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

[<cod...@go...>]

Comment #95 on issue 42 by andrewrobertjones: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

These are all fairly minor so can probably be fixed without discussion

1. I think this term need a unit: e.g.
relationship: has_units UO:0000221 ! dalton
relationship: has_units UO:0000222 ! kilodalton

[Term]
id: MS:1001361
name: alternate mass
def: "List of masses a non-standard letter code is replaced with." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001359 ! ambiguous residues

2. I don't see the point of this term:

[Term]
id: MS:1001057
name: tolerance on types
def: "Tolerance on types." [PSI:PI]
is_a: MS:1001055 ! modification parameters

3. Most of the children of quantification have errors (missing data  
type/unit) but we
can probably leave these for now:

[Term]
id: MS:1001129
name: quantification information
def: "Quantification information." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation


4. This term needs a datatype (xref: value-type:xsd\:string "The allowed  
value-type
for this CV term.")

[Term]
id: MS:1001051
name: multiple enzyme combination rules
def: "Description of multiple enzyme digestion protocol, if any." [PSI:PI]
is_a: MS:1001044 ! cleavage agent details

5. This term and related terms need units e.g.
relationship: has_units UO:0000221 ! dalton
relationship: has_units UO:0000222 ! kilodalton

[Term]
id: MS:1001201
name: DB MW filter maximum
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters


6. This term needs a URI datatype? (xsd:anyURI)

[Term]
id: MS:1001014
name: database local file path
def: "Local file path of the search database from the search engine's point  
of view."
[PSI:PI]
is_a: MS:1001011 ! search database details


7. Add date type to this (xsd:dateTime)

[Term]
id: MS:1001017
name: database release date
def: "Release date of the search database." [PSI:PI]
is_a: MS:1001011 ! search database details

8. Change string datatype to URI?

[Term]
id: MS:1001015
name: database original uri
def: "URI, from where the search database was originally downloaded."  
[PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details


9. Needs a string datatype:

[Term]
id: MS:1001016
name: database version
def: "Version of the search database ." [PSI:PI]
is_a: MS:1001011 ! search database details

10. this needs a datatype (not exactly sure if an int or a string?):

[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



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