[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

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Comment #93 on issue 42 by javizca74: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

I sent my comments to Andreas. I am not including here minor typo errors. I  
am also
attaching Andreas comments (### lines).

1) These 2 terms are somehow redundant. The def of MS:1001013 should be  
changed
(remove the examples, I guess):

[Term]
id: MS:1001011
name: search database details
def: "Details about the database searched." [PSI:PI]
is_a: MS:1001249 ! search input details


[Term]
id: MS:1001013
name: database name
def: "The name of the search database (nr, SwissProt or est_human)."  
[PSI:PI]
is_a: MS:1001011 ! search database details

##### the 1001013 term is used for mapping to
#####  
/mzIdentML/DataCollection/Inputs/SearchDatabase/DatabaseName/cvParam/@accession
##### all the child term of the 1013 are allowed here, but not the term  
itself
##### the first term is mapped to
/mzIdentML/DataCollection/Inputs/SearchDatabase/cvParam/@accession
##### and contains a large collection of terms
##### however, some of the child terms of 1001011 should not be used.
##### maybe we should restructure the CV, to only allow term that make  
sense?

2) Perhaps the def should be changed in the definition? (range:-3, +3, not  
zero,
instead of 1-6).

[Term]
id: MS:1001024
name: translation frame
def: "The translated open reading frames from a nucleotide database  
considered in the
search (range: 1-6)." [PSI:PI]
is_a: MS:1001011 ! search database details


3) Perhaps change term name DB filter on sequences” to “DB filter on amino  
acid
sequence pattern”?


[Term]
id: MS:1001027
name: DB filter on sequences
def: "Filtering applied specifically by amino acid sequence pattern."  
[PSI:PI]
is_a: MS:1001019 ! database filtering

##### maybe "DB filter on sequence pattern"? The phrase amino acid would  
restrict it
to protein databases

4)Change term name to quality estimation method details?

[Term]
id: MS:1001060
name: quality estimation details
def: "Method for quality estimation (manually or wih decoy database)."  
[PSI:PI]
is_a: MS:1001249 ! search input details

#### accepted and done

5) Delete this one?

[Term]
id: MS:1001060
name: quality estimation details
def: "Method for quality estimation (manually or wih decoy database)."  
[PSI:PI]
is_a: MS:1001249 ! search input details

#### same as above?

6) Updated def. I would change the name to “database type nucleotide”:

[Term]
id: MS:1001079
name: database type NA
def: "Database contains nucleic acid sequences." [PSI:PI]
is_a: MS:1001018 ! database type

#### accepted and done

7) I would update the term to “sequence coverage”.

[Term]
id: MS:1001093
name: coverage
def: "The percent coverage for the protein based upon the matched peptide  
sequences
(can be calculated)." [PSI:PI]
xref: value-type:xsd\:decimal "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details

#### accepted and done

8)  Update def:

[Term]
id: MS:1001115
name: scan number(s)
def: "Take from mzData. TODO: What does this mean?" [PSI:PI]
is_a: MS:1001105 ! peptide result details

9) Change this term: this is not a name for any database. It could be  
changed to
“database type EST”. Or if you are referring to the EST database from NCBI,  
it should
be called: dbEST.


[Term]
id: MS:1001178
name: database EST
is_a: MS:1001013 ! database name

10) Add synonyms to all terms containing “product ion” (fragment ion).

[Term]
id: MS:1001225
name: product ion m/z
def: "The m/z of the product ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of the product ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001227
name: product ion m/z error
def: "The product ion m/z error (ADD more docu here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

#### accepted and done

11) This term name is wrong. There is no database called EST (dbEST is the  
one from
the NCBI, for instance).

[Term]
id: MS:1001295
name: decoy DB from EST
is_a: MS:1001284 ! decoy DB derived from

#### see 9) above

12) Is it pending to add more mascot related terms?

[Term]
id: MS:1001326
name: TODO_add_others
is_a: MS:1001302 ! search engine specific input parameter

13) These terms are redundant:

[Term]
id: MS:1001343
name: NA sequence
def: "The sequence is a nucleic acid sequence." [PSI:PI]
is_a: MS:1001342 ! database sequence details

[Term]
id: MS:1001344
name: AA sequence
def: "The sequence is a amino acid sequence." [PSI:PI]
is_a: MS:1001342 ! database sequence details


There are those ones:

[Term]
id: MS:1001073
name: database type AA
def: "Database contains amino acid sequences." [PSI:PI]
is_a: MS:1001018 ! database type

[Term]
id: MS:1001079
name: database type NA
def: "Database contains nucleic acid sequences." [PSI:PI]
is_a: MS:1001018 ! database type

#### right these are redundant. However, they can be used in different  
locations
#### I would suggest to keep them



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