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A. Domain User Stories
Search for all "pre-cancerous"
...
biospecimens
...
that
...
are
...
available
...
for
...
sharing
...
at
...
Washington
...
University,
...
Thomas
...
Jefferson
...
University,
...
and
...
Fox
...
Chase
...
Cancer
...
Center.
...
Domain
...
Description
...
:
...
A
...
cancer
...
researcher
...
sits
...
down
...
to
...
his
...
console
...
with
...
the
...
intention
...
of
...
ordering
...
some
...
biospecimens
...
for
...
use
...
at
...
his
...
organization.
...
He
...
opens
...
the
...
caTissue
...
website
...
at
...
his
...
lab
...
and
...
begins
...
performing
...
the
...
search.
...
Unfortunately,
...
there
...
is
...
currently
...
a
...
shortage
...
at
...
his
...
hospital
...
of
...
suitable
...
pre-cancerous
...
tissue.
...
Therefore,
...
he
...
expands
...
his
...
search
...
to
...
Washington
...
University,
...
Thomas
...
Jefferson,
...
and
...
Fox
...
Chase,
...
all
...
of
...
which
...
are
...
in
...
driving
...
distance
...
so
...
he
...
could
...
send
...
a
...
post
...
doc
...
to
...
pick
...
them
...
up.
...
He
...
hits
...
the
...
search
...
button,
...
and
...
the
...
result
...
from
...
all
...
three
...
cancer
...
centers
...
are
...
displayed
...
on
...
his
...
web
...
page.
...
He
...
selects
...
suitable
...
biospecimens,
...
hits
...
the
...
...
button,
...
and
...
sends
...
his
...
trusty
...
post
...
doc
...
on
...
his
...
way.
...
Technical
...
Description
...
:
...
Biospecimen
...
repositories
...
are
...
deployed
...
locally,
...
as
...
well
...
as
...
Washington
...
University,
...
Thomas
...
Jefferson
...
University,
...
and
...
Fox
...
Chase
...
Cancer
...
Center.
...
Each
...
has
...
their
...
information
...
models
...
registered
...
in
...
a
...
metadata
...
repository,
...
as
...
well
...
as
...
has
...
standardized
...
APIs
...
exposed.
...
The
...
local
...
instance
...
of
...
caTissue
...
discovers
...
services
...
with
...
compatible
...
metadata
...
and
...
APIs,
...
and
...
performs
...
the
...
query.
...
The
...
data
...
returned
...
is
...
aggregated
...
based
...
on
...
standardized
...
metadata,
...
and
...
presented
...
to
...
the
...
user.
...
caTissue
...
uses
...
CDE
...
names,
...
descriptions,
...
and
...
standard
...
value
...
sets
...
to
...
display
...
data,
...
help
...
the
...
user
...
build
...
the
...
query,
...
and
...
issue
...
the
...
query.
...
Cross
...
Reference
...
:
- Support caB2B Services to integrate data on grid
...
- Requirements
...
- statement
...
- :
...
...
- [Use
...
- Case:
...
...
Identify samples obtained for glioblastoma multiforme (GBM)
...
and
...
the
...
corresponding
...
CT
...
image
...
information.
...
Domain
...
Description
...
:
...
a
...
cancer
...
researcher
...
has
...
developed
...
a
...
new
...
image
...
detection
...
algorithm
...
for
...
identifying
...
glioblastoma
...
multiforme,
...
which
...
is
...
the
...
most
...
common
...
and
...
most
...
aggressive
...
type
...
of
...
primary
...
brain
...
tumor
...
in
...
humans,
...
involving
...
glial
...
cells
...
and
...
accounting
...
for
...
52%
...
of
...
all
...
parenchymal
...
brain
...
tumor
...
cases
...
and
...
20%
...
of
...
all
...
intracranial
...
tumors.
...
When
...
viewed
...
with
...
MRI,
...
glioblastomas
...
often
...
appear
...
as
...
ring-enhancing
...
lesions.
...
The
...
appearance
...
is
...
not
...
specific,
...
however,
...
as
...
other
...
lesions
...
such
...
as
...
abscess,
...
metastasis,
...
tumefactive
...
multiple
...
sclerosis,
...
and
...
other
...
entities
...
may
...
have
...
a
...
similar
...
appearance.
...
The
...
cancer
...
researcher's
...
algorithm
...
should
...
be
...
able
...
to
...
differentiate
...
between
...
cancerous
...
lesions
...
and
...
other
...
lesions,
...
but
...
he
...
needs
...
additional
...
tissues
...
and
...
images
...
to
...
make
...
his
...
testing
...
statistically
...
significant.
...
The
...
cancer
...
researcher
...
sits
...
down
...
to
...
his
...
laptop
...
and
...
loads
...
Cancer
...
Bench-to-Bedside
...
(caB2B).
...
He
...
builds
...
a
...
search
...
on
...
all
...
known
...
tissues
...
that
...
have
...
been
...
identified
...
as
...
globlastoma
...
multiforme
...
via
...
stereotactic
...
biopsy
...
and
...
have
...
corresponding
...
CT
...
images.
...
He
...
hits
...
the
...
search
...
button,
...
gets
...
a
...
cup
...
of
...
coffee,
...
and
...
a
...
returns
...
to
...
a
...
list
...
of
...
74
...
tissues
...
with
...
465
...
images.
...
 He
...
hits
...
the
...
export
...
button,
...
which
...
downloads
...
all
...
the
...
images
...
with
...
associated
...
pathology
...
results.
...
Technical
...
Description
...
:
...
a
...
number
...
of
...
organizations
...
have
...
exposed
...
pathology
...
and
...
image
...
services
...
with
...
standardized
...
metadata.
...
 caB2B
...
uses
...
CDE
...
names,
...
descriptions,
...
and
...
value
...
sets
...
to
...
allow
...
the
...
user
...
to
...
construct
...
a
...
query
...
across
...
all
...
of
...
these
...
services.
...
 The
...
user
...
selects
...
the
...
CDEs
...
to
...
filter
...
on,
...
which
...
includes
...
a
...
join
...
across
...
information
...
models
...
(caTissue
...
annotations
...
to
...
imaging
...
annotations).
...
 A
...
semantic
...
relationship
...
between
...
the
...
two
...
models
...
based
...
on
...
biospecimen
...
identifier
...
has
...
previously
...
been
...
established.
...
 A
...
distributed
...
query
...
is
...
formulated
...
and
...
executed.
...
 The
...
resulting
...
data
...
is
...
aggregated
...
based
...
on
...
semantic
...
relationships
...
and
...
presented
...
to
...
the
...
user
...
using
...
CDE
...
names
...
and
...
descriptions.
...
Cross
...
Reference
...
:
- Support caB2B Services to integrate data on grid
- Forum posting: https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php
...
- Requirements
...
- statement
...
- :
...
...
- Use Case: https://wiki.nci.nih.gov/x/Y2RyAQ
...
Determine if each sample used in an expression profiling experiment is available for a SNP analysis experiment.
Is this a repeat of "Identify samples obtained for glioblastoma multiforme (GBM) and the corresponding CT image information"?
Search for a particular gene based on the Entrez Gene ID and its related information, for example, messenger RNA and protein information from GeneConnect.
Is this a repeat of "Search for all 'pre-cancerous' biospecimens that are available for sharing at Washington University, Thomas Jefferson University, and Fox Chase Cancer Center"?
