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

Re: [Psidev-pi-dev] [Psidev-ms-dev] Release candidate 4.0.12_rc2 of psi-ms.obo

[Neumann, S. <sne...@ip...>]

Hi,

out of curiosity, does the MS know which LC it is coupled to ?

Is the difference between "6530A Q-TOF LC/MS" and "6530B Q-TOF LC/MS"
in the MS or LC side ? And what is it called if I shoehorn 
A Waters UPLC in front of it ? 

What I am trying to say is that unless these instrument models 
are in one box, or at least such that e.g. Proteoziward msconvert 
can distinguish them, it might be good to have separate Terms 
for the LC and MS parts of the setup. 

Just my 2c,
Yours,
Steffen






On Wed, 2017-05-10 at 12:47 +0200, mayerg97 wrote:
> Dear proteomics community,
> 
> attached there's the release candidate 4.0.12_rc2 of the psi-ms.obo
> file.
> It contains new terms for Agilent instruments.
> 
> New CV terms in version 4.0.12_rc2 of psi-ms.obo:
> =================================================
> [Term]
> id: MS:1002783
> name: 6550 iFunnel Q-TOF LC/MS
> def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002784
> name: 6550A iFunnel Q-TOF LC/MS
> def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002785
> name: 6520B Q-TOF LC/MS
> def: "The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002786
> name: 6530A Q-TOF LC/MS
> def: "The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002787
> name: 6530B Q-TOF LC/MS
> def: "The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002788
> name: 6538 Q-TOF LC/MS
> def: "The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002789
> name: 6540 Q-TOF LC/MS
> def: "The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002790
> name: 6542 Q-TOF LC/MS
> def: "The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002791
> name: 6545 Q-TOF LC/MS
> def: "The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002792
> name: 6560 Q-TOF LC/MS
> def: "The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> [Term]
> id: MS:1002793
> name: 6570 Q-TOF LC/MS
> def: "The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002794
> name: 6120B Quadrupole LC/MS
> def: "The 6120B Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a single quadrupole mass
> spectrometer from the 6100 Series of Agilent mass spectrometers."
> [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002795
> name: 6150 Quadrupole LC/MS
> def: "The 6150 Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a single quadrupole mass
> spectrometer from the 6100 Series of Agilent mass spectrometers."
> [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002796
> name: 6224 Time-of-Flight LC/MS
> def: "The 6224 Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002797
> name: 6230A Time-of-Flight LC/MS
> def: "The 6230A Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002798
> name: 6230B Time-of-Flight LC/MS
> def: "The 6230B Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002799
> name: 6430 Triple Quadrupole LC/MS
> def: "The 6430 Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a Agilent triple quadrupole
> mass spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002800
> name: 6495A Triple Quadrupole LC/MS
> def: "The 6495A Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a Agilent triple quadrupole
> mass spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002801
> name: 6495B Triple Quadrupole LC/MS
> def: "The 6495B Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a Agilent triple quadrupole
> mass spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002802
> name: 7000A Triple Quadrupole GC/MS
> def: "The 7000A Quadrupole GC/MS system is a Agilent gas
> chromatography instrument combined with a Agilent triple quadrupole
> mass spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002803
> name: 7000B Triple Quadrupole GC/MS
> def: "The 7000B Quadrupole GC/MS system is a Agilent gas
> chromatography instrument combined with a Agilent triple quadrupole
> mass spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002804
> name: 7800 Quadrupole ICP-MS
> def: "The 7800 Quadrupole ICP-MS system is a Agilent inductively
> couple plasma instrument combined with a Agilent quadrupole mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> [Term]
> id: MS:1002805
> name: 8800 Triple Quadrupole ICP-MS
> def: "The 8800 Quadrupole ICP-MS system is a Agilent inductively
> couple plasma instrument combined with a Agilent quadrupole mass
> spectrometer." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> 
> 
> Changed CV terms in version 4.0.12_rc2 of psi-ms.obo:
> =====================================================
> ************ 6120 --> 6120A
> [Term]
> id: MS:1000469
> name: 6120A Quadrupole LC/MS
> def: "The 6120A Quadrupole LC/MS system is a Agilent liquid
> chromatography instrument combined with a single quadrupole mass
> spectrometer from the 6100 Series of Agilent mass spectrometers. 6120
> quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan
> speed and utilizes multiple signal acquisition." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> ************ 6520 --> 6520A
> [Term]
> id: MS:1000677
> name: 6520A Quadrupole Time-of-Flight LC/MS
> def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid
> chromatography instrument combined with a Agilent time of flight mass
> spectrometer. This time of flight mass spectrometer has a m/z range
> of 50-12000, mass accuracy of less than 2 ppm and resolution greater
> than 26,000 at m/z 2722. It has multiple ion sources and can be used
> with multimode ion sources." [PSI:MS]
> is_a: MS:1000490 ! Agilent instrument model
> 
> Best Regards,
> Gerhard
> -- 
> --------------------------------------------------------------------
> Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER
> PhD student
> Medizinisches Proteom-Center
> DEPARTMENT Medical Bioinformatics
> Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
> Fon +49 (0)234 32-21006 | 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-dev mailing list
> Psi...@li...
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[Psidev-pi-dev] Release candidate 4.0.12_rc2 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 4.0.12_rc2 of the psi-ms.obo file.
It contains new terms for Agilent instruments.

New CV terms in version 4.0.12_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002783
name: 6550 iFunnel Q-TOF LC/MS
def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002784
name: 6550A iFunnel Q-TOF LC/MS
def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002785
name: 6520B Q-TOF LC/MS
def: "The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002786
name: 6530A Q-TOF LC/MS
def: "The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002787
name: 6530B Q-TOF LC/MS
def: "The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002788
name: 6538 Q-TOF LC/MS
def: "The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002789
name: 6540 Q-TOF LC/MS
def: "The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002790
name: 6542 Q-TOF LC/MS
def: "The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002791
name: 6545 Q-TOF LC/MS
def: "The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002792
name: 6560 Q-TOF LC/MS
def: "The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1002793
name: 6570 Q-TOF LC/MS
def: "The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002794
name: 6120B Quadrupole LC/MS
def: "The 6120B Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a single quadrupole mass 
spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002795
name: 6150 Quadrupole LC/MS
def: "The 6150 Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a single quadrupole mass 
spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002796
name: 6224 Time-of-Flight LC/MS
def: "The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography 
instrument combined with a Agilent time of flight mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002797
name: 6230A Time-of-Flight LC/MS
def: "The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography 
instrument combined with a Agilent time of flight mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002798
name: 6230B Time-of-Flight LC/MS
def: "The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography 
instrument combined with a Agilent time of flight mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002799
name: 6430 Triple Quadrupole LC/MS
def: "The 6430 Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a Agilent triple quadrupole mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002800
name: 6495A Triple Quadrupole LC/MS
def: "The 6495A Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a Agilent triple quadrupole mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002801
name: 6495B Triple Quadrupole LC/MS
def: "The 6495B Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a Agilent triple quadrupole mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002802
name: 7000A Triple Quadrupole GC/MS
def: "The 7000A Quadrupole GC/MS system is a Agilent gas chromatography 
instrument combined with a Agilent triple quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002803
name: 7000B Triple Quadrupole GC/MS
def: "The 7000B Quadrupole GC/MS system is a Agilent gas chromatography 
instrument combined with a Agilent triple quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002804
name: 7800 Quadrupole ICP-MS
def: "The 7800 Quadrupole ICP-MS system is a Agilent inductively couple 
plasma instrument combined with a Agilent quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002805
name: 8800 Triple Quadrupole ICP-MS
def: "The 8800 Quadrupole ICP-MS system is a Agilent inductively couple 
plasma instrument combined with a Agilent quadrupole mass spectrometer." 
[PSI:MS]
is_a: MS:1000490 ! Agilent instrument model



Changed CV terms in version 4.0.12_rc2 of psi-ms.obo:
=====================================================
************ 6120 --> 6120A
[Term]
id: MS:1000469
name: 6120A Quadrupole LC/MS
def: "The 6120A Quadrupole LC/MS system is a Agilent liquid 
chromatography instrument combined with a single quadrupole mass 
spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 
quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan 
speed and utilizes multiple signal acquisition." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

************ 6520 --> 6520A
[Term]
id: MS:1000677
name: 6520A Quadrupole Time-of-Flight LC/MS
def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer. This time of flight mass spectrometer has a m/z range of 
50-12000, mass accuracy of less than 2 ppm and resolution greater than 
26,000 at m/z 2722. It has multiple ion sources and can be used with 
multimode ion sources." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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] Release candidate 4.0.12_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 4.0.12_rc1 of the psi-ms.obo file.
It contains two new terms for Agilent instruments.

New CV terms in version 4.0.12_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002783
name: 6550 iFunnel Q-TOF LC/MS
def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002784
name: 6550A iFunnel Q-TOF LC/MS
def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid 
chromatography instrument combined with a Agilent time of flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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 4.0.11 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 4.0.11 of the psi-ms.obo file.

It contains new and changed terms for isobaric labelling and
reporter ions used in quantification by isobaric labelling techniques.


