CV requests

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Andy, On 6/16/2011

> Some CV requests for some software we’re working on:
>
> [Term]
> id: MS:1001250
> name: local FDR
> def:"Result of quality estimation: the local FDR at the current position of a 
sorted list."  [PSI:PI]
> xref: value-type:xsd\:double"The allowed value-type for this CV term."
> is_a: MS:1001092 ! peptide quality estimation measure
> is_a: MS:1001198 ! protein quality estimation measure
> relationship: has_units UO:0000166 ! parts per notation unit
> relationship: has_units UO:0000187 ! percent
>
> I think this should be moved to is_a MS:1001405 ! spectrum identification 
result details, so we can
> use it with SpectrumIdentificationItem, correct?
>
> We would also like a general term for q-value to attach to SII, there only 
appears to be:
>
> id: MS:1001491
> name: percolator:Q value
>
> Lastly, can we also add a new term (with is_a MS:1001405 also to attach to 
SIIs) called “FDRScore” –
> defined in this paper http://www.ncbi.nlm.nih.gov/pubmed/19253293

Original issue reported on code.google.com by eisena...@googlemail.com on 17 Aug 2011 at 8:33

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Matt, mail on list 16-06-2011:
I agree that most if not all of the "peptide quality estimation" measures could 
also be SIR details.

Also, what is the parts per notation for local FDR? Q value could also be a 
percent.

Would a "general" term for Q value obsolete the Percolator one? We have the 
exact same issue for 
expect (or e-value) and p-value. We should have some consistency here. I.e. if 
your software can 
calculate its own Q value for any search engine, then perhaps it should have 
its own term.

I'm thinking we should use the "general" terms Q value, P value, and E value as 
parent terms of the 
software-specific terms. Doesn't "local FDR" fall under a type of Q value? Or 
are they both kinds of 
FDR?

And now for something completely different. I've noticed a few more CV things 
to fix as well:

I think these relationships which are currently on "intensity array" should 
also be on "product ion 
intensity."
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit (maybe we can exclude this 
one)

Likewise, "product ion m/z error" has units but "product ion m/z" does not (the 
latter should just 
have m/z, not PPM).

-Matt

Original comment by eisena...@googlemail.com on 17 Aug 2011 at 8:33

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Matt, Mail on list 16.6.2011: (see also issue 55)

Also we need protein terminal terms as children of "modification specificity 
rule".

I propose:
[Term]
id: MS:x
name: modification specificity protein N-terminus
def: "As a search engine parameter: apply the modification only at a protein 
N-terminus."
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:x
name: modification specificity protein C-terminus
def: "As a search engine parameter: apply the modification only at a protein 
C-terminus."
is_a: MS:1001056 ! modification specificity rule

Original comment by eisena...@googlemail.com on 17 Aug 2011 at 8:36

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Regarding Andys suggestion about local FDR (comment "0"): "local FDR" is also 
below "peptide result details"/"peptide quality estimation measure", so it can 
be used for SIR (in the mapping file all "spectrum identification result 
details" are allowed.
The same is true for SIR (Matts suggestion).

Original comment by eisena...@googlemail.com on 26 Aug 2011 at 5:40

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From comments "0", 1 and 2 and Matts mail about "modification motif" I 
assembled the following new and changed terms, which could go to David and the 
ms-vocab list:
(A rule to link "modification motif" have I already added to the mapping file, 
commented out for the moment):

new terms:
----------
[Term]
id: MS:100XXXX
name: q-value
def: "Quality measurement q-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide quality estimation measure
is_a: MS:1001198 ! protein quality estimation measure
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:100XXXX
name: FDRScore
def: "Quality measurement as defined in 
http://www.ncbi.nlm.nih.gov/pubmed/19253293." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:100XXXX
name: E-value
def: "Quality measurement E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide quality estimation measure
is_a: MS:1001198 ! protein quality estimation measure

[Term]
id: MS:100XXXX
name: modification specificity protein C-terminus
def: "As parameter for search engine: apply the modification only at C-terminus 
of protein." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:100XXXX
name: modification specificity protein N-terminus
def: "As parameter for search engine: apply the modification only at N-terminus 
of protein." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:100XXXX
name: modification specificity peptide C-terminus
def: "As parameter for search engine: apply the modification only at C-terminus 
of peptide." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:100XXXX
name: modification specificity peptide N-terminus
def: "As parameter for search engine: apply the modification only at N-terminus 
of peptide." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:100XXXX
name: modification motif
def: "The regular expression describing the sequence motif for a modification." 
[PSI:PI]
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:100XXXX
name: modification specificity attribute
def: "Attributes of modification specificity." [PSI:PI]
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:100XXXX
name: modification probability
def: "The a priori probability of a modification." [PSI:PI]
is_a: MS:100XXXX ! modification specificity attribute

make obsolete:
--------------
[Term]
id: MS:1001189
name: modification specificity N-term
def: "As parameter for search engine: apply the modification only N-terminal." 
[PSI:PI]
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:1001190
name: modification specificity C-term
def: "As parameter for search engine: apply the modification only C-terminal." 
[PSI:PI]
is_a: MS:1001056 ! modification specificity rule

changed terms (changed lines marked with *, please fill-in correct accession 
from newly inserted term!):
--------------------------------------------------------------------------------
-----------------------
[Term]
id: MS:1001491
name: percolator:Q value
def: "percolator:Q value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
*is_a: MS:100XXXX ! q-value

[Term]
id: MS:1001328
name: OMSSA:evalue
def: "OMSSA E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
*is_a: MS:100XXXX ! E-value

[Term]
id: MS:1001329
name: OMSSA:pvalue
def: "OMSSA p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
*is_a: MS:1001191 ! p-value

[Term]
id: MS:1001330
name: X\!Tandem:expect
def: "The X!Tandem expectation value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
*is_a: MS:100XXXX ! E-value

[Term]
id: MS:1001169
name: Paragon:expression change p-value
def: "The Paragon result 'Expression change P-value'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
*is_a: MS:1001191 ! p-value

[Term]
id: MS:1001396
name: Phenyx:PepPvalue
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
*is_a: MS:1001191 ! p-value

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of the product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information
*relationship: has_units MS:1000131 ! number of counts
*relationship: has_units MS:1000132 ! percent of base peak
*relationship: has_units MS:1000814 ! counts per second
*relationship: has_units MS:1000905 ! percent of base peak times 100

[Term]
id: MS:1001225
name: product ion m/z
def: "The m/z of the product ion." [PSI:PI]
synonym: "fragment ion m/z" EXACT []
is_a: MS:1001221 ! fragmentation information
*relationship: has_units MS:1000040 ! m/z

Original comment by eisena...@googlemail.com on 26 Aug 2011 at 6:21

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one change (value string):
[Term]
id: MS:100XXXX
name: modification motif
def: "The regular expression describing the sequence motif for a modification." 
[PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001056 ! modification specificity rule

Original comment by eisena...@googlemail.com on 31 Aug 2011 at 10:31

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I think this discussion is historic and I would like to close it. Can Martin 
and Matt please check if it is done and close it.

Original comment by andrewro...@googlemail.com on 17 Apr 2013 at 1:41

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Forwarded to Gerhard to implement new terms and changes in comments #4 and #5.

Original comment by eisena...@googlemail.com on 19 Jun 2013 at 1:21

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The terms are already in the CV

Original comment by germa64m...@gmail.com on 19 Jun 2013 at 1:44

• Changed state: Done