IRWG Generic Assay Subgroup

mewlingfawnSemiconductor

Nov 2, 2013 (3 years and 5 months ago)

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IRWG

Proposals for
LS DAM

December 16, 2010

1

Agenda


Physical vs. Virtual Entities


Specimen as a role


Building composite materials

2

Virtual Entities


A piece of DNA in a tube


A collection of copies of DNA in a tube (e.g., PCR products)


Individual copies (instances) in the collection may contain variations


The sequence of a piece of DNA (single molecule or collection)


A hypothetical DNA sequence assembled from many others


e.g., a reference sequence for an organism, but one that has never been
observed directly (in its entirety)

3

Separating the Physical from the
Virtual

4

Material (blood from person)

Experiment

MolecularSequence

SequenceRange

Features

physical things

activity that is performed to obtain information about a thing

virtual/information that describe a physical thing

….thinking about this outside of the current model….

results in

references

Data

Separating the Physical from the
Virtual 2

5

LS DAM 2.0


Molecular Biology Core

6

“Material”

Proposal


“physical”

7

Proposal


“virtual”

8

Proposal
-


9

LS DAM 2.0
-

Specimen


Already consensus to
remove
nano

material
specializations that were in
LS DAM 2.0 (
QuantumDot
,
Liposome, Fullerene,
Antibody, etc.)



ExperimentalItem.typeCode
: A code representing the
role an entity plays in an
experiment. Examples:
specimen, reagent, data
collection tool

10


We know next release of
BRIDG, Specimen will
be a role material can
play


it will describe the use
of Material obtained
from an entity


not
the Material itself


how the Material is used
is
ExperimentalItem


value of
typeCode

11

Attributes in Specimen (from
BiologicalSpecimen
) seem to be information
about the material OR about the
collection/storage of the material


not about
the USE of the material

Material

Proposal


Role of material in experiment be described by
ExperimentalItem.typeCode


Add a Tissue specialization of Material


When we need to support additional semantics around specimen (or others), specialize
ExperimentalItem

accordingly


There will be no “Specimen” class in the model


is this an issue? If yes, specialize now,
even if it is empty


Remaining ACTION: to review attributes of previous
BiologicSpecimen

and ensure all are
handled in Material or elsewhere (in collection or storage)

12

Build
-
up Physical Materials



a quantum dot
nanoparticle

has 3 components


Polymer as coat


polyethyl

glycol


Semiconductor crystal as core
-

CdSE


Semiconductor crystal as shell


ZnS


a chain of polymers
(is this right terminology?)

13

LS DAM 2.0 (modified)


Already consensus to
remove
nano

material
specializations that were
in LS DAM 2.0
(
QuantumDot
, Liposome,
Fullerene, Antibody, etc.)



Self
-
association doesn’t
support capture of
information on
relationship of the two
materials (the shell, the
core, etc.)

14

Proposal


add
MaterialRelationship
:
Defines the subcomponents of
a composite material.


functionCode
: the function the material
plays within the composite material.
Examples include: core, shell, coat,
repeat unit, <need example molecular
bio perspective>


Delete self
-
association on
Material

15

Example

a quantum dot has 3 components


Polymer as coat


polyethyl

glycol


Semiconductor crystal as
core
-

CdSE


Semiconductor crystal as
shell


ZnS

16


The composite material is an instance of Material


For each component there is an instance of
MaterialRelationship

that relates the
component to the whole and can define that components function in the whole


A composite material can have any number of components


The composite material can be used as a component of another material