New CV terms in version 4.0.11 of psi-ms.obo:
=============================================
************ New terms for isobaric labelling techniques
[Term]
id: MS:1002756
name: iodoTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher sulfhydryl-reactive 
iodo tandem mass tag (iodoTMT) labelling workflow." [PSI:PI, PMID:24926564]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002757
name: glyco-TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
glyco-tandem mass tag (glyco-TMT) labelling workflow." [PSI:PI, 
PMID:22455665]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002758
name: aminoxyTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
aminoxy tandem mass tag (aminoxyTMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002759
name: hydrazideTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
hydrazide tandem mass tag (hydrazide-TMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002760
name: iTRAQH quantitation analysis
def: "Quantification analysis using the carbonyl-reactive isobaric tags 
for relative and absolute quantification hydrazide (iTRAQH) labelling 
workflow." [PSI:PI, PMID:22926130]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002761
name: DiART quantitation analysis
def: "Quantification analysis using the amine-reactive deuterium 
isobaric amine reactive tag (DiART) labelling workflow." [PSI:PI, 
PMID:20715779]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002762
name: DiLeu quantitation analysis
def: "Quantification analysis using the amine-reactive dimethyl leucine 
(DiLeu) tag labelling workflow." [PSI:PI, PMID:20715779]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ New terms for TMT 10-plex reagents
[Term]
id: MS:1002763
name: TMT reagent 127N
def: "The name of the sample labelled with the TMT reagent 127N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002764
name: TMT reagent 127C
def: "The name of the sample labelled with the TMT reagent 127C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002765
name: TMT reagent 128N
def: "The name of the sample labelled with the TMT reagent 128N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002766
name: TMT reagent 128C
def: "The name of the sample labelled with the TMT reagent 128C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002767
name: TMT reagent 129N
def: "The name of the sample labelled with the TMT reagent 129N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002768
name: TMT reagent 129C
def: "The name of the sample labelled with the TMT reagent 129C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent
[Term]
id: MS:1002769
name: TMT reagent 130N
def: "The name of the sample labelled with the TMT reagent 130N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002770
name: TMT reagent 130C
def: "The name of the sample labelled with the TMT reagent 130C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

************ New terms for DiART labelling reagents
[Term]
id: MS:1002771
name: DiART reagent
def: "Deuterium isobaric amine reactive tag labeling reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002772
name: DiART reagent 114
def: "The name of the sample labelled with the DiART reagent 114." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002773
name: DiART reagent 115
def: "The name of the sample labelled with the DiART reagent 115." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002774
name: DiART reagent 116
def: "The name of the sample labelled with the DiART reagent 116." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002775
name: DiART reagent 117
def: "The name of the sample labelled with the DiART reagent 117." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002776
name: DiART reagent 118
def: "The name of the sample labelled with the DiART reagent 118." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002777
name: DiART reagent 119
def: "The name of the sample labelled with the DiART reagent 119." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

************ New terms for DiLeu labelling reagents
[Term]
id: MS:1002778
name: DiLeu reagent
def: "Dimethyl leucine labeling reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002779
name: DiLeu reagent 115
def: "The name of the sample labelled with the DiLeu reagent 115." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002780
name: DiLeu reagent 116
def: "The name of the sample labelled with the DiLeu reagent 116." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002781
name: DiLeu reagent 117
def: "The name of the sample labelled with the DiLeu reagent 117." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002782
name: DiLeu reagent 118
def: "The name of the sample labelled with the DiLeu reagent 118." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent


Changed CV terms in version 4.0.11 of psi-ms.obo:
=================================================
************ added is_a: MS:1001833 ! quantitation analysis summary
************ added amine-reactive to the definition
[Term]
id: MS:1001837
name: iTRAQ quantitation analysis
def: "Quantification analysis using the SCIEX amine-reactive isobaric 
tags for relative and absolute quantification (iTRAQ) labelling 
workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in 
the 114-121 m/z range." [PSI:PI, PMID:15385600]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ added amine-reactive to the definition
[Term]
id: MS:1002010
name: TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher amine-reactive 
tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are 
measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ added is_a: MS:1001833 ! quantitation analysis summary
************ and added PMID-reference
[Term]
id: MS:1002212
name: IPTL quantitation analysis
def: "Quantification analysis using a labelling strategy where both 
peptide termini are labelled so that the peptides from different 
labelling schema are isobaric." [PSI:PI, PMID:19655813]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ Changed definition to include glycoTMT, iodoTMT, aminoxyTMT 
or hydrazideTMT
[Term]
id: MS:1002615
name: TMT reagent
def: "Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT 
or hydrazideTMT isobaric labeling." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

************ Changed definition to include iTRAQH
[Term]
id: MS:1002622
name: iTRAQ reagent
def: "Isobaric tag for relative and absolute quantitation (iTRAQ or 
iTRAQH) reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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] Release candidate 4.0.11_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 4.0.11_rc1 of the psi-ms.obo file.

It contains new and changed terms for isobaric labelling and
reporter ions used in quantification by isobaric labelling techniques.


New CV terms in version 4.0.11_rc1 of psi-ms.obo:
=================================================
************ New terms for isobaric labelling techniques
[Term]
id: MS:1002756
name: iodoTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher sulfhydryl-reactive 
iodo tandem mass tag (iodoTMT) labelling workflow." [PSI:PI, PMID:24926564]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002757
name: glyco-TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
glyco-tandem mass tag (glyco-TMT) labelling workflow." [PSI:PI, 
PMID:22455665]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002758
name: aminoxyTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
aminoxy tandem mass tag (aminoxyTMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002759
name: hydrazideTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
hydrazide tandem mass tag (hydrazide-TMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002760
name: iTRAQH quantitation analysis
def: "Quantification analysis using the carbonyl-reactive isobaric tags 
for relative and absolute quantification hydrazide (iTRAQH) labelling 
workflow." [PSI:PI, PMID:22926130]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002761
name: DiART quantitation analysis
def: "Quantification analysis using the amine-reactive deuterium 
isobaric amine reactive tag (DiART) labelling workflow." [PSI:PI, 
PMID:20715779]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002762
name: DiLeu quantitation analysis
def: "Quantification analysis using the amine-reactive dimethyl leucine 
(DiLeu) tag labelling workflow." [PSI:PI, PMID:20715779]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ New terms for TMT 10-plex reagents
[Term]
id: MS:1002763
name: TMT reagent 127N
def: "The name of the sample labelled with the TMT reagent 127N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002764
name: TMT reagent 127C
def: "The name of the sample labelled with the TMT reagent 127C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002765
name: TMT reagent 128N
def: "The name of the sample labelled with the TMT reagent 128N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002766
name: TMT reagent 128C
def: "The name of the sample labelled with the TMT reagent 128C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002767
name: TMT reagent 129N
def: "The name of the sample labelled with the TMT reagent 129N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002768
name: TMT reagent 129C
def: "The name of the sample labelled with the TMT reagent 129C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent
[Term]
id: MS:1002769
name: TMT reagent 130N
def: "The name of the sample labelled with the TMT reagent 130N." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002770
name: TMT reagent 130C
def: "The name of the sample labelled with the TMT reagent 130C." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

************ New terms for DiART labelling reagents
[Term]
id: MS:1002771
name: DiART reagent
def: "Deuterium isobaric amine reactive tag labeling reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002772
name: DiART reagent 114
def: "The name of the sample labelled with the DiART reagent 114." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002773
name: DiART reagent 115
def: "The name of the sample labelled with the DiART reagent 115." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002774
name: DiART reagent 116
def: "The name of the sample labelled with the DiART reagent 116." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002775
name: DiART reagent 117
def: "The name of the sample labelled with the DiART reagent 117." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002776
name: DiART reagent 118
def: "The name of the sample labelled with the DiART reagent 118." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

[Term]
id: MS:1002777
name: DiART reagent 119
def: "The name of the sample labelled with the DiART reagent 119." [PSI:PI]
is_a: MS:1002771 ! DiART reagent

************ New terms for DiLeu labelling reagents
[Term]
id: MS:1002778
name: DiLeu reagent
def: "Dimethyl leucine labeling reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002779
name: DiLeu reagent 115
def: "The name of the sample labelled with the DiLeu reagent 115." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002780
name: DiLeu reagent 116
def: "The name of the sample labelled with the DiLeu reagent 116." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002781
name: DiLeu reagent 117
def: "The name of the sample labelled with the DiLeu reagent 117." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent

[Term]
id: MS:1002782
name: DiLeu reagent 118
def: "The name of the sample labelled with the DiLeu reagent 118." [PSI:PI]
is_a: MS:1002778 ! DiLeu reagent


Changed CV terms in version 4.0.11_rc1 of psi-ms.obo:
=====================================================
************ added is_a: MS:1001833 ! quantitation analysis summary
************ added amine-reactive to the definition
[Term]
id: MS:1001837
name: iTRAQ quantitation analysis
def: "Quantification analysis using the SCIEX amine-reactive isobaric 
tags for relative and absolute quantification (iTRAQ) labelling 
workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in 
the 114-121 m/z range." [PSI:PI, PMID:15385600]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ added amine-reactive to the definition
[Term]
id: MS:1002010
name: TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher amine-reactive 
tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are 
measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ added is_a: MS:1001833 ! quantitation analysis summary
************ and added PMID-reference
[Term]
id: MS:1002212
name: IPTL quantitation analysis
def: "Quantification analysis using a labelling strategy where both 
peptide termini are labelled so that the peptides from different 
labelling schema are isobaric." [PSI:PI, PMID:19655813]
is_a: MS:1001833 ! quantitation analysis summary
is_a: MS:1002009 ! isobaric label quantitation analysis

************ Changed definition to include glycoTMT, iodoTMT, aminoxyTMT 
or hydrazideTMT
[Term]
id: MS:1002615
name: TMT reagent
def: "Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT 
or hydrazideTMT isobaric labeling." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

************ Changed definition to include iTRAQH
[Term]
id: MS:1002622
name: iTRAQ reagent
def: "Isobaric tag for relative and absolute quantitation (iTRAQ or 
iTRAQH) reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent


Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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 4.0.10 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 4.0.10 of the psi-ms.obo file.

It contains corrections for the names of is_a relationships for several 
terms,
which result from our ontology reorganisation last summer.

Thanks Hannes, for pointing out these inconsistencies.