Automatically discover analytical steps for Illumina bead array analysis using inference based on the semantic metadata of the parameters.
Domain Description: The Illumina BeadChip is proprietary method of performing multiplex gene expression and genotyping analysis. The essential element of BeadChip technology is the attachment of oligonucleotides to silica beads An informaticist is working with a cancer researcher to study expression profiles related to proto-oncogenes in T-cell leukemias. It is the first time either has worked with this technology, and the inforaticist is in the process of developing an analytical pipeline. He performs a search for such an analytical pipeline, and a number of steps that can be linked together are presented to him based on the Illumina bead output data type and his end goal of identifying gene annotations. The pipeline that was inferred using semantic metadata is: BeadArray-specific variance stabilization and gene annotation at the probe level. The informaticist knows he needs a quality control step at the beginning to determine whether an experiment run was successful or produced bad data. He searches "quality control" and "expression data" for analytical services, and finds an option specific to Illumina bead arrays. He also knows that the control and experimental runs will need to be normalized. The results from his search apply to gene expression matrices, so he will need a translation step. He enters the bead array format as the input and the gene expression matrix as the output and finds what he needs. Fortunately, the analytical step fits right in before probe annotation, which can also work on a gene expression matrix provided the bead identifiers are included. He saves the workflow, types in some notes about it, and shares it with his cancer researcher colleague.
Technical Description: the discovery of analytical steps utilizes inference over semantic annotations of input and output parameters. The researcher selects the metadata types that will be input to the pipeline and those that will be output from the pipeline. The inference engine performs discovery steps, chaining inputs to outputs in an expanding set until all options are exhausted or the resulting type matches. Furthermore, when specific analytical steps are queries for, full-text and concept-based metadata searches are performed in conjunction with output/input matching to provide the bet possible results. Workflows are saved as a set of steps or as a set of constrains upon which workflows are dynamically generated to meet scientific goals.
Cross Reference:
- Support caB2B Services to integrate data on grid
- Forum posting: https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php
...
- Requirements
...
- statement:
...
...
- Use Case: https://wiki.nci.nih.gov/x/Y2RyAQ
...
- Brain Tumor in silico study - Pathology and Radiology data models
...
- Requirements statement: https://wiki.nci.nih.gov/x/ZwZyAQ
...
- Use Case: https://wiki.nci.nih.gov/x/3wpyAQ
...
- ICR IRWG Requirements
...
- Requirements statement: https://wiki.nci.nih.gov/x/OARyAQ
...
- Use Case: https://wiki.nci.nih.gov/x/qxJyAQ
...
Support patient to trial matching through the use of computable eligibility criteria
Domain Description: a metadata specialist works with the principle investigator of a trial to define the eligibility criteria for a study in enough detail so that eligibility can be computed from patient data. The metadata specialist defines each eligibility question as a common data element (CDE) with a description, an mathematical operator, and a data operand (what the data gets compared to). For example, the principle investigator tells the metadata specialist that all patients must be at least 21 years old. The metadata specialist defines a CDE annotated with the concept "age", the operator "greater-than or equal", and the operand "21". These steps are performed for each of the 32 eligibility criteria. The principle investigator now works with a clinical informaticist to perform a search using these computable eligibility criteria on patient data at the cancer center to see if anyone is eligible. Furthermore, prospective patients themselves can type their data into the trial matching system to compute eligibility for all known trials to determine if there are any trials for their cancer.
Technical Description: the metadata specialist defines CDEs with operator and operand annotations. These are stored in the local metadata repository, which is used by the trial matching software. When computing eligibility, data for semantically equivalent data element are computed against the eligibility metadata to determine eligibility. "Fuzzy" eligibility can be computed when data is missing or does not match.
Support the addition of data elements to an existing information model and automatically capture and publish the information about the extensions.
Domain Description: A teratoma is an encapsulated tumor with tissue or organ components resembling normal derivatives of all three germ layers. Regardless of location in the body, a teratoma is classified according to a cancer staging system: 0 or mature (benign); 1 or immature, probably benign; 2 or immature, possibly malignant (cancerous); and 3 or frankly malignant Teratomas are also classified by their content: a solid teratoma contains only tissues (perhaps including more complex structures); a cystic teratoma contain only pockets of fluid or semi-fluid such as cerebrospinal fluid, sebum, or fat; a mixed teratoma contains both solid and cystic parts. A cancer researcher would like to extend the pathology annotations associated with tissues in the center's tissue bank by adding Teratoma Content as an additional nonseminomatous germ cell tumor (NSGCT) annotation. The researcher communicates this to the director of the tissue repository, who promptly opens the administrative interface to caTissue and adds the additional pathology annotation. The system is now able to capture this, and the data and data descriptions are shareable with other organizations.
Technical Description: the cancer center is running caTissue with a local metadata repository. When a new annotation is added to caTissue, the dynamic extensions module is invoked. The caTissue information model is extended to include necessary additional classes and attributes, which in turn are propagated as new data elements in the metadata repository. These data elements represent well formed metadata that is automatically discoverable and shareable through the public interfaces. When another organization wishes to extend their caTissue model to include this type of data, they will be able to discover the metadata already created and instantiate a reference to it rather than creating it afresh.
Cross Reference:
- Reuse or create new data elements at runtime (caTissue)
...
- Requirements statement: https://wiki.nci.nih.gov/x/QRFlAQ
...
- Use Case: https://wiki.nci.nih.gov/x/t2NyAQ
...
- ICR-caIntegrator2
...
- Forum posting: https://wiki.nci.nih.gov/x/bpJ8 
...
- ;
- Requirements statement: https://wiki.nci.nih.gov/x/vn9yAQ
...
- Use Case: https://wiki.nci.nih.gov/x/wH9yAQ
...
- Brain Tumor in silico study - Pathology and Radiology data models
...
- Requirements statement: https://wiki.nci.nih.gov/x/ZwZyAQ
...
- Use Case: https://wiki.nci.nih.gov/x/3wpyAQ
...
- Â
When defining new datasets for caIntegrator's
...
data-warehouse
...
for
...
biomedical
...
data
...
collection
...
and
...
analysis,
...
automatically
...
record
...
these
...
new
...
datatypes
...
in
...
a
...
well-defined
...
and
...
federated
...
manner
...
so
...
that
...
data
...
can
...
be
...
shared.
...
Is
...
this
...
a
...
repeat
...
of
...
"Support
...
the
...
addition
...
of
...
data
...
elements
...
to
...
an
...
existing
...
information
...
model
...
and
...
automatically
...
capture
...
and
...
publish
...
the
...
information
...
about
...
the
...
extensions."?
...
Discover
...
and
...
orchestrate
...
services
...
to
...
achieve
...
LS
...
research
...
goals;
...
e.g.
...
start
...
with
...
a
...
hypothesis,
...
identify
...
relevant
...
services
...
that
...
provides
...
the
...
necessary
...
analysis
...
and
...
data,
...
create
...
the
...
worklow/pipeline,
...
report
...
findings.
...
[Baris
...
]
...
This
...
is
...
use
...
case
...
is
...
overlapping
...
with
...
"Search
...
for
...
all
...
"pre-cancerous"
...
biospecimens.."
...
and
...
"Automatically
...
discover
...
analytical
...
steps
...
for
...
Illumina.."
...
examples
...
above
Domain Description [Revised
...
From
...
ICRi
...
Use
...
Cases
...
]
...
:
...
A
...
scientist
...
is
...
trying
...
to
...
identify
...
a
...
new
...
genetic
...
biomarker
...
for
...
HER2/neu
...
negative
...
stage
...
I
...
breast
...
cancer
...
patients.
...
The
...
scientist
...
queries
...
for
...
HER2/neu
...
negative
...
tissue
...
specimens
...
of
...
Stage
...
I
...
breast
...
cancer
...
patients
...
using
...
services
...
at
...
his/her
...
cancer
...
center
...
that
...
also
...
have
...
corresponding
...
microarray
...
experiments.
...
Analysis
...
of
...
the
...
microarray
...
experiments
...
identify
...
genes
...
that
...
are
...
significantly
...
over-expressed
...
and
...
under-expressed
...
in
...
a
...
number
...
of
...
cases.
...
The
...
scientist
...
decides
...
that
...
these
...
results
...
are
...
significant,
...
and
...
related
...
literature
...
suggest
...
a
...
hypothesis
...
that
...
gene
...
A
...
may
...
serve
...
as
...
a
...
biomarker
...
in
...
HER2/neu
...
negative
...
Stage
...
I
...
breast
...
cancer.
...
To
...
validate
...
this
...
hypothesis
...
in
...
a
...
significant
...
number
...
of
...
cases
...
the
...
scientist
...
needs
...
a
...
larger
...
data
...
set,
...
so
...
he
...
queries
...
for
...
all
...
the
...
HER2/neu
...
negative
...
specimens
...
of
...
Stage
...
I
...
breast
...
cancer
...
patients
...
with
...
corresponding
...
microarray
...
data
...
and
...
also
...
for
...
appropriate
...
control
...
data
...
from
...
other
...
cancer
...
centers.
...
After
...
retrieving
...
the
...
microarray
...
experiments
...
the
...
scientist
...
analyzes
...
the
...
data
...
for
...
over-expression
...
of
...
genes
...
A.
...
Technical Description: The scientist in this case is trying to develop a workflow that will assist biomarker discovery research. S/he first needs to discover the services that provide biospecimen information with the phenotype s/he is looking for (for example, HER2/neu negative stage I breast cancer) and then the microarray experiment information. Then he needs to create a workflow (orchestrate services) where the input is a phenotype for biospecimens and output is a set of gene of interest. These steps require the support for standard terminologies (and services) and syntaxes to best describe the services' behavior and static data. Furthermore they require inference engines that relates the semantic and syntactic metadata for the inputs/outputs of the services to "assist" scientist to identify what service can be part of the workflow.
Cross References:
- Support development of workflows:
- ICR IRWG Requirements
- ICR ICRi Use Cases
Statistical computing environment and sharable metadata for statistical practice.
Domain description:Â A team of biostatistician tries to analyze the massive amount of clinical research data generated during the various phases of clinical trials. The statisticians generate various artifacts from the highly normalized data during this process such as programs for data manipulation and statistical analysis, the analysis data sets, the results of the analysis. In addition, according to the various guiding principal for a clinical trial, the data also needs to comply with various FDA Regulations and Data Standards. Therefore the real dilemma facing the team of biostatistician is how they should carry out the statistical analysis according to good statistical practices that will maintain the credibility of results and assure data integrity.
Technical description: A Statistical Computing Environment (SCE) provides a foundation for documenting rigor in the analysis and reporting of clinical trial results while increasing productivity and quality. To ensure credibility, reliability and data integrity assurance the best way is to work in an environment that tracks all of the objects. By developing a table of contents of the objects to be created one can track the objects. The table of contents itself becomes a part of the study metadata. The environment would typically include standard programs and algorithms for producing common reports of trial data. Above all, the statistical computing environment develops electronic documentation of the entire process.
Cross reference
- Requirement statements: https://wiki.nci.nih.gov/x/KDxyAQ
...
- Use
...
- cases:
...
...
Patrick:
...
This
...
is
...
a
...
very
...
interesting
...
one
...
that
...
is
...
different
...
from
...
the
...
rest.
...
However,
...
I
...
am
...
not
...
sure
...
the
...
last
...
sentence
...
in
...
the
...
domain
...
description
...
adequately
...
captures
...
it.
...
To
...
me,
...
the
...
issue
...
is
...
how
...
a
...
statistician
...
finds
...
the
...
appropriate
...
standards
...
and
...
then
...
integrates
...
them
...
into
...
their
...
own
...
statistical
...
computing
...
environment.
...
All
...
of
...
the
...
other
...
use
...
cases
...
we
...
have
...
focus
...
on
...
the
...
metadata
...
specialist
...
or
...
cancer
...
researcher
...
-
...
this
...
one
...
focuses
...
on
...
the
...
statistician
...
who
...
is
...
performing
...
the
...
analysis
...
and
...
generating
...
the
...
data.
...
We
...
need
...
to
...
drive
...
home
...
his
...
issues
...
and
...
how
...
they
...
are
...
to
...
be
...
resolved.
...
Also,
...
I
...
am
...
not
...
sure
...
I
...
understand
...
the
...
table
...
of
...
contents
...
of
...
objects.
...
caGRID should support interoperability from non grid platforms.
Domain description: A cancer researcher who is not familiar with the grid wants to collaborate with his peers from the cancer research community to identify tissue specimens, microarray, clinical trials and images of his interest. Being a total stranger to the grid he does not know the data standards and the models he needs to invoke to support his search.
Technical description: One persons object is another person's attribute". Depending on one's world view, a real life entity can be modeled in UML as Object, Attribute or value set. In caBIG models now, some model Race (and Ethnicity) as an Object while others model Race (and Ethnicity) as an attribute. This is problematic, because Race data that is modeled differently cannot be "seamlessly integrated" on caGrid (there needs to be a transform). One can start to use the SAIF language in terms of Conceptual, Platform Independent (logical) and Platform Specific (Implemented). Given that the grid has CIMs, PIMs and PSMs for applications, and BAM and a DAM and other institutions, may have their own DAMs, BAMs, CIMs, PIMs and PSMs. These elements need to be mapped to each other at whatever level needed, to get to some semantic interoperability.
Cross reference
- Requirement statement: https://wiki.nci.nih.gov/x/hAVyAQ
...
- Forum
...
- post:
...
...
- Usecases:
...
...
...
...
...
Patrick:
...
This
...
one
...
is
...
very
...
specific
...
to
...
a
...
technology
...
(caGrid).
...
It
...
needs
...
to
...
be
...
generalized.
...
I
...
am
...
not
...
sure
...
how
...
the
...
title
...
matches
...
the
...
descriptions
...
(since
...
non-grid
...
platforms
...
are
...
not
...
mentioned).
...
Also,
...
I
...
am
...
not
...
sure
...
how
...
the
...
domain
...
description
...
matches
...
the
...
technical
...
description.
...
The
...
technical
...
description
...
seems
...
to
...
focus
...
on
...
semantic
...
relationships
...
and
...
transforms,
...
whereas
...
the
...
domain
...
description
...
seems
...
to
...
focus
...
on
...
accessibility
...
to
...
non-technical
...
users.
...
Semantic search on the cancer grid.
Domain description: A cancer researcher is looking for lung cancer specimens with a histologic picture of a 'oats cell carcinoma' in males aged between 45-55 years and who have a history of smoking for at least 10 years. He invokes a data service and queries caTissue instances in DFCI, TJU, LLU for specimens and rather than using a advance query, uses a semantic query like show me all specimens of lung cancer in males aged 45-55 years who are smokers for at least 10 years and whose histologic picture is that of a oat cell carcinoma. The query runs on various instances of caTissue and comes back with the identified specimens that matched the criteria. Being able to facilitate a semantic search on the grid would facilitate greater cohesiveness of the research cancer research community.
