[Psidev-ms-dev] Release candidate 4.1.33_rc1 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new terms for the release version 4.1.33_rc1 of
the psi-ms.obo file.

It contains new terms for spectral libraries
and a term for the MS-DIAL software.

We also reorganized part of the CV, renamed some terms,
reactivated some obsolete terms and made some definitions more clear.
Please unpack and diff the two files to see the detailed changes.


New CV terms in version 4.1.33_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003033
name: molecular entity attribute
def: "A nonphysical characteristic attributed to a molecular entity." 
[PSI:PI]
relationship: part_of MS:1000881 ! molecular entity

[Term]
id: MS:1003034
name: atom
def: "Smallest constituent unit of ordinary matter that constitutes a 
chemical element." [https://en.wikipedia.org/wiki/Atom]
is_a: MS:1000881 ! molecular entity

[Term]
id: MS:1003035
name: small molecule
def: "Low molecular weight (< 900 daltons) organic compound that may 
regulate a biological process." 
[https://en.wikipedia.org/wiki/Small_molecule]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003036
name: metabolite
def: "Small molecule that is the intermediate end product of 
metabolism." [https://en.wikipedia.org/wiki/Metabolite]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003037
name: ribonucleotide
def: "Nucleotide containing ribose as its pentose component." 
[https://en.wikipedia.org/wiki/Ribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003038
name: deoxyribonucleotide
def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." 
[https://en.wikipedia.org/wiki/Deoxyribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003039
name: amino acid
def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) 
functional groups, along with a side chain (R group) that is specific to 
each amino acid." [https://en.wikipedia.org/wiki/Amino_acid]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003040
name: monosaccharide
def: "Simplest form of sugar and the most basic units of carbohydrate 
that cannot be further hydrolyzed to a simpler molecule." 
[https://en.wikipedia.org/wiki/Monosaccharide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003041
name: nucleic acid
def: "Molecule composed of a chain of nucleotides." 
[https://en.wikipedia.org/wiki/Nucleic_acid]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003042
name: polysaccharide
def: "Polymeric carbohydrate molecules composed of long chains of 
monosaccharide units bound together by glycosidic linkages." 
[https://en.wikipedia.org/wiki/Polysaccharide]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003043
name: number of residues
def: "Number of amino acid residues in a peptide, commonly referred to 
as the peptide length." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003044
name: number of missed cleavages
def: "Number of amino acid residue bonds that should have been cleaved 
by the cleavage agent used, but were not." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003045
name: peptide-to-protein mapping
def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003046
name: peptide-to-protein mapping attribute
def: "Nonphysical characteristic attributed to the result of 
peptide-to-protein mapping." [PSI:PI]
is_a: MS:1003045 ! peptide-to-protein mapping

[Term]
id: MS:1003047
name: protein sequence offset
def: "Offset in number of residues from the n terminus of the protein at 
which the peptide begins. Use 1 when the first residue of the peptide 
sequence is the first residue of the protein sequence." [PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003048
name: number of enzymatic termini
def: "Total number of termini that match standard rules for the cleavage 
agent, 2 when both termini match cleavage agent rules, 1 when only one 
terminus does, and 0 if neither terminus matches cleavage agent rules." 
[PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003049
name: peptidoform
def: "Peptide that contains zero or more mass modifications on the 
termini or side chains of its amino acid residues, and may be 
differentiated from other peptidoforms with the same peptide sequence 
but different mass modification configurations." [PSI:PI]
is_a: MS:1000860 ! peptide

[Term]
id: MS:1003050
name: peptidoform attribute
def: "Nonphysical characteristic attributed to a peptidoform." [PSI:PI]
relationship: part_of MS:1003049 ! peptidoform

[Term]
id: MS:1003051
name: peptidoform ion
def: "Peptidoform that has formed an adduct with an ion, thereby 
rendering it potentially detectable with a mass spectrometer. Commonly 
called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI]
is_a: MS:1003049 ! peptidoform
synonym: "precursor" RELATED []
synonym: "precursor ion" RELATED []
synonym: "parent ion" RELATED []

[Term]
id: MS:1003052
name: peptidoform ion property
def: "A physical characteristic of a peptidoform ion." [PSI:PI]
relationship: part_of MS:1003051 ! peptidoform ion

[Term]
id: MS:1003053
name: theoretical monoisotopic m/z
def: "Mass-to-charge ratio of a peptidoform ion composed of the most 
common isotope of each atom computed from the putative knowledge of its 
molecular constituents." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003054
name: theoretical average m/z
def: "Mass-to-charge ratio of a peptidoform ion computed from the 
putative knowledge of its molecular constituents, averaged over the 
distribution of naturally occurring isotopes." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003055
name: adduct
def: "Product of a direct addition of two or more distinct molecules, 
resulting in a single reaction product containing all atoms of all 
components. The resultant is considered a distinct molecular species." 
[https://en.wikipedia.org/wiki/Adduct]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003056
name: adduct ion property
def: "Physical measurable characteristic of an adduct ion." [PSI:PI]
relationship: part_of MS:1000353 ! adduct ion

