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

[Psidev-pi-dev] Release candidate 4.1.31_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,


following are the new and modified terms for the release version 
4.1.31_rc1 of
the psi-ms.obo file.


New CV terms in version 4.1.31_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003031
name: CPTAC accession number
def: "Main identifier of a CPTAC dataset." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier


Modified CV terms in version 4.1.31_rc1 of psi-ms.obo:
======================================================
[Term]
id: MS:1002810
name: adduct ion mass X m/z
def: "Theoretical m/z of the X component in the adduct M+X or M-X. This 
term was formerly called 'adduct ion mass', but it is not really a mass. 
It corresponds to the column mislabeled as 'Mass' at 
https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." 
[DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002809 ! adduct ion attribute

Best Regards,
Gerhard

-- 

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

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

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

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

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] New version 4.1.30 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following are the new terms for the release version 4.1.30 of
the psi-ms.obo file. It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

New CV terms in version 4.1.30 of psi-ms.obo:
=============================================
************ New term for a Mascot report parameter
[Term]
id: MS:1003030
name: Mascot:MinNumSigUniqueSeqs
def: "Minimum number of significant unique sequences required in a 
protein hit. The setting is only relevant if the protein grouping 
strategy is 'family clustering'." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1002095 ! Mascot input parameter

Best Regards,
Gerhard

-- 

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

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

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

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

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] New version 4.1.29 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,


following are the new terms for the release version 4.1.29 of
the psi-ms.obo file. It contains two CV terms for new Thermo Scientific
instruments and can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.29 of psi-ms.obo:
=============================================
************ New terms for Thermo Scientific instruments
[Term]
id: MS:1003028
name: Orbitrap Exploris 480
def: "Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS." 
[PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1003029
name: Orbitrap Eclipse
def: "Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid 
architecture consisting of quadrupole mass filter, linear ion trap and 
Orbitrap mass analyzers." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model


Best Regards,
Gerhard

-- 

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

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

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

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

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] New version 4.1.28 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following are the new terms for the release version 4.1.28 of
the psi-ms.obo file. It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

New CV terms in version 4.1.28 of psi-ms.obo:
=============================================
************ New terms for OpenPepXL
[Term]
id: MS:1003023
name: OpenPepXL
def: "Cross-Linking MS search engine." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1003024
name: OpenPepXL:score
def: "The OpenPepXL score for a cross-link spectrum match." [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:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1003025
name: named element
def: "A named element that is an attribute in a proteomics standards 
file." [PSI:PI]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Vocabularies

[Term]
id: MS:1003026
name: named element in mzIdentML
def: "A named element that is an attribute in a mzIdentML file." [PSI:PI]
is_a: MS:1003025 ! named element

[Term]
id: MS:1003027
name: named element in mzML
def: "A named element that is an attribute in a mzML file." [PSI:PI]
is_a: MS:1003025 ! named element

Changed CV terms in version 4.1.28 of psi-ms.obo:
=================================================
************ Added 'is_a: MS:1003026 ! named element in mzIdentML'
[Term]
id: MS:1003021
name: Fixed modification
def: "Post-translational modification which is assumed to be present at 
each instance of a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters
is_a: MS:1003026 ! named element in mzIdentML

[Term]
id: MS:1003022
name: Variable modification
def: "Post-translational modification which may or may not be present at 
a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters
is_a: MS:1003026 ! named element in mzIdentML

Best Regards,
Gerhard

[Psidev-pi-dev] Release candidate 4.1.28_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.28_rc1
of the psi-ms.obo file.


New CV terms in version 4.1.28_rc1 of psi-ms.obo:
=================================================
************ New terms for OpenPepXL
[Term]
id: MS:1003023
name: OpenPepXL
def: "Cross-Linking MS search engine." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1003024
name: OpenPepXL:score
def: "The OpenPepXL score for a cross-link spectrum match." [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:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1003025
name: named element
def: "A named element that is an attribute in a proteomics standards 
file." [PSI:PI]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Vocabularies

[Term]
id: MS:1003026
name: named element in mzIdentML
def: "A named element that is an attribute in a mzIdentML file." [PSI:PI]
is_a: MS:1003025 ! named element

[Term]
id: MS:1003027
name: named element in mzML
def: "A named element that is an attribute in a mzML file." [PSI:PI]
is_a: MS:1003025 ! named element


Changed CV terms in version 4.1.28_rc1 of psi-ms.obo:
=====================================================
************ Added 'is_a: MS:1003026 ! named element in mzIdentML'
[Term]
id: MS:1003021
name: Fixed modification
def: "Post-translational modification which is assumed to be present at 
each instance of a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters
is_a: MS:1003026 ! named element in mzIdentML

[Term]
id: MS:1003022
name: Variable modification
def: "Post-translational modification which may or may not be present at 
a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters
is_a: MS:1003026 ! named element in mzIdentML

Best Regards,
Gerhard

Re: [Psidev-pi-dev] [Psidev-ms-vocab] Encoding site localisation confidence for multiple modifications (mzIdentML 1.2)

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

Hi Ville,

Yes, I see that this is not a use case we covered when we designed this mechanism. All of the alternatives you propose cause some minor potential problems, and probably we would be best making a minor schema increment to fix the issue rather than trying to hack something that works. Are you happy for me to post this as an issue on GitHub, so we can track it and come up with a solution there?

