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LS DAM Overview and the Specimen Core

February 16, 2012

Core Team: Ian Fore, D.Phil., NCI CBIIT, Robert Freimuth, Ph.D., Mayo Clinic, Elaine Freund, Ph.D., 3 rd Millennium, Joyce Hernandez, Merck, Jason Hipp, M.D./Ph.D., University of Michigan, Jenny Kelley, M.A., NCI LPG, Juli Klemm, Ph.D., NCI-CBIIT, Jim McKusker, Yale, Lisa Schick, ScenPro, Inc., Mukesh Sharma, Ph.D., Washington University in St Louis, Grace Stafford, Ph.D., The Jackson Laboratory, Baris Suzek, M.S., Georgetown University

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Agenda

• What is the LS DAM?• Informing resources and alignment with BRIDG• LS DAM 2.2.2 and Core Components• Specimen Core in detail• LS DAM resources

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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• The project was initiated in February 2009 with NCI caBIG® life sciences

community as the initial stakeholder• Collaboration with the HL7 Clinical Genomics Work Group (HL7 CG WG)

began in June 2010

• Project Goals• To 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

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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.

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Informing Resources

• Many concepts drawn 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 have informed modeling decisions• ISA-TAB, FuGE, MAGE, BRIDG

• Bound to the ISO 21090 data type standard• Aligned with the Biomedical Research Integrated Domain Group (BRIDG)

model on touchpoints• Alignment is ongoing as each model continues to evolve

• Re-using concepts “owned” by BRIDG that apply to our domain• 56 of the 130 LS DAM 2.2.1 classes originate from BRIDG

• E.g., Person, Organization, Activity (and much of the hierarchy), Material

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Person, Organization, and their Roles

Document

Experiment Core

Specimen Core

Molecular Biology Core

Molecular Databases Core

Activity hierarchy (defined, planned, performed)

Material, Equipment

LS DAM 2.2.2

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LS DAM Core Components

• Experiment• Conceptual representation of the process of experimentation in both hypothesis driven and

discovery research in the Life Sciences domain• “Common” to support interoperability across expanding array of ‘omics technologies• Heavily informed by ISA-TAB and MAGE

• Molecular Biology• 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, CGOMS, FuGE, dbSNP, EndNote, various public

molecular databases• Molecular Databases

• Supports linking identifying information held in databases (such as Ensembl, UniProt, GenBank) to the molecular components defined in the Molecular Biology Core

• Specimen**• Modeling of the collection, processing and storage of physical substances originally obtained

from a biological entity • Heavily informed by caBIG® caTissue, caNanoLab and the HL7 Specimen CMET

• Took requirements supported by caTissue (primarily) and brought them into the model in manner aligned with BRIDG and the HL7 Specimen CMET, where possible

• Included in the model since LS DAM 1.0, but has not been a primary focus• Much of caBIG caTissue and caNanoLab semantics have not been harmonized into the LS DAM

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LS DAM Specimen Core Component

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Specimen Collection Subject

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Specimen Collection

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Specimen Processing

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Collection and processing of BiologicSpecimen

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LS DAM Resources

• LS DAM Wiki: https://wiki.nci.nih.gov/x/cxRlAQ• Current (and previous) version of the model and documentation

describing the changes made as part of the release• User Guide• Experiment Implementation Guide