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Discussion on examples and storyboard for AminoAcidSequence

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CLOSED - Need clarification and storyboard for examples for AminoAcidSequence (row 18)

Original Definition

DEFINITION: A representation of a linear arrangement of organic compounds containing amino (-NH2) and carboxyl (-COOH) groups.

EXAMPLE(S):  the sequence of TP53 protein, the first 20 residues of a BRCA1 protein.



Ballot Comment

note this is an example and not the first 20 residues

Proposed Definition

DEFINITION: A representation of a linear arrangement of amino acids represented in single notation

EXAMPLE(S): AMDYSLAAAL<need all residues for whatever example is chosen based on use case> (first 20 residues of a BRCA1 protein)



Proposed Disposition


Proposed Disposition Comment

Sounds like this might be a clarification helping to make the definition and example simpler. Need to verify the proposed change is OK with the life sciences subject matter experts who originally helped develop the LSDAM semantics to ensure their use case is correctly represented.

Initial Discussion

Consider adding a storyboard explanation of examples threaded throughout the MB classes so that there is consistency across all the classes – perhaps a section in the User Guide or a new element in the model somewhere. Somatic mutations and germline might be good candidates for this. Need SMEs to identify use cases/stories that would be most meaningful for them. Consider also adding lessons learned re given use cases.

Outstanding Question

Can someone provide a comprehensive, realistic and meaningful set of example values that uses the same overall scenario across all classes in the Molecular Biology sub-domain?


Lauren Becnel: The new proposed definition is [good]. The example for BRCA is fine. Let me know what is not clear here, and I can help flesh out better.

Q from WENDY (TYPE: EX): I think what Mollie wanted us to put in there for the example is not the words "the first 20 residues of a BRCA1 protein", but the actual letter codes like "AMDYSLAAAL......" where we fill in the "......" part. Also, this is the initial comment that spawned the whole conversation at the WGM about creating a comprehensive example value set across all the MB classes. That one thing (comprehensive example value set) would eliminate tons of questions and make the model more user-friendly.

DISCUSSION 20160223: change the words “first 20 residues…” to “first 10 residues…”


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