omics modeling 12/06/2011. classes reviewed until last meeting – person – biologicentity –...

Omics Modeling

12/06/2011

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– MaterialRelationship (LSDAM) and

ProductRelationship (BRIDG 3.0.3) continued

– SpecimenCollectionGroup– Protocol– PointOfContact– Data– Finding– Biomarker

Topics for discussion today• Model Review

– StorageEquipment– Container– Place

• Use Case Review

StorageEquipmentclass LSDAM - Full View

Material

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

Product

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

Equipment

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

Conta iner

+ name: ST+ containerType: CD+ dimensionOneCapacity: INT+ dimensionOneLabel: ST+ dimensionTwoCapacity: INT+ dimensionTwoLabel: ST+ dimensionThreeCapacity: INT+ dimensionThreeLabel: ST+ dimensionPointOfOrigin: ST+ descript ion: ST

MaterialRe lationship

+ typeCode: CD+ subTypeCode: CD

StorageEquipment

+ dimensionOneCapacity: INT+ dimensionOneLabel: ST+ dimensionTwoCapacity: INT+ dimensionTwoLabel: ST+ dimensionThreeCapacity: INT+ dimensionThreeLabel: ST+ dimensionPointOfOrigin: ST

0..*

is part of / includes

0. .1

0..*is enclosed by / encloses

1

1

has / is a part of

0..*

1

functions as / is a function performed by

0..*

specializes

specializes

StorageEquipment

• DEFINITION:Equipment that is used for storage purposes.

• EXAMPLES: freezers

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.

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

StorageEquipment Attributes• dimensionPointOfOrigin: The point within the

container from which definition of container capacity originates.– EXAMPLES:bottom left corner, upper left corner

Container

• DEFINITION: An object that can be used to hold things.

• EXAMPLES: slide, tube, box, rack

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.

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.

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

Container Attribute• Description: The textual representation of the

container.

Placeclass LSDAM - Container

Material::Equipment

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

Container

+ name: ST+ containerType: CD+ dimensionOneCapacity: INT+ dimensionOneLabel: ST+ dimensionTwoCapacity: INT+ dimensionTwoLabel: ST+ dimensionThreeCapacity: INT+ dimensionThreeLabel: ST+ dimensionPointOfOrigin: ST+ description: ST

Place

+ identifier: DSET<II>+ typeCode: CD+ physicalAddress: AD+ locatorTypeCode: CD+ locatorValue: ST

StorageEquipment

+ dimensionOneCapacity: INT+ dimensionOneLabel: ST+ dimensionTwoCapacity: INT+ dimensionTwoLabel: ST+ dimensionThreeCapacity: INT+ dimensionThreeLabel: ST+ dimensionPointOfOrigin: ST

0..*

is located at/is the locationof

1

0..*

is enclosed by / encloses1

0..*

is part of / includes

0..1

0..*

is containedin0..1

Place• 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

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).

Use Cases

Next Topic

• Document (i.e. including Publication)• CellCulture

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

Slides from last meeting

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

::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::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


BiologicSpecimenProduct


Equipment




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

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

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

+ 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::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:

IVL<TS.DATETIME>+ formCode: CD

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

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

class UML-Based Comprehensive ...

Common Sub-Domain::ProductRelationship

+ 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…

• 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

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 Classesclass LSDAM - Specimen

Material


BiologicSpecimenProduct


Equipment




MaterialName

+ name: EN.TN+ typeCode: CD

MaterialIdentifier



+ 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

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

Protocolclass LSDAM - Experiment and Result

Protocol

+ name: ST

Experiment

+ name: ST+ activeDateRange: IVL<TS>+ typeCode: CD+ designType: DSET<SC>+ descript ion: ST

Experime ntalItem

+ typeCode: CD

constraints{ExclusiveOr}

ExperimentalStudy

+ name: ST+ activeDateRange: IVL<TS>+ typeCode: DSET<CD>+ designType: DSET<SC>+ descript ion: ST

Data

+ creationDate: TS.DATETIME

ExperimentalFactor

+ name: ST+ typeCode: SC+ value: DSET<ANY>

Experimenta lParameter

+ name: ST+ typeCode: CD+ descript ion: ST+ statusCode: CD

0..*

is processed into / is processed from1

0..* is the result o f / results in

0..*

0..*

is used by / uses

0..*1

includes / is part of0..*

0..*

specifies / is defined by0..*

0..*

is performed as per / describesthe steps to conduct

0..*

1


0..*

specifies / is defined by

0..*

0..*

participates in / is performedon

0..*

0..*

participates in / isperformed on

0..*

0..*

is played by / plays

0. .1

0..*

is performed as per / describesthe steps to conduct 0..*

0..*uses / is used by0..*

0. .1is a collection of /isconducted as part of

0..*

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.

Dataclass LSDAM - Experiment and Result

Protocol

+ name: ST

Experiment

+ name: ST+ activeDateRange: IVL<TS>+ typeCode: CD+ designType: DSET<SC>+ descript ion: ST

Experime ntalItem

+ typeCode: CD

constraints{ExclusiveOr}

ExperimentalStudy

+ name: ST+ activeDateRange: IVL<TS>+ typeCode: DSET<CD>+ designType: DSET<SC>+ descript ion: ST

Data


ExperimentalFactor

+ name: ST+ typeCode: SC+ value: DSET<ANY>

Experimenta lParameter

+ name: ST+ typeCode: CD+ descript ion: ST+ statusCode: CD

0..*

is processed into / is processed from1

0..* is the result o f / results in

0..*

0..*

is used by / uses

0..*1


0..*

specifies / is defined by0..*

0..*

is performed as per / describesthe steps to conduct

0..*

1


0..*

specifies / is defined by

0..*

0..*

participates in / is performedon

0..*

0..*

participates in / isperformed on

0..*

0..*

is played by / plays

0. .1

0..*

is performed as per / describesthe steps to conduct 0..*

0..*uses / is used by0..*

0. .1is a collection of /isconducted as part of

0..*

Data

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

Data Attribute

• creationDate: The datetime on which the data was created.

Finding

class LSDAM - Full View

Data


Finding

Bioma rker

+ name: ST+ typeCode: CD

0..*

results in /established by

0..*

0..*

is processed into / is processed from

1

0..*is interpreted into / isderive d from

0..*

Finding

• DEFINITION: An interpretation of results of an experiment.

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.

omics modeling 12/06/2011. classes reviewed until last meeting – person – biologicentity –...

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