terms are correctly > defined. > At point 2.) I have also listed some open questions for added terms, > for > which I hope to get answers > from the community. Any feedback and further suggestions are > appreciated. > If there are no further objections and / or discussions I plan to > release the new version next tuesday (Jan 31th). > > In the attachment you'll find the obo file of the v3.17.0 release > candidate. > > > 1. Changes to already existing CV terms: > ======================================== > ************ Added Clostripain as synonym to "Arg-C" and the missing > definition field > [Term] > id: MS:1001303 > name: Arg-C > def: "Endoproteinase Arg-C." [PSI:PI] > synonym: "Clostripain" EXACT [] > is_a: MS:1001045 ! cleavage agent name > relationship: has_regexp MS:1001272 ! (?<=R)(?!P) > > ************ A new relation in "precolated plate": now also a "sample > plate type" > [Term] > id: MS:1000839 > name: precoated plate > def: "Precoated plate." [PSI:MS] > is_a: MS:1000833 ! matrix application type > is_a: MS:1001938 ! sample plate type > > ************ "paul ion trap" is now obsolete, because redundant to > quadrupole ion trap > [Term] > id: MS:1000297 > name: paul ion trap > def: "OBSOLETE A device that permits the trapping of ions by means of > an > alternating current voltage. The ejection of ions with a m/z less than > a > prescribed value and retention of those with higher mass depends on the > application of radio frequency voltages between a ring electrode and > two > end-cap electrodes to confine the ions in a circular path. The choice > of > these voltages determines the m/z below which ions are ejected." > [PSI:MS] > comment: This term was made obsolete because it is redundant to > quadrupole ion trap > synonym: "quadrupole ion trap" RELATED [] > is_a: MS:1000479 ! purgatory > is_obsolete: true > > ************ "axial ejection linear ion trap" is now a linear ion trap > [Term] > id: MS:1000078 > name: axial ejection linear ion trap > def: "A linear ion trap mass spectrometer where ions are ejected along > the axis of the analyzer." [PSI:MS] > is_a: MS:1000291 ! linear ion trap > > ************ "radial ejection linear ion trap" is now a linear ion trap > [Term] > id: MS:1000083 > name: radial ejection linear ion trap > def: "A linear ion trap mass spectrometer where ions are ejected along > the radius of the analyzer." [PSI:MS] > is_a: MS:1000291 ! linear ion trap > > > 2. Open questions (please email me further informations): > ========================================================= > What are the datatypes for the following terms? > > MS:1001919 (ProteomeXchange primary accession number) > MS:1001920 (ProteomeXchange secondary identifier) > MS:1001921 (ProteomeXchange primary accession version number) > MS:1001927 (Tranche file hash) > MS:1001928 (Tranche project hash) > > > 3. Newly added CV terms: > ======================== > [Term] > id: MS:1001914 > name: pymzML > def: "Python module to interface mzML Data." [PSI:MS] > is_a: MS:1001457 ! data processing software > > [Term] > id: MS:1001915 > name: elastase > def: "Enzyme elastase. Cleaves after A, L, I or V, except when P is > after A, L, I or V." [PSI:MS] > is_a: MS:1001045 ! cleavage agent name > relationship: has_regexp MS:1001176 ! (?<=[ALIV])(?!P) > > [Term] > id: MS:1001916 > name: proline endopeptidase > def: "Enzyme proline endopeptidase. Cleaves after P." [PSI:MS] > is_a: MS:1001045 ! cleavage agent name > relationship: has_regexp MS:1001176 ! (?<=P) > > [Term] > id: MS:1001917 > name: staphylococcal protease > def: "Staphylococcal protease. Cleaves after E." [PSI:MS] > is_a: MS:1001045 ! cleavage agent name > relationship: has_regexp MS:1001176 ! (?<=E) > > [Term] > id: MS:1001918 > name: jodobenzoate > def: "Chemical Jodobenzoate. Cleaves after W." [PSI:MS] > is_a: MS:1001045 ! cleavage agent name > relationship: has_regexp MS:1001176 ! (?<=W) > > [Term] > id: MS:1001919 > name: ProteomeXchange primary accession number > def: "Main identifier of a ProteomeXchange dataset." [PSI:PI] > is_a: MS:1000878 ! external reference identifier > > [Term] > id: MS:1001920 > name: ProteomeXchange secondary identifier > def: "Secondary identifier of a ProteomeXchange dataset." [PSI:PI] > is_a: MS:1000878 ! external reference identifier > > [Term] > id: MS:1001921 > name: ProteomeXchange primary accession version number > def: "Version number of a ProteomeXchange accession number." [PSI:PI] > is_a: MS:1000878 ! external reference identifier > > [Term] > id: MS:1001922 > name: Digital Object Identifier (DOI) > def: "DOI unique identifier." [PSI:PI] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > is_a: MS:1000878 ! external reference identifier > relationship: has_regexp MS:1001176 ! (10\.