Clarification on comments re MessengerRNA

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CLOSED - Need clarification on comments re MessengerRNA (row 31)

Current Definition

DEFINITION: A representation of a member of the class of RNA molecules in public resources (e.g., NCBI RefSeq or EBI Ensembl) that contains protein-coding information in its nucleotide sequence.

EXAMPLE(S): A messenger RNA/transcript record from ENSEMBL: http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000357654

OTHER NAME(S):

NOTE(S):

Ballot Comment

The example lists a cDNA transcript. DNA analysis reports on cDNA transcripts. The class should be changed to reflect this. Also cDNA will link to the variant representation better as it uses ATCG not AUCG. Uracil is substituted for thymine. If this is for RNA testing, then how does a lab report on cDNA transcripts?

Current Disposition

Pending Input From Submitter

Proposed Disposition Comment

Need clarification - Is it the URL that lists a cDNA transcript? Need CG and LSDAM SMEs to reconcile comments with definitions/examples to provide updated text.

Outstanding Questions

• Are the class name, definition and example inconsistent with one another?
• Assuming the class name accurately reflects what was originally intended, What should the definition be?
• Assuming the class name accurately reflects what was originally intended, What should the example be?

Responses

Lauren Becnel: I’d remove the text "in public resources (e.g., NCBI RefSeq or EBI Ensembl) “ from the definition. An mRNA isn’t biologically defined as being indexed by a public repo, and many undiscovered species have mRNAs that aren’t yet indexed in any if that makes sense.

WENDY to make change (TYPE: DEFN): take out the "in public resources (e.g., NCBI RefSeq or EBI Ensembl) "

UPDATE DONE IN THE MODEL

DISCUSSION 20160225: Lauren to investigate whether the URL is to mRNA or cDNA

Lauren Becnel, 20160226: "Homo sapiens BRCA1 transcript variant 1 mRNA, GenBank identifier NM_007294.3, is available at http://www.ncbi.nlm.nih.gov/nuccore/NM_007294.3"

UPDATE DONE IN THE MODEL

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