[Psidev-ms-dev] ProteomeXchange related terms ideally to be added to the PSI MS CV

[Juan A. V. <ju...@eb...>]

Dear all,

I would like to propose the following terms related to the ProteomeXchange submission pipeline. Ideally, we would like to have them included here since we need them not only for PRIDE purposes, but not be integrated with the other resources such as PeptideAtlas, UniProt or Tranche. 


Any feedback is welcome.

Best regards,

Juan Antonio



[Term]
id: MS: ?
name: ProteomeXchange accession number
def: Main identifier of a ProteomeXchange dataset
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: ProteomeXchange  identifier
def: Secondary identifier of a ProteomeXchange dataset
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: ProteomeXchange accession version number
def: version number of a ProteomeXchange accession number
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: Digital Object Identifier (DOI)
def: DOI unique identifier
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: Keyword
def: Free text attribute that can enrich the information about an entity
is_a: MS: 1000878 ! External reference identifier

We also need children terms for this under the previous term:

[Term]
id: MS: ?
name: Journal article keyword
def: Keyword present in a scientific publication
is_a: MS: ? ! Keyword

[Term]
id: MS: ?
name: Submitter keyword
def: Keyword assigned by the data submitter
is_a: MS: ? ! Keyword

[Term]
id: MS: ?
name: Curator keyword
def: Keyword assigned by a data curator
is_a: MS: ? ! Keyword

[Term]
id: MS: ?
name: Tranche file hash
def: Hash assigned by the Tranche resource to an individual file  
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: Tranche project hash
def: Hash  assigned by the Tranche resource to a whole project
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: PRIDE experiment URI
def: URI that allows the access to one experiment in the PRIDE database.
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: PRIDE project URI
def: URI that allows the access to one project in the PRIDE database.
is_a: MS: 1000878 ! External reference identifier


We also need three more terms to represent:

- 'Accepted manuscript'. We will use this when the data is published but the reference (PubMed ID) is not yet public.

- 'Data derived from previous dataset'. We need this term to flag is new data has been obtained by reanalysing a previous dataset.

- 'No PTMs are included in the dataset'. This may be included under the term MS:1001055 ('Modification parameters for the search engine run'), but it does not really fit there.



 I am not sure it these terms should be included here. We could just use the PRIDE CV for this.