New CV terms in version 4.0.10 of psi-ms.obo:
=============================================
************ No new terms


Changed CV terms in version 4.0.10 of psi-ms.obo:
=================================================
************ is_a: MS:1001105 ! peptide result details
************ replaced by
************ is_a: MS:1001105 ! peptide sequence-level identification 
attribute
[Term]
id: MS:1001114
name: retention time(s)
def: "OBSOLETE Retention time of the spectrum from the source file." 
[PSI:PI]
comment: This term was made obsolete because scan start time 
(MS:1000016) should be used instead.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
is_obsolete: true

************ is_a: MS:1001092 ! peptide identification confidence metric
************ replaced by
************ is_a: MS:1001092 ! peptide sequence-level identification 
statistic
[Term]
id: MS:1001191
name: p-value
def: "OBSOLETE Quality estimation by p-value." [PSI:PI]
comment: This term was made obsolete because now is split into peptide 
and protein terms.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
is_a: MS:1001198 ! protein identification confidence metric
is_obsolete: true

************ is_a: MS:1001116 ! single protein result details
************ replaced by
************ MS:1001116 ! single protein identification statistic
[Term]
id: MS:1001198
name: protein identification confidence metric
def: "Identification confidence metric for a protein." [PSI:PI]
is_a: MS:1001116 ! single protein identification statistic

************ is_a: MS:1001143 ! search engine specific score for PSMs
************ replaced by
************ is_a: MS:1001143 ! PSM-level search engine specific statistic
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated 
for PSMs from individual search engines, such that ordering of result 
quality is maintained and all FDRScore values are guaranteed to have a 
value > 0." [PMID:19253293]
comment: This term was made obsolete because it was split into the more 
specific terms for PSM-level FDRScore (1002355), distinct peptide-level 
FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein 
group-level FDRScore (MS:1002374).
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
is_obsolete: true

************ is_a: MS:1001116 ! single protein result details
************ replaced by
************ is_a: MS:1001116 ! single protein identification statistic
[Term]
id: MS:1002268
name: Byonic:Best LogProb
def: "Best (most negative) log p-value of an individual PSM." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002109 ! lower score better

************ is_a: MS:1002405 ! protein cluster details
************ replaced by
************ is_a: MS:1002405 ! protein group-level result list attribute
[Term]
id: MS:1002408
name: number of distinct protein sequences
def: "The number of protein clusters that have been identified, which 
must match the number of clusters that pass the threshold in the file." 
[PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002405 ! protein group-level result list attribute

************ is_a: MS:1002358 ! search engine specific score for 
distinct peptides
************ replaced by
************ is_a: MS:1002358 ! search engine specific peptide 
sequence-level identification statistic
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in 
the CV.
is_a: MS:1002358 ! search engine specific peptide sequence-level 
identification statistic
is_obsolete: true

************ is_a: MS:1001143 ! search engine specific score for PSMs
************ replaced by
************ is_a: MS:1001143 ! PSM-level search engine specific statistic
************ in the following six OpenXQuest terms
[Term]
id: MS:1002681
name: OpenXQuest:combined score
def: "OpenXQuest's combined 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:1002682
name: OpenXQuest:xcorr xlink
def: "OpenXQuest's cross-correlation of cross-linked ions subscore." 
[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:1002683
name: OpenXQuest:xcorr common
def: "OpenXQuest's cross-correlation of unlinked ions subscore." [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:1002684
name: OpenXQuest:match-odds
def: "OpenXQuest's match-odds subscore." [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
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002685
name: OpenXQuest:intsum
def: "OpenXQuest's sum of matched peak intensity subscore." [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
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002686
name: OpenXQuest:wTIC
def: "OpenXQuest's weighted percent of total ion current subscore." [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
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

************ is_a: MS:1001073 ! database type
************ replaced by
************ is_a: MS:1001073 ! database type amino acid
[Term]
id: MS:1002752
name: database type spectral library
def: "Database containing spectra." [PSI:PI]
is_a: MS:1001073 ! database type amino acid

************ Removed
************ is_a: MS:1001153 ! search engine specific score
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated 
for PSMs from individual search engines, such that ordering of result 
quality is maintained and all FDRScore values are guaranteed to have a 
value > 0." [PMID:19253293]
comment: This term was made obsolete because it was split into the more 
specific terms for PSM-level FDRScore (1002355), distinct peptide-level 
FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein 
group-level FDRScore (MS:1002374).
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
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.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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] Release candidate 4.0.10_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 4.0.10_rc1 of the psi-ms.obo file.

It contains corrections for the names of is_a relationships for several 
terms,
which result from our ontology reorganisation last summer.

Thanks Hannes, for pointing out these inconsistencies.


New CV terms in version 4.0.10_rc1 of psi-ms.obo:
=================================================
************ No new terms


Changed CV terms in version 4.0.10_rc1 of psi-ms.obo:
=====================================================
************ is_a: MS:1001105 ! peptide result details
************ replaced by
************ is_a: MS:1001105 ! peptide sequence-level identification 
attribute
[Term]
id: MS:1001114
name: retention time(s)
def: "OBSOLETE Retention time of the spectrum from the source file." 
[PSI:PI]
comment: This term was made obsolete because scan start time 
(MS:1000016) should be used instead.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
is_obsolete: true

************ is_a: MS:1001092 ! peptide identification confidence metric
************ replaced by
************ is_a: MS:1001092 ! peptide sequence-level identification 
statistic
[Term]
id: MS:1001191
name: p-value
def: "OBSOLETE Quality estimation by p-value." [PSI:PI]
comment: This term was made obsolete because now is split into peptide 
and protein terms.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
is_a: MS:1001198 ! protein identification confidence metric
is_obsolete: true

************ is_a: MS:1001116 ! single protein result details
************ replaced by
************ MS:1001116 ! single protein identification statistic
[Term]
id: MS:1001198
name: protein identification confidence metric
def: "Identification confidence metric for a protein." [PSI:PI]
is_a: MS:1001116 ! single protein identification statistic

************ is_a: MS:1001143 ! search engine specific score for PSMs
************ replaced by
************ is_a: MS:1001143 ! PSM-level search engine specific statistic
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated 
for PSMs from individual search engines, such that ordering of result 
quality is maintained and all FDRScore values are guaranteed to have a 
value > 0." [PMID:19253293]
comment: This term was made obsolete because it was split into the more 
specific terms for PSM-level FDRScore (1002355), distinct peptide-level 
FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein 
group-level FDRScore (MS:1002374).
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
is_obsolete: true

************ is_a: MS:1001116 ! single protein result details
************ replaced by
************ is_a: MS:1001116 ! single protein identification statistic
[Term]
id: MS:1002268
name: Byonic:Best LogProb
def: "Best (most negative) log p-value of an individual PSM." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002109 ! lower score better

************ is_a: MS:1002405 ! protein cluster details
************ replaced by
************ is_a: MS:1002405 ! protein group-level result list attribute
[Term]
id: MS:1002408
name: number of distinct protein sequences
def: "The number of protein clusters that have been identified, which 
must match the number of clusters that pass the threshold in the file." 
[PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002405 ! protein group-level result list attribute

************ is_a: MS:1002358 ! search engine specific score for 
distinct peptides
************ replaced by
************ is_a: MS:1002358 ! search engine specific peptide 
sequence-level identification statistic
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in 
the CV.
is_a: MS:1002358 ! search engine specific peptide sequence-level 
identification statistic
is_obsolete: true

************ is_a: MS:1001143 ! search engine specific score for PSMs
************ replaced by
************ is_a: MS:1001143 ! PSM-level search engine specific statistic
************ in the following six OpenXQuest terms
[Term]
id: MS:1002681
name: OpenXQuest:combined score
def: "OpenXQuest's combined 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:1002682
name: OpenXQuest:xcorr xlink
def: "OpenXQuest's cross-correlation of cross-linked ions subscore." 
[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:1002683
name: OpenXQuest:xcorr common
def: "OpenXQuest's cross-correlation of unlinked ions subscore." [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:1002684
name: OpenXQuest:match-odds
def: "OpenXQuest's match-odds subscore." [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
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002685
name: OpenXQuest:intsum
def: "OpenXQuest's sum of matched peak intensity subscore." [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
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002686
name: OpenXQuest:wTIC
def: "OpenXQuest's weighted percent of total ion current subscore." [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
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

************ is_a: MS:1001073 ! database type
************ replaced by
************ is_a: MS:1001073 ! database type amino acid
[Term]
id: MS:1002752
name: database type spectral library
def: "Database containing spectra." [PSI:PI]
is_a: MS:1001073 ! database type amino acid

************ Removed
************ is_a: MS:1001153 ! search engine specific score
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated 
for PSMs from individual search engines, such that ordering of result 
quality is maintained and all FDRScore values are guaranteed to have a 
value > 0." [PMID:19253293]
comment: This term was made obsolete because it was split into the more 
specific terms for PSM-level FDRScore (1002355), distinct peptide-level 
FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein 
group-level FDRScore (MS:1002374).
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
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.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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] [BioSharing] Record Maintenance

[<bio...@gm...>]

<p>Dear Dear BioSharing maintainer/contact,<br/><br>We are contacting you on behalf of BioSharing, an ELIXIR-UK node resource based at the University of Oxford, UK, that manually curates inter-related records on data standards, databases and data policies in the life, biomedical and environmental sciences.<br/><br>Over the last 8 months we have manually curated/reviewed every standard and database record in BioSharing as part of our curation drive.<br/><br>We note that you are listed as a contact for the following record(s). We would be grateful if you could take a look at these records and not only assess them for accuracy but also consider claiming them. This will allow you to edit these records and correct any inaccuracies and update them as necessary. All edits will be reviewed by a BioSharing engineer to ensure they conform to our curation guidelines:<ul><li>mzTab (<a href="https://biosharing.org/bsg-s000693">https://biosharing.org/bsg-s000693</a>)</li></ul></p><br><p>If you are not the appropriate contact, could we please ask you to forward this email to the appropriate person/group. We would be grateful if the appropriate person could look over the record and check the details therein to ensure it is an accurate representation of your resource.<br/><br>One of the features that makes BioSharing so powerful is the ability for users to 'claim' records. This allows a user to maintain the BioSharing record for their resource themselves, so they can edit the record and update it whenever they please. Claiming is essentially a one-off vetting of the record, as the BioSharing team can take care of the record maintenance and will only email maintainers if there is a query with the resource record that they cannot solve themselves. Another advantage of claiming the record is that any changes to that record, or linking to that record from other records, will result in an email being sent to you, allowing you to validate any changes. Records can be maintained by an individual, a number of individuals, or a group email account.<br/><br>We work with journal and funder data editors to help them pick the right resources to recommend for use by authors and fundees. Claiming your record will ensure you resource is represented correctly and increase the chances of your resource being selected for endorsement.<br><br><br/>Many thanks in advance for your time and assistance.<br>Please do not hesitate to contact us at <bio...@li...> should you have any queries.<br/><br>Yours sincerely,<br>The BioSharing team</p>

[Psidev-pi-dev] New version 4.0.9 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 4.0.9 of the psi-ms.obo file.

It contains new terms for binary data arrays and their compression
and for spectral library searches.


New CV terms in version 4.0.9 of psi-ms.obo:
============================================
[Term]
id: MS:1002742
name: noise array
def: "A data array of noise values." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002743
name: sampled noise m/z array
def: "A data array of parallel, independent m/z values for a sampling of 
noise across a spectrum (typically much smaller than MS:1000514, the m/z 
array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1002744
name: sampled noise intensity array
def: "A data array of intensity values for the amplitude of noise 
variation superposed on the baseline (MS:1002745) across a spectrum (for 
use with MS:1002743, sampled noise m/z array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000131 ! number of detector counts

[Term]
id: MS:1002745
name: sampled noise baseline array
def: "A data array of baseline intensity values (the intensity in the 
absence of analytes) for a sampling of noise across a spectrum (for use 
with MS:1002743, sampled noise m/z array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002746
name: MS-Numpress linear prediction compression followed by zlib compression
def: "Compression using MS-Numpress linear prediction compression and 
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002747
name: MS-Numpress positive integer compression followed by zlib compression
def: "Compression using MS-Numpress positive integer compression and 
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002748
name: MS-Numpress short logged float compression followed by zlib 
compression
def: "Compression using MS-Numpress short logged float compression and 
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002749
name: Mascot:IntegratedSpectralLibrarySearch
def: "Means that Mascot has integrated the search results of database 
and spectral library search into a single data set." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1002750
name: NIST MSPepSearch
def: "Search tool of the NIST (National Institute of Standrads and 
Technology) for spectral library searches." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002751
name: NIST MSP format
def: "MSP text format defined by the NIST." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1002752
name: database type spectral library
def: "Database containing spectra." [PSI:PI]
is_a: MS:1001073 ! database type

[Term]
id: MS:1002753
name: value between 0 and 1000 inclusive
def: "Value range for scores." [PSI:PI]
is_a: MS:1002304 ! domain range

[Term]
id: MS:1002754
name: MSPepSearch:score
def: "MSPepSearch score (0 for entirely dissimilar and 1000 for 
identical observed spectrum and library spectrum." [PSI:PI]
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002753 ! value between 0 and 1000 inclusive

[Term]
id: MS:1002755
name: combined ms-ms + spectral library search
def: "A combined MS2 (with fragment ions) and spectral library search." 
[PSI:PI]
is_a: MS:1001080 ! search type


Changed CV terms in version 4.0.9 of psi-ms.obo:
================================================
************ Changed web link to the new GitHub adress 
https://github.com/ms-numpress/ms-numpress
[Term]
id: MS:1002312
name: MS-Numpress linear prediction compression
def: "Compression using MS-Numpress linear prediction compression." 
[https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002313
name: MS-Numpress positive integer compression
def: "Compression using MS-Numpress positive integer compression." 
[https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002314
name: MS-Numpress short logged float compression
def: "Compression using MS-Numpress short logged float compression." 
[https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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] [Psidev-ms-dev] Release candidate 4.0.9_rc1 of psi-ms.obo

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

Thank you Gerhard. This is pretty good. I think I would like a little more
clarification on the noise terms. Some suggestions in red:



id: MS:1002742
name: noise array
def: "A data array of noise values." [PSI:MS]

id: MS:1002743
name: sampled noise m/z array
def: "A data array of parallel, independent m/z values for a sampling of
noise across a spectrum (typically much smaller than MS:1000514, the m/z
array)." [PSI:MS]

id: MS:1002744
name: sampled noise intensity array
def: "A data array of intensity values for the amplitude of noise variation
superposed on the baseline (MS:1002745) across a spectrum (for use with
MS:0002743, sampled noise m/z array)." [PSI:MS]

id: MS:1002745
name: sampled noise baseline array
def: "A data array of baseline intensity values (the intensity in the
absence of analytes) for a sampling of noise across a spectrum (for use
with MS:0002743, sampled noise m/z array)." [PSI:MS]

Does that clarify the intent accurately?



Thanks,

Eric





*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Tuesday, March 21, 2017 6:29 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* [Psidev-ms-dev] Release candidate 4.0.9_rc1 of psi-ms.obo



Dear proteomics community,

attached there's the release candidate 4.0.9_rc1 of the psi-ms.obo file.

It contains new terms for binary data arrays and their compression
and for spectral library searches.


New CV terms in version 4.0.9_rc1 of psi-ms.obo:
================================================
[Term]
id: MS:1002742
name: noise array
def: "A data array of noise values." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002743
name: sampled noise m/z array
def: "A data array of parallel, independent m/z values for a sampling of
noise across a spectrum (typically much smaller than MS:1000514, the m/z
array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1002744
name: sampled noise intensity array
def: "A data array of intensity values for a sampling of noise across a
spectrum (for use with MS:0000000, sampled noise m/z array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000131 ! number of detector counts

[Term]
id: MS:1002745
name: sampled noise baseline array
def: "A data array of signal baseline values (the signal in the absence of
analytes) for a sampling of noise across a spectrum (for use with
MS:0000000, sampled noise m/z array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002746
name: MS-Numpress linear prediction compression followed by zlib compression
def: "Compression using MS-Numpress linear prediction compression and
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002747
name: MS-Numpress positive integer compression followed by zlib compression
def: "Compression using MS-Numpress positive integer compression and zlib."
[https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002748
name: MS-Numpress short logged float compression followed by zlib
compression
def: "Compression using MS-Numpress short logged float compression and
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002749
name: Mascot:IntegratedSpectralLibrarySearch
def: "Means that Mascot has integrated the search results of database and
spectral library search into a single data set." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1002750
name: NIST MSPepSearch
def: "Search tool of the NIST (National Institute of Standrads and
Technology) for spectral library searches." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002751
name: NIST MSP format
def: "MSP text format defined by the NIST." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1002752
name: database type spectral library
def: "Database containing spectra." [PSI:PI]
is_a: MS:1001073 ! database type

[Term]
id: MS:1002753
name: value between 0 and 1000 inclusive
def: "Value range for scores." [PSI:PI]
is_a: MS:1002304 ! domain range

[Term]
id: MS:1002754
name: MSPepSearch:score
def: "MSPepSearch score (0 for entirely dissimilar and 1000 for identical
observed spectrum and library spectrum." [PSI:PI]
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002753 ! value between 0 and 1000 inclusive

[Term]
id: MS:1002755
name: combined ms-ms + spectral library search
def: "A combined MS2 (with fragment ions) and spectral library search."
[PSI:PI]
is_a: MS:1001080 ! search type


Changed CV terms in version 4.0.9_rc1 of psi-ms.obo:
====================================================
************ Changed web link to the new GitHub adress
https://github.com/ms-numpress/ms-numpress
[Term]
id: MS:1002312
name: MS-Numpress linear prediction compression
def: "Compression using MS-Numpress linear prediction compression." [
https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002313
name: MS-Numpress positive integer compression
def: "Compression using MS-Numpress positive integer compression." [
https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002314
name: MS-Numpress short logged float compression
def: "Compression using MS-Numpress short logged float compression." [
https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail *ger...@ru...

www.medizinisches-proteom-center.de

[Psidev-pi-dev] Release candidate 4.0.9_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 4.0.9_rc1 of the psi-ms.obo file.

It contains new terms for binary data arrays and their compression
and for spectral library searches.


New CV terms in version 4.0.9_rc1 of psi-ms.obo:
================================================
[Term]
id: MS:1002742
name: noise array
def: "A data array of noise values." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002743
name: sampled noise m/z array
def: "A data array of parallel, independent m/z values for a sampling of 
noise across a spectrum (typically much smaller than MS:1000514, the m/z 
array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1002744
name: sampled noise intensity array
def: "A data array of intensity values for a sampling of noise across a 
spectrum (for use with MS:0000000, sampled noise m/z array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000131 ! number of detector counts

[Term]
id: MS:1002745
name: sampled noise baseline array
def: "A data array of signal baseline values (the signal in the absence 
of analytes) for a sampling of noise across a spectrum (for use with 
MS:0000000, sampled noise m/z array)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002746
name: MS-Numpress linear prediction compression followed by zlib compression
def: "Compression using MS-Numpress linear prediction compression and 
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002747
name: MS-Numpress positive integer compression followed by zlib compression
def: "Compression using MS-Numpress positive integer compression and 
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002748
name: MS-Numpress short logged float compression followed by zlib 
compression
def: "Compression using MS-Numpress short logged float compression and 
zlib." [https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002749
name: Mascot:IntegratedSpectralLibrarySearch
def: "Means that Mascot has integrated the search results of database 
and spectral library search into a single data set." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1002750
name: NIST MSPepSearch
def: "Search tool of the NIST (National Institute of Standrads and 
Technology) for spectral library searches." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002751
name: NIST MSP format
def: "MSP text format defined by the NIST." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1002752
name: database type spectral library
def: "Database containing spectra." [PSI:PI]
is_a: MS:1001073 ! database type

[Term]
id: MS:1002753
name: value between 0 and 1000 inclusive
def: "Value range for scores." [PSI:PI]
is_a: MS:1002304 ! domain range

[Term]
id: MS:1002754
name: MSPepSearch:score
def: "MSPepSearch score (0 for entirely dissimilar and 1000 for 
identical observed spectrum and library spectrum." [PSI:PI]
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002753 ! value between 0 and 1000 inclusive

[Term]
id: MS:1002755
name: combined ms-ms + spectral library search
def: "A combined MS2 (with fragment ions) and spectral library search." 
[PSI:PI]
is_a: MS:1001080 ! search type


Changed CV terms in version 4.0.9_rc1 of psi-ms.obo:
====================================================
************ Changed web link to the new GitHub adress 
https://github.com/ms-numpress/ms-numpress
[Term]
id: MS:1002312
name: MS-Numpress linear prediction compression
def: "Compression using MS-Numpress linear prediction compression." 
[https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002313
name: MS-Numpress positive integer compression
def: "Compression using MS-Numpress positive integer compression." 
[https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002314
name: MS-Numpress short logged float compression
def: "Compression using MS-Numpress short logged float compression." 
[https://github.com/ms-numpress/ms-numpress]
is_a: MS:1000572 ! binary data compression type

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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] namespace in mzIdentML

[Witold E W. <wew...@gm...>]

Sorry if this is not the appropriate list but did not find any list
dedicated for users here: http://www.psidev.info/mailing-lists

I just have a brief question. I am trying to write the following
xpath/xquery statement

db:open("extracted","20160312_15_B1_myrimatch_2_2_140.mzid")/*:MzIdentML/*:SequenceCollection/*:Peptide

and would like to be more specific about the namespace than to use the *.

