Omics Modeling 11/15/2011. Classes reviewed until last meeting – Person – BiologicEntity – Subject – SubjectIdentifier – Performer – ExperimentalStudy

Omics Modeling

11/15/2011

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

Topics for discussion today

• Material (BiologicSpecimen) instance diagram to show how multiple identifiers can be assigned to the Material.

• Classes related to Material – For example Product, BiologicSpecimen,

MaterialRelationship, MaterialIdentifer, MaterialName, SpecimenCollectionGroup

Instance diagram-Multiple identifiers assigned to a Material

• Refer to instance diagram (in the model)– Omics DAM- Instance Diagrams -

BiologicSpecimen with multiple identifiers

Material and Few Related Classesclass 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

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

specializesspecializes

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-

http://www.fda.gov/ForIndustry/DataStandards/SubstanceRegistrationSystem-UniqueIngredientIdentifierUNII/default.htm

• NDC-http://www.fda.gov/Drugs/InformationOnDrugs/ucm142438.htm (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)?



http://www.fda.gov/Drugs/InformationOnDrugs/ucm142438.htm

Instance Diagram for NDC and UNII

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 Relationship from LSDAMclass LSDAM - Specimen

Material

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

BiologicSpecimen

Product


MaterialRe lationship

+ typeCode: CD+ subTypeCode: CD

MaterialName

+ name: EN.TN+ typeCode: CD

MaterialIdentifier


specializes

0..*

identifies

1

1. .*

names /isnam edby

1

specializes

1

functions as / is afunction performedby

0..*

1

has / is a part of

0..*

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

Material and Related Classesclass LSDAM - Specimen

Material


BiologicSpecimenProduct


Equipment

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



MaterialName


MaterialIdentifier


SpecimenCollectionGroup

+ name: ST

specializes

specializes

0..*

identifies

1

1. .*

names/ isnam edby

1

specializes

1


0..*

1

has / is a part of

0..*

0..*is part of / is composedof

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.

• typeCode: A coded value specifying the kind of material name.– EXAMPLE(S):brand name

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..*

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.

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

TO DO

• Add slides on Product Relationship and Product Part class and attribute.

Material and Related Classesclass LSDAM - Specimen

Material


BiologicSpecimenProduct


Equipment

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



MaterialName


MaterialIdentifier



+ name: ST

specializes

specializes

0..*

identifies

1

1. .*

names/ isnam edby

1

specializes

1


0..*

1

has / is a part of

0..*

0..*is part of / is composedof

1


• 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 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

Software

• Definition: A set of coded instructions, which a computer follows in processing data, performing an operation, or solving a logical problem, upon execution of the program.

Software Attributes• identifier: A unique symbol that establishes

identity of the software. – EXAMPLE(S): serial number, product number

• name: The non-unique textual identifier for the software.

• version: A form or variant of a type or original; one of a sequence of copies of a software each incorporating new modifications.

Notes: 10/25/2011- We may need to revisit the class when we are talking about cloud computing as some of the attributes may not be known (e.g. identifier).

Software Attributes• typeCode: A coded value specifying the kind of

software product. – EXAMPLE(S): data collection, instrument controlling,

data analysis, word processing, image processing, productivity, operating system

• licenseTypeCode: A coded value specifying the kind of license through which the software is available.– EXAMPLE(S):multi-site, open source, single user

• licenseEffectiveDateRange: The date and time span for when the license for this software is active.

Software Attributes• buildNumber: A non-unique identifier assigned to identify the

compiled version of the software.• buildDate: The date on which the particular state of software

was produced.• licenseKey: A non-unique textual key that certifies that the

copy of the program is original.• effectiveDateRange: The timeframe within which the software

may be used.• content: The source or binary file.Notes 10/25/2011 (Michael)- Do we really need licenseKey and content? Grace-Needed to support

LIMS. Content would be needed for the code that someone wrote (custom software). Need to revisit. Additional attributes for consideration (not a major issue)- a) URL (where open source or free software is available) to download or purchase

Equipment• An object intended for use whether alone or

in combination for diagnostic, prevention, monitoring, therapeutic, scientific, and/or experimental purposes. – EXAMPLE(S):tongue depressor, pacemaker, insulin

pump, EKG machine, x-ray machine, mass spectrometer, polymerase chain reaction (PCR) machine, microscope, pH meter

• Updated Definition: An object intended for use whether alone or in combination for diagnostic, prevention, monitoring, therapeutic, scientific, analytical, and/or experimental purposes.

Equipment Attributes

• reprocessedDeviceCode: A coded value specifying whether a device is reconditioned.– EXAMPLE(S): initial use of device, reuse, unknown– Comment (10/25/2011)- The class Equipment is

called Device in BRIDG. The class name is modified in LSDAM but not the attribute name. Suggest removing Device from attribute name

– Updated Attribute Name: reprocessedCode

Equipment Attributes

• manufactureDate: The date (and time) on which the medical device is made.– Comments (10/25/2011)The device should not be just medical device

as the equipment definition is broader.– Updated definition- The date (and time) on which the device is made.

• validationDate: The date (and time) on which the equipment is validated.

ExperimentalItem

• Definition-Entities used in the execution of an experiment.

ExperimentalItem Attributes

• typeCode: A code representing the role an entity plays in an experiment.– EXAMPLES: reagent, host, sample, data collection

tool, analytical tool• Notes 10/25/2011 (Grace)-DNA could be a reagent (Herring sperm DNA)

and would be different from patient DNA (sample). The role class helps captures this information.

• - (Joyce) Would need to bring in the entities that are needed for the experiment and are missing from the model.

• Revisit when we are reviewing Protocol class as these details could be captured in Protocol.


Protoc ol

+ name: ST

Experiment

+ name: ST+ activeDateRan ge: 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>+ description: ST

Software

+ identifier: DSET<II>+ name: ST+ version: ST+ typeCode: CD+ licenseTypeCode: CD+ licenseEffectiveDateRange:

IVL<TS.DATE>+ buildNumber: ST+ buildDate: TS.DATE+ licenseKey: ST+ effectiveDateRange:

IVL<TS>+ content: ED

ExperimentalFactor

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

0..*is performed as per /describes the steps toconduct

0..*

1

includes / is part of0..*

0..*

is played by / plays0. .1

0..*

is used by / uses

0..*

0..*

uses / is used by

0..*

0..*

is performed as per /describes the steps toconduct

0..*

0..*

specified by / specifies the use of

0..*

0..*

participates in / is performedo n

0..*

0. .1is a collection of /isconducted as part of0..*

0..*

participates in / isperformed on

0..*

1


Experimental Parameters

• Definition- Any factor that defines a system and determines (or limits) its performance. – EXAMPLES: incubation temperature, number of

mismatches in a BLAST search, scanning wavelength


Experimenta lParameter

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

NumericParameter

+ value: PQ+ range: IVL<PQ>

StringParameter

+ value: ST

Experimental Parameters Attributes

• name: A word or phrase that constitutes the distinctive designation of a parameter. – EXAMPLES: incubation temperature, scanning

wavelength

• typeCode: A term allowing the classification of parameters into categories. – EXAMPLES: centrifuge input, software analysis

Experimental Parameters Attributes

• description: A textual representation of the parameter.– EXAMPLE: temperature setting for centrifugation

procedure; analysis start point for GeneMapper 3.7

• statusCode-Indicates the condition of use of the parameter at the current time. – EXAMPLES: active, inactive, deprecated

NumericParameter (rename to PhysicalQuantityParameter)

• Definition- The numeric value associated with the experimental parameter.

• Proposed Definition- The value associated with the experimental parameter.

[Reason- as this class captures the numeric value with the optional unit (there is unit associated to the value the value captured can be more that just a number) e.g. temperature = 79.4 Degree Celsius, mass = 4 pounds]

NumericParameter Attribute

• value: The single numeric value assigned to the defined experimental parameter.– EXAMPLES: 2 minutes, 4 degrees Celsius

Proposed Definition-• value: The single numeric value with its

optional unit assigned to the defined experimental parameter. – EXAMPLES: 2 minutes, 4 degrees Celsius

NumericParameter Attribute

• range: The numeric value range assigned to the defined experimental parameter, when a range value of values is called for.– EXAMPLES: 1-4 minutes, 3-8 degrees CelsiusProposed definition

• range: The numeric value range with its optional unit assigned to the defined experimental parameter, when a range of values is called for.– EXAMPLES: 1-4 minutes, 3-8 degrees Celsius

StringParameter

• Definition- The text value associated with the experimental parameter.

StringParameter Attribute

• value: The single non-numeric value assigned to the defined experimental parameter.