[Term]
id: MS:1003057
name: scan number
def: "Ordinal number of the scan indicating its order of acquisition 
within a mass spectrometry acquisition run." [PSI:PI]
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1003058
name: spectrum property
def: "Physical measurable characteristic of a spectrum." [PSI:PI]
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1003059
name: number of peaks
def: "Number of peaks or features in a spectrum. For a peak-picked 
spectrum, this will correspond to the number of data points. For a 
non-peak-picked spectrum, this corresponds to the number of features 
discernable in the spectrum, which will be fewer than the number of data 
points." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003060
name: number of data points
def: "Number of data points in a spectrum. For a peak-picked spectrum, 
this will correspond to the number of peaks. For a non-peak-picked 
spectrum, this corresponds to the number of values in the data array, 
which are not all peaks." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003061
name: spectrum name
def: "Label attached to a spectrum uniquely naming it within a 
collection of spectra, often in a spectral library. It is often a string 
combination of peptide sequence, charge, mass modifications, collision 
energy, but will obviously be different for small molecules or 
unidentified spectra. It must be unique within a collection." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003062
name: spectrum index
def: "Integer index value associated with a spectrum within a collection 
of spectra, often in a spectral library. By custom, index counters 
should begin with 0." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003063
name: universal spectrum identifier
def: "PSI universal spectrum identifier (USI) multipart key that 
uniquely identifies a spectrum available in a ProteomeXchange datasets 
or spectral library." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003064
name: spectrum aggregation attribute
def: "Nonphysical characteristic attributed to spectrum aggregation." 
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003065
name: spectrum aggregation type
def: "Categorization of a spectrum based on the type of aggregation it 
is based on (e.g., an individual spectrum, a consensus spectrum, best 
replicate spectrum, etc.)." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003066
name: singleton spectrum
def: "Spectrum that is not the result of some aggregation process." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003067
name: consensus spectrum
def: "Spectrum that is the result of merging several replicate spectra 
to form a spectrum that is more representative of its class and ideally 
less noisy that any of its source replicates." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003068
name: best replicate spectrum
def: "Spectrum that is considered the most representative from a pool of 
replicate spectra." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003069
name: number of replicate spectra available
def: "Number of replicate spectra available for use during the 
aggregation process." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003070
name: number of replicate spectra used
def: "Number of replicate spectra used during the aggregation process. 
This is generally applicable when there are many replicates available, 
but some are discarded as being low S/N, blended, or otherwise 
unsuitable, and the remaining set is then used for merging via a 
consensus algorithm." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003071
name: spectrum origin attribute
def: "Nonphysical characteristic attributed to spectrum aggregation." 
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003072
name: spectrum origin type
def: "Categorization of a spectrum based on its type of aggregation 
(e.g., an individual spectrum, a consensus spectrum, best replicate 
spectrum, etc.)." [PSI:PI]
is_a: MS:1003071 ! spectrum origin attribute

[Term]
id: MS:1003073
name: observed spectrum
def: "Spectrum that originates from an analysis attempt of a single 
analyte species on an instrument." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003074
name: predicted spectrum
def: "Spectrum that originates from a compututational algorithm that 
attempts to predict spectra." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003075
name: demultiplexed spectrum
def: "Spectrum that originates from an attempted extraction of a single 
ion spieces from a multiplexed spectrum that contains multiple ion 
species." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003076
name: uninterpreted spectrum
def: "Spectrum provided in the form of plain numerical values without 
any information pertaining to the interpretation of features." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003077
name: interpreted spectrum
def: "Spectrum provided in a form where specific features of the 
spectrum are interpreted to provide putative explanations for some 
feature." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003078
name: interpreted spectrum attribute
def: "Nonphysical characteristic attributed to an interpreted spectrum." 
[PSI:PI]
relationship: part_of MS:1003077 ! interpreted spectrum

[Term]
id: MS:1003079
name: total unassigned intensity fraction
def: "Fraction of intensity summed from all unassigned peaks divided by 
the intensity summed from all peaks in the spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003080
name: top 20 peak unassigned intensity fraction
def: "Fraction of intensity summed from unassigned peaks among the top 
20 divided by the intensity summed from all top 20 peaks in the 
spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003081
name: unidentified modification monoisotopic mass delta
def: "Monoisotopic mass delta in Daltons of an amino acid residue 
modification whose atomic composition or molecular identity has not been 
determined. This term should not be used for modifications of known 
molecular identity such as those available in Unimod, RESID or PSI-MOD. 
This term MUST NOT be used inside the <Modification> element in 
mzIdentML." [PSI:PI]
is_a: MS:1001471 ! peptide modification details
xref: value-type:xsd\:double "The allowed value-type for this CV term."
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1003082
name: MS-DIAL
def: "MS-DIAL is a universal program for untargeted metabolomics and 
lipidomics that supports multiple instruments and MS vendors." 
[PMID:25938372]
is_a: MS:1002878 ! small molecule software
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

-- 

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

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

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

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

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

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

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