[Psidev-ms-dev] Controlled vocabulary release candidate v. 3.14.0

[David O. <do...@eb...>]

Hi community,

After the last phone conference (Nov 1st), some new terms were agreed 
(related to SQID software/algorithm and source/inlet related terms). 
I'll list them at the bottom of this mail: "Additions in the c.v. 3.14.0".
Please, check them and if anything is wrong, please send an email to the 
list (psi...@li...). If everybody agrees, I'll 
submit the new version in a couple of days.


The Peak intensity discussion, is far from finished (a new mail 
yesterday). Although the proposal about characterizing the kind of 
signal represented in spectra/chromatograms (m/z versus electro magnetic 
radiation) seems not very successful, I'll wait until everybody has 
commented about this (or something new!) related to the peak intensity.
If nothing new related to peak intensity happens in a couple of days, 
I'll send an email to the list with ALL the changes listed in Eric 
Deutsch in his Nov 1st mail (PSI MSS WG call notes) (with "all the 
changes" I mean everything after "Peak intensity discussion:" and before 
"+ Andy will check with Martin on what to do with").



Additions in the c.v. 3.14.0
======================
Four terms related to SQID software. The first, the SQID software 
definition term. The other three, search engine specific scores (related 
to peptides or proteins).
Additions proposed in mail "Request new CV terms to the PSI-MS 
Controlled Vocabulary submission" by lw...@em... on 31/10/2011.

[Term]
id: MS:1001886
name: SQID
def: "Software for data analysis of peptides and proteins." [PSI:MS]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1001887
name: SQID:score
def: "The SQID result 'Score'." [PSI:PI]
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001888
name: SQID:deltaScore
def: "The SQID result 'deltaScore'." [PSI:PI]
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001889
name: SQID:protein score
def: "The SQID result 'protein score'." [PSI:PI]
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score


A new "inlet attribute" terms and three source/inlet related terms

[Term]
id: MS:1001890
name: inlet attribute
def: "Property of an instrument inlet that needs a value." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:1001891
name: modulation time
def: "Duration of a complete cycle of modulation in a comprehensive 
two-dimensional separation system, equals the length of a second 
dimension chromatogram, i.e., the time between two successive injections 
into the second column." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000857 ! run attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1001892
name: inlet temperature
def: "Temperature of the instrument inlet." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001890 ! inlet attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree celsius

[Term]
id: MS:1001893
name: source temperature
def: "Temperature of the instrument source." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree celsius


-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD