Clarification on comments re AminoAcidSequenceFeature

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CLOSED - Need clarification on comments re AminoAcidSequenceFeature (row 20)

Current Definitions

AminoAcidSequenceFeature

DEFINITION: An annotation assigned to a defined amino acid physical location.

EXAMPLE(S): alpha helices, glycosylation sites, DNA binding domains

OTHER NAME(S):

NOTE(S):

AminoAcidSequenceFeature.typeCode

DEFINITION: A coded value that specifies a group of amino acids within a protein that confer certain characteristics upon that protein, and may be important for its overall function.

EXAMPLE(S): glycosylation site, binding site, site of post-translational modification

OTHER NAME(S):

NOTE(S): [Glycosylation Site:C16643, C37901; Binding Site:C13671]

Associations

• Included in AminoAcidPhysicalLocation
• Be reported by MolecularSequenceAnnotation

Ballot Comment

do you need a databasenamecode? Or are you restricting to a single source?

Current Disposition

Pending Input From Submitter

Proposed Disposition Comment

Need clarification - are the TYPES of amino acid sequence features (typeCode) something that is identified by a database identifier, is a CD insufficient? Or is this referring to a new attribute to capture something besides the typeCode attribute? (currently there's only one attribute in this class)

Outstanding Questions

• Is this comment suggesting that AminoAcidSequenceFeatures are captured in databases and therefore have identifiers like Proteins, Genes, Pathways, etc.?
• Currently this class only has one attribute (typeCode above) - should we add a databaseNameCode and identifier?
• Or is this comment suggesting we should change the typeCode attribute into a databaseNameCode?

Responses

Lauren Becnel: Technically, yes there are different databases that manage data on known PTMs. Phosphosite is an example. See this page on a PTM for a protein called 14-3-3eta. http://www.phosphosite.org/siteAction.action?id=23077813 It’s one of several possible PTMs for that protein, each of which can affect function in different ways.

Glycosylation is a type of post-translational modification (PTM), so are phosphorylation, ubiquitination, sumoylation, etc. Thus including glycosylation and PTM as examples as though they were on the same “level” should be avoided.

Q from WENDY (TYPE: EX & DEFN): I think this is suggesting we remove either glycosylation or PTM from the examples but I'm not sure which. Still don't know if Mollie's comment was suggesting we change the attribute AminoAcidSequenceFeature.typeCode to a databaseNameCode or just add databaseNameCode - in any case, where would the identifier/value from the database be represented?

DISCUSSION 20160223: in example on typeCode, replace “site of post-translational modification” with “phosphorylation site, ubiquitination site, sumoylation site” No need to add databaseNameCode and definition is OK, wait until we get other comments to see if other changes are needed

EXAMPLE UPDATE DONE IN MODEL

DISCUSSION 20160225: With updated examples and definition OK as is, this is OK now. DONE

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