Technical description: The Lexical Grid, coordinated by the Mayo Clinic Division of Biomedical Statistics and Informatics, provides a semantic foundation upon which multiple APIs can be developed that support consistent searching, navigation and cross terminology traversal. These open-source tools are used in a variety of projects such as the NCI Cancer Biomedical Informatics Grid, the National Center for Biomedical Ontology, the Biomedical Grid Terminology project, and the World Health Organization International Classification of Diseases (ICD-11) development process. LexGrid hosts a wide variety of terminologies and ontologies including ICD-9-CM, the Gene Ontology, the HL7 Version 3 vocabulary, and SNOMED-CT. LexGrid can also represent complete NLM Unifed Medical Language System, which currently includes over 100 source terminologies. The Lex-RDF model, maps the LexGrid model elements to corresponding constructs in W3C specifications such as RDF, OWL, and SKOS. With LexRDF, the terminological information represent in LexGrid can be translated to RDF triples, and therefore allowing LexGrid to leverage standard tools and technologies such as SPARQL and RDF triple stores.
Cross reference
...
- Requirement
...
- statement:
...
...
- Forum
...
- post:
...
...
Patrick:
...
I
...
think
...
this
...
one
...
is
...
very
...
similar
...
to
...
some
...
of
...
the
...
search
...
use
...
cases
...
earlier.
...
 Also,
...
the
...
technical
...
description
...
seems
...
to
...
focus
...
on
...
terminologies,
...
whereas
...
they
...
are
...
not
...
really
...
mentioned
...
in
...
the
...
domain
...
description.
...
Integration of radiology,
...
pathology,
...
molecular
...
and
...
genomic
...
data
...
to
...
better
...
predict
...
patient
...
outcome
...
and
...
support
...
clinical
...
decision.
...
Domain
...
Description:
...
A
...
patient
...
reports
...
to
...
a
...
hospital
...
with
...
a
...
clinical
...
condition
...
of
...
Glioblastoma
...
multiforme.
...
The
...
treating
...
oncologist
...
wants
...
to
...
find
...
out
...
the
...
likely
...
outcome
...
for
...
this
...
patient.
...
He
...
initiates
...
a
...
search
...
based
...
on
...
patient
...
presenting
...
criteria
...
in
...
Imaging,
...
histopathology
...
and
...
genomic
...
data
...
to
...
look
...
for
...
cohort
...
with
...
matching
...
criteria
...
and
...
survival
...
rate
...
to
...
better
...
predict
...
outcome
...
for
...
his
...
patients.
...
Technical
...
description:
...
A
...
service
...
is
...
needed
...
that
...
can
...
collate
...
data
...
from
...
the
...
national
...
cancer
...
imaging
...
archive,
...
caArray,
...
cancer
...
central
...
clinical
...
database
...
to
...
pull
...
out
...
information
...
for
...
a
...
patient
...
on
...
staging,
...
grading,
...
 and
...
other
...
prognostic
...
aspects
...
of
...
cancer.
...
This
...
service
...
can
...
run
...
on
...
multiple
...
instances
...
of
...
various
...
tools
...
and
...
pull
...
out
...
corresponding
...
data
...
the
...
patient.
...
This
...
service
...
can
...
also
...
be
...
extended
...
to
...
support
...
clinical
...
decision
...
like
...
if
...
a
...
particular
...
cohort
...
reports
...
better
...
outcome
...
and
...
survival
...
rates
...
with
...
treatment
...
A,
...
then
...
it
...
can
...
be
...
used
...
as
...
a
...
standard
...
line
...
of
...
treatment
...
for
...
patients
...
with
...
similar
...
picture.
...
- Requirement
...
- statement:
...
...
- Forum
...
- post:
...
...
- Use
...
- cases:
...
...
Patrick:
...
I
...
am
...
not
...
sure
...
which
...
requirements
...
in
...
this
...
are
...
not
...
captured
...
in
...
the
...
other
...
use
...
cases.
...
B.
...
Forms
...
Stories
...
Create
...
and
...
reuse
...
forms
...
Domain
...
Description
...
:
...
Forms
...
provide
...
a
...
convenient
...
paper-like
...
electronic
...
mechanism
...
to
...
capture
...
data
...
in
...
a
...
structured
...
way.
...
For
...
example,
...
when
...
a
...
patient
...
is
...
placed
...
on
...
a
...
clinical
...
trial,
...
data
...
about
...
the
...
patient's
...
demographics
...
and
...
eligibility
...
for
...
the
...
trial
...
need
...
to
...
be
...
captured.
...
The
...
trial
...
investigator
...
sits
...
with
...
the
...
forms
...
curator
...
to
...
generate
...
this
...
case
...
report
...
form.
...
The
...
forms
...
curator
...
searches
...
for
...
existing
...
demographics
...
forms
...
and
...
form
...
modules,
...
and
...
the
...
investigator
...
reviews
...
them.
...
They
...
identify
...
an
...
appropriate
...
set
...
of
...
questions,
...
and
...
include
...
them
...
in
...
the
...
case
...
report
...
form.
...
They
...
then
...
move
...
onto
...
the
...
eligibility
...
checklist.
...
The
...
investigator
...
drafted
...
the
...
checklist,
...
and
...
it
...
has
...
been
...
approved
...
by
...
the
...
IRB.
...
The
...
forms
...
curator
...
begins
...
keying
...
in
...
the
...
questions,
...
some
...
of
...
which
...
are
...
identified
...
as
...
existing
...
questions
...
and
...
reused,
...
others
...
of
...
which
...
are
...
created
...
completely
...
new.
...
The
...
form
...
is
...
marked
...
complete
...
and
...
is
...
available
...
by
...
the
...
clinical
...
research
...
staff
...
for
...
gathering
...
and
...
enrolling
...
new
...
patients.
...
Technical
...
Description
...
:
...
Forms
...
are
...
a
...
collection
...
of
...
data
...
elements
...
annotated
...
and
...
grouped
...
within
...
the
...
metadata
...
repository.
...
The
...
forms
...
curator
...
can
...
search
...
for
...
existing
...
forms
...
and
...
form
...
modules
...
(portions
...
of
...
a
...
form)
...
by
...
question
...
text,
...
annotations,
...
etc.
...
These
...
can
...
be
...
reused
...
by
...
reference,
...
or
...
imported
...
and
...
modified.
...
When
...
new
...
data
...
elements
...
are
...
being
...
curated,
...
the
...
form
...
curator
...
can
...
search
...
the
...
federated
...
set
...
of
...
all
...
metadata
...
repositories
...
to
...
identify
...
data
...
elements
...
for
...
reuse.
...
This
...
can
...
happen
...
automatically
...
within
...
the
...
curation
...
tooling
...
or
...
explicitly
...
through
...
the
...
metadata
...
web
...
interface.
...
 The
...
final
...
CRF
...
is
...
saved
...
and
...
annotated
...
within
...
the
...
local
...
metadata
...
repository.
...
Cross
...
Reference
...
:
...
- CDEs
...
- from
...
- Man.
...
- curation,
...
- UML
...
- models
...
- and
...
- CRFs
...
- Forum
...
- posting:
...
...
- Requirements
...
- statement:
...
...
- Use
...
- Case:
...
...
Support
...
of
...
form
...
annotations
...
to
...
enable
...
form
...
behavior
...
Domain
...
Description
...
:
...
a
...
forms
...
curator
...
is
...
sitting
...
down
...
to
...
create
...
the
...
case
...
report
...
forms
...
for
...
a
...
new
...
trial
...
titled
...
"Study
...
of
...
Ad.p53
...
DC
...
Vaccine
...
and
...
1-MTin
...
Metastatic
...
Invasive
...
Breast
...
Cancer."
...
Her
...
goal
...
it
...
to
...
make
...
the
...
forms
...
intuitive,
...
reduce
...
human
...
error
...
when
...
collecting
...
data,
...
and
...
as
...
precise
...
as
...
possible.
...
When
...
building
...
the
...
demographics
...
form,
...
she
...
decides
...
to
...
make
...
the
...
age
...
data
...
element
...
derived
...
from
...
the
...
date
...
of
...
birth
...
data
...
element.
...
Entering
...
data
...
that
...
can
...
simply
...
be
...
calculated
...
from
...
other
...
data
...
can
...
only
...
introduce
...
errors,
...
especially
...
since
...
date
...
of
...
birth
...
is
...
also
...
captured
...
in
...
the
...
hospital
...
system
...
so
...
can
...
easily
...
be
...
validated.
...
When
...
building
...
the
...
medical
...
history
...
CRF,
...
she
...
realizes
...
that
...
fifteen
...
of
...
the
...
questions
...
only
...
relate
...
to
...
women
...
that
...
have
...
previously
...
been
...
pregnant.
...
She
...
promptly
...
enters
...
a
...
skip
...
pattern
...
based
...
on
...
the
...
gender
...
question,
...
as
...
well
...
as
...
the
...
pregnancy
...
question.
...
That
...
should
...
significantly
...
save
...
time.
...
Now
...
that
...
all
...
the
...
questions
...
are
...
entered,
...
she
...
goes
...
back
...
to
...
edit
...
them
...
so
...
have
...
minimum
...
lengths
...
for
...
required
...
text
...
questions,
...
maximum
...
lengths
...
for
...
numeric
...
questions,
...
pick-lists
...
for
...
those
...
questions
...
with
...
a
...
particular
...
set
...
of
...
possible
...
answers,
...
and
...
a
...
data
...
mask
...
for
...
the
...
social
...
security
...
number
...
question.
...
Now,
...
the
...
clinical
...
data
...
management
...
system
...
can
...
render
...
the
...
forms
...
via
...
...
using
...
all
...
of
...
this
...
handy
...
information.
...
Technical
...
Description
...
:
...
Forms
...
provide
...
a
...
convenient
...
paper-like
...
electronic
...
mechanism
...
to
...
capture
...
data
...
in
...
a
...
structured
...
way.
...
For
...
example,
...
when
...
a
...
patient
...
is
...
placed
...
on
...
a
...
clinical
...
trial,
...
data
...
about
...
the
...
patient's
...
demographics
...
and
...
eligibility
...
for
...
the
...
trial
...
need
...
to
...
be
...
captured.
...
However,
...
forms
...
can
...
also
...
exhibit
...
specific
...
behavior
...
that
...
may
...
or
...
may
...
not
...
be
...
reusable.
...
These
...
include
...
skip
...
patterns
...
(if
...
the
...
answer
...
to
...
question
...
10
...
is
...
"Yes"
...
then
...
skip
...
to
...
question
...
15),
...
derived
...
values
...
("what
...
is
...
your
...
age"
...
and
...
"is
...
your
...
age
...
less
...
than,
...
greater
...
than,
...
or
...
equal
...
to
...
65),
...
and
...
composite
...
answers
...
("check
...
all"
...
or
...
"more
...
than
...
one
...
of
...
the
...
above").
...
Furthermore,
...
specific
...
requirements
...
about
...
how
...
a
...
form
...
is
...
rendered
...
can
...
exist.
...
For
...
example,
...
the
...
question
...
description,
...
help
...
text,
...
valid
...
values,
...
maximum
...
and
...
minimum
...
answer
...
length,
...
the
...
format
...
of
...
a
...
data
...
mask
...
(such
...
as
...
SSN),
...
etc.
...
It
...
is
...
important
...
to
...
be
...
able
...
to
...
allow
...
for
...
forms
...
to
...
be
...
annotated
...
with
...
this
...
behavior
...
such
...
that
...
tools
...
can
...
appropriately
...
render
...
and
...
act
...
upon
...
them.
...
Furthermore,
...
if
...
appropriate,
...
web
...
-
...
and
...
paper-based
...
collection
...
instruments
...
can
...
be
...
automatically
...
generated
...
from
...
this
...
metadata.
...
Extend
...
allowable
...
answers
...
with
...
additional
...
permitted
...
values
...
Domain
...
Description
...
:
...
In
...
many
...
cases,
...
data
...
elements
...
can
...
be
...
reused
...
but
...
the
...
allowable
...
values
...
need
...
to
...
be
...
extended
...
or
...
restricted.
...
For
...
example,
...
one
...
researcher
...
may
...
want
...
to
...
capture
...
diseases
...
of
...
the
...
nervous
...
system
...
while
...
another
...
may
...
want
...
to
...
capture
...
diseases
...
of
...
the
...
cirulatory
...
system.
...
These
...
both
...
can
...
be
...
captured
...
in
...
the
...
same
...
data
...
element
...
(disease)
...
using
...
the
...
same
...
controlled
...
terminology
...
(ICD-9).
...
However,
...
the
...
list
...
of
...
allowable
...
values
...
is
...
quite
...
different.
...
Furthermore,
...
yet
...
another
...
researcher
...
may
...
want
...
to
...
focus
...
only
...
on
...
certain
...
circulatory
...
diseases,
...
such
...
as
...
those
...
of
...
the
...
heart.
...
A
...
metadata
...
specialist
...
can
...
sit
...
with
...
a
...
domain
...
specialist
...
to
...
identify
...
the
...
appropriate
...
ontologies
...
and
...
constrain
...
or
...
expand
...
them
...
as
...
needed.
...
Technical
...
Description
...
:
...
the
...
metadata
...
repository
...
allows
...
for
...
data
...
element
...
to
...
have
...
a
...
value
...
domain
...
referencing
...
an
...
external
...
terminology.
...
Furthermore,
...
those
...
terminologies
...
can
...
be
...
constrained
...
or
...
expanded
...
as
...
needed
...
in
...
the
...
local
...
repository.
...
C.
...
Metadata
...
Specialist
...
Stories
...
Creation
...
of
...
metadata
...
and
...
management
...
of
...
information
...
models
...
through
...
modeling
...
and
...
web
...
tools
...
Domain
...
Description
...
:
...
the
...
imaging
...
center
...
at
...
a
...
cancer
...
center
...
has
...
just
...
purchased
...
a
...
magnetic
...
resonance
...
spectroscopy
...
(MRS)
...
machine
...
to
...
add
...
to
...
their
...
numerous
...
magnetic
...
resonance
...
imaging
...
(MRI)
...
machines.
...
MRS
...
is
...
used
...
to
...
measure
...
the
...
levels
...
of
...
different
...
metabolites
...
in
...
body
...
tissues.
...
The
...
MR
...
signal
...
produces
...
a
...
spectrum
...
of
...
resonances
...
that
...
correspond
...
to
...
different
...
molecular
...
arrangements
...
of
...
the
...
isotope
...
being
...