Best wishes
Andy



From: Ville Koskinen [mailto:vi...@ma...]
Sent: 02 July 2019 13:26
To: psi...@li...
Subject: [Psidev-ms-vocab] Encoding site localisation confidence for multiple modifications (mzIdentML 1.2)


Dear all,

we're looking at what changes are needed to export mzIdentML 1.2 from Mascot Server. One problem we've encountered so far is with site localisation scores. Here's an example query with two modifications and multiple permutations (scroll to the bottom of page):

http://www.matrixscience.com/cgi/peptide_view.pl?file=..%2Fdata%2F20190108%2FF001291.dat;_msresflags=3138;_msresflags2=266;ave_thresh=17;db_idx=2;hit=1;index=TRAP_PLAFA;px=1;query=8118;section=5

The confidence percentages are based on the score difference between adjacent ranks. There is no site-specific score; the percentage is for the joint assignment confidence of Oxidation *and* dHex(1)Hex(1).

1) One possibility is to have the same modification index for different <Modification> elements. For example:

<Peptide Id="8118_1">

  <PeptideSequence>TASCGVWDEWSPCSVTCGK</PeptideSequence>

  <Modification monoisotopicMassDelta="15.994915" location="7" residues="M">

    <cvParam cvRef="PSI-MS" accession="MS:1002504" name="modification index" value="1"/>

  </Modification>

  <Modification monoisotopicMassDelta="308.110732" location="16" residues="T">

    <cvParam cvRef="PSI-MS" accession="MS:1002504" name="modification index" value="1"/>

  </Modification>

</Peptide>
Then, under <SpectrumIdentificationResult>, the line referring to modification index 1 means a simultaneous assignment. We could then encode the 10 different permutations like:

<cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="1:19.39:7|16:true" />

<cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="1:19.39:7|14:true" />

...

<cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="1:0.61:10|3:true" />

<cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="1:0.61:10|1:true" />

This is assuming the site alternation is in the same order as the <Modification> elements (oxidation|dhex). Is this allowed, and is this the intended encoding?

2) If there must be a one-to-one mapping between modification index and modification name/delta, another possibility is to extend the regular expression constraint. Maybe something like this would work?

<cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="1:19.39:7:true,2:19.39:16:true" />

The least ambiguous syntax would be the following, but I realise this is a big departure from the existing syntax:

<cvParam cvRef="PSI-MS" accession="MS:xxxxx" name="yyyy" value="(1:7,2:16):19.39:true" />

Regards,
Ville

--

Ville Koskinen

Matrix Science

64 Baker Street

London W1U 7GB, UK

Tel: +44 (0)20 7486 1050

Fax: +44 (0)20 7224 1344



vi...@ma...<mailto:vi...@ma...>

http://www.matrixscience.com



Matrix Science Ltd. is registered in England and Wales

Company number 3533898

Re: [Psidev-pi-dev] [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

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

Yes that seems okay to me. I’m sure ontology purists would hate this approach, but it seems pragmatically useful for what we need to achieve.
Best wishes
Andy

From: Nuno Bandeira [mailto:ban...@uc...]
Sent: 07 June 2019 16:14
To: Mass spectrometry standard development <psi...@li...>
Cc: Jones, Andy <jo...@li...>; psi...@li...; psi...@li...; Eric Deutsch <ede...@sy...>; Gerhard Mayer <may...@ru...>
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

+1 makes sense to me too.

Best,

Nuno

On Fri, Jun 7, 2019, 6:57 AM Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> wrote:
I think this will be needed for the spectral library format at least since we will be needed a substantial number of concepts that are elements in mzIdentML. Pierre-Alain’s proposal seems pretty good to me. Anyone else have comments about doing it that way or refine the idea?

Thanks,
Eric


From: Binz Pierre-Alain <Pie...@ch...<mailto:Pie...@ch...>>
Sent: Thursday, June 6, 2019 11:42 PM
To: Jones, Andy <And...@li...<mailto:And...@li...>>; 'psi...@li...<mailto:psi...@li...>' <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc: Gerhard Mayer <may...@ru...<mailto:may...@ru...>>
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

Good point Andy.
If one need them for another format (these or others), should one systematically create all elements also as CV terms, have them annotated with a “is_a: MS:NNNNNN ! named element in mzIdentML “ /  mzML / etc., in order to make sure we have consistency of definition across formats?

Pierre-Alain


De : Jones, Andy <And...@li...<mailto:And...@li...>>
Envoyé : mercredi 5 juin 2019 16:43
À : 'psi...@li...<mailto:psi...@li...>' <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc : Gerhard Mayer <may...@ru...<mailto:may...@ru...>>
Objet : Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

Hi Gerhard,

Apologies for joining this conversation presumably late – these are encoded in mzIdentML via named elements. Are these CV terms needed for a different format?
Best wishes
Andy

From: Gerhard Mayer via Psidev-ms-vocab [mailto:psi...@li...]
Sent: 05 June 2019 15:40
To: psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc: Gerhard Mayer <may...@ru...<mailto:may...@ru...>>
Subject: [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo


Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.27_rc1
of the psi-ms.obo file.

