Omics Modeling

10/18/2011

Classes reviewed until last meeting– Person– BiologicEntity– Subject– SubjectIdentifier– Performer– ExperimentalStudy– Experiment– ExperimentalFactor– Activity and subclasses (defined, Planned, Performed

Activity)

Classes for discussion today

• Experimental Parameters (String Parameter, Numerical Parameter)

• Software• Equipment• ExperimentalItem

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

class LSDAM - Core Experiment plus related_for_CG_OmicsDAM

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)

class LSDAM - Core Experiment plus related_for_CG_OmicsDAM

Protoc ol

+ name: ST

Experiment

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

Experimenta lParameter

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

NumericParameter

+ value: PQ+ range: IVL<PQ>

StringPa rameter

+ value: ST

0..*

is performed as per /describes the steps toconduct

0..*

1

includes / is part of0..*

0..*

specifies / is defined by

0..*

0..*

specifies / is defined by

0..*

Association to Protocol and Experiment

Association to Software and Equipment

class LSDAM - Core Experiment plus related_for_CG_OmicsDAM

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>

Experimenta lParameter

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

NumericParameter

+ value: PQ+ range: IVL<PQ>

StringPa rameter

+ value: ST

0..*

specifies the use of /specified by

0..*

0..*

uses / defines use of

0..*

0..*

uses / defines use of

0..*

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.

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.

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

Equipment Attributes

• reprocessedDeviceCode: A coded value specifying whether a device is reconditioned.– EXAMPLE(S): initial use of device, reuse, unknown

• manufactureDate: The date (and time) on which the medical 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

class LSDAM - Core Experiment plus related_for_CG_OmicsDAM

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

includes / is part of0..*

Next Topic

• Protocol• Document (i.e. including Publication)• Point of contact• Data• Material and related class

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 last meeting

Experimental Study and Experiment

class LSDAM - Core Experiment plus related_for_CG_OmicsDAM

Experiment

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

ExperimentalStudy

+ name: ST+ activeDateRange:

IVL<TS>+ typeCode:

DSET<CD>+ designType:

DSET<SC>+ description: ST

1

includes / is part of0..*

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

0..*

1

includes / is part of0..*

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