However, namespaces  are not mentioned even once in the
http://www.psidev.info/sites/default/files/mzIdentML1.1.0.pdf

Thanks

[Psidev-pi-dev] REVISED VERSION R1: PSI recommendation document (file format proBed), 14-days public review

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

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

I received a revised version (R1) of the proBed format specification:

http://www.psidev.info/proBed-in-docproc

A “responses to reviewers” document is also included.

 

It would be great to receive your comments within two 

weeks (13th March 2017).

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBed-in-docproc) 

(or send them directly to martin.eisenacher: at : rub.de) for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

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

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

 



 

 

 

Von: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Donnerstag, 20. Oktober 2016 11:11
An: psi...@li...;
psi...@li...; psi...@li...;
ps...@eb...; psi...@eb...
Betreff: [Psidev-qc-dev] PSI recommendation document (file format proBed),
60-days public review

 

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

 <http://www.psidev.info> http://www.psidev.info for an overview of
activities).

 

A recommendation document specifying the proBed file format

has been submitted to the PSI document process.

The submission can be found here:

http://www.psidev.info/proBed-in-docproc

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 19th December 2016).

 

"The format represents systematically the output of proteogenomics

analyses, by mapping peptide identification data retrieved from 

mass spectrometry (MS)-based experiments to the genome."

(see also Cover Letter attached to the submission page)

 

The format is based on the BED format (Browser Extensive Data,

 <https://genome.ucsc.edu/FAQ/FAQformat.html#format1>
https://genome.ucsc.edu/FAQ/FAQformat.html#format1),

developed by the UCSC (University of California, Santa Cruz) team.

 

The public comment period enables the wider community to provide 

feedback on a proposed standard before it is formally accepted, and 

thus is an important step in the standardisation process.

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBed-in-docproc) 

(or send them directly to martin.eisenacher: at : rub.de) for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

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

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

 



 

Re: [Psidev-pi-dev] mzIdentML 1.2.0 - determining "donor" of cross-linked peptide

[walzer <wa...@in...>]

Dear all,

in light of some ongoing discussion about developer's adoption of mzid, 
I'd thought I bring that up for the upcoming PSI meeting. Maybe we could 
find some time to plan or start a information/PR campaign for mzid (and 
mzq and their future) .

[source] https://github.com/OpenMS/OpenMS/issues/2406#issuecomment-279343474

best,
   Mathias

Re: [Psidev-pi-dev] How stable is the psi-ms.obo URL?

[Ville K. <vi...@ma...>]

Hello Eric,

it sounds like the best we can do in Mascot is to use the latest URL at
the time of releasing the software and keep an eye on the URL for
future revisions. It's unfortunate there isn't a permanent URL
redirection in place, something like http://psidev.info/psi-ms.obo,
that would always point to the latest file.

Regards,
Ville

On Wed, 2017-02-15 at 21:55 -0800, Eric Deutsch wrote:
> Hi Ville, you're right that this CV has seen quite a lot of changes
> recently. This was mostly triggered by the close of Google Code and
> our
> decision to consolidate on GitHub. I think it is very likely that the
> current location will not change again for a long time unless there
> is
> some problem with GitHub.
> 
> I think it is generally intended that readers would use those URIs to
> fetch the ontologies that are referenced, so it is important that the
> URIs
> be correct. That said, I think it is also true that the MS CV is so
> central to most readers and writers of PSI formats that it would be
> common
> for that software to use its internal version of the MS CV, and not
> make
> use of that URI. For example, I think ProteoWizard compiles the
> latest MS
> CV into its source code and does not fetch it from the URI in the
> file. So
> I think it's a bit more important for the CVs other than the MS CV to
> have
> the URI right.
> 
> I think you can find the latest recommended URIs for the CVs in the
> example files at:
> https://github.com/HUPO-PSI/mzIdentML/tree/master/examples/1_2example
> s
> 
> I hope they're consistent.. From the PeptideShaker example:
>        <cv id="PSI-MS"
> uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-
> ms.ob
> o" fullName="PSI-MS"/>
>        <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo"
> fullName="UNIMOD"/>
>        <cv id="UO"
> uri="https://raw.githubusercontent.com/bio-ontology-research-group/un
> it-on
> tology/master/unit.obo" fullName="UNIT-ONTOLOGY"/>
>        <cv id="PRIDE"
> uri="https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pr
> ide_c
> v.obo" fullName="PRIDE"/>
> 
> I notice already one little issue is that sometimes we use the
> raw.githubusercontent form and sometimes the blob form. I don't know
> which
> is preferred, but we should probably just pick one. I think they're
> equivalent, although not sure.
> 
> Regards,
> Eric
> 
> 
> -----Original Message-----
> From: Ville Koskinen [mailto:vi...@ma...]
> Sent: Wednesday, February 15, 2017 3:49 AM
> To: psi...@li...
> Subject: [Psidev-pi-dev] How stable is the psi-ms.obo URL?
> 
> Dear list,
> 
> before moving to GitHub, the psi-ms.obo file's URL was
> 
> http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psims/
> mzML/
> controlledVocabulary/psi-ms.obo
> 
> The URL appears in a number of mzIdentML example files, of course, as
> well
> as the 1.1.0 specification document. But the current URL is now
> 
> https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo
> 
> Should newly exported mzIdentML files use the new URL or keep the old
> URL?
> How stable is the new URL? For example, in October 2015 the new URL
> was
> 
> https://github.com/HUPO-PSI/mzML/blob/master/cv/psi-ms.obo
> 
> but that's of course now dated.
> 
> Or does it make any difference what URL is output in the mzIdentML
> file?
> The mzIdentML 1.1.0 specification for the <cv> element states the uri
> attribute is the "URI of the source CV", but doesn't say whether this
> is
> for the usual namespace purposes (uniform resource
> *identifier*) or for the reader of the file to locate the .obo file
> (uniform resource *locator*). If it's a true URI, is there a table
> somewhere that records what URIs each type of CV should have?
> 
> 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...
> http://www.matrixscience.com
> 
> Matrix Science Ltd. is registered in England and Wales Company number
> 3533898
> 
> -------------------------------------------------------------------
> -------
> ----
> Check out the vibrant tech community on one of the world's most
> engaging
> tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
-- 
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...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898 

Re: [Psidev-pi-dev] How stable is the psi-ms.obo URL?

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

Hi Ville, you're right that this CV has seen quite a lot of changes
recently. This was mostly triggered by the close of Google Code and our
decision to consolidate on GitHub. I think it is very likely that the
current location will not change again for a long time unless there is
some problem with GitHub.

I think it is generally intended that readers would use those URIs to
fetch the ontologies that are referenced, so it is important that the URIs
be correct. That said, I think it is also true that the MS CV is so
central to most readers and writers of PSI formats that it would be common
for that software to use its internal version of the MS CV, and not make
use of that URI. For example, I think ProteoWizard compiles the latest MS
CV into its source code and does not fetch it from the URI in the file. So
I think it's a bit more important for the CVs other than the MS CV to have
the URI right.

I think you can find the latest recommended URIs for the CVs in the
example files at:
https://github.com/HUPO-PSI/mzIdentML/tree/master/examples/1_2examples

I hope they're consistent.. From the PeptideShaker example:
       <cv id="PSI-MS"
uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.ob
o" fullName="PSI-MS"/>
       <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo"
fullName="UNIMOD"/>
       <cv id="UO"
uri="https://raw.githubusercontent.com/bio-ontology-research-group/unit-on
tology/master/unit.obo" fullName="UNIT-ONTOLOGY"/>
       <cv id="PRIDE"
uri="https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pride_c
v.obo" fullName="PRIDE"/>

I notice already one little issue is that sometimes we use the
raw.githubusercontent form and sometimes the blob form. I don't know which
is preferred, but we should probably just pick one. I think they're
equivalent, although not sure.

Regards,
Eric


-----Original Message-----
From: Ville Koskinen [mailto:vi...@ma...]
Sent: Wednesday, February 15, 2017 3:49 AM
To: psi...@li...
Subject: [Psidev-pi-dev] How stable is the psi-ms.obo URL?

Dear list,

before moving to GitHub, the psi-ms.obo file's URL was

http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psims/mzML/
controlledVocabulary/psi-ms.obo

The URL appears in a number of mzIdentML example files, of course, as well
as the 1.1.0 specification document. But the current URL is now

https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo

Should newly exported mzIdentML files use the new URL or keep the old URL?
How stable is the new URL? For example, in October 2015 the new URL was

https://github.com/HUPO-PSI/mzML/blob/master/cv/psi-ms.obo

but that's of course now dated.

Or does it make any difference what URL is output in the mzIdentML file?
The mzIdentML 1.1.0 specification for the <cv> element states the uri
attribute is the "URI of the source CV", but doesn't say whether this is
for the usual namespace purposes (uniform resource
*identifier*) or for the reader of the file to locate the .obo file
(uniform resource *locator*). If it's a true URI, is there a table
somewhere that records what URIs each type of CV should have?

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...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales Company number
3533898

--------------------------------------------------------------------------
----
Check out the vibrant tech community on one of the world's most engaging
tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

[Psidev-pi-dev] How stable is the psi-ms.obo URL?

[Ville K. <vi...@ma...>]

Dear list,

before moving to GitHub, the psi-ms.obo file's URL was

http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psims/mzML/controlledVocabulary/psi-ms.obo

The URL appears in a number of mzIdentML example files, of course, as
well as the 1.1.0 specification document. But the current URL is now

https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo

Should newly exported mzIdentML files use the new URL or keep the old
URL? How stable is the new URL? For example, in October 2015 the new
URL was

https://github.com/HUPO-PSI/mzML/blob/master/cv/psi-ms.obo

but that's of course now dated.

Or does it make any difference what URL is output in the mzIdentML
file? The mzIdentML 1.1.0 specification for the <cv> element states the
uri attribute is the "URI of the source CV", but doesn't say whether
this is for the usual namespace purposes (uniform resource
*identifier*) or for the reader of the file to locate the .obo file
(uniform resource *locator*). If it's a true URI, is there a table
somewhere that records what URIs each type of CV should have?

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...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898 

[Psidev-pi-dev] New version 4.0.8 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 4.0.8 of the psi-ms.obo file.
It contains two new terms for proteogenomics.


