[Psidev-pi-dev] New version 4.1.35 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new and changed terms for the
version 4.1.35 of the psi-ms.obo file,
which can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.35 of psi-ms.obo:
=============================================
[Term]
id: MS:1003083
name: raw data file
def: "Data file that contains original data as generated by an 
instrument, although not necessarily in the original data format (i.e. 
an original raw file converted to a different format is still a raw data 
file)." [PSI:MS]
is_a: MS:1000577 ! source data file

[Term]
id: MS:1003084
name: processed data file
def: "File that contains data that has been substantially processed or 
transformed from what was originally acquired by an instrument." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000577 ! source data file

[Term]
id: MS:1003085
name: previous MSn-1 scan precursor intensity
def: "Intensity of the precursor ion in the previous MSn-1 scan (prior 
in time to the referencing MSn scan). For an MS2 scan, this means the 
MS1 precursor intensity. It is unspecified on whether this is an apex 
(across m/z) intensity, integrated (across m/z) intensity, a centroided 
peak intensity of unknown origin, or even summed across several 
isotopes." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001141 ! intensity of precursor ion
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003086
name: precursor apex intensity
def: "Intensity of the precursor ion current as measured by its apex 
point over time and m/z. It is unspecified whether this is the intensity 
of the selected isotope or the most intense isotope." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001141 ! intensity of precursor ion
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003087
name: supported by repository but incomplete data and/or metadata
def: "Dataset for which the identifications and/or spectra/traces are in 
formats that can be parsed by the hosting data repository such that 
internal references between identifications and spectra/traces are 
preserved and browsable at the repository. However, some metadata is not 
properly described due to lack of CV terms or some auxiliary data, such 
as data used to create a spectral library or a sequence search database 
crucial to the analysis, is not available." [PSI:PI]
is_a: MS:1002844 ! Experiment additional parameter

[Term]
id: MS:1003088
name: truncation and zlib compression
def: "Compression using truncation and zlib." 
[https://github.com/biospi/pwiz]
xref: value-type:xsd\:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1003089
name: truncation, delta prediction and zlib compression
def: "Compression using truncation, delta prediction and zlib." 
[https://github.com/biospi/pwiz]
xref: value-type:xsd\:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1003090
name: truncation, linear prediction and zlib compression
def: "Compression using truncation, linear prediction and zlib." 
[https://github.com/biospi/pwiz]
xref: value-type:xsd\:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type


Changed CV terms in version 4.1.35 of psi-ms.obo:
=================================================
************ Added is_a relation
[Term]
id: MS:1000224
name: molecular mass
def: "Mass of a molecule measured in unified atomic mass units (u or 
Da)." [https://en.wikipedia.org/wiki/Molecular_mass]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000861 ! molecular entity property
relationship: has_units UO:0000002 ! mass unit

************ renamed and added relationship: part_of MS:1002806 ! ion
[Term]
id: MS:1000507
name: ion property
def: "Nonphysical characteristic attributed to an ion." [PSI:MS]
relationship: part_of MS:1002806 ! ion

************ Added is_a relation
[Term]
id: MS:1002959
name: isomer
def: "One of several species (or molecular entities) that have the same 
atomic composition (molecular formula) but different line formulae or 
different stereochemical formulae." 
[https://goldbook.iupac.org/html/I/I03289.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000859 ! molecule

************ renamed and added is_a relation
[Term]
id: MS:1000577
name: source data file
def: "Data file from which an entity is sourced." [PSI:MS]
synonym: "source file" EXACT []
relationship: part_of MS:1001458 ! spectrum generation information
is_a: MS:1000499 ! spectrum attribute

************ changed the definition
[Term]
id: MS:1002856
name: Supported dataset by repository
def: "Dataset for which the identifications and/or spectra/traces are in 
formats that can be parsed by the hosting data repository such that 
internal references between identifications and spectra/traces are 
preserved and browsable at the repository. This is usually called a 
complete submission." [PSI:PI]
is_a: MS:1002844 ! Experiment additional parameter

[Term]
id: MS:1002857
name: Unsupported dataset by repository
def: "Dataset for which the identifications and/or spectra/traces are in 
formats that cannot be parsed by the hosting data repository and thus 
internal references between identifications and spectra/traces are not 
browsable at the repository. This is usually called a partial 
submission." [PSI:PI]
is_a: MS:1002844 ! Experiment additional parameter

Best Regards,
Gerhard

-- 

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

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

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

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

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

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

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