Transcript Omics Modeling

Omics Modeling
11/28/2011
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
Material
Product
Material Name
Material Identifier
Biologic Specimen
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
Product Part from BRIDG 3.0.2
class UML-Based Comprehensiv e BRIDG Model Diagram
BRIDG3. 0.2 - Common
Sub-Domain::
MaterialI dentifier
+
+
identifi er: II
typeCode: CD
BRIDG3. 0.2 - Common
Sub-Domain::
1. .*
Materi alName
+
+
BRIDG3.0.2 - Common
Sub-Domain::Material
identifies
0..* {is identified
by}
1
+
+
+
+
+
names
{is named by}
1
nameCode: CD
formCode: CD
description: ST
actualIndicator: BL
effectiveDateRange:
IVL<TS.DATETIME>
name: TN
typeCode: CD
BRIDG3.0.2 - Common Sub-Domain::Product
+ nameCodeModifiedText: ST
+ typeCode: CD
+ classCode: DSET<CD>
+ lotNumberText: ST.SIMPLE
+ expirationDate: TS.DATE.FULL
+ pre1938Indicator: BL
::Mat erial
+ nameCode: CD
+ formCode: CD
+ description: ST
+ actualIndicator: BL
+ effectiveDateRange: IVL<TS.DATETIME>
constraints
{Distributor Qualifier}
{Processor Qualifier}
{ProcessingSite Qualifier}
1
is a functio n performed
by
{functions as}
0..*
is part of
1
BRIDG3.0.2 - Common Sub-Domain::Biologic
::Product
+ nameCodeModifiedText: ST
+ typeCode: CD
+ classCode: DSET<CD>
+ lotNumberText: ST.SIMPLE
+ expirationDate: TS.DATE.FULL
+ pre1938Indicator: BL
::Mat erial
+ nameCode: CD
+ formCode: CD
+ description: ST
+ actualIndicator: BL
+ effectiveDateRange: IVL<TS.DATETIME>
BRIDG3.0.2 - Common Sub-Domain::Drug
::Product
+ nameCodeModifiedText: ST
+ typeCode: CD
+ classCode: DSET<CD>
+ lotNumberText: ST.SIMPLE
+ expirationDate: TS.DATE.FULL
+ pre1938Indicator: BL
::Mat erial
+ nameCode: CD
+ formCode: CD
+ description: ST
+ actualIndicator: BL
+ effectiveDateRange: IVL<TS.DATETIME>
{has as part}
0..*
BRIDG3. 0.2 - Common
Sub-Domain::ProductPart
+
+
strength: RTO<PQ,PQ>
activeIngredientIndicator: BL
Material and Related Classes
class LSDAM - Specimen
MaterialRe lationship
+
+
typeCode: CD
subTypeCode: CD
0..*
functions as / is a
function performed
by
MaterialI dentifier
+
+
identifi er: II
typeCode: CD
Materi alName
+
+
1
names
/ is
nam ed
by
1. .*
name: EN.TN
typeCode: CD
1
Material
identifies
0..*
0..*
has / is a part of
1 +
+
+
+
1 +
+
+
nameCod e: CD
typeCode: CD
subTypeCode: CD
formCode: CD
functionTypeCode: DSET<CD>
descript ion: ST
effectiveDateRange: IVL<TS.DATETIME>
specializes
specializes
Biologic Specimen
Product
+
+
+
typeCode: CD
lotNumberText : ST.SIMPLE
expirationDate: TS.DATE.FULL
specializes
Equipment
+
+
+
reprocessedDe viceCode: CD
manufactureDate : TS.DATETIME
validationDate: DSET<TS.DATETIME>
SpecimenColl ectionGroup
is part of / is composed
0..*
of
1 +
name: ST
Material and Related Classes (BRIDG 3.0.3)
class UML-Based Comprehensiv e BRIDG Model Diagram
Common Sub-Domain::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange: IVL<TS.DATETIME>
+ formCode: CD
constraints
{Distributor Qualifier}
{Processor Qualifier}
{ProcessingSite Qualifier}
+source
Common Sub-Domain::Biologic
Common Sub-Domain::
Package
+ capacityQuantity: PQ
+ capTypeCode: CD
+ handlingCode: CD
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate:
TS.DATE.FULL
+ lotNumberText:
ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange:
IVL<TS.DATETIME>
+ formCode: CD
Common Sub-Domain::FoodProduct
