omics modeling 11/28/2011. classes reviewed until last meeting – person – biologicentity –...

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 3.0.2class UML-Based Comprehensive BRIDG Model Diagram

BRIDG3.0.2 - Common Sub-Domain::Material

+ nameCode: CD+ formCode: CD+ description: ST+ actualIndicator: BL+ effectiveDateRange:

IVL<TS.DATETIME>

BRIDG3.0.2 - Common Sub-Domain::Product

+ nameCodeModifiedText: ST+ typeCode: CD+ classCode: DSET<CD>+ lotNumberText: ST.SIMPLE+ expirationDate: TS.DATE.FULL+ pre1938Indicator: BL::Material+ nameCode: CD+ formCode: CD+ description: ST+ actualIndicator: BL+ effectiveDateRange: IVL<TS.DATETIME>

constraints{Distributor Qualifier}{Processor Qualifier}{ProcessingSite Qualifier}

BRIDG3.0.2 - Common Sub-Domain::Drug

::Product+ nameCodeModifiedText: ST+ typeCode: CD+ classCode: DSET<CD>+ lotNumberText: ST.SIMPLE+ expirationDate: TS.DATE.FULL+ pre1938Indicator: BL::Material+ nameCode: CD+ formCode: CD+ description: ST+ actualIndicator: BL+ effectiveDateRange: IVL<TS.DATETIME>

BRIDG3.0.2 - Common Sub-Domain::Biologic


BRIDG3.0.2 - Common Sub-Domain::ProductPart

+ strength: RTO<PQ,PQ>+ activeIngredientIndicator: BL

BRIDG3.0.2 - Common Sub-Domain::MaterialName

+ name: TN+ typeCode: CD

BRIDG3.0.2 - Common Sub-Domain::

MaterialIdentifier

+ identifi er: II+ typeCode: CD

0..*

identifies

{is identifiedby}

1

0..*

is part of

{has as part}1

0..*

is a functio n performedby

{functions as}1

1. .*

names

{is named by} 1

Material and Related Classesclass LSDAM - Specimen

Material

+ nameCode: CD+ typeCode: CD+ subTypeCode: CD+ formCode: CD+ functionTypeCode: DSET<CD>+ descript ion: ST+ effectiveDateRange: IVL<TS.DATETIME>

BiologicSpecimenProduct

+ typeCode: CD+ lotNumberText : ST.SIMPLE+ expirationDate: TS.DATE.FULL

Equipment

+ reprocessedDeviceCode: CD+ manufactureDate : TS.DATETIME+ validationDate: DSET<TS.DATETIME>

MaterialRe lationship

+ typeCode: CD+ subTypeCode: CD

MaterialName

+ name: EN.TN+ typeCode: CD

MaterialIdentifier


SpecimenCollectionGroup

+ name: ST

specializes

specializes

0..*

identifies

1

1. .*

names/ isnam edby

1

specializes

1

functions as / is afunction performedby

0..*

1

has / is a part of

0..*

0..*is part of / is composedof

1

Material and Related Classes (BRIDG 3.0.3)class UML-Based Comprehensiv e BRIDG Model Diagram

Common Sub-Domain::Product

+ classCode: DSET<CD>+ codeModifiedText: ST+ expirationDate: TS.DATE.FULL+ lotNumberText: ST.SIMPLE+ pre1938Indicator: BL+ typeCode: CD::Material+ actualIndicator: BL+ code: CD+ description: ST+ effectiveDateRange: IVL<TS.DATETIME>+ formCode: CD


Common Sub-Domain::Package

+ capacityQuantity: PQ+ capTypeCode: CD+ handlingCode: CD::Product+ classCode: DSET<CD>+ codeModifiedText: ST+ expirationDate:

TS.DATE.FULL+ lotNumberText:

ST.SIMPLE+ pre1938Indicator: BL+ typeCode: CD::Material+ actualIndicator: BL+ code: CD+ description: ST+ effectiveDateRange:

