The Integrative Cancer Research Workspace is producing modular and interoperable tools and interfaces that provide for integration between biomedical informatics applications and data. This will ultimately enable translational and integrative research by providing for the integration of clinical and basic research data. The Workspace is developing a software-engineered, well-documented and validated biomedical informatics toolset for use throughout the research community.
General Workspace Meetings: We are gearing up to start the NCI National Cancer Informatics Program (NCIP). We are anticipating changes in the workspace structure, and we will be not having regular ICR WS meetings while we are working out the program details. We will continue to send program updates to the ICR and NCIP Announce mailing lists.
Subscribe to the ICR listserv.
Subscribe to the NCIP Announce listserv
Additional information about ICR tools is also found on the Molecular Analysis Knowledge Center wiki.
ICR WS Teleconference Speakers
Thank you very much for the many suggestions we received for ICR Workspace teleconference speakers. Based on your feedback, here are the speakers and topics for our upcoming meetings:
- No scheduled speakers
Teleconference information: 800-593-0616 passcode: 2927756
Adobe Connect: http://cbiit.acrobat.com/icrws/
ISA-TAB-Nano Paper is Publiched
BMC Biotechnology 2013, 13:2 ,14 January 2013 http://www.biomedcentral.com/1472-6750/13/2/abstract
caBIG® Life Sciences Domain Analysis Model (LS DAM) v2.2.3 is Released
We are pleased to announce the release of LS DAM 2.2.3. The 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 key updates to the LS DAM in this release are:
- Introduction of a new class, ActivityCollection, which supports the semantics around collections of activities that may be performed (or planned) regardless of purpose, such as specimen processing activities in a tissue bank or routine maintenance of equipment in a laboratory.
- Change of the data type binding from the ISO 21090 data type specification to the HL7 Abstract Data Type R2 (HL7 ADT R2) specification.
The LS DAM and associated documentation can be found on the LS DAM wiki site:
- LS DAM 2.2.3 Model Download
- LS DAM 2.2.3 HTML presentation http://www.cancer.gov/global/web/policies/page8
- LS DAM 2.2.3 Model Documentation
- LS DAM 2.2.3 Release Summary
- LS DAM 2.2.3 Change List
New Article: Informatics and Standards for Nanomedicine Technology
A recent focus article in “Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology,” explores nanotechnology and its impact on medicine and biomedical research, as well as the need for informatics standards in Nanomedicine. To read more about how Nanotechnology has the potential to make medicine more personalized, predictive, and preemptive, view the full article.
The meeting Date is hyperlinked to the notes and hyperlinks in the Executive Summary are for specific presentations
Juli Klemm, NCI: program update
Juli Klemm, NCI: program update
Richard McCombie, Ph.D. -Cold Spring Harbor Laboratory: Challenges and Opportunities in Human Genetics Using Next Generation Sequencing
Philippe Rocca-Serra, Ph.D. -University of Oxford, UK: The ISA format and supporting software: technical insights and functional overview
Rakesh Nagarajan (Washington University in St. Louis) gave a presentation on operations of the Wash U Genome Center. Kenneth Smith (Columbia University, NY) gave an update on new features in geWorkbench.
Guy Coates of the Wellcome Trust Sanger Institute will talk about the iRODS genomic data management system.
Dr. Deanna Church, NCBI project lead for the Genome Reference Consortium (GRC) and projects such as Map Viewer, Ideogram Service, Coordinate Remapping Service and CloneDB, spoke about The Human Reference Assembly and Resources for Navigating Genomic Information.
Susanna-Sansone and Philippe Rocca-Serra gave a presentation on the ISA Framework. They talked about ISA as a successful community driven initiative (organizational model, success factors, lessons learned, funding, decision making and how prioritization decisions). They will also talk about the specification, tools, and newly launched commons. You can learn more about what they are doing in the Feb's Nature Genetics issue (http://www.nature.com/ng/journal/v44/n2/index.html); with the "It's not about the data" editorial and the ISA Commons' commentary "Toward interoperable bioscience data". Also nano-Tab/ISA-TAB-Nano is on the isacommons.org website.
Presentations on working group reports concluded with reports from Mukesh Sharma and Jim McCusker. Mukesh Sharma participates in HL7 and is co-leading an effort on an OMICS DAM for the Clinical Genomics Work Group and he discussed their progress. Jim McCusker participates in W3C in the Health Care and Life Sciences (HCLS) and Provenance Interest Groups. HCLS is building a Translational Medicine Ontology (TMO) and Knowledge Base and the Provenance group is interested in defining a language for exchanging provenance information among applications.
