psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] Release candidate 4.1.9_rc2 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are new terms from the release candidate 4.1.9_rc2 of the 
psi-ms.obo file.
It contains new terms for isomer, isotopomer, isotopologue and their peaks
as well as name changes for the PEFF regular expression terms.

New CV terms in version 4.1.9_rc2 of psi-ms.obo:
================================================
[Term]
id: MS:1002955
name: hr-ms compound identification confidence level
def: "Refined High Resolution mass spectrometry confidence level for 
annotation of identified compounds as proposed by Schymanski et al. The 
value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 
2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540]
xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute

[Term]
id: MS:1002956
name: isotopic ion MS peak
def: "A mass spectrometry peak that represents one or more isotopic 
ions. The value slot contains a description of the represented isotope 
set, e.g. 'M+1 peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak

[Term]
id: MS:1002957
name: isotopomer MS peak
def: "The described isotopomer mass spectrometric signal. The value slot 
contains a description of the represented isotopomer, e.g. '13C peak', 
'15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002956 ! isotopic ion MS peak

[Term]
id: MS:1002958
name: isotopologue MS peak
def: "The described isotopologue mass spectrometric signal. The value 
slot contains a description of the represented isotopologue, e.g. '13C1 
peak' or '15N1 peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002956 ! isotopic ion MS peak

[Term]
id: MS:1002959
name: isomer
def: "One of several species (or molecular entities) that have the same 
atomic composition (molecular formula) but different line formulae or 
different stereochemical formulae." 
[https://goldbook.iupac.org/html/I/I03289.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Ontology

[Term]
id: MS:1002960
name: isotopomer
def: "An isomer that differs from another only in the spatial 
distribution of the constitutive isotopic atoms." 
[https://goldbook.iupac.org/html/I/I03352.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002959 ! isomer

[Term]
id: MS:1002961
name: isotopologue
def: "A molecular entity that differs only in isotopic composition 
(number of isotopic substitutions)." 
[https://goldbook.iupac.org/html/I/I03351.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002959 ! isomer



Changed CV terms in version 4.1.9_rc2 of psi-ms.obo:
====================================================
************ Obsoleted the following term
[Term]
id: MS:1002897
name: isotopomer peak
def: "OBSOLETE Identifies a peak when no de-isotoping has been 
performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', 
'15N', '18O', '31P'." [PSI:PI]
comment: This term was obsoleted because it was replaced by the more 
exact terms terms MS:1002956 'isotopic ion MS peak', MS:1002957 
'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead.
xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak
is_obsolete: true

************ Exchanged the name and definition for the PEFF regular 
expression
************ terms PEFF:1002001, PEFF:1002002 and PEFF:1002003 in order 
to make
************ the psi-ms.obo file loadable in OBO-Edit again (currently the
************ validator exits with an error message special characters 
are not
************ allowed in names).
[Term]
id: PEFF:1002001
name: regular expression for PEFF description line
def: "([0-9]+|[0-9]+|[a-zA-Z0-9]*)." [PSI:PEFF]
is_a: MS:1002479 ! regular expression

[Term]
id: PEFF:1002002
name: regular expression for PEFF molecular sequence type
def: 
"(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)." 
[PSI:PEFF]
is_a: MS:1002479 ! regular expression

[Term]
id: PEFF:1002003
name: regular expression for PEFF sequence status
def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF]
is_a: MS:1002479 ! regular expression


Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] Release candidate 4.1.9_rc1 of psi-ms.obo

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

Dear proteomics/metabolomics community,


following are new terms from the release candidate 4.1.9_rc1 of the 
psi-ms.obo file.
It contains new terms for isomer, isotopomer, isotopologue and their peaks.


New CV terms in version 4.1.9_rc1 of psi-ms.obo:
================================================
[Term]
id: MS:1002955
name: hr-ms compound identification confidence level
def: "Refined High Resolution mass spectrometry confidence level for 
annotation of identified compounds as proposed by Schymanski et al. The 
value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 
2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540]
xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute

[Term]
id: MS:1002956
name: isotopic ion MS peak
def: "A mass spectrometry peak that represents one or more isotopic 
ions. The value slot contains a description of the represented isotope 
set, e.g. 'M+1 peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak

[Term]
id: MS:1002957
name: isotopomer MS peak
def: "The described isotopomer mass spectrometric signal. The value slot 
contains a description of the represented isotopomer, e.g. '13C peak', 
'15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002956 ! isotopic ion MS peak

[Term]
id: MS:1002958
name: isotopologue MS peak
def: "The described isotopologue mass spectrometric signal. The value 
slot contains a description of the represented isotopologue, e.g. '13C1 
peak' or '15N1 peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002956 ! isotopic ion MS peak

[Term]
id: MS:1002959
name: isomer
def: "One of several species (or molecular entities) that have the same 
atomic composition (molecular formula) but different line formulae or 
different stereochemical formulae." 
[https://goldbook.iupac.org/html/I/I03289.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Ontology

[Term]
id: MS:1002960
name: isotopomer
def: "An isomer that differs from another only in the spatial 
distribution of the constitutive isotopic atoms." 
[https://goldbook.iupac.org/html/I/I03352.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002959 ! isomer

[Term]
id: MS:1002961
name: isotopologue
def: "A molecular entity that differs only in isotopic composition 
(number of isotopic substitutions)." 
[https://goldbook.iupac.org/html/I/I03351.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002959 ! isomer



Changed CV terms in version 4.1.9_rc1 of psi-ms.obo:
====================================================
************ Obsoleted the following term
[Term]
id: MS:1002897
name: isotopomer peak
def: "OBSOLETE Identifies a peak when no de-isotoping has been 
performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', 
'15N', '18O', '31P'." [PSI:PI]
comment: This term was obsoleted because it was replaced by the more 
exact terms terms MS:1002956 'isotopic ion MS peak', MS:1002957 
'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead.
xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak
is_obsolete: true


Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] CV term for isotopomers

[Binz Pierre-A. <Pie...@ch...>]

Hi Gerhard,
Fine to define a generic term to describe such MS signal.
But there are a few problems/questions here: There is a need to consider the correct definitions of the molecular species and the need to differentiate the description of the molecular species from the MS signals that represent these molecular species


1)      Definitions of molecular species: isotopologue and isotopomer (see IUPAC gold book : https://goldbook.iupac.org/html/I/I03351.html and https://goldbook.iupac.org/html/I/I03352.html) are terms that define specific molecular species:

-          If you want to describe is the possibility to differentiate an isotope from another, where the number of isotopic atoms differ (same chemical structure (example C2H5ON) but another isotopic atom distribution: 12C2 H5 O 14N2   vs.   13C1 12C1 H5 O 14N   vs.   12C2 H5 O 15N) In that case these are isotopologues. They also do not have, in most of the cases, the exact same mass. Please note that isotopologue has also a definition based on identity of mass number (same total number of protons and neutrons, but differently distributed in the atoms).


-          In contrast, two isotopomers have the same number of each isotopic atom but differ in the position, such as in constitutional isomers ( example ethanol : H3(13C)-(12C)H2OH vs H3(12C)-(13C)H2OH) or isotopic stereomers ((R)- and (S)-CH3CHDOH), which share an exact same mass.



2)      MS signals do represent molecular ions, but are not molecular ions themselves. In that respect, the term isotopomer has to be different from isotopomer MS signal. What you want to describe here are MS signals representing isomers (isotopomers, isotopologues, mix of them). Therefore there is a need to use isotopomer MS signal  and isotopologue MS signal  (no need to specify that they are ion signals).