New CV terms in version 4.1.27_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003021
name: fixed modification
def: "Modification which is assumed to be present at each instance of a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1003022
name: variable modification
def: "A modification which may or may not be present at a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

Best Regards,
Gerhard
--

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

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

Scientific assistant

Ruhr-Universität Bochum, Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum

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

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

Web: www.ruhr-uni-bochum.de/mpc<http://www.ruhr-uni-bochum.de/mpc>

_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...<mailto:Psi...@li...>
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-pi-dev] [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

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

I think this will be needed for the spectral library format at least since
we will be needed a substantial number of concepts that are elements in
mzIdentML. Pierre-Alain’s proposal seems pretty good to me. Anyone else
have comments about doing it that way or refine the idea?



Thanks,

Eric





*From:* Binz Pierre-Alain <Pie...@ch...>
*Sent:* Thursday, June 6, 2019 11:42 PM
*To:* Jones, Andy <And...@li...>; '
psi...@li...' <
psi...@li...>; psi...@li...;
psi...@li...
*Cc:* Gerhard Mayer <may...@ru...>
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
4.1.27_rc1 of psi-ms.obo



Good point Andy.

If one need them for another format (these or others), should one
systematically create all elements also as CV terms, have them annotated
with a “is_a: MS:NNNNNN ! named element in mzIdentML “ /  mzML / etc., in
order to make sure we have consistency of definition across formats?



Pierre-Alain





*De :* Jones, Andy <And...@li...>
*Envoyé :* mercredi 5 juin 2019 16:43
*À :* 'psi...@li...' <
psi...@li...>; psi...@li...;
psi...@li...
*Cc :* Gerhard Mayer <may...@ru...>
*Objet :* Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate
4.1.27_rc1 of psi-ms.obo



Hi Gerhard,



Apologies for joining this conversation presumably late – these are encoded
in mzIdentML via named elements. Are these CV terms needed for a different
format?

Best wishes

Andy



*From:* Gerhard Mayer via Psidev-ms-vocab [
mailto:psi...@li...
<psi...@li...>]
*Sent:* 05 June 2019 15:40
*To:* psi...@li...;
psi...@li...; psi...@li...
*Cc:* Gerhard Mayer <may...@ru...>
*Subject:* [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo



Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.27_rc1
of the psi-ms.obo file.

New CV terms in version 4.1.27_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003021
name: fixed modification
def: "Modification which is assumed to be present at each instance of a
residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1003022
name: variable modification
def: "A modification which may or may not be present at a residue type."
[PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

Best Regards,
Gerhard

-- 

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

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

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

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

*E-Mail: *ger...@ru...

*Web: *www.ruhr-uni-bochum.de/mpc

Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

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

Good point Andy.
If one need them for another format (these or others), should one systematically create all elements also as CV terms, have them annotated with a “is_a: MS:NNNNNN ! named element in mzIdentML “ /  mzML / etc., in order to make sure we have consistency of definition across formats?

Pierre-Alain


De : Jones, Andy <And...@li...>
Envoyé : mercredi 5 juin 2019 16:43
À : 'psi...@li...' <psi...@li...>; psi...@li...; psi...@li...
Cc : Gerhard Mayer <may...@ru...>
Objet : Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

Hi Gerhard,

Apologies for joining this conversation presumably late – these are encoded in mzIdentML via named elements. Are these CV terms needed for a different format?
Best wishes
Andy

From: Gerhard Mayer via Psidev-ms-vocab [mailto:psi...@li...]
Sent: 05 June 2019 15:40
To: psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc: Gerhard Mayer <may...@ru...<mailto:may...@ru...>>
Subject: [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo


Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.27_rc1
of the psi-ms.obo file.

New CV terms in version 4.1.27_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003021
name: fixed modification
def: "Modification which is assumed to be present at each instance of a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1003022
name: variable modification
def: "A modification which may or may not be present at a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

Best Regards,
Gerhard
--

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

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

Scientific assistant

Ruhr-Universität Bochum, Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum

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

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

Web: www.ruhr-uni-bochum.de/mpc<http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] New version 4.1.27 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,


following are the new modification terms for the release version 4.1.27
of the psi-ms.obo file. They were requested by Yasset for PRIDE.

It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.27 of psi-ms.obo:
=============================================
[Term]
id: MS:1003021
name: Fixed modification
def: "Post-translational modification which is assumed to be present at 
each instance of a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1003022
name: Variable modification
def: "Post-translational modification which may or may not be present at 
a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters


Best Regards,
Gerhard

-- 

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

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

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

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

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

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

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

Hi Gerhard,

Apologies for joining this conversation presumably late – these are encoded in mzIdentML via named elements. Are these CV terms needed for a different format?
Best wishes
Andy

From: Gerhard Mayer via Psidev-ms-vocab [mailto:psi...@li...]
Sent: 05 June 2019 15:40
To: psi...@li...; psi...@li...; psi...@li...
Cc: Gerhard Mayer <may...@ru...>
Subject: [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo


Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.27_rc1
of the psi-ms.obo file.

New CV terms in version 4.1.27_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003021
name: fixed modification
def: "Modification which is assumed to be present at each instance of a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1003022
name: variable modification
def: "A modification which may or may not be present at a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

Best Regards,
Gerhard
--


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

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

Scientific assistant

Ruhr-Universität Bochum, Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum

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

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

Web: www.ruhr-uni-bochum.de/mpc<http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] Release candidate 4.1.27_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.27_rc1
of the psi-ms.obo file.