New CV terms in version 4.0.8 of psi-ms.obo:
============================================
[Term]
id: MS:1002740
name: unmapped peptide
def: "Within the context of a proteogenomics approach, a peptide 
sequence that has not been mapped to a genomic location." [PSI:PI]
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002741
name: unmapped protein
def: "Within the context of a proteogenomics approach, a protein 
sequence that has not been mapped to a genomic location." [PSI:PI]
is_a: MS:1002636 ! proteogenomics attribute

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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] FW: ProteoAnnotator_1_2.mzid

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

Hi all,

I think on balance we should go with option 2, and add the following new terms to the CV:

Term: “unmapped peptide”
Def: Within the context of a proteogenomics approach, a peptide sequence that has not been mapped to a genomic location
is_a: MS:1002636 ! proteogenomics attribute

Term: “unmapped protein”
Def: Within the context of a proteogenomics approach, a protein sequence that has not been mapped to a genomic location
is_a: MS:1002636 ! proteogenomics attribute

Please shout if you’d like to change these, otherwise we will update the specs (say by the end of the week) and the validator.

Best wishes
Andy



From: mayerg97 [mailto:ger...@ru...]
Sent: 01 February 2017 08:00
To: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: ProteoAnnotator_1_2.mzid


Hi all,

from the validation side, it makes not much difference, if option 1 or 2 is choosen,
but option 2 is much clearer to read.

Cheers,
Gerhard

Am 31.01.2017 um 16:20 schrieb Jones, Andy:
Hi all,

The validation of proteogenomics example files has revealed a minor flaw in the proteogenomics specs. We use a MUST rule that says every peptide and protein that is not a decoy must state its genomic location. This doesn’t make sense for two reasons:


-          Some peptides may have been  identified but not mappable to a chromosome, due to the approach taken i.e. the protein database and gene models are not consistent for sensible reasons

-          As we have done, we have a merged result file from hits to Ensembl and Uniprot (Uniprot hits are not mapped).

Solutions:


1.      Relax the MUST rule, to say that CV terms should be added for all mapped peptides/proteins.

a.       Downside: hard to encode this logic in the validator

2.      Introduce another CV term for “unmapped peptide” and “unmapped protein” to cater for this case explicitly.

Option 2 seems more formally sensible, but makes more work for data exporters to add CV terms to every peptide/protein, even if they only intended to map one subset.

If possible, can people give opinions fairly quickly. We now have a time pressure to get MCP paper resubmitted within around 2 weeks otherwise it is a new submission.

Best wishes
Andy




From: mayerg97 [mailto:ger...@ru...]
Sent: 26 January 2017 13:33
To: Jones, Andy <jo...@li...><mailto:jo...@li...>; Ghali, Fawaz <fg...@li...><mailto:fg...@li...>
Subject: Re: ProteoAnnotator_1_2.mzid


Hi Fawaz and Andy,

e.g.
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000004093|" id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>

is referenced by

  <PeptideEvidence dBSequence_ref="dbseq_generic|B_GENSCAN00000004093|" peptide_ref="FAALDNEEEDK_" start="241" end="251" pre="K" post="E" isDecoy="false" id="FAALDNEEEDK_generic|B_GENSCAN00000004093|_241_251"></PeptideEvidence>

but this PeptideEvidence is not a decoy and has also no genome mapping information defined,
but the specification document defines in Figure 5 that the CV terms must be present on every PeptideEvidence, unless ifDecoy="true"

Best wishes,
Gerhard


Am 26.01.2017 um 13:52 schrieb mayerg97:

Hi Fawaz and Andy,

it's because there are DBSequences contained, which have no genome mapping defined, e.g.

  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000004093|" id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000027223|" id="dbseq_generic|B_GENSCAN00000027223|"></DBSequence>
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000009965|" id="dbseq_generic|B_GENSCAN00000009965|"></DBSequence>
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000034417|" id="dbseq_generic|B_GENSCAN00000034417|"></DBSequence>

If we want to allow here both sequences with and without genome mapping, we can change the

ProteogenomicsDBSequence_must_rule
into a SHOULD rule instead.

Best wishes,
Gerhard


Am 26.01.2017 um 13:14 schrieb Jones, Andy:

Hi Fawaz,



I don't see anything wrong with this - Gerhard, do you have any ideas?

Thanks

Andy



-----Original Message-----

From: Ghali, Fawaz

Sent: 26 January 2017 11:55

To: Jones, Andy <jo...@li...><mailto:jo...@li...>

Subject: ProteoAnnotator_1_2.mzid



Hi Andy,





ProteoAnnotator_1_2.mzid has an error:



Message 1:

    Rule ID: ProteogenomicsDBSequence_must_rule

    Level: ERROR

    Context(/cvParam/@accession ) in 380 locations

    --> None of the given CvTerms were found at '/MzIdentML/SequenceCollection/DBSequence/cvParam/@accession' because no values were found:

  - The sole term MS:1002637 (chromosome name) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.

  - The sole term MS:1002638 (chromosome strand) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.

  - The sole term MS:1002644 (genome reference version) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.







Example:



  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|A_ENSP00000395953|" id="dbseq_generic|A_ENSP00000395953|">

    <cvParam cvRef="PSI-MS" accession="MS:1002637" name="chromosome name" value="11"></cvParam>

    <cvParam cvRef="PSI-MS" accession="MS:1002638" name="chromosome strand" value="+"></cvParam>

    <cvParam cvRef="PSI-MS" accession="MS:1002644" name="genome reference version" value="Homo_sapiens.GRCh38.77.gff3"></cvParam>

  </DBSequence>







Why it's complaining about the name?







Best wishes,

Fawaz

--

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

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

PhD student

Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-21006 | 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.049a | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554

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

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

PhD student

Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-21006 | 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] FW: ProteoAnnotator_1_2.mzid

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

Hi all,

from the validation side, it makes not much difference, if option 1 or 2 
is choosen,
but option 2 is much clearer to read.

Cheers,
Gerhard


Am 31.01.2017 um 16:20 schrieb Jones, Andy:
>
> Hi all,
>
> The validation of proteogenomics example files has revealed a minor 
> flaw in the proteogenomics specs. We use a MUST rule that says every 
> peptide and protein that is not a decoy must state its genomic 
> location. This doesn’t make sense for two reasons:
>
> -Some peptides may have been  identified but not mappable to a 
> chromosome, due to the approach taken i.e. the protein database and 
> gene models are not consistent for sensible reasons
>
> -As we have done, we have a merged result file from hits to Ensembl 
> and Uniprot (Uniprot hits are not mapped).
>
> Solutions:
>
> 1.Relax the MUST rule, to say that CV terms should be added for all 
> mapped peptides/proteins.
>
> a.Downside: hard to encode this logic in the validator
>
> 2.Introduce another CV term for “unmapped peptide” and “unmapped 
> protein” to cater for this case explicitly.
>
> Option 2 seems more formally sensible, but makes more work for data 
> exporters to add CV terms to every peptide/protein, even if they only 
> intended to map one subset.
>
> If possible, can people give opinions fairly quickly. We now have a 
> time pressure to get MCP paper resubmitted within around 2 weeks 
> otherwise it is a new submission.
>
> Best wishes
>
> Andy
>
> *From:*mayerg97 [mailto:ger...@ru...]
> *Sent:* 26 January 2017 13:33
> *To:* Jones, Andy <jo...@li...>; Ghali, Fawaz 
> <fg...@li...>
> *Subject:* Re: ProteoAnnotator_1_2.mzid
>
> Hi Fawaz and Andy,
>
> e.g.
>
> <DBSequence searchDatabase_ref="SearchDB_1" 
> accession="generic|B_GENSCAN00000004093|" 
> id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>
>
> is referenced by
>
>   <PeptideEvidence 
> dBSequence_ref="dbseq_generic|B_GENSCAN00000004093|" 
> peptide_ref="FAALDNEEEDK_" start="241" end="251" pre="K" post="E" 
> isDecoy="false" 
> id="FAALDNEEEDK_generic|B_GENSCAN00000004093|_241_251"></PeptideEvidence>
>
> but this PeptideEvidence is not a decoy and has also no genome mapping 
> information defined,
> but the specification document defines in Figure 5 that the CV terms 
> must be present on every PeptideEvidence, unless ifDecoy="true"
>
> Best wishes,
> Gerhard
>
> Am 26.01.2017 um 13:52 schrieb mayerg97:
>
>     Hi Fawaz and Andy,
>
>     it's because there are DBSequences contained, which have no genome
>     mapping defined, e.g.
>
>       <DBSequence searchDatabase_ref="SearchDB_1"
>     accession="generic|B_GENSCAN00000004093|"
>     id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>
>       <DBSequence searchDatabase_ref="SearchDB_1"
>     accession="generic|B_GENSCAN00000027223|"
>     id="dbseq_generic|B_GENSCAN00000027223|"></DBSequence>
>       <DBSequence searchDatabase_ref="SearchDB_1"
>     accession="generic|B_GENSCAN00000009965|"
>     id="dbseq_generic|B_GENSCAN00000009965|"></DBSequence>
>       <DBSequence searchDatabase_ref="SearchDB_1"
>     accession="generic|B_GENSCAN00000034417|"
>     id="dbseq_generic|B_GENSCAN00000034417|"></DBSequence>
>
>     If we want to allow here both sequences with and without genome
>     mapping, we can change the
>
>     ProteogenomicsDBSequence_must_rule
>
>     into a SHOULD rule instead.
>
>     Best wishes,
>     Gerhard
>
>     Am 26.01.2017 um 13:14 schrieb Jones, Andy:
>
>         Hi Fawaz,
>
>         I don't see anything wrong with this - Gerhard, do you have any ideas?
>
>         Thanks
>
>         Andy
>
>         -----Original Message-----
>
>         From: Ghali, Fawaz
>
>         Sent: 26 January 2017 11:55
>
>         To: Jones, Andy<jo...@li...> <mailto:jo...@li...>
>
>         Subject: ProteoAnnotator_1_2.mzid
>
>         Hi Andy,
>
>         ProteoAnnotator_1_2.mzid has an error:
>
>         Message 1:
>
>              Rule ID: ProteogenomicsDBSequence_must_rule
>
>              Level: ERROR
>
>              Context(/cvParam/@accession ) in 380 locations
>
>              --> None of the given CvTerms were found at '/MzIdentML/SequenceCollection/DBSequence/cvParam/@accession' because no values were found:
>
>            - The sole term MS:1002637 (chromosome name) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>
>            - The sole term MS:1002638 (chromosome strand) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>
>            - The sole term MS:1002644 (genome reference version) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>
>         Example:
>
>            <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|A_ENSP00000395953|" id="dbseq_generic|A_ENSP00000395953|">
>
>              <cvParam cvRef="PSI-MS" accession="MS:1002637" name="chromosome name" value="11"></cvParam>
>
>              <cvParam cvRef="PSI-MS" accession="MS:1002638" name="chromosome strand" value="+"></cvParam>
>
>              <cvParam cvRef="PSI-MS" accession="MS:1002644" name="genome reference version" value="Homo_sapiens.GRCh38.77.gff3"></cvParam>
>
>            </DBSequence>
>
>         Why it's complaining about the name?
>
>         Best wishes,
>
>         Fawaz
>
>     -- 
>
>     *--------------------------------------------------------------------*
>
>     *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
>     *PhD student*
>
>     *Medizinisches Proteom-Center*
>
>     *DEPARTMENT Medical Bioinformatics*
>
>     *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
>
>     *Fon *+49 (0)234 32-21006 | *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.049a | Universitätsstraße 150 | D-44801 Bochum
>
> *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554
>
> *E-mail *ger...@ru... <mailto:ger...@ru...>
>
> www.medizinisches-proteom-center.de 
> <http://www.medizinisches-proteom-center.de/>
>
> ------------------------------------------------------------------------
>
> No virus found in this message.
> Checked by AVG - www.avg.com <http://www.avg.com/email-signature>
> Version: 2016.0.7998 / Virus Database: 4749/13832 - Release Date: 01/25/17
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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] ProteoAnnotator_1_2.mzid