3)      A MS signal at M+1 (nominal mass of the monoisotopic form + 1Da, low res instruments) is often a mix of isotopologues and isotopomers (one 13C OR one 15N OR one 2H (deuterium) distributed on the ion/molecule). In that case the signal cannot discriminate. Both strict terms isotopomer and isotopologue are not full correct. One should use the term isobar (same mass number). Only if the signals can be discriminated at very high resolving power instruments (which can discriminate the isobars 12C15N from 13C14N one can specify them as different isotopologues)



4)      In all cases the definition field of the PSI-MS CV term must not be restricted to quantified peak as it is proposed. This term isotopomer describes a (group of) molecules or a (group of) ion(s). This  should be available for quant as well as for ID. It should only represent a descriptor of what isotopomer is considered in a data analysis process. Please remove the restriction to quant in the definition of the terms here



My proposal:   use three terms for the definition of the molecular species MS signals: isotopic ion MS peak, isotopomer MS peak, isotopologue MS peak, and create also terms for the definition of the molecular species themselves.



id: MS:nnnnnnn
name: isotopic ion MS peak
def: " A MS peak that represents one or more isotopic ions. The value slot contains description of the represented isotope set , e.g. 'M+1 peak'." [PSI:PI]." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

id: MS:nnnnnnn
name: isotopomer MS peak
def: " The described isotopomer MS signal. The value slot contains description of the represented isotopomer, e.g. '13C peak' or '15N peak'." [PSI:PI]." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology
is_a: MS:nnnnnnn ! isotopic ion MS signal


id: MS:nnnnnnn
name: isotopologue MS peak
def: " The described isotopologue MS signal. The value slot contains description of the represented isotopologue , e.g. '13C1 peak' or '15N1 peak'." [PSI:PI]." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology
is_a: MS:nnnnnnn ! isotopic ion MS signal


id: MS:1002955
name: isotopomer
def: " An isomer that differ from another only in the spatial distribution of the constitutive isotopic atoms." [PSI:PI]." [https://goldbook.iupac.org/html/I/I03352.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology
is_a: MS:nnnnnnn ! isomer


id: MS:nnnnnnn
name: isotopologue
def: " A molecular entity that differs only in isotopic composition (number of isotopic substitutions),." [PSI:PI]." [https://goldbook.iupac.org/html/I/I03351.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology
is_a: MS:nnnnnnn ! isomer


id: MS:nnnnnnn
name: isomer
def: " One of several species (or molecular entities ) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae " [PSI:PI]." [https://goldbook.iupac.org/html/I/I03289.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology


Pierre-Alain


De : mayerg97 via Psidev-pi-dev <psi...@li...>
Envoyé : vendredi 8 juin 2018 12:32
À : psi...@li...
Cc : psi...@li...; Mass spectrometry standard development <psi...@li...>; jones, Andy <And...@li...>
Objet : Re: [Psidev-pi-dev] [Psidev-ms-vocab] CV term for isotopomers

Hi all,

I would propose to add a generic term with a string value like e.g.

[Term]
id: MS:1002955
name: isotopomer
def: "The quantified isotopomer. The value slot contains the quantified peak, e.g. '13C peak' or '15N peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

Cheers,
Gerhard
Am 06.06.2018 um 17:21 schrieb Jones, Andy:
Hi all,

I have a potential term request for mzTab-M in this section, where we allow the exporter to state if quant is being provided for an assumed peak other than the monoisotopic one (for quant approaches that are not de-isotoping features). I don't see any such term already in PSI-MS, does this seem sensible to add, or should we just add a specification for a number e.g. +1, +2 (relative to the monoisotopic peak). I recognize that for very-high res instruments one might be able to resolve separately a 13C and a 15N peak, I think this is done here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838547/. For these kinds of approaches, it would seem useful to be able to state some other knowledge about the peak being quantified.

Let me know any thoughts!
Best wishes
Andy


6.4.5. isotopomer
Description:

If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here e.g. "+1", "+2", "13C peak" using cvParams, otherwise (i.e. for approaches where SMF rows are de-isotoped features) this MUST be null.

Type:

Parameter

Is Nullable:

TRUE

Example:

SFH SMF_ID ... isotopomer ...
SMF 1 ... [MS,MS:1000XX,"13C peak", ]...







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--

--------------------------------------------------------------------

Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER

PhD student

Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29272 | Fax +49 (0)234 32-14554

E-mail ger...@ru...<mailto:ger...@ru...>

www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de/>

Re: [Psidev-ms-dev] [Psidev-ms-vocab] CV term for isotopomers

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

Hi all,

I would propose to add a generic term with a string value like e.g.

[Term]
id: MS:1002955
name: isotopomer
def: "The quantified isotopomer. The value slot contains the quantified 
peak, e.g. '13C peak' or '15N peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Ontology

Cheers,
Gerhard

Am 06.06.2018 um 17:21 schrieb Jones, Andy:
>
> Hi all,
>
> I have a potential term request for mzTab-M in this section, where we 
> allow the exporter to state if quant is being provided for an assumed 
> peak other than the monoisotopic one (for quant approaches that are 
> not de-isotoping features). I don’t see any such term already in 
> PSI-MS, does this seem sensible to add, or should we just add a 
> specification for a number e.g. +1, +2 (relative to the monoisotopic 
> peak). I recognize that for very-high res instruments one might be 
> able to resolve separately a 13C and a 15N peak, I think this is done 
> here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838547/ 
> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838547/>. For these 
> kinds of approaches, it would seem useful to be able to state some 
> other knowledge about the peak being quantified.
>
> Let me know any thoughts!
>
> Best wishes
>
> Andy
>
> 6.4.5. isotopomer
>
> *Description:*
>
> 	
>
> If de-isotoping has not been performed, then the isotopomer quantified 
> MUST be reported here e.g. “+1”, “+2”, “13C peak” using cvParams, 
> otherwise (i.e. for approaches where SMF rows are de-isotoped 
> features) this MUST be null.
>
> *Type:*
>
> 	
>
> Parameter
>
> *Is Nullable:*
>
> 	
>
> *TRUE*
>
> *Example:*
>
> 	
>
> SFH SMF_ID … isotopomer …
>
> SMF 1 … *[MS,MS:1000XX,”13C peak”, ]…*
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>
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> Psidev-ms-vocab mailing list
> Psi...@li...
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-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] New version 4.1.8 of psi-ms.obo

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

Dear proteomics/metabolomics community,


the new version 4.1.8 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains new terms for the TopPIC and TopMG software.


New CV terms in version 4.1.8 of psi-ms.obo:
============================================
[Term]
id: MS:1002899
name: msalign format
def: "msalign file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002900
name: feature format
def: "TopFD feature file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002901
name: TopPIC
def: "TopPIC: a software tool for top-down mass spectrometry-based 
proteoform identification and characterization." [PMID:27423895, 
http://proteomics.informatics.iupui.edu/software/toppic/index.html]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002902
name: TopFD
def: "Top-down mass spectral feature detection." 
[http://proteomics.informatics.iupui.edu/software/toppic/index.html]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002903
name: TopMG
def: "A mass graph-based approach for the identification of modified 
proteoforms using top-down tandem mass spectra." [PMID:28453668, 
http://proteomics.informatics.iupui.edu/software/topmg/index.html]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002904
name: proteoform-level identification attribute
def: "Proteoform level information." [PSI:PI]
is_a: MS:1002694 ! single identification result attribute

[Term]
id: MS:1002905
name: proteoform-level identification statistic
def: "Identification confidence metric for a proteoform." [PSI:PI]
is_a: MS:1002904 ! proteoform-level identification attribute

[Term]
id: MS:1002906
name: search engine specific score for proteoforms
def: "Search engine specific proteoform scores." [PSI:PI]
is_a: MS:1002905 ! proteoform-level identification statistic

[Term]
id: MS:1002907
name: proteoform-level global FDR
def: "Estimation of the global false discovery rate of proteoforms." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002905 ! proteoform-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002908
name: proteoform-level local FDR
def: "Estimation of the local false discovery rate of proteoforms." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002905 ! proteoform-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002909
name: proteoform-level statistical threshold
def: "Estimated statistical threshold at proteoform-level." [PSI:PI]
is_a: MS:1002573 ! spectrum identification statistical threshold

[Term]
id: MS:1002910
name: proteoform-level global FDR threshold
def: "Threshold for the global false discovery rate of proteoforms." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002909 ! proteoform-level statistical threshold

[Term]
id: MS:1002911
name: proteoform-level local FDR threshold
def: "Threshold for the local false discovery rate of proteoforms." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002909 ! proteoform-level statistical threshold

[Term]
id: MS:1002912
name: TopPIC input parameter
def: "Search engine input parameters specific to TopPIC." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002913
name: TopPIC:fixed modification
def: "Fixed modifications for TopPIC searching." [PSI:PI]
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002914
name: TopPIC:N-term form
def: "N-terminal forms of proteins allowed in TopPIC searching." [PSI:PI]
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002915
name: TopPIC:error tolerance
def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002916
name: TopPIC:max shift
def: "Maximum value of the mass shift (in Dalton) of an unexpected 
modification." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002917
name: TopPIC:min shift
def: "Minimum value of the mass shift (in Dalton) of an unexpected 
modification." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002918
name: TopPIC:shift num
def: "Maximum number of unexpected modifications in a proteoform 
spectrum match." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002919
name: TopPIC:spectral cutoff type
def: "Spectrum-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002920
name: TopPIC:spectral cutoff value
def: "Spectrum-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002921
name: TopPIC:proteoform-level cutoff type
def: "Proteoform-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002922
name: TopPIC:proteoform-level cutoff value
def: "Proteoform-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002923
name: TopPIC:generating function
def: "P-value and E-value estimation using generating function." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002924
name: TopPIC:combined spectrum number
def: "Number of combined spectra." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002925
name: TopPIC:mod file
def: "The text file containing the information of common PTMs." [PSI:PI]
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002926
name: TopPIC:thread number
def: "Number of threads used in TopPIC." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002927
name: TopPIC:use TopFD feature
def: "Proteoform identification using TopFD feature file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002928
name: TopPIC:spectral E-value
def: "TopPIC spectrum-level E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002353 ! PSM-level e-value
relationship: has_order MS:1002109 ! lower score better

[Term]
id: MS:1002929
name: TopPIC:spectral FDR
def: "TopPIC spectrum-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002351 ! PSM-level local FDR

[Term]
id: MS:1002930
name: TopPIC:proteoform-level FDR
def: "TopPIC proteoform-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002901 ! search engine specific score for proteoforms

[Term]
id: MS:1002931
name: TopPIC:spectral p-value
def: "TopPIC spectrum-level p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002352 ! PSM-level p-value

[Term]
id: MS:1002932
name: TopPIC:MIScore
def: "Modification identification score." [PMID:27291504]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic

[Term]
id: MS:1002933
name: TopPIC:MIScore threshold
def: "TopPIC:MIScore threshold." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002934
name: TopMG input parameter
def: "Search engine input parameters specific to TopMG." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002935
name: TopMG:fixed modification
def: "Fixed modifications for TopMG searching." [PSI:PI]
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002936
name: TopMG:N-term form
def: "N-terminal forms of proteins allowed in TopMG searching." [PSI:PI]
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002937
name: TopMG:error tolerance
def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002938
name: TopMG:max shift
def: "Maximum value of the mass shift (in Dalton)." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002939
name: TopMG:spectral cutoff type
def: "Spectrum-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002940
name: TopMG:spectral cutoff value
def: "Spectrum-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002941
name: TopMG:proteoform-level cutoff type
def: "Proteoform-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002942
name: TopMG:proteoform-level cutoff value
def: "Proteoform-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002943
name: TopMG:mod file
def: "The text file containing the information of common PTMs." [PSI:PI]
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002944
name: TopMG:thread number
def: "Number of threads used in TopMG." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002945
name: TopMG:use TopFD feature
def: "Proteoform identification using TopFD feature file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002946
name: TopMG:proteoform graph gap size
def: "Gap size in constructing proteoform graph." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002947
name: TopMG:variable PTM number
def: "Maximum number of variable PTMs." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002948
name: TopMG:variable PTM number in proteoform graph gap
def: "Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002949
name: TopMG:use ASF-DIAGONAL
def: "Protein filtering using ASF-DIAGONAL method." [PMID:29327814]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002950
name: TopMG:spectral E-value
def: "TopMG spectrum-level E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better

[Term]
id: MS:1002951
name: TopMG:spectral FDR
def: "TopMG spectrum-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002351 ! PSM-level local FDR
is_a: MS:1001143 ! PSM-level search engine specific statistic

[Term]
id: MS:1002952
name: TopMG:proteoform-level FDR
def: "TopMG proteoform-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002901 ! search engine specific score for proteoforms

[Term]
id: MS:1002953
name: TopMG:spectral p-value
def: "TopMG spectrum-level p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002352 ! PSM-level p-value
is_a: MS:1001143 ! PSM-level search engine specific statistic

[Term]
id: MS:1002954
name: collisional cross sectional area
def: "Structural molecular descriptor for the effective interaction area 
between the ion and neutral gas measured in ion mobility mass 
spectrometry." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1000861 ! chemical compound attribute
relationship: has_units UO:0000324 ! square angstrom


Changed CV terms in version 4.1.8 of psi-ms.obo:
================================================
No changed CV terms


Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] Release candidate 4.1.8_rc1 of psi-ms.obo

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

Dear proteomics community,

following are new terms from the release candidate 4.1.8_rc1 of the 
psi-ms.obo file.
It contains new terms for the TopPIC and TopMG software.


New CV terms in version 4.1.8_rc1 of psi-ms.obo:
================================================
[Term]
id: MS:1002899
name: msalign format
def: "msalign file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002900
name: feature format
def: "TopFD feature file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002901
name: TopPIC
def: "TopPIC: a software tool for top-down mass spectrometry-based 
proteoform identification and characterization." [PMID:27423895, 
http://proteomics.informatics.iupui.edu/software/toppic/index.html]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002902
name: TopFD
def: "Top-down mass spectral feature detection." 
[http://proteomics.informatics.iupui.edu/software/toppic/index.html]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002903
name: TopMG
def: "A mass graph-based approach for the identification of modified 
proteoforms using top-down tandem mass spectra." [PMID:28453668, 
http://proteomics.informatics.iupui.edu/software/topmg/index.html]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002904
name: proteoform-level identification attribute
def: "Proteoform level information." [PSI:PI]
is_a: MS:1002694 ! single identification result attribute

[Term]
id: MS:1002905
name: proteoform-level identification statistic
def: "Identification confidence metric for a proteoform." [PSI:PI]
is_a: MS:1002904 ! proteoform-level identification attribute

[Term]
id: MS:1002906
name: search engine specific score for proteoforms
def: "Search engine specific proteoform scores." [PSI:PI]
is_a: MS:1002905 ! proteoform-level identification statistic

[Term]
id: MS:1002907
name: proteoform-level global FDR
def: "Estimation of the global false discovery rate of proteoforms." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002905 ! proteoform-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002908
name: proteoform-level local FDR
def: "Estimation of the local false discovery rate of proteoforms." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002905 ! proteoform-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002909
name: proteoform-level statistical threshold
def: "Estimated statistical threshold at proteoform-level." [PSI:PI]
is_a: MS:1002573 ! spectrum identification statistical threshold

[Term]
id: MS:1002910
name: proteoform-level global FDR threshold
def: "Threshold for the global false discovery rate of proteoforms." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002909 ! proteoform-level statistical threshold

[Term]
id: MS:1002911
name: proteoform-level local FDR threshold
def: "Threshold for the local false discovery rate of proteoforms." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002909 ! proteoform-level statistical threshold

[Term]
id: MS:1002912
name: TopPIC input parameter
def: "Search engine input parameters specific to TopPIC." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002913
name: TopPIC:fixed modification
def: "Fixed modifications for TopPIC searching." [PSI:PI]
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002914
name: TopPIC:N-term form
def: "N-terminal forms of proteins allowed in TopPIC searching." [PSI:PI]
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002915
name: TopPIC:error tolerance
def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002916
name: TopPIC:max shift
def: "Maximum value of the mass shift (in Dalton) of an unexpected 
modification." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002917
name: TopPIC:min shift
def: "Minimum value of the mass shift (in Dalton) of an unexpected 
modification." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002918
name: TopPIC:shift num
def: "Maximum number of unexpected modifications in a proteoform 
spectrum match." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002919
name: TopPIC:spectral cutoff type
def: "Spectrum-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002920
name: TopPIC:spectral cutoff value
def: "Spectrum-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002921
name: TopPIC:proteoform-level cutoff type
def: "Proteoform-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002922
name: TopPIC:proteoform-level cutoff value
def: "Proteoform-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002923
name: TopPIC:generating function
def: "P-value and E-value estimation using generating function." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002924
name: TopPIC:combined spectrum number
def: "Number of combined spectra." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002925
name: TopPIC:mod file
def: "The text file containing the information of common PTMs." [PSI:PI]
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002926
name: TopPIC:thread number
def: "Number of threads used in TopPIC." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002927
name: TopPIC:use TopFD feature
def: "Proteoform identification using TopFD feature file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002928
name: TopPIC:spectral E-value
def: "TopPIC spectrum-level E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002353 ! PSM-level e-value
relationship: has_order MS:1002109 ! lower score better

[Term]
id: MS:1002929
name: TopPIC:spectral FDR
def: "TopPIC spectrum-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002351 ! PSM-level local FDR

[Term]
id: MS:1002930
name: TopPIC:proteoform-level FDR
def: "TopPIC proteoform-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002901 ! search engine specific score for proteoforms

[Term]
id: MS:1002931
name: TopPIC:spectral p-value
def: "TopPIC spectrum-level p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002352 ! PSM-level p-value

[Term]
id: MS:1002932
name: TopPIC:MIScore
def: "Modification identification score." [PMID:27291504]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic

[Term]
id: MS:1002933
name: TopPIC:MIScore threshold
def: "TopPIC:MIScore threshold." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002934
name: TopMG input parameter
def: "Search engine input parameters specific to TopMG." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002935
name: TopMG:fixed modification
def: "Fixed modifications for TopMG searching." [PSI:PI]
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002936
name: TopMG:N-term form
def: "N-terminal forms of proteins allowed in TopMG searching." [PSI:PI]
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002937
name: TopMG:error tolerance
def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002938
name: TopMG:max shift
def: "Maximum value of the mass shift (in Dalton)." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002939
name: TopMG:spectral cutoff type
def: "Spectrum-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002940
name: TopMG:spectral cutoff value
def: "Spectrum-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002941
name: TopMG:proteoform-level cutoff type
def: "Proteoform-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002942
name: TopMG:proteoform-level cutoff value
def: "Proteoform-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002943
name: TopMG:mod file
def: "The text file containing the information of common PTMs." [PSI:PI]
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002944
name: TopMG:thread number
def: "Number of threads used in TopMG." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002945
name: TopMG:use TopFD feature
def: "Proteoform identification using TopFD feature file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002946
name: TopMG:proteoform graph gap size
def: "Gap size in constructing proteoform graph." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002947
name: TopMG:variable PTM number
def: "Maximum number of variable PTMs." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002948
name: TopMG:variable PTM number in proteoform graph gap
def: "Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002949
name: TopMG:use ASF-DIAGONAL
def: "Protein filtering using ASF-DIAGONAL method." [PMID:29327814]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002950
name: TopMG:spectral E-value
def: "TopMG spectrum-level E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better

[Term]
id: MS:1002951
name: TopMG:spectral FDR
def: "TopMG spectrum-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002351 ! PSM-level local FDR
is_a: MS:1001143 ! PSM-level search engine specific statistic

[Term]
id: MS:1002952
name: TopMG:proteoform-level FDR
def: "TopMG proteoform-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002901 ! search engine specific score for proteoforms

[Term]
id: MS:1002953
name: TopMG:spectral p-value
def: "TopMG spectrum-level p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002352 ! PSM-level p-value
is_a: MS:1001143 ! PSM-level search engine specific statistic

[Term]
id: MS:1002954
name: collisional cross sectional area
def: "Structural molecular descriptor for the effective interaction area 
between the ion and neutral gas measured in ion mobility mass 
spectrometry." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1000861 ! chemical compound attribute
relationship: has_units UO:0000324 ! square angstrom


Changed CV terms in version 4.1.8_rc1 of psi-ms.obo:
====================================================
No changed CV terms


Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] New version 4.1.7 of psi-ms.obo

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

Dear proteomics/metabolomics community,

the new version 4.1.7 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains new and changed terms for mzTab-M annotation.


New CV terms in version 4.1.7 of psi-ms.obo:
============================================
[Term]
id: MS:1002894
name: InChIKey
def: "Unique chemical structure identifier for chemical compounds." 
[PMID:273343401]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1002895
name: small molecule identification attribute
def: "Compound identification information." [PSI:PI]
is_a: MS:1002694 ! single identification result attribute

[Term]
id: MS:1002896
name: compound identification confidence level
def: "Confidence level for annotation of identified compounds as defined 
by the Metabolomics Standards Initiative (MSI). The value slot can have 
the values 'Level 0' until 'Level 4'." [PMID:29748461]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute

[Term]
id: MS:1002897
name: isotopomer peak
def: "Identifies a peak when no de-isotoping has been performed. The 
value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', 
'31P'." [PSI:PI]
xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak

[Term]
id: MS:1002898
name: Shimadzu Biotech QTOF nativeID format
def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:PI]
is_a: MS:1000767 ! native spectrum identifier format


Changed CV terms in version 4.1.7 of psi-ms.obo:
================================================
************ Changed definition and added publication reference 
[PMID:27824832]
[Term]
id: MS:1002599
name: splash key
def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details

Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.7_rc1 of psi-ms.obo

[Brian P. <bs...@pr...>]

Apologies if I'm being pedantic, but shouldn't "InChI key" really be
"InChIKey"?

I've not seen it as two words before, and that's not how the InChI folks
use it: http://inchi.info/inchikey_overview_en.html.

