Omics Modeling 11/01/2011

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

Classes for discussion today Material Other classes related to Material (e.g. Product, BiologicSpecimen, MaterialRelationship, MaterialIdentifer, MaterialName, SpecimenCollectionGroup)

Material and Few Related Classes

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 shouldnt 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

Material and Few Related Classes

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)- Do we need a NDC code? or SRS number to describe the drug (e.g. Acetaminophen)-Continue next week

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

Material and Related Classes

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

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 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

Material and Related Classes

SpecimenCollectionGroup 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 last meeting

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.

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

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 Celsius Proposed 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)

Association to Protocol and Experiment

Association to Software and Equipment

StringParameter.value Attributeexample1: GeneMapper 3.7 input parameter Parameter Parameter.dataValueG52100 Parameter.descriptionGeneMapper v3.7 Dye Set G5 for 5 color dye analysis modules. Analysis end point for GeneMapper v3.7 Parameter.nameGM37_DyeSetGM37_Start Parameter.statusCodeactive Parameter.typeCodesoftwareAnalysis Parameter.rangeNA

Slides from previous meetings

Experimental Study and Experiment

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