New CV terms in version 4.1.27_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003021
name: fixed modification
def: "Modification which is assumed to be present at each instance of a 
residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1003022
name: variable modification
def: "A modification which may or may not be present at a residue type." 
[PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

Best Regards,
Gerhard

-- 

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

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

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

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

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

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] New version 4.1.26 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,


following are the new/changed terms for the version 4.1.26 of the
psi-ms.obo file. It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.26 of psi-ms.obo:
=============================================
[Term]
id: MS:1003019
name: pressure chromatogram
def: "Representation of chromatographic pressure versus time." [PSI:MS]
is_a: MS:1000626 ! chromatogram type


[Term]
id: MS:1003020
name: flow rate chromatogram
def: "Representation of the chromatographic flow rate versus time." [PSI:MS]
is_a: MS:1000626 ! chromatogram type


Changed CV terms in version 4.1.26 of psi-ms.obo:
=================================================
************ Changed definition from
************ 'The representation of detector response versus time.' to
************ 'Representation of a chromatographic separation attribute 
measurement versus time.'
[Term]
id: MS:1000625
name: chromatogram
def: "Representation of a chromatographic separation attribute 
measurement versus time." [PSI:MS]
relationship: part_of MS:1001458 ! spectrum generation information


************ Changed definition from
************ 'Broad category or type of a chromatogram.' to
************ 'Type of chromatogram measurement being represented.'
[Term]
id: MS:1000626
name: chromatogram type
def: "Type of chromatogram measurement being represented." [PSI:MS]
relationship: part_of MS:1000625 ! chromatogram


************ Changed name from
************ 'mass chromatogram' to
************ 'ion current chromatogram'
************ and definition from
************ 'A plot of the relative abundance of a beam or other 
collection of ions as a function of the retention time.' to
************ 'Representation of the current of ions versus time.'
[Term]
id: MS:1000810
name: ion current chromatogram
def: "Representation of the current of ions versus time." [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type


************ Changed definition from
************ 'The measurement of electromagnetic properties as a 
function of the retention time.' to
************ 'Representation of electromagnetic properties versus time.'
[Term]
id: MS:1000811
name: electromagnetic radiation chromatogram
def: "Representation of electromagnetic properties versus time." [PSI:MS]
synonym: "EMR radiation chromatogram" EXACT []
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type


************ Changed definition from
************ 'The measurement of light absorbed by the sample as a 
function of the retention time.' to
************ 'Representation of light absorbed by the sample versus time.'
[Term]
id: MS:1000812
name: absorption chromatogram
def: "Representation of light absorbed by the sample versus time." [PSI:MS]
is_a: MS:1000811 ! electromagnetic radiation chromatogram


************ Changed definition from
************ 'The measurement of light emitted by the sample as a 
function of the retention time.' to
************ 'Representation of light emitted by the sample versus time.'
[Term]
id: MS:1000813
name: emission chromatogram
def: "Representation of light emitted by the sample versus time." [PSI:MS]
is_a: MS:1000811 ! electromagnetic radiation chromatogram


************ Changed definition from
************ 'Chromatogram obtained by plotting the total ion current 
detected in each of a series of mass spectra recorded as a function of 
retention time.' to
************ 'Representation of the total ion current detected in each 
of a series of mass spectra versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000235
name: total ion current chromatogram
def: "Representation of the total ion current detected in each of a 
series of mass spectra versus time." [PSI:MS]
synonym: "TIC chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a specific single ion current at each time point.' to
************ 'Representation of an array of the measurements of a 
specific single ion current versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000627
name: selected ion current chromatogram
def: "Representation of an array of the measurements of a specific 
single ion current versus time." [PSI:MS]
synonym: "SIC chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the most 
intense peaks at each time point.' to
************ 'Representation of an array of the most intense peaks 
versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000628
name: basepeak chromatogram
def: "Representation of an array of the most intense peaks versus time." 
[PSI:MS]
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a selectively monitored ion at each time point.' to
************ 'Representation of an array of the measurements of a 
selectively monitored ion versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001472
name: selected ion monitoring chromatogram
def: "Representation of an array of the measurements of a selectively 
monitored ion versus time." [PSI:MS]
synonym: "SIM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a selectively monitored reaction at each time point.' to
************ 'Representation of an array of the measurements of a 
selectively monitored reaction versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001473
name: selected reaction monitoring chromatogram
def: "Representation of an array of the measurements of a selectively 
monitored reaction versus time." [PSI:MS]
synonym: "SRM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'OBSOLETE Chromatogram created by creating an array of the 
measurements of a series of monitored reactions at each time point.' to
************ 'OBSOLETE Representation of an array of the measurements of 
a series of monitored reactions versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001474
name: consecutive reaction monitoring chromatogram
def: "OBSOLETE Representation of an array of the measurements of a 
series of monitored reactions versus time." [PSI:MS]
comment: This term was made obsolete because, by design, it can't be 
properly represented in mzML 1.1. CRM experiments must be represented in 
a spectrum-centric way.
synonym: "CRM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram
is_obsolete: true


Best Regards,
Gerhard

-- 

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

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

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

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

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

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] Release candidate 4.1.26_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following are the new/changed terms for the release candidate 4.1.26_rc1
of the psi-ms.obo file.


New CV terms in version 4.1.26_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003019
name: pressure chromatogram
def: "Representation of chromatographic pressure versus time." [PSI:MS]
is_a: MS:1000626 ! chromatogram type


[Term]
id: MS:1003020
name: flow rate chromatogram
def: "Representation of the chromatographic flow rate versus time." [PSI:MS]
is_a: MS:1000626 ! chromatogram type


Changed CV terms in version 4.1.26_rc1 of psi-ms.obo:
=====================================================
************ Changed definition from
************ 'The representation of detector response versus time.' to
************ 'Representation of a chromatographic separation attribute 
measurement versus time.'
[Term]
id: MS:1000625
name: chromatogram
def: "Representation of a chromatographic separation attribute 
measurement versus time." [PSI:MS]
relationship: part_of MS:1001458 ! spectrum generation information


************ Changed definition from
************ 'Broad category or type of a chromatogram.' to
************ 'Type of chromatogram measurement being represented.'
[Term]
id: MS:1000626
name: chromatogram type
def: "Type of chromatogram measurement being represented." [PSI:MS]
relationship: part_of MS:1000625 ! chromatogram


************ Changed name from
************ 'mass chromatogram' to
************ 'ion current chromatogram'
************ and definition from
************ 'A plot of the relative abundance of a beam or other 
collection of ions as a function of the retention time.' to
************ 'Representation of the current of ions versus time.'
[Term]
id: MS:1000810
name: ion current chromatogram
def: "Representation of the current of ions versus time." [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type


************ Changed definition from
************ 'The measurement of electromagnetic properties as a 
function of the retention time.' to
************ 'Representation of electromagnetic properties versus time.'
[Term]
id: MS:1000811
name: electromagnetic radiation chromatogram
def: "Representation of electromagnetic properties versus time." [PSI:MS]
synonym: "EMR radiation chromatogram" EXACT []
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type


************ Changed definition from
************ 'The measurement of light absorbed by the sample as a 
function of the retention time.' to
************ 'Representation of light absorbed by the sample versus time.'
[Term]
id: MS:1000812
name: absorption chromatogram
def: "Representation of light absorbed by the sample versus time." [PSI:MS]
is_a: MS:1000811 ! electromagnetic radiation chromatogram


************ Changed definition from
************ 'The measurement of light emitted by the sample as a 
function of the retention time.' to
************ 'Representation of light emitted by the sample versus time.'
[Term]
id: MS:1000813
name: emission chromatogram
def: "Representation of light emitted by the sample versus time." [PSI:MS]
is_a: MS:1000811 ! electromagnetic radiation chromatogram


************ Changed definition from
************ 'Chromatogram obtained by plotting the total ion current 
detected in each of a series of mass spectra recorded as a function of 
retention time.' to
************ 'Representation of the total ion current detected in each 
of a series of mass spectra versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000235
name: total ion current chromatogram
def: "Representation of the total ion current detected in each of a 
series of mass spectra versus time." [PSI:MS]
synonym: "TIC chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a specific single ion current at each time point.' to
************ 'Representation of an array of the measurements of a 
specific single ion current versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000627
name: selected ion current chromatogram
def: "Representation of an array of the measurements of a specific 
single ion current versus time." [PSI:MS]
synonym: "SIC chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the most 
intense peaks at each time point.' to
************ 'Representation of an array of the most intense peaks 
versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000628
name: basepeak chromatogram
def: "Representation of an array of the most intense peaks versus time." 
[PSI:MS]
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a selectively monitored ion at each time point.' to
************ 'Representation of an array of the measurements of a 
selectively monitored ion versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001472
name: selected ion monitoring chromatogram
def: "Representation of an array of the measurements of a selectively 
monitored ion versus time." [PSI:MS]
synonym: "SIM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a selectively monitored reaction at each time point.' to
************ 'Representation of an array of the measurements of a 
selectively monitored reaction versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001473
name: selected reaction monitoring chromatogram
def: "Representation of an array of the measurements of a selectively 
monitored reaction versus time." [PSI:MS]
synonym: "SRM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'OBSOLETE Chromatogram created by creating an array of the 
measurements of a series of monitored reactions at each time point.' to
************ 'OBSOLETE Representation of an array of the measurements of 
a series of monitored reactions versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001474
name: consecutive reaction monitoring chromatogram
def: "OBSOLETE Representation of an array of the measurements of a 
series of monitored reactions versus time." [PSI:MS]
comment: This term was made obsolete because, by design, it can't be 
properly represented in mzML 1.1. CRM experiments must be represented in 
a spectrum-centric way.
synonym: "CRM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram
is_obsolete: true

Best Regards,
Gerhard

-- 

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

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

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

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

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

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] New version 4.1.25 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new/changed terms for the version 4.1.25 of the
psi-ms.obo file. It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


@Felipe: I left out PTMProphet:PTM Score (see Eric's last email):
"
PTM Prophet has quite a substantial number of metrics.
     At the PSM level, we have:
         normalized information content
         number of localized modifications
     At the site level, we have:
         modification localization probability
         O-score
         M-score
"

If you need such PTMProphet metrics, then please send me a list with
proposal for their exact name and definitions.