Cheers

Brian Pratt

On Fri, May 18, 2018 at 5:50 AM, mayerg97 via Psidev-ms-vocab <
psi...@li...> wrote:

> Dear proteomics/metabolomics community,
>
> following are new/changed terms from the release candidate 4.1.7_rc1 of
> the psi-ms.obo file.
> It contains new and changed terms for mzTab-M annotation.
>
>
> New CV terms in version 4.1.7_rc1 of psi-ms.obo:
> ================================================
> [Term]
> id: MS:1002894
> name: InChI key
> def: "Unique chemical structure identifier for chemical compounds."
> [PMID:273343401]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001405 ! spectrum identification result details
>
> [Term]
> id: MS:1002895
> name: small molecule identification attribute
> def: "Compound identification information." [PSI:PI]
> is_a: MS:1002694 ! single identification result attribute
>
> [Term]
> id: MS:1002896
> name: compound identification confidence level
> def: "Confidence level for annotation of identified compounds as defined
> by the Metabolomics Standards Initiative (MSI). The value slot can have the
> values 'Level 0' until 'Level 4'." [PMID:29748461]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002895 ! small molecule identification attribute
>
> [Term]
> id: MS:1002897
> name: isotopomer peak
> def: "Identifies a peak when no de-isotoping has been performed. The value
> slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'."
> [PSI:PI]
> xref: value-type:xsd:string "The allowed value-type for this CV term."
> is_a: MS:1000231 ! peak
>
>
> Changed CV terms in version 4.1.7_rc1 of psi-ms.obo:
> ====================================================
> ************ Changed definition and added publication reference
> [PMID:27824832]
> [Term]
> id: MS:1002599
> name: splash key
> def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001405 ! spectrum identification result details
>
> Best Regards,
> Gerhard
> --
>
> *--------------------------------------------------------------------*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
> *PhD student*
>
> *Medizinisches Proteom-Center*
>
> *DEPARTMENT Medical Bioinformatics*
>
> *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum
>
> *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554
>
> *E-mail* ger...@ru...
>
> www.medizinisches-proteom-center.de
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Psidev-ms-vocab mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
>
>

[Psidev-ms-dev] Release candidate 4.1.7_rc1 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are new/changed terms from the release candidate 4.1.7_rc1 of 
the psi-ms.obo file.
It contains new and changed terms for mzTab-M annotation.


New CV terms in version 4.1.7_rc1 of psi-ms.obo:
================================================
[Term]
id: MS:1002894
name: InChI key
def: "Unique chemical structure identifier for chemical compounds." 
[PMID:273343401]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1002895
name: small molecule identification attribute
def: "Compound identification information." [PSI:PI]
is_a: MS:1002694 ! single identification result attribute

[Term]
id: MS:1002896
name: compound identification confidence level
def: "Confidence level for annotation of identified compounds as defined 
by the Metabolomics Standards Initiative (MSI). The value slot can have 
the values 'Level 0' until 'Level 4'." [PMID:29748461]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute

[Term]
id: MS:1002897
name: isotopomer peak
def: "Identifies a peak when no de-isotoping has been performed. The 
value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', 
'31P'." [PSI:PI]
xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak


Changed CV terms in version 4.1.7_rc1 of psi-ms.obo:
====================================================
************ Changed definition and added publication reference 
[PMID:27824832]
[Term]
id: MS:1002599
name: splash key
def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details

Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] New version 4.1.6 of psi-ms.obo

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

Dear proteomics/metabolomics community,

the new version 4.1.6 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains new and modified CV terms for ion mobility.


New CV terms in version 4.1.6 of psi-ms.obo:
============================================
[Term]
id: MS:1002892
name: ion mobility attribute
def: "An attribute describing ion mobility searches." [PSI:PI]
is_a: MS:1000503 ! scan attribute
is_a: MS:1002345 ! PSM-level attribute

[Term]
id: MS:1002893
name: ion mobility array
def: "An array of ion mobility data." [PSI:PI]
is_a: MS:1000513 ! binary data array


Changed CV terms in version 4.1.6 of psi-ms.obo:
================================================
************ New parent term (ion mobility attribute)
[Term]
id: MS:1001581
name: FAIMS compensation voltage
def: "The DC potential applied to the asymmetric waveform in FAIMS that 
compensates for the difference between high and low field mobility of an 
ion." [PSI:MS]
synonym: "FAIMS CV" EXACT []
is_a: MS:1002892 ! ion mobility attribute

************ New parent term (ion mobility attribute)
[Term]
id: MS:1002476
name: ion mobility drift time
def: "Drift time of an ion or spectrum of ions as measured in an ion 
mobility mass spectrometer. This time might refer to the central value 
of a bin into which all ions within a narrow range of drift time have 
been aggregated." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1002892 ! ion mobility attribute
relationship: has_units UO:0000028 ! millisecond

************ New parent term (ion mobility attribute)
[Term]
id: MS:1002815
name: inverse reduced ion mobility
def: "Ion mobility measurement for an ion or spectrum of ions as 
measured in an ion mobility mass spectrometer. This might refer to the 
central value of a bin into which all ions within a narrow range of 
mobilities have been aggregated." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1002892 ! ion mobility attribute
relationship: has_units MS:1002814 ! "volt-second per square centimeter"

************ New parent term (ion mobility array)
[Term]
id: MS:1002477
name: mean drift time array
def: "Array of drift times, averaged from a matrix of binned m/z and 
drift time values, corresponding to spectrum of individual peaks encoded 
with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second

************ Renamed 'mean ion mobility array'
************     --> 'mean inverse reduced ion mobility array'
************ and new parent term (ion mobility array)
[Term]
id: MS:1002816
name: mean inverse reduced ion mobility array
def: "Array of drift times or inverse reduced ion mobilities, averaged 
from a matrix of binned m/z and ion mobility values, corresponding to a 
spectrum of individual peaks encoded with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
relationship: has_units MS:1002814 ! "volt-second per square centimeter"

************ Added a value to the following 3 CV-terms
[Term]
id: MS:1002889
name: Progenesis MetaScope score
def: "The confidence score produced by Progenesis QI." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002888 ! small molecule confidence measure

[Term]
id: MS:1002890
name: fragmentation score
def: "The fragmentation confidence score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002888 ! small molecule confidence measure

[Term]
id: MS:1002891
name: isotopic fit score
def: "The isotopic fit confidence score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002888 ! small molecule confidence measure


Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] Release candidate 4.1.6_rc1 of psi-ms.obo

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

Dear proteomics/metabolomics community,


following are the new terms from the release candidate 4.1.6_rc1 of the 
psi-ms.obo file.
It contains new and modified CV terms for ion mobility.


New CV terms in version 4.1.6_rc1 of psi-ms.obo:
================================================
[Term]
id: MS:1002892
name: ion mobility attribute
def: "An attribute describing ion mobility searches." [PSI:PI]
is_a: MS:1000503 ! scan attribute
is_a: MS:1002345 ! PSM-level attribute

[Term]
id: MS:1002893
name: ion mobility array
def: "An array of ion mobility data." [PSI:PI]
is_a: MS:1000513 ! binary data array


Changed CV terms in version 4.1.6_rc1 of psi-ms.obo:
====================================================
************ New parent term (ion mobility attribute)
[Term]
id: MS:1001581
name: FAIMS compensation voltage
def: "The DC potential applied to the asymmetric waveform in FAIMS that 
compensates for the difference between high and low field mobility of an 
ion." [PSI:MS]
synonym: "FAIMS CV" EXACT []
is_a: MS:1002892 ! ion mobility attribute

************ New parent term (ion mobility attribute)
[Term]
id: MS:1002476
name: ion mobility drift time
def: "Drift time of an ion or spectrum of ions as measured in an ion 
mobility mass spectrometer. This time might refer to the central value 
of a bin into which all ions within a narrow range of drift time have 
been aggregated." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1002892 ! ion mobility attribute
relationship: has_units UO:0000028 ! millisecond

