Difference between revisions of "Discussion on examples and storyboard for AminoAcidSequence"
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− | ===Need clarification and storyboard for examples for AminoAcidSequence (row 18)=== | + | ===CLOSED - Need clarification and storyboard for examples for AminoAcidSequence (row 18)=== |
− | ====Original Definition | + | ====Original Definition==== |
DEFINITION: A representation of a linear arrangement of organic compounds containing amino (-NH2) and carboxyl (-COOH) groups. | DEFINITION: A representation of a linear arrangement of organic compounds containing amino (-NH2) and carboxyl (-COOH) groups. | ||
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note this is an example and not the first 20 residues | note this is an example and not the first 20 residues | ||
− | ====Proposed Definition | + | ====Proposed Definition==== |
DEFINITION: A representation of a linear arrangement of amino acids represented in single notation | DEFINITION: A representation of a linear arrangement of amino acids represented in single notation | ||
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====Outstanding Question==== | ====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? | |
====Responses==== | ====Responses==== | ||
− | + | 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. | ||
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+ | DISCUSSION 20160223: change the words “first 20 residues…” to “first 10 residues…” | ||
+ | |||
+ | UPDATES DONE IN MODEL | ||
Return to [[BRIDG]] | Return to [[BRIDG]] |
Latest revision as of 03:30, 26 February 2016
Return to BRIDG
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.
OTHER NAME(S):
NOTE(S):
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)
OTHER NAME(S):
NOTE(S):
Proposed Disposition
Persuasive
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?
Responses
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…”
UPDATES DONE IN MODEL
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