[Gerben M. <ger...@gm...>]

Hi all,

I would also choose option 2. Because of multiple reasons identified
peptides can be not mappable (mutations, indels, differences between used
search space and genomic annotation, etc...).
The "unmapped" feature is something being used in the the proteogenomics
formats (proBAM and proBed) as well. See descriptions on the psi-dev
websites (http://www.psidev.info/proBAM and http://www.psidev.info/probed).
These CV's could be introduces there as well.

Cheers,
Gerben


On Tue, Jan 31, 2017 at 6:26 PM, Juan Antonio Vizcaino <ju...@eb...>
wrote:

> Hi all,
>
> On 31 Jan 2017, at 15:20, Jones, Andy <And...@li...>
> wrote:
>
> Hi all,
>
> The validation of proteogenomics example files has revealed a minor flaw
> in the proteogenomics specs. We use a MUST rule that says every peptide and
> protein that is not a decoy must state its genomic location. This doesn’t
> make sense for two reasons:
>
> -          Some peptides may have been  identified but not mappable to a
> chromosome, due to the approach taken i.e. the protein database and gene
> models are not consistent for sensible reasons
> -          As we have done, we have a merged result file from hits to
> Ensembl and Uniprot (Uniprot hits are not mapped).
>
> Solutions:
>
> 1.       Relax the MUST rule, to say that CV terms should be added for
> all mapped peptides/proteins.
> a.       Downside: hard to encode this logic in the validator
> 2.       Introduce another CV term for “unmapped peptide” and “unmapped
> protein” to cater for this case explicitly.
>
> Option 2 seems more formally sensible, but makes more work for data
> exporters to add CV terms to every peptide/protein, even if they only
> intended to map one subset.
>
> If possible, can people give opinions fairly quickly. We now have a time
> pressure to get MCP paper resubmitted within around 2 weeks otherwise it is
> a new submission.
>
>
> I would support option 2. It is more consistent and makes life easier for
> readers. Also, in most usual use cases (at least for the best annotated
> genomes), the number of unmapped peptides should be low.
>
> Cheers,
>
> Juan
>
>
>
>
>
> Best wishes
> Andy
>
>
>
>
> *From:* mayerg97 [mailto:ger...@ru... <ger...@ru...>]
> *Sent:* 26 January 2017 13:33
> *To:* Jones, Andy <jo...@li...>; Ghali, Fawaz <
> fg...@li...>
> *Subject:* Re: ProteoAnnotator_1_2.mzid
>
>
> Hi Fawaz and Andy,
>
> e.g.
>
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000004093|"
> id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>
>
> is referenced by
>
>   <PeptideEvidence dBSequence_ref="dbseq_generic|B_GENSCAN00000004093|"
> peptide_ref="FAALDNEEEDK_" start="241" end="251" pre="K" post="E"
> isDecoy="false" id="FAALDNEEEDK_generic|B_GENSCAN00000004093|_241_251"><
> /PeptideEvidence>
>
> but this PeptideEvidence is not a decoy and has also no genome mapping
> information defined,
> but the specification document defines in Figure 5 that the CV terms must
> be present on every PeptideEvidence, unless ifDecoy="true"
>
> Best wishes,
> Gerhard
>
> Am 26.01.2017 um 13:52 schrieb mayerg97:
>
> Hi Fawaz and Andy,
>
> it's because there are DBSequences contained, which have no genome mapping
> defined, e.g.
>
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000004093|"
> id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000027223|"
> id="dbseq_generic|B_GENSCAN00000027223|"></DBSequence>
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000009965|"
> id="dbseq_generic|B_GENSCAN00000009965|"></DBSequence>
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000034417|"
> id="dbseq_generic|B_GENSCAN00000034417|"></DBSequence>
>
> If we want to allow here both sequences with and without genome mapping,
> we can change the
>
> ProteogenomicsDBSequence_must_rule
>
> into a SHOULD rule instead.
>
> Best wishes,
> Gerhard
>
> Am 26.01.2017 um 13:14 schrieb Jones, Andy:
>
> Hi Fawaz,
>
>
>
> I don't see anything wrong with this - Gerhard, do you have any ideas?
>
> Thanks
>
> Andy
>
>
>
> -----Original Message-----
>
> From: Ghali, Fawaz
>
> Sent: 26 January 2017 11:55
>
> To: Jones, Andy <jo...@li...> <jo...@li...>
>
> Subject: ProteoAnnotator_1_2.mzid
>
>
>
> Hi Andy,
>
>
>
>
>
> ProteoAnnotator_1_2.mzid has an error:
>
>
>
> Message 1:
>
>     Rule ID: ProteogenomicsDBSequence_must_rule
>
>     Level: ERROR
>
>     Context(/cvParam/@accession ) in 380 locations
>
>     --> None of the given CvTerms were found at '/MzIdentML/SequenceCollection/DBSequence/cvParam/@accession' because no values were found:
>
>   - The sole term MS:1002637 (chromosome name) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>
>   - The sole term MS:1002638 (chromosome strand) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>
>   - The sole term MS:1002644 (genome reference version) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>
>
>
>
>
>
>
> Example:
>
>
>
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|A_ENSP00000395953|" id="dbseq_generic|A_ENSP00000395953|">
>
>     <cvParam cvRef="PSI-MS" accession="MS:1002637" name="chromosome name" value="11"></cvParam>
>
>     <cvParam cvRef="PSI-MS" accession="MS:1002638" name="chromosome strand" value="+"></cvParam>
>
>     <cvParam cvRef="PSI-MS" accession="MS:1002644" name="genome reference version" value="Homo_sapiens.GRCh38.77.gff3"></cvParam>
>
>   </DBSequence>
>
>
>
>
>
>
>
> Why it's complaining about the name?
>
>
>
>
>
>
>
> Best wishes,
>
> Fawaz
>
>
> --
>
> *--------------------------------------------------------------------*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
> *PhD student*
>
> *Medizinisches Proteom-Center*
>
> *DEPARTMENT Medical Bioinformatics*
>
> *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
>
> *Fon *+49 (0)234 32-21006 <+49%20234%203221006> | *Fax *+49 (0)234
> 32-14554 <+49%20234%203214554>
>
> *E-mail *ger...@ru...
>
> www.medizinisches-proteom-center.de
>
>
> --
>
> *--------------------------------------------------------------------*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
> *PhD student*
>
> *Medizinisches Proteom-Center*
>
> *DEPARTMENT Medical Bioinformatics*
>
> *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
>
> *Fon *+49 (0)234 32-21006 <+49%20234%203221006> | *Fax *+49 (0)234
> 32-14554 <+49%20234%203214554>
>
> *E-mail *ger...@ru...
>
> www.medizinisches-proteom-center.de
> ------------------------------
> No virus found in this message.
> Checked by AVG - www.avg.com <http://www.avg.com/email-signature>
> Version: 2016.0.7998 / Virus Database: 4749/13832 - Release Date: 01/25/17
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org <http://slashdot.org/>! http://
> sdm.link/slashdot_______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>
>

Re: [Psidev-pi-dev] ProteoAnnotator_1_2.mzid

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

Hi all,

> On 31 Jan 2017, at 15:20, Jones, Andy <And...@li...> wrote:
> 
> Hi all,
>  
> The validation of proteogenomics example files has revealed a minor flaw in the proteogenomics specs. We use a MUST rule that says every peptide and protein that is not a decoy must state its genomic location. This doesn’t make sense for two reasons:
>  
> -          Some peptides may have been  identified but not mappable to a chromosome, due to the approach taken i.e. the protein database and gene models are not consistent for sensible reasons
> -          As we have done, we have a merged result file from hits to Ensembl and Uniprot (Uniprot hits are not mapped).
>  
> Solutions:
>  
> 1.       Relax the MUST rule, to say that CV terms should be added for all mapped peptides/proteins.
> a.       Downside: hard to encode this logic in the validator
> 2.       Introduce another CV term for “unmapped peptide” and “unmapped protein” to cater for this case explicitly.
>  
> Option 2 seems more formally sensible, but makes more work for data exporters to add CV terms to every peptide/protein, even if they only intended to map one subset.
>  
> If possible, can people give opinions fairly quickly. We now have a time pressure to get MCP paper resubmitted within around 2 weeks otherwise it is a new submission.

I would support option 2. It is more consistent and makes life easier for readers. Also, in most usual use cases (at least for the best annotated genomes), the number of unmapped peptides should be low.

