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Omics Modeling

Omics Modeling. 11/15/2011. Classes reviewed until last meeting. Activity and subclasses (defined, Planned, Performed Activity) ExperimentalParameters (String Parameter, Numerical Parameter) Software Equipment ExperimentalItem Material. Person BiologicEntity Subject SubjectIdentifier

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Omics Modeling

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  1. Omics Modeling 11/15/2011

  2. Classes reviewed until last meeting • Activity and subclasses (defined, Planned, Performed Activity) • ExperimentalParameters (String Parameter, Numerical Parameter) • Software • Equipment • ExperimentalItem • Material • Person • BiologicEntity • Subject • SubjectIdentifier • Performer • ExperimentalStudy • Experiment • ExperimentalFactor

  3. 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

  4. Instance diagram-Multiple identifiers assigned to a Material • Refer to instance diagram (in the model) • Omics DAM- Instance Diagrams - BiologicSpecimen with multiple identifiers

  5. Material and Few Related Classes

  6. 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.

  7. 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.

  8. 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)?

  9. Instance Diagram for NDC and UNII

  10. Product Part from BRIDG 3.0.2

  11. Material Relationship from LSDAM

  12. Product-Ingredient Example For Instance Diagram

  13. 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.

  14. Material and Related Classes

  15. MaterialName • DEFINITION: The non-unique textual identification of a material in a specified context

  16. 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

  17. Material Relationship from LSDAM

  18. 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.

  19. 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.

  20. MaterialRelationship (LSDAM) • DEFINITION: Specifies the link between one material and another.

  21. 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

  22. TO DO • Add slides on Product Relationship and Product Part class and attribute.

  23. Material and Related Classes

  24. SpecimenCollectionGroup • DEFINITION: Represents a group of specimens collected from the same participant in the same accession event.

  25. SpecimenCollectionGroup Attributes • name: Unique name given to the specimen collection group

  26. Next Topic • Protocol • Point of Contact • Document (i.e. including Publication) • Data • CellCulture • StorageEquipment • Container • Place

  27. Slides from previous meetings

  28. Material and Few Related Classes

  29. 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.

  30. 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

  31. Material Attribute • description: The textual representation of the material. • effectiveDateRange: The date and time span for when the material is active.

  32. 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- • The typeCode and subTypeCode needs to be flipped (as molecular can not be subtype of DNA). • The definition for subTypeCode needs to be completed

  33. 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

  34. 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.

  35. 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).

  36. 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.

  37. 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

  38. 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.

  39. 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

  40. 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.

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

  42. 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.

  43. 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

  44. 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

  45. 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

  46. 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]

  47. 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

  48. 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

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