Thread: [Psidev-ms-dev] Controlled vocabulary release candidate v. 3.12.0

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Dear all,

Sorry about the really long mail.
I've divided the several things we had to do in two blocks: changes that 
I considered for the next release ("Changes and additions" section) and 
pending changes related to things not clarified ("Pending things").
Attached to this mail, there's a release candidate (new version number 
will be 3.12.0). Please check the changes and additions. I expect 
everything is OK. If you don't agree with the changes, please, email the 
list and we'll change whatever is needed. As soon everything is agreed, 
I'll publish the new version.

=====================================================
Changes and additions
=====================================================

- Two new terms proposed by Steve Robles (last mail Oct 10th, "Request 
for new terms"): MS:1001878 ("Offset Voltage") and MS:1001879 
("In-source collision-induced dissociation").
Eric Deutsch commented a possible overlapping between the first one 
(MS:1001878-> "Offset Voltage") and the next two terms MS:1000876 ("cone 
voltage") and MS:1000877 ("tube lens").
No mails following this point.
I should add that the last term's name ("tube lens"), maybe is better 
described as "tube lens voltage". (change not included in the temporal 
obo file).
The two new terms:

[Term]
id: MS:1001878
name: Offset Voltage
def: "The potential difference between two adjacent interface voltages 
affecting in-source collision induced dissociation." [PSI:MS]
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000218 ! volt

[Term]
id: MS:1001879
name: In-source collision-induced dissociation
def: "The dissociation of an ion as a result of collisional excitation 
during ion transfer from an atmospheric pressure ion source and the mass 
spectrometer vacuum." [PSI:MS]
is_a: MS:1000044 ! dissociation method

- Change in definition for MS:1000932 ("...MDS SCIEX TripleTOF 5500..." 
changed by "...MDS SCIEX TripleTOF 5600...") (last mail Oct 10th, 
"Request for new terms")

- A definition for the term MS:1000672 (name: Cliquid) (last mail Oct 
10th, "Request for new terms"). Is an Applied Biosystems software. 
Browsing I found that maybe the definition could be something like this:
def: "AB SCIEX or Applied Biosystems software for data analysis and 
quantitation." [PSI:MS]
I found the most complete descripcion of the software in this link:
http://www.mass-spec-capital.com/product/cliquid-software-applied-biosystems-abi-unit-life-technologies-2001-18662.html 

- New term added for the mz5 format (last mail Oct 10th, "Request for 
new terms")(last mail Oct 10th, "Request for new terms"):
[Term]
id: MS:1001880
name: mz5 file
def: "mz5 file format, modeled after mzML, developed by the Steen Lab." 
[PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

- Space removed in 1000139 name "4000 Q TRAP" à “4000 QTRAP”. (last mail 
Oct 10th, "Request for new terms")
Does this cause a problem with obsoleted term of same name (id: 
MS:1000870)? No problems reported.

- Adding 3 transition validation attributes (last mail Oct 10th, 
"Request for new terms"):
[Term]
id: MS:1001881
name: transition validation attribute
def: "Attributes of the quality of a transition that affect its 
selection as appropriate." [PSI:MS]
relationship: part_of MS:1000908 ! transition

[Term]
id: MS:1001882
name: coefficient of variation
def: "Variation of a set of signal measurements calculated as the 
standard deviation relative to the mean." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001881 ! transition validation attribute

[Term]
id: MS:1001883
name: signal-to-noise ratio
def: "Unitless number providing the ratio of the total measured 
intensity of a signal relative to the estimated noise level for that 
signal." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001881 ! transition validation attribute

- Adding 1 command-line parameter term as suggested by Magnus (last mail 
Oct 10th, "Request for new terms"):

[Term]
id: MS:1001884
name: command-line parameters
def: "Parameters string passed to a command-line interface software 
application." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter

- Two terms (MS:1001843 and id: MS:1001844 -peak intensity and area- now 
sons of MS:1000042 ! peak intensity) proposed by Eric Deutsch about 
“peak area” and “peak height” (last email Oct 10th "PSI-MS CV: peak 
intensity area terms").
Related to this, the term MS:1001845 ("peak area" too) has been 
obsoleted because duplicated toMS:1001844.

=====================================================
Pending things
=====================================================

Pending things 1 -> Some comments in Eric Deutsch mail (Oct 10th) not 
yet implemented in the controlled vocabulary and to be discussed :
2) Is there really a difference between “peak area” and “XIC area”. I 
suspect not. If there really is an intended subtle difference (e.g. 
“peak area” takes into account background removal, which “XIC area” is 
irrespective of background) then we should define this.
3) It seems to me that all these term names are incomplete and 
potentially misleading. For example, the “peak area” term is not really 
for the concept of “peak area”; it is the concept of “quantifying signal 
by measuring peak area”. One can infer this by knowing the parent, but 
if our goal is to create term names that can stand on their own, I think 
these should be clarified. It will be tempting to users to use the “peak 
area” term to provide a measurement of a peak area.
4) For 1859, normalized to what?
5) For 1130, can peptides have an area? Mass specs don’t see peptides, 
they see peptide ions. And they see them as peaks. So it would see that 
“peptide raw area” is a badly named term that probably when decomposed 
means the same as “peak area”. Or, if I’m wrong, can we improve the 
definition?

Pending things 2 -> Some comments by David Ovelleiro (mail Sept 27th, 
"Possible need of changing some things under "identification result 
details" (MS:1001405)") not yet implemented in the controlled vocabulary:
- comment 1: there are two terms, MS:1001362 and MS:1001114, which in 
addition to be children to their respective parents (MS:1001116 and 
MS:1001105 resp), are also direct children to MS:1001405. The problem I 
see here is that the two parents, are also direct descendants of 
MS:1001405. Is this not redundant and unnecessary? My proposal is to 
remove the is_a (direct) relationship to MS:1001405.
Please, check the picture "screen1.jpg" for a more graphical description.
- comment 2: the term "Mascot query number" (MS:1001528) is direct child 
to "spectrum identification result details" (MS:1001405). Don't you 
think that this term would be better placed under "search engine 
specific score" (MS:1001153) (child to the previous MS:1001528)
- comment 3: the terms related to the "False Discovery Rate" are, in my 
opinion, some confusing at this point. I attach a screen-shot called 
screen2.jpg to illustrate what I'm saying. At least two of the terms 
("pep:global FDR" and "prot:global FDR") seem miss located to me. Maybe 
they should work like "local FDR", with a unique term called "global 
FDR" child to both "peptide" and "proteine" / "identification confidence 
metric" (MS:1001198 and MS:1001092). Or maybe two terms could be used 
(the way is now), but children to MS:1001198 and MS:1001092 and changing 
the prefix "pep:" and "prot:" by the proper "peptide" and "protein".

Two replies (Eric Deutsch and David Creasy, mails Sept 27th) seem to 
give support to the first point. Second point rejected. Third point 
extended in Eric Deutsch mail.

Pending things 3 -> the "modification specificity N-term/C-term" related 
terms were NOT modified following the proposal in Martin Eisenacher mail 
(Sept 1st). In mail sent by David Ovelleiro (Sept 16th) changes related 
to modifications specificity were put to a stop until more consensus was 
reached. This should be clarified (pretty sure a final soultion for this 
is needed).

=================================================================================

Thanks for your attention.

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

Thread: [Psidev-ms-dev] Controlled vocabulary release candidate v. 3.12.0

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