+
stabilityDuration:
IVL<TS.DATETIME>
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange:
IVL<TS.DATETIME>
+ formCode: CD
+ handlingCode: CD
+ riskCode: CD
+ stabilityDuration: IVL<TS.DATETIME>
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange: IVL<TS.DATETIME>
+ formCode: CD
1+target
has
has
as
as
{is the target for}
{is the target
source
source
for}
Common Sub-Domain::Drug
Common Sub-Domain::Cosmetic
+ stabilityDuration: IVL<TS.DATETIME>
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange: IVL<TS.DATETIME>
+ formCode: CD
1
+ handlingCode: CD
+ riskCode: CD
+ stabilityDuration: IVL<TS.DATETIME>
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange: IVL<TS.DATETIME>
+ formCode: CD
Common Sub-Domain::
ProductRelationship
+source
+target +
0..* +
0..*
+
Common Sub-Domain::Dev ice
+
+
+
+
+
+
+
/age: PQ.TIME
availableForEvaluationIndicator: BL
handlingCode: CD
manufactureDate: TS.DATETIME
overTheCounterProductIndicator: BL
reprocessedDeviceCode: CD
returnedToReprocessorDate:
TS.DATETIME
+ riskCode: CD
+ singleUseDeviceIndicator: BL
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange: IVL<TS.DATETIME>
+ formCode: CD
+
+
+
activeIngredientIndicator: BL
confidentialityCode:
DSET<CD>
effectiveDateRange:
IVL<TS.DATETIME>
identifier: II
quantity: RTO<PQ,PQ>
typeCode: CD
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
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)
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
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)
class UML-Based Comprehensiv e ...
ProductRelationship
Common Sub -Domain::
ProductRel ationship
• DEFINITION: Specifies the link
between one product and another.
• EXAMPLE(S): lot, content, kind, part,
ingredient, package, assembly, specialized,
equivalent
+
identifier: II
+
typeCode: CD
+
quantity: RT O<PQ,PQ>
+
confidentialityCode :
DSET <CD>
+
activeIngredientIndicator: BL
+
effectiveDateRange :
IVL<T S.DAT ET IME>
• 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
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 drugs—START NEXT WEEK HERE
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
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.
Material and Related Classes
class LSDAM - Specimen
MaterialRe lationship
+
+
typeCode: CD
subTypeCode: CD
0..*
functions as / is a
function performed
by
MaterialI dentifier
+
+
identifi er: II
typeCode: CD
Materi alName
+
+
1
names
/ is
nam ed
by
1. .*
name: EN.TN
typeCode: CD
1
Material
identifies
0..*
0..*
has / is a part of
1 +
+
+
+
1 +
+
+
nameCod e: CD
typeCode: CD
subTypeCode: CD
formCode: CD
functionTypeCode: DSET<CD>
descript ion: ST
effectiveDateRange: IVL<TS.DATETIME>
specializes
specializes
Biologic Specimen
Product
+
+
+
typeCode: CD
lotNumberText : ST.SIMPLE
expirationDate: TS.DATE.FULL
specializes
Equipment
+
+
+
reprocessedDe viceCode: CD
manufactureDate : TS.DATETIME
validationDate: DSET<TS.DATETIME>
SpecimenColl ectionGroup
is part of / is composed
0..*
of
1 +
name: ST
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.
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
Protocol
• DEFINITION: A composite activity that serves
as a rule which guides how activities should
be performed.
Protocol Attribute
• name: The designation by which the protocol
is referenced.
