[Psidev-ms-dev] Release candidate 4.1.16_rc1 of psi-ms.obo

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Dear proteomics/metabolomics community,

following are new terma and changes for the release candidate 4.1.16_rc1 of
the psi-ms.obo file. It contains two new digestion terms and new terms for
the IdentiPy software and the their scores.

In addition several terms are chanegd in order to remove redundant 
subclassing
(superfluous is_a relations are removed now).

New CV terms in version 4.1.16_rc1 of psi-ms.obo:
=================================================
************ New digestion terms
[Term]
id: MS:1002985
name: in-gel digestion
def: "Digestion of proteins separated by gel electrophoresis for mass 
spectrometric characterization of proteins and proteomes." [PSI:PI]
is_a: MS:1000831 ! sample preparation

[Term]
id: MS:1002986
name: in-solution digestion
def: "Digestion of proteins in solution for mass spectrometric 
characterization of proteins and proteomes." [PSI:PI]
is_a: MS:1000831 ! sample preparation

************ New search engine / score / software terms
[Term]
id: MS:1002987
name: IdentiPy
def: "IdentiPy." [PMID:29682971, https://bitbucket.org/levitsky/identipy]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002988
name: IdentiPy:RHNS
def: "The IdentiPy result 'RHNS'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002989
name: IdentiPy:hyperscore
def: "The IdentiPy result 'hyperscore'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002990
name: ms_deisotope
def: "ms_deisotope, a library for deisotoping and charge state 
deconvolution of mass spectra." 
[https://github.com/mobiusklein/ms_deisotope]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002991
name: python-psims
def: "python-psims, a library for generating mzML and mzIdentML." 
[https://github.com/mobiusklein/psims]
is_a: MS:1002333 ! conversion software

Changed CV terms in version 4.1.16_rc1 of psi-ms.obo:
*********** REMOVED REDUNDANT SUBCLASSINGS **********
=====================================================

************ Removed the redundant is_a: MS:1001457 ! data processing 
software
************ for the following three terms
[Term]
id: MS:1002334
name: ProCon
def: "Java software designed to convert one of several proteomics 
identification results formats into mzIdentML or PRIDE XML." [PSI:PI, 
http://www.medizinisches-proteom-center.de/procon]
is_a: MS:1002333 ! conversion software

[Term]
id: MS:1002335
name: PRIDE Converter2
def: "Java software designed to convert one of several proteomics 
identification results formats into PRIDE XML." [PMID:22949509]
is_a: MS:1002333 ! conversion software

[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein 
inference and identification analysis." [PSI:PI, 
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002414 ! postprocessing software
is_a: MS:1001456 ! analysis software

************ Removed the redundant is_a: MS:1001833 ! quantitation 
analysis summary
************ for the following ten terms
[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:1002009 ! isobaric label quantitation analysis

[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:1002009 ! isobaric label quantitation analysis

[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:1002009 ! isobaric label quantitation analysis

[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: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: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: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: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: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: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:1002009 ! isobaric label quantitation analysis

************ Removed the redundant is_a: MS:1001459 ! file format
[Term]
id: MS:1000914
name: tab delimited text format
def: "A file format that has two or more columns of tabular data where 
each column is separated by a TAB character." [PSI:MS]
is_a: MS:1001040 ! intermediate analysis format

************ Removed the redundant is_a: MS:1001455 ! acquisition software
************ Removed the redundant is_a: MS:1001456 ! analysis software
************ Removed the redundant is_a: MS:1001457 ! data processing 
software
[Term]
id: MS:1001878
name: MALDI Solutions Microbial Identification
def: "Shimadzu Biotech software for data acquisition, processing, and 
analysis." [PSI:MS]
is_a: MS:1001558 ! MALDI Solutions

************ Removed the redundant is_a: MS:1001405 ! spectrum 
identification result details
[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
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
is_obsolete: true

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

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