Omics Modeling 11/28/2011

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

Topics for discussion today Classes related to Material – Review discussion on ProductPart, ProductRelationship and MaterialRelationship from last meeting (Slides from last meeting) – Review additional Material related classes, for example MaterialRelationship (LSDAM), ProductRelationship (BRIDG3.0.3), SpecimenCollectionGroup Protocol PointOfContact

Product Part from BRIDG 3.0.2

Material and Related Classes

Material and Related Classes (BRIDG 3.0.3)

MaterialRelationship (LSDAM) DEFINITION: Specifies the link between one material and another. Question? – Will this class be deleted from Omics DAM or – IS it okay to have both MaterialRelationship and ProductPart (from BRIDG reused in Omics DAM) in the Omics DAM? – Note: The renamed class has new attributes that are needed for research (JH). 11/22 BRIDG has a renamed ProductPart called ProductRelationship that has added attributes

Notes on ProductRelationship class (BRIDG 3.0.3) Attributes are very drug centric (Grace) in ProductRelationship class Issue: How to capture the drug and its ingredient relationships (e.g. Tylenol caplets and acetaminophen)? – Need to harmonize ProductRelationship (BRIDG 3.0.3) and Material Relationship (LSDAM). We will wait for LSDAM to harmonize the two classes. We will communicate this to LSDAM. At minimum we need the ProductRelationship attributes in the MaterialRelationship class…..and should be generalized to capture information on more than just drugs. Look into how the updated class would relate to software or equipment. – For now, 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. – Note: we are using ProductRelationship (BRIDG 3.0.3) and not ProductPart (BRIDG 3.0.2)

MaterialRelationship Attributes typeCode: Specifies the type of material relationship. – EXAMPLES: linkage, part subTypeCode: Further specifies the type of material relationship, based on the relationship type. – EXAMPLES: for linkage: entrapment, encapsulation; for part: core, shell, coat

ProductRelationship Class from BRIDG – 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)

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 typeocde while the other examples (package, content, ingredients) are values for typeCode. Joyce to reach out to BRIDG folks

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 is not clear. In what situations should we use ProductRelationship.identifier? For same ingredient used in multiple drugsSTART NEXT WEEK HERE

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

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.

Material and Related Classes

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..* Material) should be MaterialIdentfied-1..* Material as all BiologicSpecimens should have an identified for us to track them properly.

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

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

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

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

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

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.

PointOfContact Attributes telecomAddress: A sequence of digits or characters used to identify a particular telephone, fax, or 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 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.

Next Topic Document (i.e. including Publication) Data CellCulture StorageEquipment Container Place

Slides from last meeting

Omics Modeling 11/22/2011

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 – Biologic Specimen

Topics for discussion today Revisit modeling of NDC and UNII identifiers for Product Classes related to Material – For example MaterialRelationship, MaterialIdentifer, MaterialName, SpecimenCollectionGroup

NDC and UNII identifiers for Product The issue was discussed in last meeting and teh resolution is below – NDC and UNII can be handled by MaterialIdentifier from (BRIDG 3.0.2). The ProductPart class will be used to capture the relationships to build the product. For example, UNII will be given to the individual ingredients (e.g. Acetaminophen) while the NDC is given to the final product (e.g. Tylenol Caplets 500mg). ProductPart will be used to define the relationship between the final product and its composing materials e.g. Acetaminophen and Tylenol Caplets 500mg. – Note from JH: that we need to use the ProductRelationship class from BRIDG instead of ProductPart from BRIDG See slide 14 for resolution of this issue.

NDC and UNII identifiers for Product The issue was discussed in last meeting – Issue pending was regarding capturing Package information LS DAM has Container (defined as-An object that can be used to hold things.) BRIDG defines Package as A container within which the product is packaged or shipped Package information can be captured in the container class of LSDAM but may need review of the attributes and harmonize

Instance Diagram for NDC and UNII

Product Part from BRIDG 3.0.2

Material and Related Classes

MaterialName DEFINITION: The non-unique textual identification of a material in a specified context

MaterialName Attributes name: A non-unique textual identifier for the material. – EXAMPLE(S):The therapeutic agent used in a chemotherapy clinical trial. (11/22 Note: Need the name of the therapeutic agent as example). For example Taxol, paclitaxel typeCode: A coded value specifying the kind of material name. – EXAMPLE(S):brand name, generic

MaterialIdentifier DEFINTION: The unique identification of a material in a specific context. – NOTE(S): This class is a resolution of the requirement for noting the type of an identifier which is not handled by the purely technical HL7 II data type.

MaterialIdentifier Attributes Identifier: A unique symbol that establishes identity of the material. – EXAMPLE(S): serial number, product number, model number typeCode: A coded value specifying the kind of material identifier.

