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Life Sciences Domain Analysis Model (LS DAM)

The LS DAM is being integrated with the BRIDG model. Going forward, information about ongoing support for this this combined domain analysis model will be available available on the BRIDG wiki.

 

 

Overview of the LS DAM

The caBIG Life Sciences Domain Analysis Model (LS DAM) is a shared view of the semantics for Life Sciences which includes hypothesis driven basic and pre-clinical research as well as discovery sciences. The effort was initiated as a means to provide a foundation for achieving semantic interoperability among various applications across caBIG.

This is a collaborative effort, currently engaging stakeholders from the National Cancer Institute (NCI), including the Cancer Biomedical Informatics Grid (caBIG) project, the HL7 Clinical Genomics Work Group (HL7 CG WG), and the Biomedical Research Integrated Domain Group (BRIDG).

The LS DAM is aligned, where appropriate, with the Biomedical Research Integrated Domain Group (BRIDG) model, which is a separate DAM that supports the domain of protocol driven clinical and pre-clinical research. The points of alignment highlight the touch points between life sciences and clinical research, and through these touch points, the two models can be used together to support semantic interoperability across the translational research continuum.

The intent is for the LS DAM to continue to evolve over time, becoming more refined and expanding to describe the full breadth of scope, as the model is used and the user community brings new concepts forward to be included.

The LS DAM is modeled in UML through Enterprise Architect. It is fully described through UML class and instance diagrams. The LS DAM is bound to the ISO 21090 data type standard.

What is a Domain Analysis Model (DAM)?

A Domain Analysis Model (DAM) :

  • An implementation-independent view of a domain of interest
  • Represents a shared understanding of concepts
  • Uses domain terminology and is understandable to domain experts who may have little or no UML skills but yet, are a primary consumer
  • Includes unambiguous definitions
  • Uses complex data types designed specifically for the domain of focus, in our case healthcare
  • Follows good modeling practices
  • Enables interoperability when systems share a common understanding
  • Is built by analysts and subject matter experts who develop consensus
  • Informs development of downstream artifacts

LS 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.

LS DAM Context:
Concepts important to Clinical Research are contained in the BRIDG domain analysis model. The LS DAM and BRIDG models are harmonized on key concepts that can be used as touch points to allow utilization of elements from both models.

LS DAM Project Team Members and Stakeholders

Name

Affiliation

Role

Juli Klemm*

NCI CBIIT

Government Sponsor, ICR Workspace Federal Lead

Ian Fore*

NCI CBIIT

TBPT Workspace Federal Lead

Mervi Heiskanen*

NCI CBIIT

ICR Workspace Facilitator

Anna Fernandez*

Booz Allen Hamilton

TBPT Workspace Facilitator

Robert Freimuth*

Mayo Clinic

IRWG Lead

Elaine Freund

3rd Millennium

ICR Workspace Facilitator

Joyce Hernandez*

Merck

HL7 Clinical Genomics WG

Jason Hipp

University of Michigan

IRWG

Jenny Kelley

NCI LPG

IRWG

Sue Pan

SAIC

IRWG

Fred Prior

Washington University in St. Louis

IRWG

Konrad Rokicki

SAIC

IRWG

Lisa Schick*

ScenPro

LS DAM Analyst

Mukesh Sharma*

Washington University in St. Louis

IRWG, HL7 Clinical Genomics WG

Grace Stafford*

The Jackson Laboratory

IRWG

Todd Stokes

Georgia Tech

IRWG

Baris Suzek*

Georgetown University

IRWG

*Current Participant

Release History

LS DAM Version

Release Date

Primary Focus

2.2.3

May 2012

Harmonization of specimen procesing protocol and binding to HL7 Abstract Data Type Release 2

2.2.2

January 2012

Re-alignment of Experiment Core to ISA-TAB as per community feedback

2.2.1

May 2011

Correction to technical (non-domain semantics) issues

2.2

April 2011

Further refinement of Experiment and Molecular Biology Core and introduction of Experiment Implementation Guide

2.1

February 2011

Resolution of concerns within Molecular Biology and Experiment Cores

2.0

October 2010

Alignment with BRIDG 3.0.2 and formalization of Experiment Core

1.2

February 2010

Addition of key semantics from ICR nano sub-domain

1.1

October 2009

Further alignment with BRIDG 3.0.1

1.0

July 2009

Initial release

** Anticipated

Examples of Use in the Community

The caBIG Molecular Annotation Service (MAS) is a resource for accessing molecular annotations from curated data sources. The information model that supports this service is derived from the LS DAM, primarily from the Molecular Biology Core (for example, genes, proteins and genetic variations).

The caLIMS v.2.0 was a project focused on the development of an open source Laboratory Information Management System. The project team leveraged and extended several concepts originating in the LS DAM as needed to support their specific project requirements.

The development of the HL7 Omics DAM, a product of the HL7 Clinical Genomics (CG) Work Group, has been heavily informed by the LS DAM Experiment and Molecular Biology cores. The Omics DAM was posted for informative ballot as part of the HL7 May 2012 ballot cycle.

The HL7 Specimen DAM Project is a collaborative effort involving participants from several HL7 Work Groups (including: Orders & Observations (O&O), Clinical Genomics (CG), and Anatomic Pathology (AP)), aimed at building a Specimen DAM that will support the cross work group requirements. The project team has elected to use the LS DAM Specimen Core as a basis on which their model will be built.

Next Steps

For information on identified recommendations and next steps, see the Future Activities Compilation on the IRWG wiki.

Interested in Participating or Submitting Feedback?

For information on participating in the LS DAM Project or to submit feedback, see the IRWG LS DAM Feedback page on the IRWG wiki.

  
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