Translational Bioinformatics

 

For more information or to schedule this course, please contact  JDiane Rein <drein@buffalo.edu>.

The major goals of this face-to-face course are to familiarize participants with 1) clinical bioinformatics databases; 2) acquisition of expert level search strategies within these database; and 3) acquisition of human genetics principles and vocabulary.

The morning sessions will cover Clinical Bioinformatics, and its relationship to translational medicine, biomedical informatics, clinical informatics, and electronic medical and health records. This will be supplemented with a module covering the biology and vocabulary in genetics, genomic variation and mutations, implementing that vocabulary through searching the Human Gene Mutation Database. The afternoon sessions concentrate to searching two major clinical bioinformatics databases: Online Mendelian Inheritance in Man (OMIM) which integrates biological data with human disease data and information; and 2) PharmGKB, the NIH-designated personalized medicine database which interrelates biological data with pharmacological and other pharmaceutical-related drug information. The workshop ends with an overview and demonstration of clinical bioinformatics public health databases.

Although many investigators have used bioinformatics methodologies at the laboratory research bench in many subject disciplines, only since 2009 have researchers shifted the role of bioinformatics in asking and answering questions related to human health and disease. Genetics, both the “traditional” genetics as well as the new genetics of mutations, genomic variations, and chromosomal architecture discoveries arising out of the early application of bioinformatics to inheritable and acquired pathologies and traits, is very much the vocabulary and database search strings of this new kind of medical research and practice which is typically referred to generically as “genomic medicine” and/or “personalized medicine”. Bioinformatics (that biological data related to gene and protein sequences, their genetic expression and concomitant pathological processes and disease phenotypes) is rapidly becoming an integral component of biomedical education, clinical practice and translational medicine efforts which aim to bring the “bench to the bedside”.

The 1000Genomes Project which, regardless of its name, is currently sequencing over 2000 individual human genomes from various populations and ethnicities worldwide to create a comprehensive, foundational resource in human genetic variation, now generates more biodata in one day than the entire Human Genome Project did in 10 years. Clinical bioinformatics is intricately associate with, as well as a major driver of, data archiving, storage and institutional repository efforts. The practice of clinical bioinformatics from bench to bedside requires that these stored data by linked to patient medical and health records in a way that generates new diagnostic tools and clinical practice. To link health-associated bioinformatics data to clinical practice, NIH and AMIA (American Medical Informatics Association which has taken the lead in the translational bioinformatics area) have designated several existing bioinformatics databases to be expanded to hold aggregated patient data, linking it to patient biological data. Thus bioinformatics, as related to medical research and clinical practice, is intimately associated with both data archiving and electronic health records initiatives.

Although librarians and libraries are familiar with data archiving and electronic health records, understanding the role of bioinformatics in health is very much an outlier to librarian education and library-based products and services. The single attempt to train both bioresearchers and librarians in bioinformatics arose out of the National Center for Biotechnology Information (NCBI) at the National Library of Medicine. In early 2008, after less than five years of providing 1-5 day bioinformatics sessions for librarians and information specialists, all bioinformatics educational librarian outreach programs were discontinued by NCBI. This has left a gap that not only remains unfilled and but has created a new one: those who were initially trained cannot continue their training process as bioinformatics continues to explode into new directions and usage. Discussion of this lack of bioinformatics training has been discussed considerably amongst librarians and their various SIGs.



Learning Objectives

Upon completion of the Clinical Bioinformatics Overview and Resource Module participants will:

1) be able to define clinical bioinformatics and understand its relationship to translational medicine, biomedical informatics, and electronic health and medical record;

2) have acquired a working genetics and molecular genetics vocabulary of inherited and acquired diseases and pathologies;

3) identify the major genetics data databases;

4) have developed effective bioinformatics search strategies to retrieve human clinical bioinformatics data and information related to gene-disease relationships (OMIM) or to gene-drug-disease relationships (PharmGKB); and

5) be able to identify the major clinical bioinformatics public health databases and the content they contain.


Agenda

NOTE: Bioinformatics changes rapidly. The agenda below is a representative framework. 

This workshop is available in two different formats:

8 C.E. hours for the complete full -day workshop
4 C.E. hours for clinical bioinformatics database and search Modules 4-5


MODULE 1: 8:30-9:00AM, Introductions; 
MODULE 2: 9:00-10:15AM, Clinical Bioinformatics Overview, lecture and discussion;
BREAK 10:15-10:30;
MODULE 3: 10:30-Noon, Enabling Searching: The Vocabulary, Biology and Databases of Clinical Bioinformatics, lecture, discussion and search
exercises;
LUNCH: Noon-1 PM;
MODULE 4, Part 1: 1:00-2:30—Clinical Bioinformatics Database search and exercises; 2:30-2:45PM,
BREAK;
MODULE 4, Part 2: 2:45-4:00PM, Clinical Bioinformatics database search and exercises;
MODULE 5: 4:00-5:00PM; Public Health Clinical Bioinformatics Databases, overview and demonstration exercises; 5:00-5:30PM, Summary and
evaluations.



This project has been funded in whole or in part with Federal funds from the National Library of Medicine, National Institutes of Health, Department of Health and Human Services, under contract No. N01-LM-6-3501 with the New York University School of Medicine


Participant Materials

Participants will be provided with a full-color combination workbook/handout, both as print and electronic versions. The handout will also include step-by-step instructions and screenshots to resolving the problems and exercises covered in the workshop, and an appendix of resources.

Facility Requirements

Computer work stations for both participants and instructor with access to the Internet. LAN connection preferred over wireless, if possible. Projector and screen required. Most recent web browser version of Internet Explorer or Firefox. Firefox is greatly preferred. Instructor’s computer connected to external room speakers and sound. Whiteboard or flipboard available with markers.

MLA CE Credits: 4 or 8

8 C.E. hours for the complete full -day workshop
4 C.E. hours for clinical bioinformatics database and search Modules 4-5