"excited".
...
Magnetic
...
resonance
...
spectroscopic
...
imaging
...
(MRSI)
...
combines
...
both
...
spectroscopic
...
and
...
imaging
...
methods
...
to
...
produce
...
spatially
...
localized
...
spectra
...
from
...
within
...
the
...
sample
...
or
...
patient.
...
 A
...
metadata
...
specialist
...
has
...
been
...
assigned
...
to
...
enhance
...
their
...
imaging
...
repository
...
to
...
handle
...
this
...
new
...
type
...
data
...
He
...
opens
...
his
...
modeling
...
tool,
...
and
...
begins
...
to
...
add
...
additional
...
classes
...
related
...
to
...
metabolic
...
signatures.
...
As
...
the
...
metadata
...
specialist
...
types
...
the
...
class
...
name
...
"Metabolite"
...
into
...
the
...
modeling
...
tool,
...
a
...
number
...
of
...
existing
...
classes
...
and
...
concepts
...
are
...
suggested
...
to
...
him
...
automatically.
...
One
...
of
...
these
...
peak's
...
his
...
interest,
...
and
...
he
...
clicks
...
on
...
the
...
link
...
for
...
more
...
information.
...
His
...
web
...
browser
...
pops
...
up
...
showing
...
him
...
the
...
data
...
element
...
from
...
a
...
system
...
focused
...
on
...
drug
...
discovery
...
and
...
pharmokenetics.
...
This
...
is
...
the
...
perfect
...
term
...
to
...
reuse,
...
and
...
this
...
type
...
of
...
linkage
...
should
...
provide
...
for
...
a
...
convenient
...
way
...
to
...
easily
...
match
...
potential
...
drugs
...
with
...
MRS
...
results.
...
He
...
imports
...
the
...
class
...
into
...
his
...
modeling
...
tool,
...
bringing
...
with
...
it
...
an
...
number
...
of
...
associated
...
classes
...
and
...
attributes
...
that
...
may
...
be
...
of
...
use.
...
Technical
...
Description
...
:
...
all
...
data
...
elements
...
and
...
referenced
...
concepts
...
in
...
the
...
metadata
...
repository
...
are
...
indexed
...
and
...
easily
...
accessible
...
by
...
type-ahead
...
and
...
other
...
integrated
...
tooling
...
solutions.
...
The
...
model
...
browser
...
is
...
a
...
convenient
...
interface
...
for
...
exploring
...
the
...
metadata
...
in
...
a
...
UML
...
or
...
data
...
element
...
centric
...
way.
...
Furthermore,
...
the
...
repository
...
supports
...
the
...
import
...
and
...
export
...
of
...
modeling
...
standards,
...
such
...
as
...
XMI,
...
which
...
facilitates
...
direct
...
reuse.
...
Managing
...
semantic
...
relationships
...
in
...
order
...
to
...
link
...
and
...
share
...
data
...
Domain
...
Descriptions
...
:
...
a
...
metadata
...
specialist
...
has
...
been
...
tasked
...
with
...
cross-linking
...
the
...
hospital
...
system
...
and
...
the
...
clinical
...
systems
...
in
...
her
...
organization.
...
Fortunately,
...
both
...
systems
...
have
...
been
...
modeled
...
with
...
well
...
defined
...
metadata,
...
which
...
has
...
been
...
registered
...
in
...
a
...
metadata
...
repository.
...
Unfortunately,
...
the
...
information
...
models
...
used
...
by
...
the
...
systems
...
are
...
not
...
harmonized,
...
so
...
data
...
cannot
...
easily
...
be
...
integrated.
...
Therefore,
...
the
...
metadata
...
specialist
...
defines
...
semantic
...
relationships
...
between
...
the
...
elements
...
that
...
she
...
knows
...
are
...
related,
...
though
...
they
...
do
...
not
...
share
...
the
...
exact
...
same
...
common
...
data
...
elements.
...
For
...
example,
...
she
...
semantically
...
links
...
Patient
...
Last
...
Name
...
in
...
the
...
hospital
...
system
...
to
...
Subject
...
Surname
...
in
...
the
...
clinical
...
system.
...
Once
...
all
...
of
...
the
...
appropriate
...
relationships
...
are
...
made,
...
clinicians
...
are
...
able
...
to
...
navigate
...
between
...
the
...
system
...
seamlessly.
...
Furthermore,
...
the
...
antiquated
...
data
...
warehouse
...
where
...
all
...
of
...
this
...
information
...
is
...
painstakingly
...
transformed
...
and
...
poorly
...
linked
...
can
...
be
...
retired,
...
and
...
quality
...
of
...
care
...
queries
...
can
...
now
...
be
...
carried
...
out
...
using
...
semantic
...
relationships.
...
Technical
...
Description
...
:
...
semantic
...
relationship
...
and
...
rules
...
between
...
data
...
elements
...
can
...
be
...
formed,
...
stored,
...
and
...
shared
...
in
...
the
...
metadata
...
repository.
...
Furthermore,
...
these
...
relationships
...
can
...
be
...
reasoned
...
on
...
using
...
a
...
inference
...
engines
...
and
...
query
...
systems.
...
Cross Reference:
- ICR IRWG Requirements
...
- Requirements
...
- statement:
...
...
- Use
...
- Case:
...
...
Supporting
...
interoperability
...
standards
...
(for
...
example,
...
Healthcare
...
Datatypes)
...
Domain
...
Description
...
:
...
ISO
...
21090,
...
otherwise
...
known
...
as
...
HL7
...
Healthcare
...
Datatypes,
...
provide
...
a
...
basic
...
representation
...
of
...
common
...
chunks
...
of
...
data
...
exchanged
...
in
...
the
...
healthcare
...
community,
...
such
...
as
...
Address,
...
Document,
...
and
...
Coded
...
List.
...
A
...
metadata
...
specialist
...
has
...
been
...
tasked
...
to
...
expose
...
some
...
clinical
...
research
...
data
...
in
...
a
...
standards-based
...
approach.
...
She
...
sits
...
down
...
to
...
her
...
modeling
...
tool,
...
and,
...
as
...
a
...
first
...
step,
...
imports
...
the
...
healthcare
...
data
...
types
...
from
...
the
...
caBIG
...
metadata
...
repository.
...
She
...
begins
...
replacing
...
what
...
were
...
complex
...
sets
...
of
...
classes
...
and
...
attributes
...
in
...
her
...
existing
...
model
...
with
...
these
...
standard
...
datatypes.
...
The
...
resulting
...
system
...
is
...
not
...
only
...
simplified,
...
but
...
is
...
also
...
interoperable
...
by
...
virtue
...
of
...
using
...
ISO
...
21090.
...
Technical
...
Description
...
:
...
the
...
metadata
...
repository
...
allows
...
for
...
the
...
representation
...
of
...
any
...
standard
...
as
...
long
...
as
...
it
...
can
...
be
...
encoded
...
in
...
UML.
...
 ISO
...
21090
...
is
...
such
...
as
...
standard,
...
and
...
can
...
easily
...
be
...
exported
...
into
...
XMI
...
and
...
imported
...
into
...
a
...
modeling
...
tool.
...
In
...
UML,
...
these
...
classes
...
can
...
be
...
represented
...
as
...
complex
...
types
...
and
...
applied
...
to
...
attributes
...
rather
...
than
...
associations.
...
Cross
...
