1 LS DAM Overview August 7, 2012 Current Core Team: Ian Fore, D.Phil., NCI CBIIT, Robert Freimuth, Ph.D., Mayo Clinic, Mervi Heiskanen, NCI-CBIIT, Joyce Hernandez, Merck, Juli Klemm, Ph.D., NCI-CBIIT, Lisa Schick, ScenPro, Mukesh Sharma, Ph.D., Washington University in St Louis, Grace Stafford, Ph.D., The Jackson Laboratory, Baris Suzek, M.S., Georgetown University

2 Agenda What is it? Informing resources and alignment with BRIDG LS DAM Core Components Examples of the LS DAM in use 2

3 Life Sciences Domain Analysis Model (LS DAM) – What is it? The LS DAM Project grew out of the desire to support interoperability across several NCI cancer Bioinformatics Grid (caBIG®) life sciences applications Initiated in February 2009 with NCI caBIG life sciences community as the initial stakeholder Collaboration with HL7 Clinical Genomics Work Group (HL7 CG) began June 2010 Omics DAM Collaboration with HL7 Orders and Observations Work Group (HL7 O&O) began February 2012 Specimen DAM Project Goals Produce a shared view, in UML, of the static semantics of the domain of hypothesis- driven and discovery research at the organism, cell, and molecular level in order to facilitate human and computable semantic interoperability in that domain Maintain alignment of the LS DAM with BRIDG as it also evolves, in order to facilitate human and computable semantic interoperability across the translational research continuum 3

4 Life Sciences DAM Scope Statement Life Sciences research includes (i) in vivo, experiments (ii) ex vivo, in vitro or in situ experiments, and (iii) in silico experiments modeling and analyzing processes or other biological phenomena. The Life Sciences Domain Analysis Model (LS DAM) focuses on concepts important for conducting hypothesis driven and discovery science at the organismal, cellular and molecular level. The LS DAM includes and defines relationships between concepts that are central to specimen collection, processing and banking (human, model organism, cell lines, etc.), in vitro imaging, and molecular biology.

5 Informing Resources Leveraged caBIG ICRi and Enterprise scenarios to define scope of initial version of model Drew support for concepts from well-established, community-vetted caBIG projects E.g., tissue banking related (caTissue), microarray data management (caArray), laboratory information management system (caLIMS), nanomaterial data sharing portal (caNanoLab) Standard reference models and data exchange formats widely used in the life sciences community have informed modeling decisions ISA-TAB (Investigation, Study, Assay data exchange format) FuGE (Functional Genomics Experiment model) MAGE (Microarray Gene Expression model) Aligned with the BRIDG model on touchpoints Alignment to be ongoing as each model continues to evolve Approximately 1/3 of the LS DAM classes are BRIDG 3.0.2

6 Alignment with BRIDG to support translational research Subject touch point supports traversing from LS DAM to BRIDG to support use cases as needed LS DAM includes distinct specialization of BRIDG.Subject to support the specific requirements around SpecimenCollectionPr otocolSubject Touch points can be leveraged in support of the translational research continuum

7 7 Experiment Core Specimen Core Molecular Biology Core Molecular Databases Core LS DAM Common

8 LS DAM Experiment Core Component Conceptual representation of the process of experimentation in both hypothesis driven and discovery research in the Life Sciences domain Collaborative effort with HL7 CG WG to model common representation that can support interoperability around expanding array of ‘omics technologies Heavily informed by ISA-TAB and MAGE Includes concepts such as: ExperimentalStudy, Experiment, ExperimentalParameter, ExperimentalFactor

9 LS DAM Experiment Core 9

10 LS DAM Experiment Core - ActivityItem 10

11 LS DAM Molecular Biology Core Component Modeling of the molecular components of cells and organisms that will enable linking to genomic and proteomic annotations and experimental findings Heavily informed by ISA-TAB, MAGE-TAB, FuGE, dbSNP, various public molecular databases Includes concepts such as Gene, Protein, NucleicAcidSequence, AminoAcidSequence, GeneticVariation

12 LS DAM Molecular Biology Core 12

13 LS DAM Molecular Databases Core Component Supports linking identifying information held in databases (such as Ensembl, UniProt, GenBank) to the molecular components defined in the molecular biology core Includes concepts such as GeneIdentifier, ProteinIdentifier, SNPIdentifier

14 LS DAM Molecular Databases Core 14

15 LS DAM Specimen Core Component Modeling of the collection, processing and storage of physical substances originally obtained from a biological entity Heavily informed by caBIG caTissue, caNanoLab Includes concepts such as Material, BiologicSpecimen, PeformedSpecimenCollection, PerformedSpecimenProcessing, SpecimenCollectionProtocol

16 LS DAM Specimen Core Component 16

17 Examples of LS DAM in use caBIG® Molecular Annotation Service (MAS) A resource for accessing molecular annotations from curated data sources Information model supporting this service derived from the LS DAM Requested support for annotation of genes and gene products in LS DAM HL7 CG WG Omics DAM A DAM to support genetic testing scenarios from contact with a participant through the collection of specimens, the molecular assays performed on the specimen or a derivative, and the lab reports generated as a result LS DAM leveraged as the backbone of the effort Several requests submitted, many addressed in next LS DAM release caBIG® caLIMS2 A laboratory information management system Leveraged several LS DAM concepts that are relevant to a laboratory environment while developing the project’s information model Requested support for several identified gap concepts in LS DAM nano-TAB An ISA-TAB based standard format for describing data related to investigations, nanomaterials, specimens, and assays in nanomedicine Has been mapped to LS DAM in an effort to align the two standards

18 Resources LS DAM Wiki: Links to current and previous releases Background information 18