New CV terms in version 4.1.25 of psi-ms.obo:
=============================================
[Term]
id: MS:1003011
name: pFind
def: "Sequence-tag-based search engine pFind." [PMID:30295672]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003012
name: KSDP score
def: "Kernel mass spectral dot product scoring function." [PMID:15044235]
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1003013
name: i3tms
def: "i3-tms search engine and data-analysis software." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003014
name: MSFragger
def: "A database search-based peptide identification tool." [PMID:28394336]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003015
name: razor peptide
def: "A peptide which is shared between protein groups and assigned to 
the protein group with the largest number of identified peptides." [PSI:PI]
is_a: MS:1000860 ! peptide

[Term]
id: MS:1003016
name: ProteinProphet:peptide weight
def: "Fraction of peptide evidence attributable to a protein or a set of 
indistinguishable proteins." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002490 ! peptide-level scoring
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1003017
name: ProteinProphet:peptide group weight
def: "Fraction of peptide evidence attributable to a group of proteins." 
[PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002490 ! peptide-level scoring
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1003018
name: Philosopher
def: "General proteomics processing toolkit for shotgun proteomics." 
[https://philosopher.nesvilab.org/]
is_a: MS:1001456 ! analysis software



Changed CV terms in version 4.1.25 of psi-ms.obo:
=================================================
************ adde synonym 'InterProphet'
[Term]
id: MS:1002288
name: iProphet
def: "A program in the TPP that calculates distinct peptide 
probabilities based on several lines of corroborating evidence including 
search results from multiple search engines via the pepXML format." 
[PMID:21876204]
synonym: "InterProphet" EXACT []
is_a: MS:1002286 ! Trans-Proteomic Pipeline software


Best Regards,
Gerhard

-- 

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

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

Scientific assistant

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

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

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

Hi Gerhard, Felipe, thanks for this proposal, I have a few suggested
amendments, below in red (and *** in case color doesn't come through):



-----Original Message-----
From: mayerg97 via Psidev-ms-vocab <psi...@li...>

Dear proteomics/metabolomics community,



following are the new/changed terms for the release candidate 4.1.25_rc1 of
the psi-ms.obo file.





New CV terms in version 4.1.25_rc1 of psi-ms.obo:

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

[Term]

id: MS:1003011

name: pFind

def: "Sequence-tag-based search engine pFind." [PMID:30295672]

is_a: MS:1001456 ! analysis software



[Term]

id: MS:1003012

name: KSDP score

def: "Kernel mass spectral dot product scoring function." [PMID:15044235]

is_a: MS:1001143 ! PSM-level search engine specific statistic

relationship: has_order MS:1002108 ! higher score better



[Term]

id: MS:1003013

name: i3tms

def: "i3-tms search engine and data-analysis software." [PSI:PI]

is_a: MS:1001456 ! analysis software



[Term]

id: MS:1003014

name: MSFragger

def: "A database search-based peptide identification tool." [PMID:28394336]

is_a: MS:1002286 ! Trans-Proteomic Pipeline software



[Term]

id: MS:1003015

name: razor peptide

def: "A peptide which is shared between protein groups and assigned to

the protein group with the largest number of identified peptides." [PSI:PI]

is_a: MS:1000860 ! peptide



*** Begin

The following term should not be added as is. PTMProphet doesn’t have a
“PTM Score”.

x [Term]

x id: MS:1003016

x name: PTMProphet:PTM Score

x def: "The PTM score from PTMProphet software." [PSI:MS]

x xref: value-type:xsd\:string "The allowed value-type for this CV term."

X is_a: MS:1001968 ! PTM localization PSM-level statistic

X relationship: has_regexp MS:1002505 ! regular expression for modification
localization scoring

*** PTM Prophet has quite a substantial number of metrics.

At the PSM level, we have:

normalized information content

number of localized modifications

At the site level, we have:

               modification localization probability

               O-score

M-score

So I think we may actually want 5 terms, not a single term (and not called
PTM Score).

@Felipe, are you eager to write terms, or were you just thinking that we
will need something eventually?

The paper is currently under revision. I suggest we exclude 3016 from this
RC, and circle back in a few weeks to provide a more complete set of terms
and definitions. Does that sound okay?

*** End





[Term]

id: MS:1003017

name: ProteinProphet:peptide weight

def: "Peptide weight used for FDR filtering." [PSI:PI]

***def: "Fraction of peptide evidence attributable to a protein or a set of
indistinguishable proteins." [PSI:PI]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1002490 ! peptide-level scoring

is_a: MS:1001153 ! search engine specific score

relationship: has_order MS:1002108 ! higher score better

relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

*** NOTE: Although some may use this for filtering, any score could
potentially be used for filtering, and I suggest that a potential use
should not be part of the definition, or else 100 other terms would also be
characterized as “for FDR filtering” (but I discourage that)



[Term]

id: MS:1003018

name: ProteinProphet:peptide group weight

def: "Peptide group weight used for FDR filtering." [PSI:PI]

***def: "Fraction of peptide evidence attributable to a group of proteins."
[PSI:PI]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1002490 ! peptide-level scoring

is_a: MS:1001153 ! search engine specific score

relationship: has_order MS:1002108 ! higher score better

relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive





Changed CV terms in version 4.1.25_rc1 of psi-ms.obo:

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

************ added synonym 'InterProphet'

[Term]

id: MS:1002288

name: iProphet

def: "A program in the TPP that calculates distinct peptide

probabilities based on several lines of corroborating evidence including

search results from multiple search engines via the pepXML format."

[PMID:21876204]

synonym: "InterProphet" EXACT []

is_a: MS:1002286 ! Trans-Proteomic Pipeline software



Best Regards,

Gerhard



-- 



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



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



Scientific assistant



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







_______________________________________________

Psidev-ms-vocab mailing list

Psi...@li...

https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

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

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

Dear proteomics/metabolomics community,

following are the new/changed terms for the release candidate 4.1.25_rc1 
of the
psi-ms.obo file.


New CV terms in version 4.1.25_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003011
name: pFind
def: "Sequence-tag-based search engine pFind." [PMID:30295672]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003012
name: KSDP score
def: "Kernel mass spectral dot product scoring function." [PMID:15044235]
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1003013
name: i3tms
def: "i3-tms search engine and data-analysis software." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003014
name: MSFragger
def: "A database search-based peptide identification tool." [PMID:28394336]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

[Term]
id: MS:1003015
name: razor peptide
def: "A peptide which is shared between protein groups and assigned to 
the protein group with the largest number of identified peptides." [PSI:PI]
is_a: MS:1000860 ! peptide

[Term]
id: MS:1003016
name: PTMProphet:PTM Score
def: "The PTM score from PTMProphet software." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1003017
name: ProteinProphet:peptide weight
def: "Peptide weight used for FDR filtering." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002490 ! peptide-level scoring
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1003018
name: ProteinProphet:peptide group weight
def: "Peptide group weight used for FDR filtering." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002490 ! peptide-level scoring
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive


Changed CV terms in version 4.1.25_rc1 of psi-ms.obo:
=====================================================
************ added synonym 'InterProphet'
[Term]
id: MS:1002288
name: iProphet
def: "A program in the TPP that calculates distinct peptide 
probabilities based on several lines of corroborating evidence including 
search results from multiple search engines via the pepXML format." 
[PMID:21876204]
synonym: "InterProphet" EXACT []
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

Best Regards,
Gerhard

-- 

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

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

Scientific assistant

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

[Psidev-pi-dev] New version 4.1.24 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new/changed terms for the new release 4.1.24 of the
psi-ms.obo file. It contains a new term for the LPPtiger software.


New CV terms in version 4.1.24 of psi-ms.obo:
=============================================
[Term]
id: MS:1003010
name: LPPtiger
def: "Software for lipidome-specific prediction and identification of 
oxidized phospholipids from LC-MS datasets." [PMID:29123162]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software


Best Regards,
Gerhard

-- 

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

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

*Scientific assistant*

*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-pi-dev] New version 4.1.23 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new/changed terms for the new release 4.1.23 of the
psi-ms.obo file. The obsolete term 'database version' was reactivated.


New CV terms in version 4.1.23 of psi-ms.obo:
=============================================
No new terms


Changed CV terms in version 4.1.23 of psi-ms.obo:
=================================================
************ reactivated an obsolete term (for usage e.g. in mzTab)
[Term]
id: MS:1001016
name: database version
def: "Version of the search database. In mzIdentML use the attribute 
instead." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details


Best Regards,
Gerhard

-- 

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

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

*Scientific assistant*

*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-pi-dev] Training materials

[Horvatovich, P.L. <p.l...@ru...>]

Dear Andy and All,

Unfortunately, I will be not attending the meeting but would be interested
both for any tutorial materials and/or or materials (slides documents etc)
summarising the outcome of the meeting.

With best regards,

Peter Horvatovich

On Tue, Mar 12, 2019 at 12:30 PM Jones, Andy <And...@li...>
wrote:

> Hi all,
>
>
>
> Apologies for the cross-posting. The PSI meeting kicks off next Monday in
> Cape Town and hoping to see lots of you there. We are going to have lots of
> local participation from individuals new to PSI processes and standards,
> and as such, we have decided to give various tutorials in different slots
> to bring people up to speed.
>
>
>
> If you have any slides introducing one of the core PSI standards, data
> submission to a public repository or some other relevant aspect of data
> sharing, please send them over to me (off the mailing list), and I will add
> them to a shared drive that various people can access when we’re in Cape
> Town, so that we can be flexible at who gives a tutorial dependent on
> availability during the meeting.
>
>
>
> Best wishes
>
> Andy
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>


-- 

Peter Horvatovich
Associate Professor

University of Groningen
Faculty of Sciences and Engineering
Groningen Research Institute of Pharmacy
Analytical Biochemistry

Building 3226, Room 6.9
Antonius Deusinglaan 1
9713 AV Groningen
Internal Zip Code XB20
P.O. Box 196
9700 AD Groningen
The Netherlands

Telephone: +31-(0)50-363 3341
Fax: +31 (0)50 363 7582
Mobile: +31 (0)6 2459 7203
Email: p.l...@ru...
Homepage: www.biomac.nl

[Psidev-pi-dev] Training materials

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

Hi all,

Apologies for the cross-posting. The PSI meeting kicks off next Monday in Cape Town and hoping to see lots of you there. We are going to have lots of local participation from individuals new to PSI processes and standards, and as such, we have decided to give various tutorials in different slots to bring people up to speed.