************ New parent term (ion mobility attribute)
[Term]
id: MS:1002815
name: inverse reduced ion mobility
def: "Ion mobility measurement for an ion or spectrum of ions as 
measured in an ion mobility mass spectrometer. This might refer to the 
central value of a bin into which all ions within a narrow range of 
mobilities have been aggregated." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1002892 ! ion mobility attribute
relationship: has_units MS:1002814 ! "volt-second per square centimeter"

************ New parent term (ion mobility array)
[Term]
id: MS:1002477
name: mean drift time array
def: "Array of drift times, averaged from a matrix of binned m/z and 
drift time values, corresponding to spectrum of individual peaks encoded 
with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second

************ Renamed 'mean ion mobility array'
************     --> 'mean inverse reduced ion mobility array'
************ and new parent term (ion mobility array)
[Term]
id: MS:1002816
name: mean inverse reduced ion mobility array
def: "Array of drift times or inverse reduced ion mobilities, averaged 
from a matrix of binned m/z and ion mobility values, corresponding to a 
spectrum of individual peaks encoded with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
relationship: has_units MS:1002814 ! "volt-second per square centimeter"

************ Added a value to the following 3 CV-terms
[Term]
id: MS:1002889
name: Progenesis MetaScope score
def: "The confidence score produced by Progenesis QI." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002888 ! small molecule confidence measure

[Term]
id: MS:1002890
name: fragmentation score
def: "The fragmentation confidence score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002888 ! small molecule confidence measure

[Term]
id: MS:1002891
name: isotopic fit score
def: "The isotopic fit confidence score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002888 ! small molecule confidence measure


Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

Re: [Psidev-ms-dev] New version 4.1.5 of psi-ms.obo

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

> Dear proteomics/metabolomics community,
>
> the new version 4.1.5 of the psi-ms.obo file can be downloaded from
> https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
>
> It contains new CV terms for usage in mzTab-M files.
>
> New CV terms in version 4.1.5 of psi-ms.obo:
> ============================================
> [Term]
> id: MS:1002878
> name: small molecule analysis software
> def: "Software for the analysis of small molecules." [PSI:PI]
> is_a: MS:1001456 ! analysis software
>
> [Term]
> id: MS:1002879
> name: Progenesis QI
> def: "Metabolomics analysis software for LC-MS data from Nonlinear 
> Dynamics." [PSI:PI]
> is_a: MS:1002878 ! small molecule analysis software
>
> [Term]
> id: MS:1002880
> name: Compound Discoverer
> def: "Metabolomics analysis software from Thermo Fisher Scientific." 
> [PSI:PI]
> is_a: MS:1002878 ! small molecule analysis software
>
> [Term]
> id: MS:1002881
> name: MyCompoundID
> def: "Metabolite identification tool MyCompoundID." [PSI:PI, 
> PMID:23373753]
> is_a: MS:1002878 ! small molecule analysis software
>
> [Term]
> id: MS:1002882
> name: study variable average function
> def: "Function used to calculate the study variable quantification 
> value." [PSI:PI]
> is_a: MS:1001184 ! search statistics
>
> [Term]
> id: MS:1002883
> name: median
> def: "Median function." [PSI:PI]
> is_a: MS:1002882 ! study variable average function
>
> [Term]
> id: MS:1002884
> name: study variable variation function
> def: "Function used to calculate the study variable quantification 
> variation value." [PSI:PI]
> is_a: MS:1001184 ! search statistics
>
> [Term]
> id: MS:1002885
> name: standard error
> def: "Standard error function." [PSI:PI]
> is_a: MS:1002884 ! study variable variation function
>
> [Term]
> id: MS:1002886
> name: small molecule quantification datatype
> def: "The value reported in a small molecule quantification." [PSI:PI]
> is_a: MS:1001805 ! quantification datatype
>
> [Term]
> id: MS:1002887
> name: Progenesis QI normalised abundance
> def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002886 ! small molecule quantification datatype
>
> [Term]
> id: MS:1002888
> name: small molecule confidence measure
> def: "The confidence score produced by a small molecule analysis 
> software." [PSI:PI]
> is_a: MS:1002694 ! single identification result attribute
>
> [Term]
> id: MS:1002889
> name: Progenesis MetaScope score
> def: "The confidence score produced by Progenesis QI." [PSI:PI]
> is_a: MS:1002888 ! small molecule confidence measure
>
> [Term]
> id: MS:1002890
> name: fragmentation score
> def: "The fragmentation confidence score." [PSI:PI]
> is_a: MS:1002888 ! small molecule confidence measure
>
> [Term]
> id: MS:1002891
> name: isotopic fit score
> def: "The isotopic fit confidence score." [PSI:PI]
> is_a: MS:1002888 ! small molecule confidence measure
>
>
> Best Regards,
> Gerhard
>
> -- 
>
> *--------------------------------------------------------------------*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
> *PhD student*
>
> *Medizinisches Proteom-Center*
>
> *DEPARTMENT Medical Bioinformatics*
>
> *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum
>
> *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554
>
> *E-mail***ger...@ru... <mailto:ger...@ru...>
>
> www.medizinisches-proteom-center.de 
> <http://www.medizinisches-proteom-center.de/>
>

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] New version 4.1.5 of psi-ms.obo

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

Dear proteomics/metabolomics community,

the new version 4.1.5 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains new CV terms for usage in mzTab-M files.

New CV terms in version 4.1.5 of psi-ms.obo:
============================================
[Term]
id: MS:1002878
name: small molecule analysis software
def: "Software for the analysis of small molecules." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002879
name: Progenesis QI
def: "Metabolomics analysis software for LC-MS data from Nonlinear 
Dynamics." [PSI:PI]
is_a: MS:1002878 ! small molecule analysis software

[Term]
id: MS:1002880
name: Compound Discoverer
def: "Metabolomics analysis software from Thermo Fisher Scientific." 
[PSI:PI]
is_a: MS:1002878 ! small molecule analysis software

[Term]
id: MS:1002881
name: MyCompoundID
def: "Metabolite identification tool MyCompoundID." [PSI:PI, PMID:23373753]
is_a: MS:1002878 ! small molecule analysis software

[Term]
id: MS:1002882
name: study variable average function
def: "Function used to calculate the study variable quantification 
value." [PSI:PI]
is_a: MS:1001184 ! search statistics

[Term]
id: MS:1002883
name: median
def: "Median function." [PSI:PI]
is_a: MS:1002882 ! study variable average function

[Term]
id: MS:1002884
name: study variable variation function
def: "Function used to calculate the study variable quantification 
variation value." [PSI:PI]
is_a: MS:1001184 ! search statistics

[Term]
id: MS:1002885
name: standard error
def: "Standard error function." [PSI:PI]
is_a: MS:1002884 ! study variable variation function

[Term]
id: MS:1002886
name: small molecule quantification datatype
def: "The value reported in a small molecule quantification." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002887
name: Progenesis QI normalised abundance
def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002886 ! small molecule quantification datatype

[Term]
id: MS:1002888
name: small molecule confidence measure
def: "The confidence score produced by a small molecule analysis 
software." [PSI:PI]
is_a: MS:1002694 ! single identification result attribute

[Term]
id: MS:1002889
name: Progenesis MetaScope score
def: "The confidence score produced by Progenesis QI." [PSI:PI]
is_a: MS:1002888 ! small molecule confidence measure

[Term]
id: MS:1002890
name: fragmentation score
def: "The fragmentation confidence score." [PSI:PI]
is_a: MS:1002888 ! small molecule confidence measure

[Term]
id: MS:1002891
name: isotopic fit score
def: "The isotopic fit confidence score." [PSI:PI]
is_a: MS:1002888 ! small molecule confidence measure


Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] Release candidate 4.1.5_rc1 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new terms from the release candidate 4.1.5_rc1 of the 
psi-ms.obo file.
It contains new CV terms for usage in mzTab-M files.