PointOfContact
• DEFINITION: A person or organization (e.g.,
helpdesk) serving as the coordinator or focal
point of an activity or program.
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.
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.
Next Topic
•
•
•
•
•
•
Document (i.e. including Publication)
Data
CellCulture
StorageEquipment
Container
Place
Slides from last meeting
Omics Modeling
11/22/2011
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
Material
Product
Biologic Specimen
Topics for discussion today
• Revisit modeling of NDC and UNII identifiers
for Product
• Classes related to Material
– For example MaterialRelationship,
MaterialIdentifer, MaterialName,
SpecimenCollectionGroup
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.
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
Instance Diagram for NDC and UNII
Product Part from BRIDG 3.0.2
class UML-Based Comprehensiv e BRIDG Model Diagram
BRIDG3. 0.2 - Common
Sub-Domain::
MaterialI dentifier
+
+
identifi er: II
typeCode: CD
BRIDG3. 0.2 - Common
Sub-Domain::
1. .*
Materi alName
+
+
BRIDG3.0.2 - Common
Sub-Domain::Material
identifies
0..* {is identified
by}
1
+
+
+
+
+
names
{is named by}
1
nameCode: CD
formCode: CD
description: ST
actualIndicator: BL
effectiveDateRange:
IVL<TS.DATETIME>
name: TN
typeCode: CD
BRIDG3.0.2 - Common Sub-Domain::Product
+ nameCodeModifiedText: ST
+ typeCode: CD
+ classCode: DSET<CD>
+ lotNumberText: ST.SIMPLE
+ expirationDate: TS.DATE.FULL
+ pre1938Indicator: BL
::Mat erial
+ nameCode: CD
+ formCode: CD
+ description: ST
+ actualIndicator: BL
+ effectiveDateRange: IVL<TS.DATETIME>
constraints
{Distributor Qualifier}
{Processor Qualifier}
{ProcessingSite Qualifier}
1
is a functio n performed
by
{functions as}
0..*
is part of
1
BRIDG3.0.2 - Common Sub-Domain::Biologic
::Product
+ nameCodeModifiedText: ST
+ typeCode: CD
+ classCode: DSET<CD>
+ lotNumberText: ST.SIMPLE
+ expirationDate: TS.DATE.FULL
+ pre1938Indicator: BL
::Mat erial
+ nameCode: CD
+ formCode: CD
+ description: ST
+ actualIndicator: BL
+ effectiveDateRange: IVL<TS.DATETIME>
BRIDG3.0.2 - Common Sub-Domain::Drug
::Product
+ nameCodeModifiedText: ST
+ typeCode: CD
+ classCode: DSET<CD>
+ lotNumberText: ST.SIMPLE
+ expirationDate: TS.DATE.FULL
+ pre1938Indicator: BL
::Mat erial
+ nameCode: CD
+ formCode: CD
+ description: ST
+ actualIndicator: BL
+ effectiveDateRange: IVL<TS.DATETIME>
{has as part}
0..*
BRIDG3. 0.2 - Common
Sub-Domain::ProductPart
+
+
strength: RTO<PQ,PQ>
activeIngredientIndicator: BL
Material and Related Classes
class LSDAM - Specimen
MaterialRe lationship
+
+
typeCode: CD
subTypeCode: CD
0..*
functions as / is a
function performed
by
MaterialI dentifier
+
+
identifi er: II
typeCode: CD
Materi alName
+
+
1
names
/ is
nam ed
by
1. .*
name: EN.TN
typeCode: CD
1
Material
identifies
0..*
0..*
has / is a part of
1 +
+
+
+
1 +
+
+
nameCod e: CD
typeCode: CD
subTypeCode: CD
formCode: CD
functionTypeCode: DSET<CD>
descript ion: ST
effectiveDateRange: IVL<TS.DATETIME>
specializes
specializes
Biologic Specimen
Product
+
+
+
typeCode: CD
lotNumberText : ST.SIMPLE
expirationDate: TS.DATE.FULL
specializes
Equipment
+
+
+
reprocessedDe viceCode: CD
manufactureDate : TS.DATETIME
validationDate: DSET<TS.DATETIME>
SpecimenColl ectionGroup
is part of / is composed
0..*
of
1 +
name: ST
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.