(\d)+(\.(\d)*)?/[^\*].+) > > [Term] > id: MS:1001923 > name: external reference keyword > def: "Free text attribute that can enrich the information about an > entity." [PSI:PI] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > is_a: MS:1000878 ! external reference identifier > > [Term] > id: MS:1001924 > name: journal article keyword > def: "Keyword present in a scientific publication." [PSI:PI] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > is_a: MS:1001923 ! external reference keyword > > [Term] > id: MS:1001925 > name: submitter keyword > def: "Keyword assigned by the data submitter." [PSI:PI] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > is_a: MS:1001923 ! external reference keyword > > [Term] > id: MS:1001926 > name: curator keyword > def: "Keyword assigned by a data curator." [PSI:PI] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > is_a: MS:1001923 ! external reference keyword > > [Term] > id: MS:1001927 > name: Tranche file hash > def: "Hash assigned by the Tranche resource to an individual file." > [PSI:PI] > is_a: MS:1000878 ! external reference identifier > > [Term] > id: MS:1001928 > name: Tranche project hash > def: "Hash assigned by the Tranche resource to a whole project." > [PSI:PI] > is_a: MS:1000878 ! external reference identifier > > [Term] > id: MS:1001929 > name: PRIDE experiment URI > def: "URI that allows the access to one experiment in the PRIDE > database." [PSI:PI] > xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." > is_a: MS:1000878 ! external reference identifier > > [Term] > id: MS:1001930 > name: PRIDE project URI > def: "URI that allows the access to one project in the PRIDE database." > [PSI:PI] > xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." > is_a: MS:1000878 ! external reference identifier > > [Term] > id: MS:1001931 > name: source interface > def: "The source interface." [PSI:MS] > relationship: part_of MS:1000458 ! source > > [Term] > id: MS:1001932 > name: source interface model > def: "The source interface model." [PSI:MS] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > relationship: part_of MS:1001931 ! source interface > > [Term] > id: MS:1001933 > name: source sprayer > def: "The source sprayer." [PSI:MS] > relationship: part_of MS:1000458 ! source > > [Term] > id: MS:1001934 > name: source sprayer type > def: "The source sprayer type." [PSI:MS] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > relationship: part_of MS:1001933 ! source sprayer > > [Term] > id: MS:1001935 > name: source sprayer manufacturer > def: "The source sprayer manufacturer." [PSI:MS] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > relationship: part_of MS:1001933 ! source sprayer > > [Term] > id: MS:1001936 > name: source sprayer model > def: "The source sprayer model." [PSI:MS] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > relationship: part_of MS:1001933 ! source sprayer > > [Term] > id: MS:1001937 > name: sample plate > def: "Plate where the sample solution is spotted in a MALDI or similar > instrument." [PSI:MS] > relationship: part_of MS:1000458 ! source > > [Term] > id: MS:1001938 > name: sample plate type > def: "The sample plate type." [PSI:MS] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > relationship: part_of MS:1001937 ! sample plate > > [Term] > id: MS:1001939 > name: stainless steel plate > def: "Stainless steel plate." [PSI:MS] > is_a: MS:1001938 ! sample plate type > > [Term] > id: MS:1001940 > name: coated glass plate > def: "Coated glass plate." [PSI:MS] > is_a: MS:1001938 ! sample plate type > > [Term] > id: MS:1001941 > name: electrospray supply type > def: "Whether the sprayer is fed or is loaded with sample once." > [PSI:MS] > relationship: part_of MS:1000458 ! source > > [Term] > id: MS:1001942 > name: static supply electrospray > def: "The sprayer is loaded with sample once." [PSI:MS] > is_a: MS:1001941 ! electrospray supply type > > [Term] > id: MS:1001943 > name: fed supply electrospray > def: "The sprayer is continuously fed with sample." [PSI:MS] > is_a: MS:1001941 ! electrospray supply type > > [Term] > id: MS:1001944 > name: Collision cell exit potential > def: "Potential difference between Q2 and Q3 in a triple quadrupole > instrument in volts." [PSI:MS] > xref: value-type:xsd\:float "The allowed value-type for this CV term." > is_a: MS:1000510 ! precursor activation attribute > relationship: has_units UO:0000218 ! volt > synonym: "CXP" EXACT [] > > Best regards, > Gerhard > > -- > --- > Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer > BioInformatik > Medizinisches-Proteom-Center (MPC) > Ruhr-Universität Bochum > Zentrum für klinische Forschung I (ZKF I) > E.042 > Universitätsstrasse 150 > D-44801 Bochum > > Phone: +49(0)234/32-29836 > Fax: +49(0)234/32-14554 > Email: Ger...@ru... > Web: http://www.medizinisches-proteom-center.de |
From: Juan A. V. <ju...@eb...> - 2012-01-25 15:44:55
|
Hi Steffen, Oliver explained the way we tried to solve it in the case of mzTab. There have been several e-mails and conversations in the past about the general problem here and this is the adaptation of proteomics data format (such as traML or mzML) to work with metabolomics data. For instance, our colleagues here at the EBI (the group headed by C. Steinbeck) are going to use mzML and also mzTab for the MS derived data because there is not much well established in the metabolomics field. So the general problem is should we really try to move this really forward? This of course would mean a lot of extra work like, you say, working with new ontologies. But in my opinion is something that will need to get done sooner or later. I would like to know your opinion on this. Anyone else's opinion is of course also welcome. Maybe, a lot of things have already been done and I am not aware of them. Thanks, Juan On 25 Jan 2012, at 15:06, Oliver Kohlbacher wrote: > Steffen, > > you might want to have a look at the mzTab specification, more precisely > at the 'small molecule table' therein. > The approach chosen there is rather pragmatic: a database ID and a chemical > formula. Chemical formula is of course well specified and for most practical > purposes database IDs like PubChem or HMDB are entirely sufficient imho. > > http://code.google.com/p/mztab/wiki/FileFormat#Format_Specification > > CHeers, > Oliver > > > On Jan 25, 2012, at 3:12 PM, Steffen Neumann wrote: > >> Hi, >> >> I am currently preparing a set of MRM Transitions >> as showcase for TraML in Metabolomics. >> >> I'll need to specify for which <Compound> a transition >> was obtained. Currently, we only have cvParams >> for "predicted isoelectric point", "theoretical mass" >> and children of "chemical compound formula": >> http://www.peptideatlas.org/schemas/TraML/1.0.0/TraML1.0.0.html#Compound >> >> This is a) far from complete, and b) underspecified, >> because MS:1000867 "structural formula" does not specify >> whether the value shall be SMILES, InChI or whatever. >> >> Is there a way to embrace (pun intended :-) >> the EDAM (EMBRACE Data and Methods) ontology of [...] identifiers >> for <Compound> ? Then we'd have something like this: >> >> <TraML> >> <cv URI="http://edamontology.org/ontology?format=obo" >> fullName="EDAM (EMBRACE Data And Methods)" id="EDAM" version="unknown" /> >> ... >> <Compound> >> <cvParam accession="EDAM_data:1172" cvRef="EDAM" name="PubChem CID" value="932" /> >> </Compound> >> >> EDAM has entries for a gazillion different compound identifiers: >> http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM&termId=EDAM_data:1086&termName=Compound%20identifier >> >> and InChI, SMILES, molecular formula: >> http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM&termId=EDAM_format%3A2035&termName=Chemical%20formula%20format >> >> The only downside I can see is that the converters and validators >> need to slurp in another ontology of respectable size. >> >> Thoughts ? >> >> 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 >> >> >> >> ------------------------------------------------------------------------------ >> Keep Your Developer Skills Current with LearnDevNow! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-d2d >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > --- > Oliver Kohlbacher (oli...@un...) > Professor, Applied Bioinformatics, Center for Bioinformatics Tuebingen > Dept. of Computer Science, University of Tuebingen > phone: +49-7071-29-70457 http://abi.inf.uni-tuebingen.de > > vCard at: http://abi.inf.uni-tuebingen.de/People/kohlbach/vCard > > > > > > > > > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
From: Oliver K. <koh...@in...> - 2012-01-25 15:07:01
|
Steffen, you might want to have a look at the mzTab specification, more precisely at the 'small molecule table' therein. The approach chosen there is rather pragmatic: a database ID and a chemical formula. Chemical formula is of course well specified and for most practical purposes database IDs like PubChem or HMDB are entirely sufficient imho. http://code.google.com/p/mztab/wiki/FileFormat#Format_Specification CHeers, Oliver On Jan 25, 2012, at 3:12 PM, Steffen Neumann wrote: > Hi, > > I am currently preparing a set of MRM Transitions > as showcase for TraML in Metabolomics. > > I'll need to specify for which <Compound> a transition > was obtained. Currently, we only have cvParams > for "predicted isoelectric point", "theoretical mass" > and children of "chemical compound formula": > http://www.peptideatlas.org/schemas/TraML/1.0.0/TraML1.0.0.html#Compound > > This is a) far from complete, and b) underspecified, > because MS:1000867 "structural formula" does not specify > whether the value shall be SMILES, InChI or whatever. > > Is there a way to embrace (pun intended :-) > the EDAM (EMBRACE Data and Methods) ontology of [...] identifiers > for <Compound> ? Then we'd have something like this: > > <TraML> > <cv URI="http://edamontology.org/ontology?format=obo" > fullName="EDAM (EMBRACE Data And Methods)" id="EDAM" version="unknown" /> > ... > <Compound> > <cvParam accession="EDAM_data:1172" cvRef="EDAM" name="PubChem CID" value="932" /> > </Compound> > > EDAM has entries for a gazillion different compound identifiers: > http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM&termId=EDAM_data:1086&termName=Compound%20identifier > > and InChI, SMILES, molecular formula: > http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM&termId=EDAM_format%3A2035&termName=Chemical%20formula%20format > > The only downside I can see is that the converters and validators > need to slurp in another ontology of respectable size. > > Thoughts ? > > 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 > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev --- Oliver Kohlbacher (oli...@un...) Professor, Applied Bioinformatics, Center for Bioinformatics Tuebingen Dept. of Computer Science, University of Tuebingen phone: +49-7071-29-70457 http://abi.inf.uni-tuebingen.de vCard at: http://abi.inf.uni-tuebingen.de/People/kohlbach/vCard |
From: Gerhard M. <Ger...@ru...> - 2012-01-25 14:32:53
|
Hello all, I took over the CV maintenance of the psi-ms.obo file from David. David, in the name of the community I would like to thank you so much for your efforts in maintaining the CV during the last year. In the following you find a list of all requests and proposals which I found in the ms-vocab list since the last official release at Nov 24th, 2011 of the obo file (version 3.16.0). In addition I made sure that each definition ends with a period (full stop) according to the "Guidelines for the development of Controlled Vocabularies". Please check if the list is complete and the terms are correctly defined. At point 2.) I have also listed some open questions for added terms, for which I hope to get answers from the community. Any feedback and further suggestions are appreciated. If there are no further objections and / or discussions I plan to release the new version next tuesday (Jan 31th). In the attachment you'll find the obo file of the v3.17.0 release candidate. 1. Changes to already existing CV terms: ======================================== ************ Added Clostripain as synonym to "Arg-C" and the missing definition field [Term] id: MS:1001303 name: Arg-C def: "Endoproteinase Arg-C." [PSI:PI] synonym: "Clostripain" EXACT [] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001272 ! (?<=R)(?!P) ************ A new relation in "precolated plate": now also a "sample plate type" [Term] id: MS:1000839 name: precoated plate def: "Precoated plate." [PSI:MS] is_a: MS:1000833 ! matrix application type is_a: MS:1001938 ! sample plate type ************ "paul ion trap" is now obsolete, because redundant to quadrupole ion trap [Term] id: MS:1000297 name: paul ion trap def: "OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected." [PSI:MS] comment: This term was made obsolete because it is redundant to quadrupole ion trap synonym: "quadrupole ion trap" RELATED [] is_a: MS:1000479 ! purgatory is_obsolete: true ************ "axial ejection linear ion trap" is now a linear ion trap [Term] id: MS:1000078 name: axial ejection linear ion trap def: "A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer." [PSI:MS] is_a: MS:1000291 ! linear ion trap ************ "radial ejection linear ion trap" is now a linear ion trap [Term] id: MS:1000083 name: radial ejection linear ion trap def: "A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer." [PSI:MS] is_a: MS:1000291 ! linear ion trap 2. Open questions (please email me further informations): ========================================================= What are the datatypes for the following terms? MS:1001919 (ProteomeXchange primary accession number) MS:1001920 (ProteomeXchange secondary identifier) MS:1001921 (ProteomeXchange primary accession version number) MS:1001927 (Tranche file hash) MS:1001928 (Tranche project hash) 3. Newly added CV terms: ======================== [Term] id: MS:1001914 name: pymzML def: "Python module to interface mzML Data." [PSI:MS] is_a: MS:1001457 ! data processing software [Term] id: MS:1001915 name: elastase def: "Enzyme elastase. Cleaves after A, L, I or V, except when P is after A, L, I or V." [PSI:MS] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001176 ! (?