New CV terms in version 4.1.5_rc1 of psi-ms.obo:
================================================
[Term]
id: MS:1002878
name: small molecule analysis software
def: "Software for the analysis of small molecules." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002879
name: Progenesis QI
def: "Metabolomics analysis software for LC-MS data from Nonlinear 
Dynamics." [PSI:PI]
is_a: MS:1002878 ! small molecule analysis software

[Term]
id: MS:1002880
name: Compound Discoverer
def: "Metabolomics analysis software from Thermo Fisher Scientific." 
[PSI:PI]
is_a: MS:1002878 ! small molecule analysis software

[Term]
id: MS:1002881
name: MyCompoundID
def: "Metabolite identification tool MyCompoundID." [PSI:PI, PMID:26415007]
is_a: MS:1002878 ! small molecule analysis software

[Term]
id: MS:1002882
name: study variable average function
def: "Function used to calculate the study variable quantification 
value." [PSI:PI]
is_a: MS:1001184 ! search statistics

[Term]
id: MS:1002883
name: median
def: "Median function." [PSI:PI]
is_a: MS:1002882 ! study variable average function

[Term]
id: MS:1002884
name: study variable variation function
def: "Function used to calculate the study variable quantification 
variation value." [PSI:PI]
is_a: MS:1001184 ! search statistics

[Term]
id: MS:1002885
name: standard error
def: "Standard error function." [PSI:PI]
is_a: MS:1002884 ! study variable variation function

[Term]
id: MS:1002886
name: small molecule quantification datatype
def: "The value reported in a small molecule quantification." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002887
name: Progenesis QI normalised abundance
def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002886 ! small molecule quantification datatype

[Term]
id: MS:1002888
name: small molecule confidence measure
def: "The confidence score produced by a small molecule analysis 
software." [PSI:PI]
is_a: MS:1002694 ! single identification result attribute

[Term]
id: MS:1002889
name: Progenesis MetaScope score
def: "The confidence score produced by Progenesis QI." [PSI:PI]
is_a: MS:1002888 ! small molecule confidence measure

[Term]
id: MS:1002890
name: fragmentation score
def: "The fragmentation confidence score." [PSI:PI]
is_a: MS:1002888 ! small molecule confidence measure

[Term]
id: MS:1002891
name: isotopic fit score
def: "The isotopic fit confidence score." [PSI:PI]
is_a: MS:1002888 ! small molecule confidence measure

Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] Fwd: [Psi-sc] Bus timetable for attendees

[Mayer, G. <may...@ru...>]

see message from Sandra


-------- Weitergeleitete Nachricht --------
Betreff: 	[Psi-sc] Bus timetable for attendees
Datum: 	Tue, 17 Apr 2018 12:25:01 +0100
Von: 	Sandra Orchard <or...@eb...>
An: 	ps...@eb..., ps...@eb..., psi...@eb...



Hi

As I suspect Andy is traveling and has the attendee mailing list, I've
pasted the bus timetable to get you up to EMBL in the mornings on the
event webpage

http://www.psidev.info/content/hupo-psi-meeting-2018

Please spread the word to anyone you see in Heidelberg who is not on any
of these mailing lists, and also please can someone forward to the mass
spec list. German buses leave promptly so don't be late.

If you are making your own way up the hill, please head for the Large
Operon. It costs about E15 in a taxi.

Sandra


-- 
Sandra Orchard

Protein Function Content Team Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

phone: 01223 494675
fax: 01223 494468
email: or...@eb...

_______________________________________________
Psi-sc mailing list
Ps...@eb...
https://listserver.ebi.ac.uk/mailman/listinfo/psi-sc

[Psidev-ms-dev] New version 4.1.4 of psi-ms.obo

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

Dear proteomics community,

the new version 4.1.4 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains four new terms for Thermo Scientific instruments.

New CV terms in version 4.1.4 of psi-ms.obo:
============================================
[Term]
id: MS:1002874
name: TSQ Altis
def: "Thermo Scientific TSQ Altis Triple Quadrupole MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002875
name: TSQ Quantis
def: "Thermo Scientific TSQ Quantis Triple Quadrupole MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002876
name: TSQ 9000
def: "Thermo Scientific TSQ 9000 Triple Quadrupole MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002877
name: Q Exactive HF-X
def: "Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS." 
[PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] Release candidate 4.1.4_rc1 of psi-ms.obo

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

Dear proteomics community,

following are the changes for the release candidate 4.1.4_rc1 of the 
psi-ms.obo file.
There are four new terms for Thermo Scientific instruments.

New CV terms in version 4.1.4_rc1 of psi-ms.obo:
================================================
[Term]
id: MS:1002874
name: TSQ Altis
def: "Thermo Scientific TSQ Altis Triple Quadrupole MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002875
name: TSQ Quantis
def: "Thermo Scientific TSQ Quantis Triple Quadrupole MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002876
name: TSQ 9000
def: "Thermo Scientific TSQ 9000 Triple Quadrupole MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002877
name: Q Exactive HF-X
def: "Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS." 
[PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] New version 4.1.3 of psi-ms.obo

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

Dear proteomics community,

the new version 4.1.3 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains two new terms for the Panorama repository.


New CV terms in version 4.1.3 of psi-ms.obo:
============================================
[Term]
id: MS:1002872
name: Panorama Public dataset identifier
def: "Dataset identifier issued by the Panorama Public repository. A 
dataset can refer to either a single sample as part of a study, or all 
samples that are part of the study corresponding to a publication." [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:1002873
name: Panorama Public dataset URI
def: "URI that allows the access to one dataset in the Panorama Public 
repository. A dataset can refer to either a single sample as part of a 
study, or all samples that are part of the study corresponding to a 
publication." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] New version 4.1.2 of psi-ms.obo

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

Dear proteomics community,

the new version 4.1.2 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains three new terms for Bioconductor software packages.


New CV terms in version 4.1.2 of psi-ms.obo:
============================================
[Term]
id: MS:1002869
name: mzR
def: "Bioconductor package mzR for reading and writing mass spectrometry 
data files." [PSI:PI]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002870
name: MSnbase
def: "Bioconductor package MSnbase provides infrastructure for 
manipulation, processing and visualization of mass spectrometry and 
proteomics data, ranging from raw to quantitative and annotated data." 
[PMID:22113085]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002871
name: CAMERA
def: "Bioconductor package CAMERA for annotation of peak lists generated 
by xcms, rule based annotation of isotopes and adducts, isotope 
validation, EIC correlation based tagging of unknown adducts and 
fragments." [PMID:22111785]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] Release candidate 4.1.2_rc1 of psi-ms.obo

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

Dear proteomics community,

following are the changes for the release candidate 4.1.2_rc1 of the 
psi-ms.obo file.
There are three new terms for Bioconductor software packages.

