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Omics Modeling

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Title: Omics Modeling


1
Omics Modeling
  • 11/28/2011

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

3
Topics for discussion today
  • Classes related to Material
  • Review discussion on ProductPart,
    ProductRelationship and MaterialRelationship
    from last meeting (Slides from last meeting)
  • Review additional Material related classes, for
    example MaterialRelationship (LSDAM),
    ProductRelationship (BRIDG3.0.3),
    SpecimenCollectionGroup
  • Protocol
  • PointOfContact

4
Product Part from BRIDG 3.0.2
5
Material and Related Classes
6
Material and Related Classes (BRIDG 3.0.3)
7
MaterialRelationship (LSDAM)
  • DEFINITION Specifies the link between one
    material and another.
  • Question?
  • Will this class be deleted from Omics DAM or
  • IS it okay to have both MaterialRelationship and
    ProductPart (from BRIDG 3.0.2 reused in Omics
    DAM) in the Omics DAM?
  • Note The renamed class has new attributes that
    are needed for research (JH).
  • 11/22 BRIDG 3.0.3 has a renamed ProductPart
    called ProductRelationship that has added
    attributes

8
Notes on ProductRelationship class (BRIDG 3.0.3)
  • Attributes are very drug centric (Grace) in
    ProductRelationship class
  • Issue How to capture the drug and its ingredient
    relationships (e.g. Tylenol caplets and
    acetaminophen)?
  • Need to harmonize ProductRelationship (BRIDG
    3.0.3) and Material Relationship (LSDAM). We
    will wait for LSDAM to harmonize the two classes.
    We will communicate this to LSDAM. At minimum
    we need the ProductRelationship attributes in the
    MaterialRelationship class..and should be
    generalized to capture information on more than
    just drugs. Look into how the updated class
    would relate to software or equipment.
  • For now, leave a note in the model that if the
    use case is related to DRUGS then use
    ProductRelationship class otherwise use
    MaterialRelationship e.g. for Nanoparticles.
  • Note we are using ProductRelationship (BRIDG
    3.0.3) and not ProductPart (BRIDG 3.0.2)

9
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

10
ProductRelationship
  • Class from BRIDG 3.0.3
  • Needs to be added to omics DAM
  • We will leave a note in the model that if the use
    case is related to DRUGS then use
    ProductRelationship class otherwise use
    MaterialRelationship e.g. for Nanoparticles.
    (from 11/22 discussion)

11
ProductRelationship
  • DEFINITION Specifies the link
  • between one product and another.
  • EXAMPLE(S) lot, content, kind, part, ingredient,
    package, assembly, specialized, equivalent
  • Note 11/28 Lot may not be a good example as we
    are using the Material Identifier to define the
    Lot number. LotNumber is an attribute of
    Product. So, decided to delete Lot from eg.
  • Updated Example content, kind, part, ingredient,
    package, assembly, specialized, equivalent
  • What is the use case for giving kind as an
    example. Kind is a same things as typeocde
    while the other examples (package, content,
    ingredients) are values for typeCode. Joyce to
    reach out to BRIDG folks

12
ProductRelationship Attributes
  • Identifier A unique symbol that establishes
    identity of the product within the context of
    another product.
  • NOTE(S) There are multiple ways in which an
    identifier can be associated to a product
    inherited from MaterilaIdentifier.identifier, the
    association to ProcessedProduct.identifier, and
    the association to ProductRelationship.identifier.
    If there is no context associated with the
    identifier, then MaterialIdentifier.identifier
    should be used. However, if the identifier for a
    product would be different in different context,
    one of the other identifiers should be used. If
    the product is used in multiple assemblies, and
    in each assembly it would be assigned a different
    identifier, then ProductRelationship.identifier
    should be used. If a kind of product is produced
    by different processors, and each processor
    assigns the product a different identifier, then
    ProcessedProduct.identifier should be used.
  • Notes 11/28 The note above from BRIDG 3.0.3 is
    not clear. In what situations should we use
    ProductRelationship.identifier? For same
    ingredient used in multiple drugsSTART NEXT WEEK
    HERE