IVL<TS.DATETIME>+ formCode: CD

Common Sub-Domain::Dev ice

+ /age: PQ.TIME+ availableForEvaluationIndicator: BL+ handlingCode: CD+ manufactureDate: TS.DATETIME+ overTheCounterProductIndicator: BL+ reprocessedDeviceCode: CD+ returnedToReprocessorDate:

TS.DATETIME+ riskCode: CD+ singleUseDeviceIndicator: BL::Product+ classCode: DSET<CD>+ codeModifiedText: ST+ expirationDate: TS.DATE.FULL+ lotNumberText: ST.SIMPLE+ pre1938Indicator: BL+ typeCode: CD::Material+ actualIndicator: BL+ code: CD+ description: ST+ effectiveDateRange: IVL<TS.DATETIME>+ formCode: CD

Common Sub-Domain::Drug

+ handlingCode: CD+ riskCode: CD+ stabilityDuration: IVL<TS.DATETIME>::Product+ classCode: DSET<CD>+ codeModifiedText: ST+ expirationDate: TS.DATE.FULL+ lotNumberText: ST.SIMPLE+ pre1938Indicator: BL+ typeCode: CD::Material+ actualIndicator: BL+ code: CD+ description: ST+ effectiveDateRange: IVL<TS.DATETIME>+ formCode: CD

Common Sub-Domain::Biologic


Common Sub-Domain::FoodProduct

+ stabilityDuration: IVL<TS.DATETIME>

::Product+ classCode: DSET<CD>+ codeModifiedText: ST+ expirationDate: TS.DATE.FULL+ lotNumberText: ST.SIMPLE+ pre1938Indicator: BL+ typeCode: CD::Material+ actualIndicator: BL+ code: CD+ description: ST+ effectiveDateRange:


Common Sub-Domain::Cosmetic

+ stabilityDuration: IVL<TS.DATETIME>::Product+ classCode: DSET<CD>+ codeModifiedText: ST+ expirationDate: TS.DATE.FULL+ lotNumberText: ST.SIMPLE+ pre1938Indicator: BL+ typeCode: CD::Material+ actualIndicator: BL+ code: CD+ description: ST+ effectiveDateRange: IVL<TS.DATETIME>+ formCode: CD

Common Sub-Domain::ProductRelationship

+ activeIngredientIndicator: BL+ confidentialityCode:

DSET<CD>+ effectiveDateRange:

IVL<TS.DATETIME>+ identifier: II+ quantity: RTO<PQ,PQ>+ typeCode: CD

+source

0..*

hasastarget{is the target for}

+target 1

+target

0..*

hasassource

{is thesourcefor}

+source 1

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 3.0.2 reused in Omics DAM) in the Omics DAM?

– Note: The renamed class has new attributes that are needed for research (JH).

• 11/22 BRIDG 3.0.3 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 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)

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

class UML-Based Comprehensive ...


+ identifier: II+ typeCode: CD+ quantity: RTO<PQ,PQ>+ confidentialityCode:

DSET<CD>+ activeIngredientIndicator: BL+ effectiveDateRange:

IVL<TS.DATETIME>

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—START 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




Equipment




MaterialName


MaterialIdentifier



+ name: ST

specializes

specializes

0..*

identifies

1

1. .*

names/ isnam edby

1

specializes

1


0..*

1

has / is a part of

0..*


1

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.


• 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 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.

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 3.0.3 instead of ProductPart from BRIDG 3.0.2. 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 3.0.3 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




IVL<TS.DATETIME>













MaterialIdentifier


0..*

identifies

{is identifiedby}

1

0..*

is part of

{has as part}1

0..*


{functions as}1

1. .*

names

{is named by} 1


Material




Equipment




MaterialName


MaterialIdentifier



+ name: ST

specializes

specializes

0..*

identifies

1

1. .*

names/ isnam edby

1

specializes

1


0..*

1

has / is a part of

0..*


1

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 3.0.3 reused in Omics DAM) in the Omics DAM?

– Note: The renamed class has new attributes that are needed for research (JH).

• 11/22 BRIDG 3.0.3 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




Equipment




MaterialName


MaterialIdentifier



+ name: ST

specializes

specializes

0..*

identifies

1

1. .*

names/ isnam edby

1

specializes

1


0..*

1

has / is a part of

0..*


1

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.


