[Psidev-ms-dev] New version 3.84.0 of psi-ms.obo

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Dear proteomics community,

here's the new version 3.84.0 of the psi-ms.obo file.
It contains mainly new terms for proteogenomics searches.

New CV terms in version 3.84.0 of psi-ms.obo:
=============================================
************
[Term]
id: MS:1002631
name: Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)
def: "A dissociation process combining electron-transfer and 
higher-energy collision dissociation (EThcD). It combines ETD (reaction 
time) followed by HCD (activation energy)." [PSI:PI]
synonym: "EThcD" EXACT []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1002632
name: jPOST dataset identifier
def: "Dataset identifier issued by the jPOST repository. A dataset can 
refer to either a single sample as part of a study, or all samples that 
are part of the study corresponding to a publication." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002633
name: jPOST dataset URI
def: "URI that allows the access to one dataset in the jPOST repository. 
A dataset can refer to either a single sample as part of a study, or all 
samples that are part of the study corresponding to a publication." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002634
name: Q Exactive Plus
def: "Thermo Scientific Q Exactive Plus." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002635
name: proteogenomics search
def: "Proteogenomics search performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002636
name: proteogenomics attribute
def: "Proteogenomics attribute." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002637
name: chromosome name
def: "The name or number of the chromosome to which a given peptide has 
been mapped." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002638
name: chromosome strand
def: "The strand (+ or -) to which the peptide has been mapped." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002639
name: peptide start on chromosome
def: "The overall start position on the chromosome to which a peptide 
has been mapped i.e. the position of the first base of the first codon, 
using a zero-based counting system." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002640
name: peptide end on chromosome
def: "The overall end position on the chromosome to which a peptide has 
been mapped i.e. the position of the third base of the last codon, using 
a zero-based counting system." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002641
name: peptide exon count
def: "The number of exons to which the peptide has been mapped." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002642
name: peptide exon nucleotide sizes
def: "A comma separated list of the number of DNA bases within each exon 
to which a peptide has been mapped. Assuming standard operation of a 
search engine, the peptide exon sizes should sum to exactly three times 
the peptide length." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which 
the peptide has been mapped, relative to peptide-chromosome start." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002644
name: genome reference version
def: "The reference genome and versioning string as used for mapping. 
All coordinates are within this frame of reference." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002645
name: MSDK
def: "Mass Spectrometry Development Kit (MSDK) is a Java library of 
algorithms for processing of mass spectrometry data." [PSI:PI, 
http://msdk.github.io/]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

Changed CV terms in version 3.84.0 of psi-ms.obo:
=================================================
************ added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001031
name: spectral library search
def: "A search using a library of spectra." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ added relationship: has_units UO:0000169 ! parts per million
[Term]
id: MS:1001412
name: search tolerance plus value
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001411 ! search tolerance specification
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000169 ! parts per million
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

************ added relationship: has_units UO:0000169 ! parts per million
[Term]
id: MS:1001413
name: search tolerance minus value
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001411 ! search tolerance specification
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000169 ! parts per million
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

************ added value-type:xsd\:float to the following six 
PeptideShaker terms
[Term]
id: MS:1002466
name: PeptideShaker PSM score
def: "The probability based PeptideShaker PSM score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002467
name: PeptideShaker PSM confidence
def: "The probability based PeptideShaker PSM confidence." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002468
name: PeptideShaker peptide score
def: "The probability based PeptideShaker peptide score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002358 ! search engine specific score for distinct peptides
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002469
name: PeptideShaker peptide confidence
def: "The probability based PeptideShaker peptide confidence." [PSI:PI]
xref: value-type:xsd\:float "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:1002470
name: PeptideShaker protein group score
def: "The probability based PeptideShaker protein group score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002471
name: PeptideShaker protein group confidence
def: "The probability based PeptideShaker protein group confidence." 
[PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

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/>