Proposed Definition-• value: The single textual value assigned to the

defined experimental parameter.(Reason- non numeric is not the best way to

define String)


Protoc ol

+ name: ST

Experiment




NumericParameter


StringPa rameter

+ value: ST

0..*

is performed as per /describes the steps toconduct

0..*

1


0..*

specifies / is defined by

0..*

0..*

specifies / is defined by

0..*

Association to Protocol and Experiment

Association to Software and Equipment


Software

+ identifier: DSET<II>+ name: ST+ version: ST+ typeCode: CD+ licenseTypeCode: CD+ licenseEffectiveDateRange:

IVL<TS.DATE>+ buildNumber: ST+ buildDate: TS.DATE+ licenseKey: ST+ effectiveDateRange:

IVL<TS>+ content: ED

Equipment

+ reprocessedDe viceCode: CD+ manufactureDate : TS.DATETIME+ validationDate: DSET<TS.DATETIME>



NumericParameter


StringPa rameter

+ value: ST

0..*

specifies the use of /specified by

0..*

0..*

uses / defines use of

0..*

0..*

uses / defines use of

0..*

StringParameter.valueAttribute example1: GeneMapper 3.7

input parameterexample1: GeneMapper 3.7 input parameter

Parameter

Parameter.dataValue G5 2100

Parameter.description GeneMapper v3.7 Dye Set G5 for 5 color dye analysis modules.

Analysis end point for GeneMapper v3.7

Parameter.name GM37_DyeSet GM37_Start

Parameter.statusCode active active

Parameter.typeCode softwareAnalysis softwareAnalysis

Parameter.range NA

Slides from previous meetings

Experimental Study and Experiment


Experiment


ExperimentalStudy

+ name: ST+ activeDateRange:

IVL<TS>+ typeCode:

DSET<CD>+ designType:

DSET<SC>+ description: ST

1


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

0..*

1


sharmam

The Cardinality needs to be changed from 0..1 to 0 to many (Experiment--Experimental Study)

Definitions

• ExperimentStudy-– Current Definition: A detailed examination or

analysis designed to discover facts about a system under investigation. Systems may include intact organisms, biologic specimens, natural or synthetic materials, diseases, and pathways.

– The definition is application for research, clinical studies and clinical diagnosis that involves molecular testing.

Definitions

• Experiment-– Current Definition: A coordinated set of actions

and observations designed to generate data, with the ultimate goal of discovery or hypothesis testing.

– Proposed Definition: A coordinated set of actions and observations designed to generate data, with the ultimate goal of either discovery/hypothesis or diagnostic testing.

ExperimentalStudy Attributes• name: A non-unique identifier by which the experimental

study is know or referred.• activeDateRange: The timeframe within which the

experiment is ongoing.• typeCode: Identifies the type of experimental study.

EXAMPLES: microarray experiment, model organism experiment

• designType: A term allowing the classification of the study based on the overall experimental study design. EXAMPLES: time-course design, cross-over design, parallel group design, titration study.

• Description: A textual explanation of the study, with components, such as objectives or goals. (source: ISA-TAB)

Experiment Attribute• name: The designation by which an experiment is referenced.• activeDateRange: The timeframe within which the experiment is ongoing.• typeCode: Identifies the type of experiment.

EXAMPLES: microarray experiment, model organism experiment• designType: A term allowing the classification of the experiment based on

the overall experimental design. EXAMPLES: factorial designs, covariance designs, blocking designs. – Comment (Michael Miller): Do we need the designType in class experiment?

It seems duplicate of ExperimentalStudy. Are there examples that show a ExperimentalStudyDesign deciding the design of the Experiment (ExperimentDesign)?

– TCGA project is nested at top design type is multi-omics, within that multiple omics experiments-within which multiple centers producing data through “runs”

• Description: A textual explanation of the experiment, with components, such as objectives or goals. (source: ISA-TAB)

Other Topics Discussed today • Activity and subclasses (defined, Planned, Performed Activity) and relationship to

ExperimentalStudy and Experiment.

• ExperimentalFactor– Question (9/29/2011) Michael in Omics call- The Experimenatalfactor has an attribute value

as DSET but in the current model we can not associate an experiment to an individual time (we will have all the time associated to the experiment).

– Suggestion to LSDAM- Create a separate class called "ExperimentFactorValue". Attributes- 1) value 2) unit. The class will exist between Experimental Factor and Experiment. (Business rule: An experiment has one and only 1 value for each experimental factor).

– Would need to delete "Value" attribute from ExperimentalFactor.

– Change Request sent to Lisa (9/27/2011)

– Need to make change in our model here.

Next Topic

• ExperimentalItem• Material and related class

Documents

Omics Modeling 11/15/2011. Classes reviewed until last meeting – Person – BiologicEntity – Subject – SubjectIdentifier – Performer – ExperimentalStudy