Cheers,

Juan




>  
> Best wishes
> Andy
>  
>  
>  
>  
> From: mayerg97 [mailto:ger...@ru... <mailto:ger...@ru...>] 
> Sent: 26 January 2017 13:33
> To: Jones, Andy <jo...@li... <mailto:jo...@li...>>; Ghali, Fawaz <fg...@li... <mailto:fg...@li...>>
> Subject: Re: ProteoAnnotator_1_2.mzid
>  
> Hi Fawaz and Andy,
> 
> e.g. 
> 
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000004093|" id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>
> 
> is referenced by 
> 
>   <PeptideEvidence dBSequence_ref="dbseq_generic|B_GENSCAN00000004093|" peptide_ref="FAALDNEEEDK_" start="241" end="251" pre="K" post="E" isDecoy="false" id="FAALDNEEEDK_generic|B_GENSCAN00000004093|_241_251"></PeptideEvidence>
> 
> but this PeptideEvidence is not a decoy and has also no genome mapping information defined,
> but the specification document defines in Figure 5 that the CV terms must be present on every PeptideEvidence, unless ifDecoy="true"
> 
> Best wishes,
> Gerhard
> 
> 
> Am 26.01.2017 um 13:52 schrieb mayerg97:
> Hi Fawaz and Andy,
> 
> it's because there are DBSequences contained, which have no genome mapping defined, e.g.
> 
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000004093|" id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000027223|" id="dbseq_generic|B_GENSCAN00000027223|"></DBSequence>
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000009965|" id="dbseq_generic|B_GENSCAN00000009965|"></DBSequence>
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000034417|" id="dbseq_generic|B_GENSCAN00000034417|"></DBSequence>
> 
> If we want to allow here both sequences with and without genome mapping, we can change the
> 
> ProteogenomicsDBSequence_must_rule
> into a SHOULD rule instead.
> 
> Best wishes,
> Gerhard
> 
> 
> Am 26.01.2017 um 13:14 schrieb Jones, Andy:
> Hi Fawaz,
>  
> I don't see anything wrong with this - Gerhard, do you have any ideas?
> Thanks
> Andy 
>  
> -----Original Message-----
> From: Ghali, Fawaz 
> Sent: 26 January 2017 11:55
> To: Jones, Andy <jo...@li...> <mailto:jo...@li...>
> Subject: ProteoAnnotator_1_2.mzid
>  
> Hi Andy,
>  
>  
> ProteoAnnotator_1_2.mzid has an error:
>  
> Message 1:
>     Rule ID: ProteogenomicsDBSequence_must_rule
>     Level: ERROR
>     Context(/cvParam/@accession ) in 380 locations
>     --> None of the given CvTerms were found at '/MzIdentML/SequenceCollection/DBSequence/cvParam/@accession' because no values were found:
>   - The sole term MS:1002637 (chromosome name) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>   - The sole term MS:1002638 (chromosome strand) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>   - The sole term MS:1002644 (genome reference version) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>  
>  
>  
> Example:
>  
>   <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|A_ENSP00000395953|" id="dbseq_generic|A_ENSP00000395953|">
>     <cvParam cvRef="PSI-MS" accession="MS:1002637" name="chromosome name" value="11"></cvParam>
>     <cvParam cvRef="PSI-MS" accession="MS:1002638" name="chromosome strand" value="+"></cvParam>
>     <cvParam cvRef="PSI-MS" accession="MS:1002644" name="genome reference version" value="Homo_sapiens.GRCh38.77.gff3"></cvParam>
>   </DBSequence>
>  
>  
>  
> Why it's complaining about the name?
>  
>  
>  
> Best wishes,
> Fawaz
>  
> -- 
> --------------------------------------------------------------------
> 
> Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER
> 
> PhD student
> 
> Medizinisches Proteom-Center
> 
> DEPARTMENT Medical Bioinformatics
> 
> Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
> 
> Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554
> 
> E-mail ger...@ru... <mailto:ger...@ru...>
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[Psidev-pi-dev] FW: ProteoAnnotator_1_2.mzid

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

Hi all,

The validation of proteogenomics example files has revealed a minor flaw in the proteogenomics specs. We use a MUST rule that says every peptide and protein that is not a decoy must state its genomic location. This doesn’t make sense for two reasons:


-          Some peptides may have been  identified but not mappable to a chromosome, due to the approach taken i.e. the protein database and gene models are not consistent for sensible reasons

-          As we have done, we have a merged result file from hits to Ensembl and Uniprot (Uniprot hits are not mapped).

Solutions:


1.       Relax the MUST rule, to say that CV terms should be added for all mapped peptides/proteins.

a.       Downside: hard to encode this logic in the validator

2.       Introduce another CV term for “unmapped peptide” and “unmapped protein” to cater for this case explicitly.

Option 2 seems more formally sensible, but makes more work for data exporters to add CV terms to every peptide/protein, even if they only intended to map one subset.

If possible, can people give opinions fairly quickly. We now have a time pressure to get MCP paper resubmitted within around 2 weeks otherwise it is a new submission.

Best wishes
Andy




From: mayerg97 [mailto:ger...@ru...]
Sent: 26 January 2017 13:33
To: Jones, Andy <jo...@li...>; Ghali, Fawaz <fg...@li...>
Subject: Re: ProteoAnnotator_1_2.mzid


Hi Fawaz and Andy,

e.g.
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000004093|" id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>

is referenced by

  <PeptideEvidence dBSequence_ref="dbseq_generic|B_GENSCAN00000004093|" peptide_ref="FAALDNEEEDK_" start="241" end="251" pre="K" post="E" isDecoy="false" id="FAALDNEEEDK_generic|B_GENSCAN00000004093|_241_251"></PeptideEvidence>

but this PeptideEvidence is not a decoy and has also no genome mapping information defined,
but the specification document defines in Figure 5 that the CV terms must be present on every PeptideEvidence, unless ifDecoy="true"

Best wishes,
Gerhard

Am 26.01.2017 um 13:52 schrieb mayerg97:

Hi Fawaz and Andy,

it's because there are DBSequences contained, which have no genome mapping defined, e.g.

  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000004093|" id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000027223|" id="dbseq_generic|B_GENSCAN00000027223|"></DBSequence>
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000009965|" id="dbseq_generic|B_GENSCAN00000009965|"></DBSequence>
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000034417|" id="dbseq_generic|B_GENSCAN00000034417|"></DBSequence>

If we want to allow here both sequences with and without genome mapping, we can change the

ProteogenomicsDBSequence_must_rule
into a SHOULD rule instead.

Best wishes,
Gerhard

Am 26.01.2017 um 13:14 schrieb Jones, Andy:

Hi Fawaz,



I don't see anything wrong with this - Gerhard, do you have any ideas?

Thanks

Andy



-----Original Message-----

From: Ghali, Fawaz

Sent: 26 January 2017 11:55

To: Jones, Andy <jo...@li...><mailto:jo...@li...>

Subject: ProteoAnnotator_1_2.mzid



Hi Andy,





ProteoAnnotator_1_2.mzid has an error:



Message 1:

    Rule ID: ProteogenomicsDBSequence_must_rule

    Level: ERROR

    Context(/cvParam/@accession ) in 380 locations

    --> None of the given CvTerms were found at '/MzIdentML/SequenceCollection/DBSequence/cvParam/@accession' because no values were found:

  - The sole term MS:1002637 (chromosome name) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.

  - The sole term MS:1002638 (chromosome strand) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.

  - The sole term MS:1002644 (genome reference version) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.







Example:



  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|A_ENSP00000395953|" id="dbseq_generic|A_ENSP00000395953|">

    <cvParam cvRef="PSI-MS" accession="MS:1002637" name="chromosome name" value="11"></cvParam>

    <cvParam cvRef="PSI-MS" accession="MS:1002638" name="chromosome strand" value="+"></cvParam>

    <cvParam cvRef="PSI-MS" accession="MS:1002644" name="genome reference version" value="Homo_sapiens.GRCh38.77.gff3"></cvParam>

  </DBSequence>







Why it's complaining about the name?







Best wishes,

Fawaz

--

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

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

PhD student

Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-21006 | 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.049a | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554

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

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

________________________________
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Re: [Psidev-pi-dev] [Psidev-ms-vocab] New version 4.0.7 of psi-ms

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

Looks good to me, thanks

From: mayerg97 [mailto:ger...@ru...]
Sent: 30 January 2017 15:39
To: psi...@li...; psi...@li...; psi...@li...
Subject: [Psidev-ms-vocab] New version 4.0.7 of psi-ms


Dear proteomics community,

attached there's the new version 4.0.7 of the psi-ms.obo file.


Changed CV terms in version 4.0.7 of psi-ms.obo:
================================================
************ parent term of the new sub-terms
************ changed the definition
[Term]
id: MS:1001805
name: quantification datatype
def: "The data type of the value reported in a QuantLayer." [PSI:MS]
is_a: MS:1001129 ! quantification information

************ former childs of MS:1001805
************ are now childs of the new sub-terms of MS:1001805, e.g.
[Term]
id: MS:1001842
name: sequence-level spectral count
def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype

[Term]
id: MS:1002733
name: peptide-level spectral count
def: "The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype

[Term]
id: MS:1002734
name: peptide ion-level spectral count
def: "The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype


New CV terms in version 4.0.7 of psi-ms.obo:
============================================
************ added new sub-childs to MS:1001805
[Term]
id: MS:1002735
name: feature-level quantification datatype
def: "The data type of the value reported in a QuantLayer for a feature." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002736
name: PSM-level quantification datatype
def: "The data type of the value reported in a QuantLayer for a PSM." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002737
name: peptide-level quantification datatype
def: "The data type of the value reported in a QuantLayer for a peptide." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002738
name: protein-level quantification datatype
def: "The data type of the value reported in a QuantLayer for a protein." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002739
name: protein group-level quantification datatype
def: "The data type of the value reported in a QuantLayer for a protein group." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

Best Regards,
Gerhard
--

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

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

PhD student

Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-21006 | 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] [HUPO-PSI/mzIdentML] mzIdentML-Validator GUI 1.4.25

[Gerhard M. <not...@gi...>]

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You are receiving this because you are subscribed to this thread.
View it on GitHub:
https://github.com/HUPO-PSI/mzIdentML/releases/tag/mzIdentMLValidator_GUI_v1.4.25-SNAPSHOT