1. Omics Modeling 12/06/2011

2. Classes reviewed until last meeting – Person – BiologicEntity – Subject – SubjectIdentifier – Performer – ExperimentalStudy – Experiment – ExperimentalFactor – Activity and subclasses (defined, Planned, Performed Activity) – ExperimentalParameters (String Parameter, Numerical Parameter) – Software – Equipment – ExperimentalItem – Material – Product – Material Name – Material Identifier – Biologic Specimen – MaterialRelationship (LSDAM) and ProductRelationship (BRIDG 3.0.3) continued – SpecimenCollectionGroup – Protocol – PointOfContact – Data – Finding – Biomarker

3. Topics for discussion today Model Review – StorageEquipment – Container – Place Use Case Review

4. StorageEquipment

5. DEFINITION:Equipment that is used for storage purposes. EXAMPLES: freezers

6. StorageEquipment Attributes dimensionOneCapacity: The maximum amount that can be contained, in the first dimension of size of the equipment. dimensionOneLabel:A descriptive marker assigned to the first dimension of the container. – EXAMPLES: rows, columns dimensionTwoCapacity: The maximum amount that can be contained, in the second dimension of size of the equipment.

7. StorageEquipment Attributes dimensionTwoLabel: A descriptive marker assigned to the second dimension of the container. – EXAMPLES: rows, columns dimensionThreeCapacity: The maximum amount that can be contained, in the third dimension of size of the equipment. dimensionThreeLabel: A descriptive marker assigned to the third dimension of the container. – EXAMPLES: rows, columns

8. StorageEquipment Attributes dimensionPointOfOrigin: The point within the container from which definition of container capacity originates. – EXAMPLES:bottom left corner, upper left corner

9. Container DEFINITION: An object that can be used to hold things. EXAMPLES: slide, tube, box, rack

10. Container Attribute Name:A non-unique textual identifier for the container. containerType:Container type in which specimen is placed – EXAMPLE(S): clot tube, KEDTA, ACD, sterile specimen cup dimensionOneCapacity: The maximum amount that can be contained, in the first dimension of size of the container.

11. Container Attribute dimensionOneLabel:A descriptive marker assigned to the first dimension of the container. – EXAMPLE(S):rows, columns dimensionTwoCapacity: The maximum amount that can be contained, in the second dimension of size of the container. dimensionTwoLabel: A descriptive marker assigned to the second dimension of the container.

12. Container Attribute dimensionThreeCapacity: The maximum amount that can be contained, in the third dimension of size of the container. dimensionThreeLabel: A descriptive marker assigned to the third dimension of the container. – EXAMPLE(S):rows, columns dimensionPointOfOrigin: The point within the container from which definition of container capacity originates. – EXAMPLE(S): bottom left corner, upper left corner

13. Container Attribute Description: The textual representation of the container.

14. Place

15. DEFINITION: A bounded physical location which may contain structures. EXAMPLE(S):ambulance, helicopter, manufacturing site, service delivery location, home, emergency department, surgical suite, patient room

16. Place NOTE(S) (from LSDAM model): – Constraints: Place may be natural or man-made. The geographic position of a place may or may not be constant. – Discussion: Places may be work facilities (where relevant acts occur), homes (where people live) or offices (where people work). Places may contain sub-places (floor, room, booth, bed). Places may also be sites that are investigated in the context of health care, social work, public health administration (e.g., buildings, picnic grounds, day care centers, prisons, counties, states, and other focuses of epidemiological events).

17. Use Cases

18. Next Topic Document (i.e. including Publication) CellCulture

19. Use Case Review In scope uses cases from Gene Expression DAM (Refer- previously balloted; Gene Expression Domain Analysis Model_Version2_May-2010_Ballot) – 2.1 Sponsor-Agency Storyboard – 2.2 Sponsor-Lab Storyboard: – 2.3 Healthcare Breast Cancer Recurrence Risk Assessment Using Gene Expression Profiling

20. Slides from last meeting

21. Product Part from BRIDG 3.0.2

22. Material and Related Classes

23. Material and Related Classes (BRIDG 3.0.3)

24. ProductRelationship Class from BRIDG 3.0.3 – Needs to be added to omics DAM – We will leave a note in the model that if the use case is related to DRUGS then use ProductRelationship class otherwise use MaterialRelationship e.g. for Nanoparticles. (from 11/22 discussion)

