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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