Presentation on theme: "Brief review of what Crimson does Scope of the i2b2 Crimson cell –(1) i2b2 sample ontology + ontology management for source LIMS broadcasting samples to."— Presentation transcript:
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/
Crimson Cohort CMV Samples (Discarded or Dedicated) Query IRB Sys. A Timely Clinical Data f OR Consented cohort Retrospective Clinical Data Sys. B Sys. C i2b2 (CDR) High-throughput and cost-effective performance of genomic studies Consented Samples IRB Phenotypic Data IRB Analyses
Crimson Usage/Use Cases: 75K samples for ~70 studies
Sample Utilization Category% samples that have undergone some analysis Biorepositories6-10% Clinical trials67% i2b2 DBPs77% (will be >95% shortly) Discarded: Anon/de-ID (with or without external cohort) 93% Discarded: Consented (consented cohort) 94% >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
Webservice Layer 3. Cohort Mgmt 4. EMSI 1. Sample Ont Mgmt Business Logic Layer i2b2 Crimson Cell 5. Crimson Widget in i2b2 Client Crimson Webservice Layer Business Layer i2b2 hive PM LIMS Honest Broker Criteria Engine Crimson Map Study Mgmt Subject Mgmt LIMS X Map 2. IRB data Ont 1. Sample ontology Project Plan
(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.