New CV terms in version 4.1.2_rc1 of psi-ms.obo:
================================================
[Term]
id: MS:1002869
name: mzR
def: "Bioconductor package mzR for reading and writing mass spectrometry 
data files." [PSI:PI]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002870
name: MSnbase
def: "Bioconductor package MSnbase provides infrastructure for 
manipulation, processing and visualization of mass spectrometry and 
proteomics data, ranging from raw to quantitative and annotated data." 
[PMID:22113085]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002871
name: CAMERA
def: "Bioconductor package CAMERA for annotation of peak lists generated 
by xcms, rule based annotation of isotopes and adducts, isotope 
validation, EIC correlation based tagging of unknown adducts and 
fragments." [PMID:22111785]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software


Changed CV terms in version 4.1.2_rc1 of psi-ms.obo:
====================================================
************ No changed terms

Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] drift time question

[Hannes R. <han...@gm...>]

Dear list

I have a question regarding the drift time array:

[Term]
id: MS:1002816
name: mean ion mobility array
def: "Array of drift times or inverse reduced ion mobilities, averaged
from a matrix of binned m/z and ion mobility values, corresponding to
a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000513 ! binary data array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
relationship: has_units MS:1002814 ! "volt-second per square centimeter"

it seems to me that the formulation is somewhat unclear, what does
"averaged from a maxtrix of binned m/z and ion mobility values" mean
here. It seems strange that we have this term but no term for the
general case where we simply want to display ion mobility data. I
therefore suggest to change the existing term or add a new term

[Term]
id: MS:xxx
name: ion mobility array
def: "Array of drift times or inverse reduced ion mobilities
corresponding to a spectrum of individual peaks encoded with an m/z
array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000513 ! binary data array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
relationship: has_units MS:1002814 ! "volt-second per square centimeter"


I think this would allow us to reprenst 3 dimensional data with one
array of m/z, one of intensity and one of ion mobility, right? Or
maybe I misunderstood the point of MS:1002816

Best

Hannes

[Psidev-ms-dev] PSI 2018 Spring meeting

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

Dear colleagues,

I am sending a reminder about the upcoming PSI meeting next month, details below. We hope to see lots of you there!
Best wishes
Andy

http://www.psidev.info/content/hupo-psi-meeting-2018


*********************

We are pleased to announce that the PSI 2018 Spring meeting is open for registration (http://www.psidev.info/content/hupo-psi-meeting-2018). PSI2018 will take place April 18-20th 2018 at EMBL, Heidelberg in Germany. The meeting is free of charge for participants (including lunches, refreshments and a workshop dinner).

The main topics for discussion will working on the new spectral library data format, the Universal spectrum ID, PEFF (extended fasta format) and PROXI (web services API). There will be a track focussing on metabolomics (mzTab format), further work on quality control (qcML) and developments in the molecular interactions group including implementations of MI XML 3.0, CausalTab format, and identification of novel interactions in interactomes.

The PSI always welcomes new participants with an interest in getting involved in proteomics data standards. Please feel free to register and come along to see what we are doing, or forward this message on to other colleagues who may be interested.

[Psidev-ms-dev] FW: Scalable and Reproducible Structural Bioinformatics Workshop & Hackathon 2018

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

Hi everyone, I’m sure this will be a great workshop and hackathon for those
interested in protein structures. See below if you’re interested..





On Thu, Mar 1, 2018 at 11:04 PM, Peter Rose <pwr...@gm...> wrote:

Hi Eric and Gustavo,



We are hosting our second MMTF workshop. If you or anyone you know is
interested in attending, please forward this information. We have funds to
pay for travel and accommodation!


--------



We are pleased to announce the second MMTF workshop:  *Scalable and
Reproducible Structural Bioinformatics Workshop & Hackathon 2018*. This
workshop will be held May 7 – 9, 2018 at the University of California, San
Diego and hosted by the Structural Bioinformatics Laboratory at the San
Diego Supercomputer Center.



*Sponsorship* This workshop is sponsored by the NIH Big Data to Knowledge
(BD2K) initiative. Air travel and 4-day lodging can be provided for
non-commercial participants, including a limited number of international
participants. Applicants will be selected based on the best fit to the
program on a rolling basis.



*Apply now to secure your place in the workshop.*

https://www.eiseverywhere.com/mmtfworkshop2018/



*Application deadline: April 1, 2018.*



This 3-day hands-on workshop and hackathon introduces you to:

• Application of state-of-the-art Big Data technologies to Structural
Bioinformatics

• Data mining and machine learning

• 2D/3D visualization and deployment in Jupyter Notebooks



The first two days of the workshop combine lectures, hands-on applications,
and programming sessions. On the third day, participants apply the new
technologies to their own projects.



This workshop is aimed at graduate students, postdocs, staff, faculty,
industrial researchers, and scientific software developers. Experience with
Python is required.



-- 

Peter Rose, Ph.D.

Director, Structural Bioinformatics Laboratory

San Diego Supercomputer Center

UC San Diego

+1-858-822-5497

Re: [Psidev-ms-dev] hyperlink to mzML 1.1.0 xsd is broken

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

Hi Damon, thank you for reporting. I have updated the link to the correct
location:



https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.0.xsd







*From:* Damon Barbacci [mailto:dam...@gm...]
*Sent:* Friday, January 26, 2018 6:05 AM
*To:* psi...@li...
*Subject:* [Psidev-ms-dev] hyperlink to mzML 1.1.0 xsd is broken



The hyperlink to "mzml1.1.0.xsd (main schema)" on the PSI webpage
http://psidev.info/mzml_1_0_0%20  is broken.  The hyperlink tries to go to



http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/schema/mzML1.1.0.xsd



but the following error is show in the browser



The psidev project's CVS data is in read-only mode, so the project may have
switched over to another source-code-management system. To check,
visit the Project
Summary Page for psidev <https://sourceforge.net/projects/psidev> and see
if the menubar lists a newer code repository, such as SVN or Git.

The CVS data can be accessed as follows. You can run a per-module CVS
checkout via pserver protocol:

·  *cvs -z3 -d:pserver:anonymous@a.cvs.sourceforge.net:/cvsroot/psidev co
-P htdocs*

·  *cvs -z3 -d:pserver:anonymous@a.cvs.sourceforge.net:/cvsroot/psidev co
-P ppp*

·  *cvs -z3 -d:pserver:anonymous@a.cvs.sourceforge.net:/cvsroot/psidev co
-P psi*

·  *cvs -z3 -d:pserver:anonymous@a.cvs.sourceforge.net:/cvsroot/psidev co
-P psi-ms*

You can view a list of files or copy all the CVS repository data via rsync
(the 1st command lists the files, the 2nd copies):

·  *rsync -a a.cvs.sourceforge.net::cvsroot/psidev/*

·  *rsync -ai a.cvs.sourceforge.net::cvsroot/psidev/ /my/local/dest/dir/*

If you are a project admin for psidev, you can request that this page
redirect to another repo on your project by submitting a support request
<https://sourceforge.net/support>.

Re: [Psidev-ms-dev] correct URL for namespace and QName missing namespace

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

Hi Damon, thank you for the report. Where are you finding the
imzML1.1.0.xsd schema?



Regarding the namespace, I’m not certain what to do. You’re right this is
not a useful URL and that’s unfortunate. But I’m not certain it’s worth
changing the schema to fix it. I don’t know that it needs to be a valid
URL, as long as it’s a unique string?



Regarding QName and the definition you show, this does not appear to be in
mzML1.1.0.xsd. Perhaps it is in imzML1.1.0.xsd, as you state. But imzML is
not an official PSI product. It is just a PSI-similar/compatible format.
I’m guessing you found that here:

https://github.com/imzML/imzML



Searching for “QName” and “none” doesn’t turn up anything either.



So, I don’t understand your statement. Would you elaborate?



Thanks,

Eric





*From:* Damon Barbacci [mailto:dam...@gm...]
*Sent:* Friday, January 26, 2018 6:13 AM
*To:* psi...@li...
*Subject:* [Psidev-ms-dev] correct URL for namespace and QName missing
namespace



Following the xlmns link within the imzML1.1.0.xsd doesn't go anywhere, the
link needs to be updated.



schema xmlns:dx="http://psi.hupo.org/ms/mzml"



The following generates an error because the type is missing a namespace.



<xs:element name="binary" type="none">