25. ProductRelationship DEFINITION: Specifies the link between one product and another. EXAMPLE(S): lot, content, kind, part, ingredient, package, assembly, specialized, equivalent Note 11/28: Lot may not be a good example as we are using the Material Identifier to define the Lot number. LotNumber is an attribute of Product. So, decided to delete Lot from eg. – Updated Example: content, kind, part, ingredient, package, assembly, specialized, equivalent What is the use case for giving kind as an example. Kind is a same things as typecode while the other examples (package, content, ingredients) are values for typeCode. AI: Joyce to reach out to BRIDG folks

26. ProductRelationship Attributes Identifier: A unique symbol that establishes identity of the product within the context of another product. NOTE(S): There are multiple ways in which an identifier can be associated to a product; inherited from MaterilaIdentifier.identifier, the association to ProcessedProduct.identifier, and the association to ProductRelationship.identifier. If there is no context associated with the identifier, then MaterialIdentifier.identifier should be used. However, if the identifier for a product would be different in different context, one of the other identifiers should be used. If the product is used in multiple assemblies, and in each assembly it would be assigned a different identifier, then ProductRelationship.identifier should be used. If a kind of product is produced by different processors, and each processor assigns the product a different identifier, then ProcessedProduct.identifier should be used. Notes 11/28: The note above from BRIDG 3.0.3 is not clear. In what situations should we use ProductRelationship.identifier? For same ingredient used in multiple drugs… 12/6/2011: AI: to revisit the note in future. An example would help. Joyce has reached out to BRIDG team and Juli Evans will reach out to developers with a use case provided by Joyce

27. ProductRelationship Attributes typeCode: A coded value specifying the kind of relationship a product has with another product. – EXAMPLE(S): lot, content, kind, part, ingredient, package, assembly, specialized, equivalent Quantity: An indication of the amount of one product contained in another product. – EXAMPLE(S): 50 mg per tablet; 300 ml / liter

28. ProductRelationship Attributes confidentialityCode: A coded value specifying the privacy requirements for information about this relationship. – EXAMPLE(S):A manufacturer considers an ingredient in a product to be a trade secret. activeIngredientIndicator: Specifies whether the ingredient is an active ingredient. effectiveDateRange: The date and time span for when the product relationship is active.

29. Material and Related Classes

30. BiologicSpecimen Definition: Any material sample taken from a biological entity, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products (source: NCIt, modified). Question- Where is the specimen quantity captured? The specimen quality is captured in PerformedSpecimenReviewResult. Comment/Change request- Add to constraints for BilogicSpecimen class- Cardinality of association between (MaterialIdentfied-0..* --- 1-Material) should be MaterialIdentfied-1..* --- 1-Material as all BiologicSpecimens should have an identified for us to track them properly.

31. SpecimenCollectionGroup DEFINITION: Represents a group of specimens collected from the same participant in the same accession event.

32. SpecimenCollectionGroup Attributes name: Unique name given to the specimen collection group

33. Protocol

34. DEFINITION: A composite activity that serves as a rule which guides how activities should be performed.

35. Protocol Attribute name: The designation by which the protocol is referenced.

36. PointOfContact DEFINITION: A person or organization (e.g., helpdesk) serving as the coordinator or focal point of an activity or program.

37. PointOfContact Attributes typeCode: A coded value specifying the kind of role the contact person plays. – EXAMPLES: Principal Investigator, Submitter, Research Technician, Service Representative postalAddress: A contact point used to send physical forms of communication to the person.

38. PointOfContact Attributes telecomAddress: A sequence of digits or characters used to identify a particular telephone, fax, or email of the person. – EXAMPLE(S):The set of digits that serves as the address for a telephone device. Included in the phone number are country, city, and area codes needed to uniquely address the telephone. A URL or e-mail would be similarly described. effectiveDateRange: The date and time span for when the point of contact is active. primaryIndicator: Specifies whether this is the main or principal point of contact.

39. Data

40. DEFINITION: A collection or single item of factual information, derived from measurement or research or other data, from which conclusions may be drawn.

41. Data Attribute creationDate: The datetime on which the data was created.

42. Finding

43. DEFINITION: An interpretation of results of an experiment.

44. Biomarker DEFINITION: Measurable and quantifiable biological parameters (e.g., specific enzyme concentration, specific hormone concentration, specific gene phenotype distribution in a population, presence of biological substances) which serve as indices for health- and physiology-related assessments, such as disease risk, psychiatric disorders, environmental exposure and its effects, disease diagnosis, metabolic processes, substance abuse, pregnancy, cell line development, epidemiologic studies, etc. (Source: MESH) Notes (12/6/2011): Joyce will try to map the Viral Genetics data that she has to the DAM-Start here next week.