News

BioInformatics Seminar Series

The NCI Center for BioInformatics sponsors an ongoing series of seminars that are open to the NIH and the general public. Topics cover a broad range of informatics subjects that are relevant to biology and/or medicine. Contact Frank Hartel at (301) 435-3869 or MaryAnn Fuss at 301-435-1520 for additional information about these seminars.

• Rolling Schedule of Seminar Dates
  This is the Seminar Schedule. This schedule is revised as topics are assigned to future seminar dates and as seminar logistics are firmed up. Below is a list of topics that have been scheduled to date. 

• Knowledge Representation in Clinical Trials
  On April 9, 2001 at 2 PM in Room EPN/7107, Dr Mark Musen discussed his work on representation of knowledge in the clinical trials environment. Dr Musen is the Head of Stanford Medical Informatics and Associate Professor of Medicine at Stanford University. 

• Description Logic Modeling of Biomedical Vocabulary
  On April 16, 2001 at 8 AM in EPN Conference Room H, a panel of speakers discussed use of formal description logic as applied to biological and medical terminology. Mr Eric Mayes of Apelon Inc. presented an overview of description logic as applied to biomedical vocabulary. Dr Keith Campbell of Inoveon Corp. discussed scalability issues in description logic vocabulary. Dr Michael Stearns of the American College of Pathologists described some lessons learned by the College in building the large SNOMED/RT vocabulary. Drs. Fred Rosenberg and Frank Hartel of NCI Center for BioInformatics discussed NCI's work on using description logic to model gene and protein related vocabulary. Video tape of the presentations is available upon request. 

• Relevance of HL7, ASTM and ISO Standards to Cancer Research and Treatment
  On May 7, 2001 at 9 AM in EPN Conference Room H, Drs. Chris Chute and Peter Elkin of the Mayo Clinic described recent and pending national and international standards developments  and discussed their relevance to NCI and to the larger cancer community. Dr. Chute's presentation focused on HL7, while Dr Elkin focused on ASTM E31 standards. Video tape of the presentations is available upon request. 

• HIPAA and Clinical Research
  On May 30, 2001 at 9 AM in the Natcher Center (Bldg 45) Balcony A, Dr. J. Michael Fitzmaurice of the Agency for Healthcare Research and Quality described the four components of HIPAA (transactions and codes, identifiers, security, and privacy) giving the most recent updated information about the contents of these standards, dates of first release, and dates of final rules. Dr. Fitzmaurice's presentation  also addressed the HIPAA Privacy Rule, a standard that protects individually identifiable health information in the hands of entities that are covered by HIPAA. Video tape of the presentations is available upon request. 

• XML, RDF, and Biological Data
  On June 11, 2001 at 9 AM Mr Joseph Futrelle of the National Computer Science Alliance, University of Illinois discussed ongoing progress in using XML, RDF and open source software  to parse, group and retrieve data in the Digital Library community. Mr. Futrelle highlighted opportunities to adapt these developments to various types of biological information. 

• XML in Bioinformatics
  On July 23, 2001 at 9 AM, in 6116 Executive Blvd, Room 3056B, Jonathan A. Borden, M.D., Director Boston Gamma Knife Center and Assistant Professor of Neurosurgery at Tuft University New England Medical Center presented an overview of XML document storage, query and retrieval systems and distributed document repositories. The Semantic Web, RDF, RDDL and DAML, and application of these techniques for healthcare applications were discussed. An overview of the DAML ontology and knowledge representation language was given. Particular attention was given to the application of these new Semantic Web technologies to cancer research.

• Computational Bioinformatics at SDSC * POSTPONED *
  This seminar, scheduled for September 17, 2001 at 9 AM, in the Neuroscience Bldg, 6001 Executive Blvd., Conf. Room A1/A2, was postponed. No newdate has been established. This flyer describes the focus of the presentations as they were originally planned.

• A New Theory of Gene Regulation
  On January 28, 2002 at 9 AM, in the Executive Plaza Conference Center, Richard J. Feldmann, Global Determinants, Inc. presented his theory of gene regulation being a function of the sequences flanking genes. The slides from the semianr are available for download.

• Extraction of Information from the Molecular Biology Literature
  On May 13, 2002 at 9 AM, in the Executive Plaza Conference Center Room H, Dr. Carol Friedman of Queens College CUNY and Columbia University described her work using natural language processing (NLP) to autonomously acquire knowledge associated with bimolecular interactions from the published literature.

• Ontologies and Terminologies in Biomedical Research: Desiderata for Original and Classical Data Sharing and Reuse On March 31, 2003 at 9 AM, in the 6116 Executive Blvd. Conference Room 3056A/B, Dr. Yves Lussier and Dr. Eneida Mendonca of the Department of Biomedical Informatics College of Physician and Surgeons, Columbia University described their work using ontologies and terminologies for data mapping, indexing, sharing, analysis and reuse. Dr. Lussier's slides (MS-PowerPoint or HTML) and Dr. Mendonca slides are available for download.

• Protein Naming and Protein Classification
  On June 23 at 9 AM, in the 6116 Executive Blvd.Conference Room 3056A/B, Dr. Anastasia Nikolskaya of Georgetown University will discuss her work on Functional Analysis of Protein Sequences and Protein Classification and Dr. Inderjeet Mani of the MITRE Corporation will describe his work on Extraction of Protein Names from MEDLINE. A précis of the talks is available.