13
ProductRelationship Attributes
  • typeCode A coded value specifying the kind of
    relationship a product has with another product.
  • EXAMPLE(S) lot, content, kind, part, ingredient,
    package, assembly, specialized, equivalent
  • Quantity An indication of the amount of one
    product contained in another product.
  • EXAMPLE(S) 50 mg per tablet 300 ml / liter

14
ProductRelationship Attributes
  • confidentialityCode A coded value specifying the
    privacy requirements for information about this
    relationship.
  • EXAMPLE(S)A manufacturer considers an ingredient
    in a product to be a trade secret.
  • activeIngredientIndicator Specifies whether the
    ingredient is an active ingredient.
  • effectiveDateRange The date and time span for
    when the product relationship is active.

15
Material and Related Classes
16
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.

17
SpecimenCollectionGroup
  • DEFINITION Represents a group of specimens
    collected from the same participant in the same
    accession event.

18
SpecimenCollectionGroup Attributes
  • name Unique name given to the specimen
    collection group

19
Protocol
  • DEFINITION A composite activity that serves as a
    rule which guides how activities should be
    performed.

20
Protocol Attribute
  • name The designation by which the protocol is
    referenced.

21
PointOfContact
  • DEFINITION A person or organization (e.g.,
    helpdesk) serving as the coordinator or focal
    point of an activity or program.

22
PointOfContact Attributes
  • typeCode A coded value specifying the kind of
    role the contact person plays.
  • EXAMPLES Principal Investigator, Submitter,
    Research Technician, Service Representative
  • postalAddress A contact point used to send
    physical forms of communication to the person.

23
PointOfContact Attributes
  • telecomAddress A sequence of digits or
    characters used to identify a particular
    telephone, fax, or email of the person.
  • EXAMPLE(S)The set of digits that serves as the
    address for a telephone device. Included in the
    phone number are country, city, and area codes
    needed to uniquely address the telephone. A URL
    or e-mail would be similarly described.
  • effectiveDateRange The date and time span for
    when the point of contact is active.
  • primaryIndicator Specifies whether this is the
    main or principal point of contact.

24
Next Topic
  • Document (i.e. including Publication)
  • Data
  • CellCulture
  • StorageEquipment
  • Container
  • Place

25
Slides from last meeting
26
Omics Modeling
  • 11/22/2011

27
Classes reviewed until last meeting
  • ExperimentalParameters (String Parameter,
    Numerical Parameter)
  • Software
  • Equipment
  • ExperimentalItem
  • Material
  • Product
  • Biologic Specimen
  • Person
  • BiologicEntity
  • Subject
  • SubjectIdentifier
  • Performer
  • ExperimentalStudy
  • Experiment
  • ExperimentalFactor
  • Activity and subclasses (defined, Planned,
    Performed Activity)

28
Topics for discussion today
  • Revisit modeling of NDC and UNII identifiers for
    Product
  • Classes related to Material
  • For example MaterialRelationship,
    MaterialIdentifer, MaterialName,
    SpecimenCollectionGroup

29
NDC and UNII identifiers for Product
  • The issue was discussed in last meeting and teh
    resolution is below
  • NDC and UNII can be handled by MaterialIdentifier
    from (BRIDG 3.0.2). The ProductPart class will be
    used to capture the relationships to build the
    product. For example, UNII will be given to
    the individual ingredients (e.g. Acetaminophen)
    while the NDC is given to the final product
    (e.g. Tylenol Caplets 500mg). ProductPart will
    be used to define the relationship between the
    final product and its composing materials e.g.
    Acetaminophen and Tylenol Caplets 500mg.
  • Note from JH that we need to use the
    ProductRelationship class from BRIDG 3.0.3
    instead of ProductPart from BRIDG 3.0.2. See
    slide 14 for resolution of this issue.