If you have any slides introducing one of the core PSI standards, data submission to a public repository or some other relevant aspect of data sharing, please send them over to me (off the mailing list), and I will add them to a shared drive that various people can access when we're in Cape Town, so that we can be flexible at who gives a tutorial dependent on availability during the meeting.

Best wishes
Andy

[Psidev-pi-dev] New version 4.1.22 of psi-ms.obo

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

Dear proteomics/metabolomics community,

the new version 4.1.22 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

New CV terms in version 4.1.22 of psi-ms.obo:
=============================================
[Term]
id: MS:1003004
name: maXis II
def: "Bruker Daltonics' maXis II." [PSI:MS]
is_a: MS:1001547 ! Bruker Daltonics maXis series

[Term]
id: MS:1003005
name: timsTOF Pro
def: "Bruker Daltonics' timsTOF Pro." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1003006
name: mean inverse reduced ion mobility array
def: "Array of 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 MS:1002814 ! volt-second per square centimeter

[Term]
id: MS:1003007
name: raw ion mobility array
def: "Array of raw drift times." [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

[Term]
id: MS:1003008
name: raw inverse reduced ion mobility array
def: "Array of raw inverse reduced ion mobilities." [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 MS:1002814 ! volt-second per square centimeter

[Term]
id: MS:1003009
name: Shimadzu Biotech LCD format
def: "Shimadzu Biotech LCD file format." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: PEFF:0001035
name: initiator methionine
def: "N-terminal methionine residue of a protein that can be 
co-translationally cleaved." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for each 
VariantSimple item



Changed CV terms in version 4.1.22 of psi-ms.obo:
=================================================
************    "volt-second per square centimeter"
************ --> volt-second per square centimeter
[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

************    Removed relationship: has_units MS:1002814 ! volt-second 
per square centimeter
[Term]
id: MS:1002816
name: mean ion mobility array
def: "Array of drift times, 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

************     MS:1002901 ! search engine specific score for proteoforms
************ --> MS:1002906 ! search engine specific score for proteoforms
[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:1002906 ! search engine specific score for proteoforms

[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:1002906 ! search engine specific score for proteoforms

Best Regards,
Gerhard

-- 

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

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

*Scientific assistant*

*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-pi-dev] PSI2019

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

Hi all,
A polite reminder to register for the PSI 2019 meeting, which will take place in Cape Town, SA, March 18-20 : http://psidev.info/hupo-psi-meeting-2019 if you are interested in data sharing for proteomics. We are also planning to run some training activities as part of the meeting, so that new participants can learn about existing standards and related software.

There is no cost to register for the meeting, although participants must pay their own travel and hotel costs. Please forward this on to anyone who you think might be interested in attending – we are always keen to attract new participants.

Best wishes
Andy

[Psidev-pi-dev] Release candidate 4.1.22_rc1 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new terms for the release candidate 4.1.22_rc1 of the
psi-ms.obo file. It contains some added terms for Bruker instruments, for
a Shimadzu format, some error corrections and the updated terms for the
ion mobility arrays.


New CV terms in version 4.1.22_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003004
name: maXis II
def: "Bruker Daltonics' maXis II." [PSI:MS]
is_a: MS:1001547 ! Bruker Daltonics maXis series

[Term]
id: MS:1003005
name: timsTOF Pro
def: "Bruker Daltonics' timsTOF Pro." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1003006
name: mean inverse reduced ion mobility array
def: "Array of 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 MS:1002814 ! volt-second per square centimeter

[Term]
id: MS:1003007
name: raw ion mobility array
def: "Array of raw drift times." [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

[Term]
id: MS:1003008
name: raw inverse reduced ion mobility array
def: "Array of raw inverse reduced ion mobilities." [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 MS:1002814 ! volt-second per square centimeter

[Term]
id: MS:1003009
name: Shimadzu Biotech LCD format
def: "Shimadzu Biotech LCD file format." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: PEFF:0001035
name: initiator methionine
def: "N-terminal methionine residue of a protein that can be 
co-translationally cleaved." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for each 
VariantSimple item



Changed CV terms in version 4.1.22_rc1 of psi-ms.obo:
=====================================================
************    "volt-second per square centimeter"
************ --> volt-second per square centimeter
[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

************    Removed relationship: has_units MS:1002814 ! volt-second 
per square centimeter
[Term]
id: MS:1002816
name: mean ion mobility array
def: "Array of drift times, 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

************     MS:1002901 ! search engine specific score for proteoforms
************ --> MS:1002906 ! search engine specific score for proteoforms
[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:1002906 ! search engine specific score for proteoforms

[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:1002906 ! search engine specific score for proteoforms


Best Regards,
Gerhard

-- 

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

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

*Scientific assistant*

*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-pi-dev] PSI2019

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

Hi all,

I am pleased to announce that registration is now open for the PSI 2019 meeting, which will take place in Cape Town, SA, March 18-20 : http://psidev.info/hupo-psi-meeting-2019. As a reminder, there is no cost to register for the meeting, although participants must pay their own travel and hotel costs. Please forward this on to anyone who you think might be interested in attending – we are always keen to attract new participants.

We hope to see you there!
Best wishes
Andy