MaterialRelationship (LSDAM) DEFINITION: Specifies the link between one material and another. Question? – Will this class be deleted from Omics DAM or – IS it okay to have both MaterialRelationship and ProductPart (from BRIDG reused in Omics DAM) in the Omics DAM? – Note: The renamed class has new attributes that are needed for research (JH). 11/22 BRIDG has a renamed ProductPart called ProductRelationship that has added attributes

Notes on ProductRelationship class (BRIDG 3.0.3) Attributes are very drug centric (Grace) in ProductRelationship class Issue: How to capture the drug and its ingredient relationships (e.g. Tylenol caplets and acetaminophen)? – Need to harmonize ProductRelationship (BRIDG 3.0.3) and Material Relationship (LSDAM). We will wait for LSDAM to harmonize the two classes. We will communicate this to LSDAM. At minimum we need the ProductRelationship attributes in the MaterialRelationship class…..and should be generalized to capture information on more than just drugs. Look into how the updated class would relate to software or equipment. – For now, leave a note in the model that if the use case is related to DRUGS then use ProductRelationship class otherwise useuse MaterialRelationship e.g. for Nanoparticles.

MaterialRelationship Attributes typeCode: Specifies the type of material relationship. – EXAMPLES: linkage, part subTypeCode: Further specifies the type of material relationship, based on the relationship type. – EXAMPLES: for linkage: entrapment, encapsulation; for part: core, shell, coat

Material and Related Classes

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..* Material) should be MaterialIdentfied-1..* Material as all BiologicSpecimens should have an identified for us to track them properly.

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

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

Next Topic Protocol Point of Contact Document (i.e. including Publication) Data CellCulture StorageEquipment Container Place

Slides from previous meetings

Material and Related Classes (BRIDG 3.0.3)

Product Part from BRIDG 3.0.2

Material Relationship from LSDAM

Material and Few Related Classes

Product DEFINITION: A thing produced by or resulting from a process. – EXAMPLE(S): drug, device – The FDA list of regulated products: animal and human drugs; therapeutic biologics; allergenics; cell, tissue and gene therapy products; blood components; blood derivative products; devices; and animal (pets and livestock) and human food/feed (medicated and un-medicated); cosmetics; pet treats; and dietary supplements.

Product Attribute typeCode: A coded value specifying the kind of product. – EXAMPLE(S):veterinary medicine, diagnostic device – NOTE(S): All members of a type share similar functions and general characteristics, especially the purpose for which they are used.

Product Attribute lotNumberText: An alphanumeric string used to identify a particular batch of the product. expirationDate: The date (and time), assigned by the manufacturer, on which the product should not be used. Comment (Joyce/Helena-11/1/2011)- Do we need a National Drug Code? Or UNII to describe the drug (e.g. Acetaminophen)- Continue next week – Questions (11/8/2011): Is this an ID and can this be captured in a similar way as described for the Material (BiologicSpecimen multiple ID instance diagram)? Do we need both NDC and UNII ? and how would we model this? UNII- UniqueIngredientIdentifierUNII/default.htmhttp:// UniqueIngredientIdentifierUNII/default.htm NDC- (published 10/6/2011) – NDC code is at the product level and SRS is at the ingredients level. Is this correct? – How do we capture the ingredients (some are active some and in active). The SRS-UNII helps identify the ingredients uniquely. Need to bring in ProductRelationship class (3.0.3) or ProductPart (3.0.2) from BRIDG. Does MaterialRelationship class capture this? Does UNII belong within the ProductRelationship class (as id)?

Instance Diagram for NDC and UNII

Product Part from BRIDG 3.0.2

Material Relationship from LSDAM

Active IngredientsInactive Ingredients Caplet Acetaminophen 500 mg in each caplet Cellulose, corn starch, FD&C Red #40, hypromellose, magnesium stearate, polyethylene glycol, sodium starch glycolate Product-Ingredient Example For Instance Diagram

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..* Material) should be MaterialIdentfied-1..* Material as all BiologicSpecimens should have an identified for us to track them properly.

Material and Few Related Classes

Material A class adapted from BRIDG model. Definition: A physical substance. – EXAMPLE(S):drug, device, specimen Comment-Need to revisit the association cardinality (between Material and PerformedMaterialProcessStep)- A material after processing can produce more than 1 material.

Material Attribute nameCode: A coded value specifying the non- unique textual identifier for the material. – EXAMPLE(S): aspirin, tobacco, caffeine – NOTE(S): The granularity of the code may vary depending on the specificity of the material. For example, acetaminophen, Tylenol, Tylenol 250 mg gel cap. formCode: A coded value specifying the state and nature of the material. – EXAMPLE(S): solid, liquid, gas, tablet, ointment, gel

Material Attribute description: The textual representation of the material. effectiveDateRange: The date and time span for when the material is active.

Material Attribute (added by LSDAM) typeCode: Indicates the type of material. – EXAMPLES: protein material, DNA material subTypeCode: The class of a specimen that involves……??? – EXAMPLES: tissue, fluid, cell, molecular Questions – If the class is modified from BRIDG then shouldnt LSDAM to rename the class? – The typecode and subtype code needs to be flipped around i.e. type examples are in subtype and subtype examples are in type? – Change Request- a)The typeCode and subTypeCode needs to be flipped (as molecular can not be subtype of DNA). b)The definition for subTypeCode needs to be completed

Material Attribute (added by LSDAM) functionTypeCode: The characteristic behavior of the material that results from the chemical and physical composition and properties of the entity. – EXAMPLES:kinase, RNAse