Protein

: Public Class

Created:	9/9/2008 4:05:40 PM
Modified:	3/26/2015 6:04:07 PM

Project:
Author:
Version:	1.0
Phase:	1.0
Status:
Complexity:	Easy
Difficulty:
Priority:
Multiplicity:
Advanced:
UUID:	{0BAEBAD3-7914-4c24-A811-F98252387CC0}
Appears In:	UML-Based Comprehensive BRIDG Model Diagram, View EX: Experiment, View MB: Molecular Biology

DEFINITION: A representation of an organic macromolecule in public resources (e.g., UniProt or NCBI RefSeq) composed of one or more chains (linear polymers) of alpha-L-amino acids linked by peptide bonds and ranging in size from a few thousand to over 1 million Daltons. Comment Requested: In interest of re-using existing standards, should the above definition of Protein be replaced by the following from the NLM -- : A molecule made up of amino acids that are needed for the body to function properly. Proteins are the basis of body structures such as skin and hair and of substances such as enzymes, cytokines, and antibodies. [Source: http://ghr.nlm.nih.gov/glossary=protein] EXAMPLE(S): A protein record from UniProt Knowledgebase: http://www.uniprot.org/uniprot/P38398 OTHER NAME(S): NOTE(S):

Attributes
Associations To
Associations From
Tagged Values

Attribute

Public DSET<SC>
name

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to *
Transient:	False
Derived:	False
IsID:	False

Map:LSDAM=Protein.symbol
Map:LSDAM=Protein.name
Map:PGx v1.0=PB.PBGENRI

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;A textual identifier using human-readable language identifying a protein defined by an organization that assigns such things.#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S): #lt;br /#gt;#lt;/p#gt;#lt;p#gt;Breast cancer type 1 susceptibility protein#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;Question for SMEs: Question for SMEs: Should this attribute be remodeled in a related class with an association to the Organization class to represent the organization assigning the name?#lt;br /#gt;#lt;/p#gt;

Public DSET<SC>
symbol

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to *
Transient:	False
Derived:	False
IsID:	False

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;An acronym, abbreviation or other short name for a protein defined by an organization that assigns such things.#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S): #lt;br /#gt;#lt;/p#gt;#lt;p#gt;BRCA1 protein#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;Question for SMEs: Should this attribute be remodeled in a related class with an association to the Organization class to represent the organization assigning the symbol?#lt;br /#gt;#lt;/p#gt;

Element	Source Role	Target Role
Material Class	Name: characterizingProtein	Name: characterizedMaterial
Details: DESCRIPTION:<br /></p><p>Each Protein might characterize one or more Material. Each Material might be characterized by one or more Protein.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
AminoAcidSequence Class	Name: representedProtein	Name: representingAminoAcidSequence
Details: DESCRIPTION:<br /></p><p>Each Protein might be represented by one or more AminoAcidSequence. Each AminoAcidSequence might represent one or more Protein.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>

Element	Source Role	Target Role
ProteinIdentifier Class	Name: identifyingProteinIdentifier	Name: identifiedProtein
Details: DESCRIPTION:<br /></p><p>Each ProteinIdentifier always identifies one Protein. Each Protein might be identified by one or more ProteinIdentifier.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
Pathway Class	Name: involvingPathway	Name: involvedProtein
Details: DESCRIPTION:<br /></p><p>Each Pathway might involve one or more Protein. Each Protein might be involved in one or more Pathway. <br /></p><p> <br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
MolecularBiomarkerGroup Class	Name: basingMolecularBiomarkerGroup	Name: basedProtein
Details: DESCRIPTION:<br /></p><p>Each MolecularBiomarkerGroup might be based on one or more Protein. Each Protein might be the basis of one or more MolecularBiomarkerGroup.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
Gene Class	Name: encodingGene	Name: encodedProtein
Details: DESCRIPTION:<br /></p><p>Each Gene might encode one or more Protein. Each Protein might be encoded by one or more Gene.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
Biomarker Class	Name: basingBiomarker	Name: basedProtein
Details: DESCRIPTION:<br /></p><p>Each Biomarker might be based on one or more Protein. Each Protein might be the basis of one or more Biomarker.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>

Tag	Value
Map:LSDAM	Protein
Details:
Map:LSDAMv2.2.3Plus	Protein
Details:
Map:PGx v1.0	PB.PBGENTYP
Details: