Transcript IRB data: New PM v1.4 tables

• Brief review of what Crimson does
• Scope of the i2b2 Crimson cell
– (1) i2b2 sample ontology + ontology management for source LIMS
broadcasting samples to i2b2.
– (2) Entry/management of IRB data (PM cell v1.4)
– (3) Cohort Manager
• Prospective collection (Crimson): (a) Forwarded from i2b2CRC
or (b) “return-trip” cohorts from Crimson or other source LIMS.
• Manage query/requests from retrospective repositories
(Crimson or other source LIMS).
– (4) Enterprise Master Specimen Index (EMSI)
– Project materials will be posted to
http://i2b2crimson.partners.org/
Sys.
A
Retrospective
Clinical Data
Sys.
B
Sys.
C
Timely Clinical Data
f
OR
Consented cohort
Crimson
i2b2
IRB
(CDR)
Cohort
IRB
Consented
Samples
IRB
Query
IRB
Phenotypic
Data
Analyses
CMV
Samples
(Discarded or Dedicated)
High-throughput and cost-effective
performance of genomic studies
Crimson Usage/Use Cases: 75K samples for ~70 studies
Sample Utilization
Category
% samples that have
undergone some analysis
Biorepositories
6-10%
Clinical trials
67%
i2b2 DBPs
77% (will be >95% shortly)
Discarded: Anon/de-ID
93%
(with or without external cohort)
Discarded: Consented
94%
(consented cohort)
>40K samples released for researcher use.
Crimson-i2b2 R01 (NLM)
• What we’re creating:
– (1) i2b2 Sample Ontology
– (2) Manage IRB data in
i2b2 (for purposes of
sample collection but
available for other uses).
– (3) Cohort Manager for
sample collection:
prospective or requests
from retrospective
repositories.
– (4) Enterprise Master
Specimen Index (EMSI)
• What we’re not creating:
– Rebuilding Crimson
– Building a de novo LIMS for
sample handling/management
i2b2 hive
5. Crimson Widget
in i2b2 Client
PM Ont
2. IRB data
1. Sample
ontology
Webservice Layer
Webservice Layer
Business Logic Layer
Business Layer
1. Sample
Ont Mgmt
Crimson
Map
LIMS X
Map
3. Cohort
Mgmt
4. EMSI
i2b2 Crimson Cell
Project Plan
Honest
Broker
Criteria
Engine
Study
Mgmt
Subject
Mgmt
LIMS
Crimson
(1) Sample Ontology
• Fluids, Microbes, Solid Tissues
– Fluids and microbes first (blood, CSF, DNA, B.
cepacia, MRSA..).
• SNOMED and WHO coding.
– Solid tissues to build upon SNOMED, HL7/sample
segments and caBIG nomenclatures.
• LOINC great for results and procedures but not for
sample types or microbes.
• Relational ontology
– Primary vs. derivative samples
– Sample query tool to select sample type(s),
preservatives/fixatives, etc. for prospective or
retrospective query.
Sample Ontology Manager
• Source LIMS providing samples can map
their local ontology into the Crimson cell via
an adapter.
– Vocabulary terms in Sample ontology treated as
vocabulary items or as “results” in different LIMS.
• Examples: Crimson, Sunquest LIS, Powerpath APLIS,
LabVantage LIMS..
• Ability to update ontologies in an i2b2
webclient UI (bank’s “LabAdmin” role).
(2) IRB data: New PM v1.4
tables
• Create a Templating System for the PM cell:
– PM_OBJECTS table (new)
• Support creation of “n” objects for the PM cell
– PM_ATTRIBUTES table (new)
• Supports creation of “n” attributes per object.
– PM_PERMISSIONS table has added columns to
define relations with attributes.
• Stores data associated with instances of an object
IRB-related objects
•
•
•
•
GRANTING_ENTITY
IRB_PROTOCOL
SPONSOR
MULTISITE_PROTOCOL
– Link to 1 or more local IRB protocols
– Plus anything else a given i2b2 site might
want to define..
IRB data entry
• AJAX/webclient UI for PM cell
• Create/edit IRB protocols.
• Add/remove IRB protocol to an
i2b2Group.
• Enter IRB-specific elements driving
sample collection and release.
(3) Cohort-forwarding
• Crimson cell will receive cohorts from the
i2b2CRC or from Crimson.
• Validate cohorts and manage QA processes.
• Forward to receiving system.
– Initiate prospective collection (forward to
Crimson/QA)
– Generate datamart (Crimson -> i2b2)
– Find samples (with EMSI)
• Generate picklists that go to a source LIMS which will
release samples.
(4) EMSI
• Enterprise Master Specimen Index
– Tracks instances of samples across an enterprise.
– Dataset includes sample availability, accession#s
assigned by different LIS/LIMS.
• Source LIMS can broadcast samples into the
EMSI to indicate availability (public or for
specific studies/private).
– Handles consented, de-ID and anon samples.
• Developed within Partners Healthcare
– Serve Partners-wide biorepository (blood +
derivatives first, tissues later).
– Within Partners, Crimson (webservice) and
Sunquest LIS (HL7 + Ensemble) broadcast
samples into EMSI.
http://i2b2crimson.partners.org
• BWH Pathology
– Lynn Bry
– Neil Herring
• Partners i2b2/PPMB teams
– Shawn Murphy
– Mike Mendis
–
–
–
–
Natalie Boutin
Ana Holzbach
Kevin Enbree
Neeta Rathi
• HSPH/WHO
– John Stelling
– Hubert Lison
• Extension Engine
–
–
–
–
Bob Allard
Niksa Radovic
Ofri Markus
Dusko Dobrijevic
• Daedalus Software
–
–
–
–
Erik Lickerman
Nighat Afsheen
Ahmed Balia
Azita Sharif
• Funding
– NLM