• Open Vocabulary Server Development and Extraction of Biological Entities from the Literature
  On July 18 at 9 AM, in the 6116 Executive Blvd. Conference Room 3056A/B, Harold Solbrig of the Mayo Clinic discussed his work on open, distributed terminology server software and Dr. Lynette Hirschman of the MITRE Corporation described her work on identification of biological entities and extraction of relations, complexes and pathways from the biomedical literature. A précis of the talks is available as are Mr. Solbrig's slides.

• Integrating Gene Expression And Proteomic Data With Other Biological Data Types: Human Disease Associations, Literature Mining, and Biological Pathways
  On January 26, 2004 at 2 PM, in the 6116 Executive Blvd. Conference Room 3056A/B, Kevin Becker of the Gene Expression Genomics Unit, National Institute on Aging discussed three publicly accessible web based tools, which are useful for the integration of high throughput gene expression and proteomic data. These include: PubMatrix for high throughput semi-automated literature searching http://pubmatrix.grc.nia.nih.gov/; the Genetic Association Database for the integration of human genetic data http://geneticassociationdb.nih.gov and BBID-The Biological Biochemical Image Database http://bbid.grc.nia.nih.gov/. A précis of the talks is available.

• Formal Principles for Biomedical Ontologies
  On February 9, 2004 at 2 PM, in 6130 Executive Blvd. (EPN), Conf. Room H, Barry Smith of the University at Buffalo and Leipzig University discussed a number of structural and formal problems that are common in biological ontologies, and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Professor Smith argued that these problems can be avoided through adherence to formal organizing principles drawn from philosophical ontology, principles which represent best practices in classification and definition. He discussed how their neglect is associated in systematic ways with certain kinds of coding errors, and will conclude by sketching the potential benefits of a formally more adequate regime of classification and definition in the future. A précis of the talks is available, as are Dr Smith’s slides.

• Foundational Model of Anatomy in Cross-Correlation of Neoplasia and Anatomical Entities
  On March 3, 2004 at 9 AM, in 6130 Executive Blvd. (EPN), Conf. Room H, Cornelius Rosse of the School of Medicine, University of Washington, Seattle, WA will illustrate how the Foundation Model of Anatomy (FMA) can be partitioned and filtered to provide the view and granularity that meets the needs of NCI knowledge modelers. Particular examples will be used as mockups to show the kinds of neoplasias that can affect certain kinds of anatomical entities and how the FMA can provide the framework for associating gene expression data and other etiological information with particular anatomical entities. A précis of the talk is available.

• Formal Principles for Biomedical Ontologies
  On April 15, 2004 at 2 PM, in 6130 Executive Blvd. (EPN), Conf. Room H, Chris Stoeckert and Trish Whetzel, of the Department of Genetics, University of Pennsylvania, discussed MGED Ontology (MO). The relationship of MO to the Minimum Amount of Information about a Microarray Experiment (MIAME), a standard developed by the Microarray Gene Expression Data (MGED) Society (http://www.mged.org) was described. MGED has also generated a set of guidelines called the MicroArray Object Model (MAGE-OM) to represent this domain, and has created the MGED Ontology (MO) to provide the semantics for MIAME and MAGE. MO provides terms for the annotation of microarray experiments through classes, properties, and instances to describe the design, the biological materials, and the technical elements of a microarray experiment. MO also provides a framework to reference terms from external ontologies to take advantage of existing ontologies. In principle, MO can be extended to describe additional types of functional genomics experiments. A précis of the talk and Dr. Stoeckert's slides are available.

• Data Integration Support for Cancer Research
  On June 4, 2004 at 1 PM, in 6116 Executive Blvd. (EPN), Conf. Room 6006, Michael Becich, and Rebecca Crowley of the University of Pittsburgh Cancer Center discussed the Pittsburgh Cancer Center's overall shared vision of an integrated environment for cancer research (Becich), followed by a description of several areas in which we have maturing development efforts (Crowley). A précis of the talk is available, as are the speakers’ slides. The slides are in a ZIP file that is large, about 25MB.

• Using Protégé to Bridge Vocabulary and Information Spaces
  On October 18, 2004 at 10 AM, in 6116 Executive Blvd., Conf. Room 6006 Harold Solbrig of the Mayo Clinic Division of Biomedical Informatics will describe one way that Protégé can be used to define the various elements of an information model using external terminologies. Mr. Solbrig will discuss how terminology can be imported and used in conjunction with the sort of modeling tasks that Protégé is frequently used for, such as defining entry forms, information models, etc., and how the various components of this model relate to the information model described in Part 3 of the ISO/IEC 11179 standard on metadata registries. A précis of the talk is available.

• Utilizing Nomenclatures to Improve Data Representation and Information Management in Support of Cancer Research
  On November 10, 2004 at 1 PM, in 6116 Executive Blvd. Conf. Room 607, Dr. Peter Elkin of the Mayo Clinic College of Medicine will discuss the theory behind compositional systems for data representation in the context of a working J2EE terminology server. He will demonstrate the server and several applications that have been built around the terminology server which demonstrate the power of ontologic support (compositional concept based indexing) in support of cancer research. To date Dr Elkin has explored using his terminology server to support numerous applications. In this Seminar, he will describe results to date relative to automated indexing of clinical documents and expert systems for quality reviews or clinical trials support, and will touch on image management and web site indexing and knowledge management as time permits. A précis of the talk is available.