30
NDC and UNII identifiers for Product
  • The issue was discussed in last meeting
  • Issue pending was regarding capturing Package
    information
  • LS DAM has Container (defined as-An object that
    can be used to hold things.)
  • BRIDG 3.0.3 defines Package as  A container
    within which the product is packaged or shipped
  • Package information can be captured in the
    container class of LSDAM but may need review of
    the attributes and harmonize

31
Instance Diagram for NDC and UNII
32
Product Part from BRIDG 3.0.2
33
Material and Related Classes
34
MaterialName
  • DEFINITION The non-unique textual identification
    of a material in a specified context

35
MaterialName Attributes
  • name A non-unique textual identifier for the
    material.
  • EXAMPLE(S)The therapeutic agent used in a
    chemotherapy clinical trial.
  • (11/22 Note Need the name of the therapeutic
    agent as example). For example Taxol, paclitaxel
  • typeCode A coded value specifying the kind of
    material name.
  • EXAMPLE(S)brand name, generic

36
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.

37
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.

38
MaterialRelationship (LSDAM)
  • DEFINITION Specifies the link between one
    material and another.
  • Question?
  • Will this class be deleted from Omics DAM or
  • IS it okay to have both MaterialRelationship and
    ProductPart (from BRIDG 3.0.3 reused in Omics
    DAM) in the Omics DAM?
  • Note The renamed class has new attributes that
    are needed for research (JH).
  • 11/22 BRIDG 3.0.3 has a renamed ProductPart
    called ProductRelationship that has added
    attributes

39
Notes on ProductRelationship class (BRIDG 3.0.3)
  • Attributes are very drug centric (Grace) in
    ProductRelationship class
  • Issue How to capture the drug and its ingredient
    relationships (e.g. Tylenol caplets and
    acetaminophen)?
  • Need to harmonize ProductRelationship (BRIDG
    3.0.3) and Material Relationship (LSDAM). We
    will wait for LSDAM to harmonize the two classes.
    We will communicate this to LSDAM. At minimum
    we need the ProductRelationship attributes in the
    MaterialRelationship class..and should be
    generalized to capture information on more than
    just drugs. Look into how the updated class
    would relate to software or equipment.
  • For now, leave a note in the model that if the
    use case is related to DRUGS then use
    ProductRelationship class otherwise useuse
    MaterialRelationship e.g. for Nanoparticles.

40
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

41
Material and Related Classes
42
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.

43
SpecimenCollectionGroup
  • DEFINITION Represents a group of specimens
    collected from the same participant in the same
    accession event.

44
SpecimenCollectionGroup Attributes
  • name Unique name given to the specimen
    collection group

45
Next Topic
  • Protocol
  • Point of Contact
  • Document (i.e. including Publication)
  • Data
  • CellCulture
  • StorageEquipment
  • Container
  • Place

46
Slides from previous meetings
47
Material and Related Classes (BRIDG 3.0.3)
48
Product Part from BRIDG 3.0.2
49
Material Relationship from LSDAM
50
Material and Few Related Classes
51
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.

52
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.

53
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-UniqueIngredientIdenti
    fierUNII/default.htm
  • NDC-http//www.fda.gov/Drugs/InformationOnDrugs/uc
    m142438.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)?

54
Instance Diagram for NDC and UNII
55
Product Part from BRIDG 3.0.2
56
Material Relationship from LSDAM
57
Product-Ingredient Example For Instance Diagram
Active Ingredients Inactive Ingredients
Caplet Acetaminophen 500 mg in each caplet Cellulose, corn starch, FDC Red 40, hypromellose, magnesium stearate, polyethylene glycol, sodium starch glycolate
58
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.

59
Material and Few Related Classes
60
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.

61
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

62
Material Attribute
  • description The textual representation of the
    material.
  • effectiveDateRange The date and time span for
    when the material is active.

63
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-
  • The typeCode and subTypeCode needs to be flipped
    (as molecular can not be subtype of DNA).
  • The definition for subTypeCode needs to be
    completed

64
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.
  • EXAMPLESkinase, RNAse
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