• 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)class UML-Based Comprehensiv e BRIDG Model Diagram

Common Sub-Domain::Product

+ classCode: DSET<CD>+ codeModifiedText: ST+ expirationDate: TS.DATE.FULL+ lotNumberText: ST.SIMPLE+ pre1938Indicator: BL+ typeCode: CD::Material+ actualIndicator: BL+ code: CD+ description: ST+ effectiveDateRange: IVL<TS.DATETIME>+ formCode: CD


Common Sub-Domain::Package

+ capacityQuantity: PQ+ capTypeCode: CD+ handlingCode: CD::Product+ classCode: DSET<CD>+ codeModifiedText: ST+ expirationDate:

TS.DATE.FULL+ lotNumberText:

ST.SIMPLE+ pre1938Indicator: BL+ typeCode: CD::Material+ actualIndicator: BL+ code: CD+ description: ST+ effectiveDateRange:


Common Sub-Domain::Dev ice

+ /age: PQ.TIME+ availableForEvaluationIndicator: BL+ handlingCode: CD+ manufactureDate: TS.DATETIME+ overTheCounterProductIndicator: BL+ reprocessedDeviceCode: CD+ returnedToReprocessorDate:

TS.DATETIME+ riskCode: CD+ singleUseDeviceIndicator: BL::Product+ classCode: DSET<CD>+ codeModifiedText: ST+ expirationDate: TS.DATE.FULL+ lotNumberText: ST.SIMPLE+ pre1938Indicator: BL+ typeCode: CD::Material+ actualIndicator: BL+ code: CD+ description: ST+ effectiveDateRange: IVL<TS.DATETIME>+ formCode: CD

Common Sub-Domain::Drug


Common Sub-Domain::Biologic


Common Sub-Domain::FoodProduct

+ stabilityDuration: IVL<TS.DATETIME>

::Product+ classCode: DSET<CD>+ codeModifiedText: ST+ expirationDate: TS.DATE.FULL+ lotNumberText: ST.SIMPLE+ pre1938Indicator: BL+ typeCode: CD::Material+ actualIndicator: BL+ code: CD+ description: ST+ effectiveDateRange:


Common Sub-Domain::Cosmetic

+ stabilityDuration: IVL<TS.DATETIME>::Product+ classCode: DSET<CD>+ codeModifiedText: ST+ expirationDate: TS.DATE.FULL+ lotNumberText: ST.SIMPLE+ pre1938Indicator: BL+ typeCode: CD::Material+ actualIndicator: BL+ code: CD+ description: ST+ effectiveDateRange: IVL<TS.DATETIME>+ formCode: CD


+ activeIngredientIndicator: BL+ confidentialityCode:

DSET<CD>+ effectiveDateRange:

IVL<TS.DATETIME>+ identifier: II+ quantity: RTO<PQ,PQ>+ typeCode: CD

+source

0..*

hasastarget{is the target for}

+target 1

+target

0..*

hasassource

{is thesourcefor}

+source 1




IVL<TS.DATETIME>













MaterialIdentifier


0..*

identifies

{is identifiedby}

1

0..*

is part of

{has as part}1

0..*


{functions as}1

1. .*

names

{is named by} 1

Material Relationship from LSDAMclass LSDAM - Specimen

Material


BiologicSpecimen

Product




MaterialName


MaterialIdentifier


specializes

0..*

identifies

1

1. .*

names /isnam edby

1

specializes

1


0..*

1

has / is a part of

0..*

Material and Few Related Classes

class LSDAM - Core Experiment plus related_for_CG_OmicsDAM

Material

+ nameCod e: CD+ typeCode: CD+ subTypeCode: CD+ formCode: CD+ functionTypeCode: DSET<CD>+ descript ion: ST+ effectiveDateRange: IVL<TS.DATETIME>

Biologic SpecimenProduct


specializesspecializes

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 shouldn’t 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

omics modeling 11/28/2011. classes reviewed until last meeting – person – biologicentity –...

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