Reference
...
:
...
- Mapping/transformation
...
- support
...
- for
...
- ISO21090
...
- data
...
- types
...
- Requirements
...
- statement:
...
...
- Use
...
- Case:
...
...
Capturing
...
data
...
in
...
a
...
standard
...
way
...
using
...
data
...
element
...
reuse
...
Is
...
this
...
one
...
redundant
...
with
...
"Creation
...
of
...
metadata
...
and
...
management
...
of
...
information
...
models
...
through
...
modeling
...
and
...
web
...
tools"
...
and
...
"Finding
...
touch
...
points
...
with
...
other
...
systems
...
when
...
building
...
a
...
population
...
science
...
application"?
...
Description
...
:
...
Core
...
to
...
interoperability
...
is
...
capturing
...
data
...
in
...
a
...
standard
...
way
...
using
...
the
...
same
...
or
...
similar
...
data
...
elements.
...
Data
...
elements
...
individually
...
can
...
be
...
reused,
...
for
...
example
...
allowing
...
for
...
patient
...
data
...
to
...
be
...
joined
...
across
...
systems
...
using
...
the
...
Patient
...
Medical
...
Record
...
Number.
...
Forms
...
in
...
their
...
entirety
...
can
...
be
...
reused,
...
such
...
as
...
eligibility
...
forms
...
for
...
multi-site
...
clinical
...
trials.
...
Data
...
formats
...
for
...
encoding
...
biomedical
...
data
...
can
...
be
...
shared,
...
such
...
as
...
MAGE-ML
...
for
...
gene
...
expression
...
data.
...
This
...
allows
...
for
...
data
...
to
...
be
...
captured
...
in
...
a
...
standard
...
way,
...
shared
...
across
...
platforms
...
and
...
systems,
...
for
...
users
...
to
...
search
...
based
...
on
...
the
...
data
...
that
...
is
...
encoded
...
using
...
type-ahead
...
Google-like
...
functionality,
...
and
...
for
...
users
...
to
...
build
...
new
...
systems
...
based
...
on
...
the
...
standards
...
that
...
are
...
already
...
in
...
use.
...
Cross
...
Reference
...
:
...
- ICR
...
- IRWG
...
- Requirements
...
- Forum
...
- posting:
...
...
- Requirements
...
- statement:
...
...
- Use
...
- Case:
...
...
- CDEs
...
- from
...
- Man.
...
- curation,
...
- UML
...
- models
...
- and
...
- CRFs
...
- Forum
...
- posting:
...
...
- Requirements
...
- statement:
...
...
- Use
...
- Case:
...
...
Finding
...
touch
...
points
...
with
...
other
...
systems
...
when
...
building
...
a
...
population
...
science
...
application
...
Domain
...
Description
...
:
...
The
...
mission
...
of
...
population
...
science
...
is
...
to
...
reduce
...
the
...
risk,
...
incidence,
...
and
...
deaths
...
from
...
cancer
...
as
...
well
...
as
...
enhance
...
the
...
quality
...
of
...
life
...
for
...
cancer
...
survivors.
...
Genetic,
...
epidemiologic,
...
behavioral,
...
applied,
...
and
...
surveillance
...
cancer
...
research
...
are
...
typical
...
activities
...
of
...
population
...
science
...
researchers,
...
which
...
combines
...
clinical,
...
basic,
...
and
...
population
...
scientists
...
to
...
further
...
individual
...
and
...
population
...
health.
...
Patients
...
are
...
often
...
followed
...
for
...
months
...
or
...
years
...
after
...
diagnosis
...
and/or
...
treatment.
...
A
...
cancer
...
population
...
sciences
...
researcher
...
is
...
studying
...
chemotherapy
...
use
...
in
...
young
...
and
...
elderly
...
patients
...
with
...
advanced
...
lung
...
cancer.
...
For
...
this
...
type
...
of
...
cancer,
...
physicians
...
and
...
patients
...
often
...
have
...
to
...
choose
...
between
...
platinum-based
...
chemotherapy
...
or
...
non-platinum-based
...
chemotherapy.
...
Platinum-based
...
treatment
...
is
...
generally
...
considered
...
to
...
be
...
more
...
aggressive
...
and
...
effective,
...
but
...
it
...
is
...
also
...
more
...
toxic.
...
It
...
is
...
unclear
...
whether
...
physicians
...
are
...
avoiding
...
platinum-based
...
treatments
...
in
...
the
...
elderly
...
because
...
of
...
concerns
...
about
...
frailty
...
and
...
toxicity.
...
The
...
cancer
...
researcher
...
consults
...
with
...
a
...
metadata
...
specialist
...
for
...
designing
...
the
...
information
...
model
...
that
...
will
...
include
...
patient,
...
clinical,
...
pathology,
...
tissue,
...
and
...
imaging
...
data.
...
The
...
metadata
...
specialist
...
selects
...
a
...
number
...
of
...
information
...
models
...
that
...
are
...
currently
...
being
...
used
...
by
...
other
...
researchers,
...
and
...
overlays
...
them
...
to
...
determine
...
the
...
data
...
elements
...
that
...
are
...
important
...
for
...
linking
...
and
...
capturing
...
such
...
diverse
...
data.
...
These
...
are
...
exported
...
from
...
the
...
metadata
...
repositories
...
and
...
imported
...
into
...
his
...
modeling
...
tool
...
to
...
be
...
enhanced
...
with
...
the
...
new
...
fields
...
for
...
the
...
population
...
science
...
research.
...
Technical
...
Description
...
:
...
each
...
information
...
model
...
has
...
well
...
defined
...
metadata
...
available
...
in
...
distributed
...
metadata
...
repositories.
...
The
...
nature
...
of
...
the
...
metadata
...
is
...
such
...
that
...
simple
...
queries
...
can
...
determine
...
overlapping
...
data
...
elements.
...
This
...
can
...
be
...
visualized
...
side-by-side
...
in
...
a
...
tabular
...
format,
...
or
...
graphically
...
in
...
a
...
UML
...
class
...
model.
...
The
...
metadata
...
repository
...
can
...
output
...
data
...
using
...
UML
...
standards,
...
such
...
as
...
XMI,
...
which
...
can
...
easily
...
be
...
aggregated
...
and
...
imported
...
into
...
a
...
modeling
...
tool.
...
Support
...
data
...
transformations
...
in
...
order
...
to
...
allow
...
different
...
flow
...
cytrometry
...
tools
...
to
...
work
...
together
...
Domain
...
Description
...
:
...
Flow
...
cytometry
...
(FCM)
...
is
...
a
...
technique
...
for
...
counting
...
and
...
examining
...
microscopic
...
particles,
...
which
...
is
...
routinely
...
used
...
in
...
the
...
diagnosis
...
of
...
health
...
disorders,
...
especially
...
blood
...
cancers,
...
but
...
has
...
many
...
other
...
applications
...
in
...
both
...
research
...
and
...
clinical
...
practice.
...
Automated
...
identification
...
systems
...
could
...
potentially
...
help
...
findings
...
of
...
rare
...
and
...
hidden
...
populations.
...
An
...
informatics
...
specialist
...
is
...
working
...
on
...
objectively
...
comparing
...
many
...
of
...
the
...
FCM
...
analytical
...
methods
...
available
...
in
...
the
...
community
...
for
...
use
...
in
...
automated
...
population
...
identification
...
using
...
computational
...
methods.
...
The
...
primary
...
barrier
...
to
...
this
...
evaluation
...
is
...
the
...
wide
...
variety
...
of
...
data
...
standards
...
used
...
by
...
the
...
tooling,
...
which
...
includes
...
MIFlowCyt,
...
ACS,
...
NetCDF,
...
Gating-ML,
...
FuGEFlow,
...
and
...
OBI.
...
The
...
informaticist
...
decides
...
to
...
take
...
an
...
approach
...
of
...
defining
...
semantic
...
relationships
...
and
...
transformation
...
services. The result is a system in which FCM analytical workflows are able to discover and perform translations as needed during analytical comparisons.
Technical Description: semantic relationship and rules between data elements can be formed, stored, and shared in the metadata repository. Furthermore, these relationships can be reasoned on using a inference engines and workflow engines. Translation services can be defined and identified as such, which would allow for them to be discovered and applied as needed.
Content Driven browser
An informatics scientist modeling a new tool is browsing the CDE browsers to find the CDEs of his interest.
The CDE browser in its current shape has some usability issues. Non-regular users using the browser find the terminology used very technical and it requires training to understand. For curators whose job it is to work with these tools that may be acceptable. However, if these tools are to be usable by outside researchers, the terminology should be a better fit with less-technical terms, those researchers are likely to use. The visual presentation of controls/action is problematic and the relationship between the browse tree and the search forms (Search for CDEs, Search for Forms) is not intuitive.
Given the numerous usability issues with the CDE browser the need is to come up with an alternative and a more efficient search workflow.
Cross reference
- New CDE browser workflow:https://wiki.nci.nih.gov/pages/viewpageattachments.action?pageId=24259415
...
- Requirement
...
- statement:
...
...
- Forum
...
- post:
...
...
- Patrick:
...
- I
...
- think
...
- the
...
- domain
...
- description
...
- needs
...
- to
...
- be
...
- worked
...
- up
...
- a
...
- bit
...
- to
...
- be
...
- believable.
...
D.
...
Developer
...
Stories
...
Iterative
...
development
...
and
...
management
...
of
...
information
...
models
...
Domain
...
Description
...
:
...
Iterative
...
and
...
Incremental
...
development
...
is
...
a
...
cyclic
...
software
...
development
...
process
...
developed
...
in
...
response
...
to
...
the
...
weaknesses
...
of
...
the
...
waterfall
...
model.
...
It
...
starts
...
with
...
an
...
initial
...
planning
...
and
...
ends
...
with
...
deployment
...
with
...
the
...
cyclic
...
interaction
...
in
...
between.
...
The
...
basic
...
idea
...
behind
...
iterative
...
enhancement
...
is
...
to
...
develop
...
a
...
software
...
system
...
incrementally,
...
allowing
...
the
...
developer
...
to
...
take
...
advantage
...
of
...
what
...
was
...
being
...
learned
...
during
...
the
...
development
...
of
...
earlier,
...
incremental,
...
deliverable
...
versions
...
of
...
the
...
system.
...
Learning
...
comes
...
from
...
both
...
the
...
development
...
and
...
use
...
of
...
the
...
system,
...
where
...
possible
...
key
...
steps
...
in
...
the
...
process
...
are
...
to
...
start
...
with
...
a
...
simple
...
implementation
...
of
...
a
...
subset
...
of
...
the
...
software
...
requirements
...
and
...
iteratively
...
enhance
...
the
...
evolving
...
sequence
...
of
...
versions
...
until
...
the
...
full
...
system
...
is
...
implemented.
...
At
...
each
...
iteration,
...
design
...
modifications
...
are
...
made
...
and
...
new
...
functional
...
capabilities
...
are
...
added.
...
In
...
order
...
to
...
support
...
an
...
iterative
...
development
...
process,
...
it
...
is
...
necessary
...
that
...
the
...
metadata
...
itself
...
be
...
iteratively
...
developed.
...
The
...
information
...
model
...
is
...
enhanced,
...
semantics
...
added
...
and
...
removed,
...
on
...
a
...
monthly
...
basis.
...
Technical
...
Description
...
:
...
The
...
metadata
...
repository
...
supports
...
software
...
engineers
...
and
...
metadata
...
specialists
...
to
...
create
...
mod
...
The
...
metadata
...
repository
...
itself
...
must
...
support
...
the
...
developer
...
to
...
create,
...
modify,
...
and
...
remove
...
metadata
...
on
...
an
...
ongoing
...
basis.
...
Cross
...
Reference
...
:
...
- Automate
...
- Loading
...
- process
...
- Forum
...
- posting:
...
...
- Requirements
...
- statement:
...
...
- Use
...
- Case:
...
...
- Automate
...
- &
...
- Streamline
...
- caDSR
...
- Model
...
- Submission
...
- Process
...
- Forum
...
- posting:
...
...
- Requirements
...
- statement:
...
...
- Use
...
- Case:
...
...
- Simplify
...
- and
...
- streamline
...
- recording
...
- data
...
- semantics
...
- Forum
...
- posting:
...
...
- Use
...
- Case:
...
...
- Automate
- Forum posting:
...
...
- Requirements
...
- statement:
...
...
- Use
...
- Case:
...
...
- Use
...
- Case:
...
...
- ICR
...
- IRWG
...
- Requirements
...
- Forum
...
- posting:
...
...
- Requirements
...
- statement:
...
...
- Use
...
- Case:
...
...
Support
...
standardized
...
processes
...
for
...
software
...
development
...
and
...
conformance
...
Domain
...
Description
...
:
...
caEHR
...
is
...
the
...
flagship
...
project
...
that
...
is
...
applying
...
the
...
ECCF
...
process,
...
which,
...
when
...
applied
...
effectively,
...
should
...
produce
...
specifications
...
that
...
can
...
be
...
used
...
to
...
evaluate
...
how
...
and
...
at
...
what
...
levels
...
various
...
information
...
systems
...
are
...
interoperable.
...
This
...
is
...
important
...
to
...
enabling
...
coordination
...
of
...
IT
...
resources
...
across
...
the
...
community
...
of
...
NCI
...
stakeholders.
...
The
...
caEHR
...
project
...
is
...
currently
...
creating
...
and
...
managing
...
various
...
artifacts
...
(CFSS,
...
PIM,
...
PSM)
...
manually.
...
Significant
...
challenges
...
include:
...
1)
...
managing
...
traceability
...
and
...
change;
...
2)
...
formulating
...
conformance
...
assertions
...
so
...
that
...
they
...
can
...
be
...
evaluated;
...
3)
...
collaborating
...
on
...
model
...
elements
...
(i.e.
...
distributed
...
model
...
authoring).
...
The
...
application
...
of
...
the
...
ECCF
...
process
...
is
...
facilitated
...
by
...
providing
...
a
...
formal
...
model
...
of
...
ECCF
...
artifacts.
...
As
...
an
...
example,
...
this
...
supports
...
traceability
...
among
...
artifacts,
...
the
...
ability
...
to
...
generate
...
artifacts,
...
and
...
the
...
synchronization
...
of
...
artifacts.
...
Technical
...
Description
...
:
...
ECCF
...
artifacts
...
can
...
be
...
defined
...
fully
...
within
...
UML,
...
which
...
can
...
be
...
stored
...
in
...
the
...
metadata
...
repository.
...
 This
...
would
...
allow
...
the
...
artifacts
...
to
...
be
...
queried,
...
manipulated,
...
compared,
...
and
...
exported.
...
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