(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
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 (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
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.
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
class LSDAM - Specimen
MaterialRe lationship
+
+
typeCode: CD
subTypeCode: CD
0..*
functions as / is a
function performed
by
MaterialI dentifier
+
+
identifi er: II
typeCode: CD
Materi alName
+
+
1
names
/ is
nam ed
by
1. .*
name: EN.TN
typeCode: CD
1
Material
identifies
0..*
0..*
has / is a part of
1 +
+
+
+
1 +
+
+
nameCod e: CD
typeCode: CD
subTypeCode: CD
formCode: CD
functionTypeCode: DSET<CD>
descript ion: ST
effectiveDateRange: IVL<TS.DATETIME>
specializes
specializes
Biologic Specimen
Product
+
+
+
typeCode: CD
lotNumberText : ST.SIMPLE
expirationDate: TS.DATE.FULL
specializes
Equipment
+
+
+
reprocessedDe viceCode: CD
manufactureDate : TS.DATETIME
validationDate: DSET<TS.DATETIME>
SpecimenColl ectionGroup
is part of / is composed
0..*
of
1 +
name: ST
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.
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 previous meetings
Material and Related Classes (BRIDG 3.0.3)
class UML-Based Comprehensiv e BRIDG Model Diagram
Common Sub-Domain::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange: IVL<TS.DATETIME>
+ formCode: CD
constraints
{Distributor Qualifier}
{Processor Qualifier}
{ProcessingSite Qualifier}
+source
Common Sub-Domain::Biologic
Common Sub-Domain::
Package
+ capacityQuantity: PQ
+ capTypeCode: CD
+ handlingCode: CD
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate:
TS.DATE.FULL
+ lotNumberText:
ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange:
IVL<TS.DATETIME>
+ formCode: CD
Common Sub-Domain::FoodProduct
+
stabilityDuration:
IVL<TS.DATETIME>
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange:
IVL<TS.DATETIME>
+ formCode: CD
+ handlingCode: CD
+ riskCode: CD
+ stabilityDuration: IVL<TS.DATETIME>
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange: IVL<TS.DATETIME>
+ formCode: CD
1+target
has
has
as
as
{is the target for}
{is the target
source
source
for}
Common Sub-Domain::Drug
Common Sub-Domain::Cosmetic
+ stabilityDuration: IVL<TS.DATETIME>
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange: IVL<TS.DATETIME>
+ formCode: CD
1
+ handlingCode: CD
+ riskCode: CD
+ stabilityDuration: IVL<TS.DATETIME>
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange: IVL<TS.DATETIME>
+ formCode: CD
Common Sub-Domain::
ProductRelationship
+source
+target +
0..* +
0..*
+
Common Sub-Domain::Dev ice
+
+
+
+
+
+
+
/age: PQ.TIME
availableForEvaluationIndicator: BL
handlingCode: CD
manufactureDate: TS.DATETIME
overTheCounterProductIndicator: BL
reprocessedDeviceCode: CD
returnedToReprocessorDate:
TS.DATETIME
+ riskCode: CD
+ singleUseDeviceIndicator: BL
::Product
+ classCode: DSET<CD>
+ codeModifiedText: ST
+ expirationDate: TS.DATE.FULL
+ lotNumberText: ST.SIMPLE
+ pre1938Indicator: BL
+ typeCode: CD
::Material
+ actualIndicator: BL
+ code: CD
+ description: ST
+ effectiveDateRange: IVL<TS.DATETIME>
+ formCode: CD
+
+
+
activeIngredientIndicator: BL
confidentialityCode:
DSET<CD>
effectiveDateRange:
IVL<TS.DATETIME>
identifier: II
quantity: RTO<PQ,PQ>
typeCode: CD
Product Part from BRIDG 3.0.2
class UML-Based Comprehensiv e BRIDG Model Diagram
BRIDG3. 0.2 - Common
Sub-Domain::
MaterialI dentifier
+
+
identifi er: II
typeCode: CD
BRIDG3. 0.2 - Common
Sub-Domain::
1. .*
Materi alName
+
+
BRIDG3.0.2 - Common
Sub-Domain::Material
identifies
0..* {is identified
by}
1
+
+
+
+
+
names
{is named by}
1
nameCode: CD
formCode: CD
description: ST
actualIndicator: BL
effectiveDateRange:
IVL<TS.DATETIME>
name: TN
typeCode: CD
BRIDG3.0.2 - Common Sub-Domain::Product
+ nameCodeModifiedText: ST
+ typeCode: CD
+ classCode: DSET<CD>
+ lotNumberText: ST.SIMPLE
+ expirationDate: TS.DATE.FULL
+ pre1938Indicator: BL
::Mat erial
+ nameCode: CD
+ formCode: CD
+ description: ST
+ actualIndicator: BL
+ effectiveDateRange: IVL<TS.DATETIME>
constraints
{Distributor Qualifier}
{Processor Qualifier}
{ProcessingSite Qualifier}
1
is a functio n performed
by
{functions as}
0..*
is part of
1
BRIDG3.0.2 - Common Sub-Domain::Biologic
::Product
+ nameCodeModifiedText: ST
+ typeCode: CD
+ classCode: DSET<CD>
+ lotNumberText: ST.SIMPLE
+ expirationDate: TS.DATE.FULL
+ pre1938Indicator: BL
::Mat erial
+ nameCode: CD
+ formCode: CD
+ description: ST
+ actualIndicator: BL
+ effectiveDateRange: IVL<TS.DATETIME>
BRIDG3.0.2 - Common Sub-Domain::Drug
::Product
+ nameCodeModifiedText: ST
+ typeCode: CD
+ classCode: DSET<CD>
+ lotNumberText: ST.SIMPLE
+ expirationDate: TS.DATE.FULL
+ pre1938Indicator: BL
::Mat erial
+ nameCode: CD
+ formCode: CD
+ description: ST
+ actualIndicator: BL
+ effectiveDateRange: IVL<TS.DATETIME>
{has as part}
0..*
BRIDG3. 0.2 - Common
Sub-Domain::ProductPart
+
+
strength: RTO<PQ,PQ>
activeIngredientIndicator: BL
Material Relationship from LSDAM
class LSDAM - Specimen
MaterialRe lationship
+
+
typeCode: CD
subTypeCode: CD
0..*
functions as / is a
function performed
by
MaterialI dentifier
+
+
identifi er: II
typeCode: CD
Materi alName
+
+
name: EN.TN
typeCode: CD
1. .*
names /
is
nam ed
by
1
1
Material
identifies
0..*
0..*
has / is a part of
1 +
+
+
+
1 +
+
+
nameCod e: CD
typeCode: CD
subTypeCode: CD
formCode: CD
functionTypeCode: DSET<CD>
descript ion: ST
effectiveDateRange: IVL<TS.DATETIME>
specializes
specializes
Biologic Specimen
Product
+
+
+
typeCode: CD
lotNumberText : ST.SIMPLE
expirationDate: TS.DATE.FULL
Material and Few Related Classes
class LSDAM - Core Experiment plus related_for_CG_OmicsDAM
Material
+
+
+
+
+
+
+
nameCod e: CD
typeCode: CD
subTypeCode: CD
formCode: CD
functionTypeCode: DSET<CD>
descript ion: ST
effectiveDateRange: IVL<TS.DATETIME>
specializes
specializes
Product
+
+
+
typeCode: CD
lotNumberText : ST.SIMPLE
expirationDate: TS.DATE.FULL
Biologic Specimen
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 nonunique 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 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 Requesta) 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