Dr. Dan Stanzione from the U of Texas at Austin’s Texas Advanced Computing Center, spoke about iPlant. iPlant Collaborative is a community of plant and computer scientists and educators developing an infrastructure of computing resources, interoperable analysis software and data services in a collaborative environment. iPlant activities and mission are shaped by community driven questions and requirements and resources are provided to advance the science being done by community members.
John Speakman, Chief Program Officer, Center for Biomedical Informatics and Information Technology, National Cancer Institute, provided a caBIG^®^ Program Update
Dr. David Wheeler, Director of cancer genomics and Assistant Director of the Baylor College of Medicine's Human Genome Sequencing Center, spoke about approaches and challenges with next generation sequence data analysis pipelines.
Jennifer Fostel presented the Ontology for Biomedical Investigations (OBI). The OBI project is developing an integrated ontology for the description of life-science and clinical investigations. OBI is built using BFO principles and provides terms for annotation of biomedical investigations, regardless of the particular field of study.
Dr. Ray Fergerson is from the Stanford Center for Biomedical Informatics Research and is the NCBO Project Director. He is one of the developers of the Protégé OWL plugin. He spoke about the NCBO organization, outreach and factors for success.
Carlo Torniai, an ontologist from Oregon Health and Science University, spoke on the eagle-I consortium and their research resource discovery network for biomedical scientists.
Amnon Shabo (slides on request firstname.lastname@example.org) spoke about the HL7 Clinical Gemonics Work Group - From Healthcare to Research.
Mike Hucka (slides on request email@example.com) from Caltech spoke about SBML (Systems Biology Markup Language) as an open community standard initiative. SBML is a representation format, based on XML, for communicating and storing computational models of biological processes. Mike reviewed past, present and future directions for the community and provided lessons learned – what went right (involved actual stakeholders, addressed real needs -not perceived ones, transparent and inclusive process, etc.) and where there were challenges (testing, complexity creep, not formalizing processes sufficiently).
Cecilia Neomi Arighi from U of Delaware presented on Protein Ontology. (PRO) provides the ontological representation of proteins and protein complexes and shows the relationships between them. It encompasses three sub-ontologies: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). There is a website with extensive browse and search capabilities and includes additional annotations using other ontologies like Pfam and GO.
John Speakman, NCI CBIIT CPO kicked-off the workspace call with a caBIG Program Update. Mike Smoot, UCSD, is lead developer for Cytoscape. He provided an overview of the Cytoscape software platform for visualizing molecular interactions and pathways and integrating these with annotations and data. His talk also focused on the active Cytoscape community.
Mark Bray from the Broad Institute gave a presentation on CellProfiler. It is a tool which integrates various algorithms. It is capable of extracting measurements for every individual cell in an image-based screen, ranging from standard assays (e.g., cell count, size, per-cell protein levels) as well as more complex morphological assays (e.g., cell/organelle shape or subcellular patterns of DNA or protein staining).
The ICR workspace heard reports on the recent BioIT and AACR meetings from Mark Adams (BAH) and Jens Poschet (Sapient) respectively.
The ICR participants presented on their assigned projects.
Alex Kanous from the DSIC Knowledge Center provided a presentation on the electronic Data Use Agreement tool. The tool may be used for generating DUAs for outgoing data based on a catalog of standardized, modular contract clauses, each of which corresponds to one of the E-DSSF’s sensitivity ratings.
Anton Nekrutenko and Daniel Blankenberg and of The Pennsylvania State University gave a presentation on Galaxy, an open-source next generation sequence (NGS) analysis software system. It addresses the need to empower the scientists without access to extensive infrastructure to do the analysis. Galaxy is a free web service, and has a plethora of analysis tools and has workflow generation capabilities
caArray Users Meeting featured upcoming plugin architecture for support the addition of new parsers and data storage mechanisms.
Jenny Kelley, NCI Population Sciences, updated the community on caLIMS v2 new features. She also provided a thorough demonstration of the tool.
The ICR Workspace is hearing reports on activities for the last period.
Looking for older notes? Access ICR Meeting Notes Archive Jan 2008 - Nov 2010