<=[ALIV])(?!P) [Term] id: MS:1001916 name: proline endopeptidase def: "Enzyme proline endopeptidase. Cleaves after P." [PSI:MS] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001176 ! (?<=P) [Term] id: MS:1001917 name: staphylococcal protease def: "Staphylococcal protease. Cleaves after E." [PSI:MS] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001176 ! (?<=E) [Term] id: MS:1001918 name: jodobenzoate def: "Chemical Jodobenzoate. Cleaves after W." [PSI:MS] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001176 ! (?<=W) [Term] id: MS:1001919 name: ProteomeXchange primary accession number def: "Main identifier of a ProteomeXchange dataset." [PSI:PI] is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001920 name: ProteomeXchange secondary identifier def: "Secondary identifier of a ProteomeXchange dataset." [PSI:PI] is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001921 name: ProteomeXchange primary accession version number def: "Version number of a ProteomeXchange accession number." [PSI:PI] is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001922 name: Digital Object Identifier (DOI) def: "DOI unique identifier." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier relationship: has_regexp MS:1001176 ! (10\.(\d)+(\.(\d)*)?/[^\*].+) [Term] id: MS:1001923 name: external reference keyword def: "Free text attribute that can enrich the information about an entity." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001924 name: journal article keyword def: "Keyword present in a scientific publication." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword [Term] id: MS:1001925 name: submitter keyword def: "Keyword assigned by the data submitter." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword [Term] id: MS:1001926 name: curator keyword def: "Keyword assigned by a data curator." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword [Term] id: MS:1001927 name: Tranche file hash def: "Hash assigned by the Tranche resource to an individual file." [PSI:PI] is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001928 name: Tranche project hash def: "Hash assigned by the Tranche resource to a whole project." [PSI:PI] is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001929 name: PRIDE experiment URI def: "URI that allows the access to one experiment in the PRIDE database." [PSI:PI] xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001930 name: PRIDE project URI def: "URI that allows the access to one project in the PRIDE database." [PSI:PI] xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1001931 name: source interface def: "The source interface." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1001932 name: source interface model def: "The source interface model." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001931 ! source interface [Term] id: MS:1001933 name: source sprayer def: "The source sprayer." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1001934 name: source sprayer type def: "The source sprayer type." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001933 ! source sprayer [Term] id: MS:1001935 name: source sprayer manufacturer def: "The source sprayer manufacturer." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001933 ! source sprayer [Term] id: MS:1001936 name: source sprayer model def: "The source sprayer model." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001933 ! source sprayer [Term] id: MS:1001937 name: sample plate def: "Plate where the sample solution is spotted in a MALDI or similar instrument." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1001938 name: sample plate type def: "The sample plate type." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001937 ! sample plate [Term] id: MS:1001939 name: stainless steel plate def: "Stainless steel plate." [PSI:MS] is_a: MS:1001938 ! sample plate type [Term] id: MS:1001940 name: coated glass plate def: "Coated glass plate." [PSI:MS] is_a: MS:1001938 ! sample plate type [Term] id: MS:1001941 name: electrospray supply type def: "Whether the sprayer is fed or is loaded with sample once." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1001942 name: static supply electrospray def: "The sprayer is loaded with sample once." [PSI:MS] is_a: MS:1001941 ! electrospray supply type [Term] id: MS:1001943 name: fed supply electrospray def: "The sprayer is continuously fed with sample." [PSI:MS] is_a: MS:1001941 ! electrospray supply type [Term] id: MS:1001944 name: Collision cell exit potential def: "Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000218 ! volt synonym: "CXP" EXACT [] Best regards, Gerhard -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |