Archive for the ‘Informatics’ Category
Health science librarians are invited to participate in a rigorous online bioinformatics training course, Fundamentals of Bioinformatics and Searching, sponsored by the National Library of Medicine (NLM), the National Center for Biotechnology Information (NCBI), and the National Network of Libraries of Medicine, NLM Training Center (NTC). The course provides basic knowledge and skills for librarians interested in helping patrons use online molecular databases and tools from the NCBI. Attending this course will improve your ability to initiate or extend bioinformatics services at your institution. Prior knowledge of molecular biology and genetics is not required. The major goal of this course is to provide an introduction to bioinformatics theory and practice in support of developing and implementing library-based bioinformatics products and services. This material is essential for decision-making and implementation of these programs, particularly instructional and reference services.
This course is offered online (asynchronously) from January 11 – February 19, 2016. The format includes video lectures, readings, a molecular vocabulary exercise, an NCBI discovery exercise, and other hands-on exercises. The instructor is Diane Rein, Ph.D., MLS, Bioinformatics and Molecular Biology Liaison from the Health Science Library, University at Buffalo. The course is a prerequisite for the face-to-face workshop, Librarian’s Guide to NCBI. Participants who complete the required coursework and earn full continuing education credit will be eligible to apply to attend the 5-day Librarian’s Guide in the future.
Due to limited enrollment, interested participants are required to complete an application form. The deadline for completing the application is December 7, 2015; participants will be notified of acceptance on December 21, 2015. The course is offered at no cost to participants. Participants who complete all assignments and the course evaluation by the due dates will receive 25 hours of MLA CE credit. No partial CE credit is granted. For questions, contact the course organizers.
The next session of the National Library of Medicine Informatics Lecture Series will be held on November 4, at 11:00am-12:00pm PST, with the feature presentation Use of Clinical Big Data to Inform Precision Medicine. The speaker will be Joshua Denny, MD, Associate Professor in the Departments of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. This talk will be broadcast live and archived.
At Vanderbilt, Dr. Denny and his team have linked phenotypic information from de-identified electronic health records (EHRs) to a DNA repository of nearly 200,000 samples, creating a ‘virtual’ cohort. This approach allows study of genomic basis of disease and drug response using real-world clinical data. Finding the right information in the EHR can be challenging, but the combination of billing data, laboratory data, medication exposures, and natural language processing has enabled efficient study of genomic and pharmacogenomic phenotypes. The Vanderbilt research team has put many of these discovered pharmacogenomic characteristics into practice through clinical decision support. The EHR also enables the inverse experiment – starting with a genotype and discovering all the phenotypes with which it is associated – a phenome-wide association study (PheWAS). Dr. Denny’s research team has used PheWAS to replicate more than 300 genotype-phenotype associations, characterize pleiotropy, and discover new associations. They have also used PheWAS to identify characteristics within disease subtypes.
Dr. Denny is part of the NIH-supported Electronic Medical Records and Genomics (eMERGE) network, Pharmacogenomics Research Network (PGRN), and Implementing Genomics in Practice (IGNITE) networks. He is a past recipient of the American Medical Informatics Association New Investigator Award, Homer Warner Award, and Vanderbilt Chancellor’s Award for Research. Dr. Denny remains active in clinical care and in teaching students. He is also a member of the National Library of Medicine Biomedical Library and Informatics Review Committee.
Applications are now being accepted for the 2016 National Library of Medicine (NLM) Georgia Biomedical Informatics Courses to be held April 3-9 and September 11-17 at Brasstown Valley Conference Center in Young Harris, Georgia. Applications will be accepted until December 7. All applicants will be notified by the end of January/early February of their application status. Successful applicants will be asked for a commitment to attend the entire course and all sessions. Travel, hotel, and meals of all successful applicants will be paid for by Georgia Regents University (soon to be Augusta University). For questions, feel free to contact Adrienne Hayes.
The National Library of Medicine (NLM) has released a new web page, Nursing Resources for Standards and Interoperability. The page is a resource for nurses, students, informaticians, and anyone interested in nursing terminologies for systems development. It describes the role of SNOMED CT and Laboratory Observation Identifiers Names and Codes (LOINC) in implementing Meaningful Use in the United States, specifically for the nursing care domain.
NLM has provided this resource in response to the position statement released by the American Nurses Association (ANA) that reaffirms support for use of recognized terminologies in coding nursing problems, interventions and observations (SNOMED CT), and in nursing assessments and outcomes (LOINC). In addition to SNOMED CT and LOINC, the Nursing Resources for Standards and Interoperability page provides information about other highly utilized nursing terminologies. The resource page provides a new two-minute video tutorial that describes how to use the Unified Medical Language System (UMLS) Metathesaurus Browser to find Concept Unique Identifiers (CUIs) and extract concept-level synonyms between SNOMED CT and other nursing terminologies. Additionally, links to other NLM Terminology resources and helpful resources are provided.
NLM welcomes feedback on the Nursing Resources for Standards and Interoperability page. Please send comments to NLM Customer Service.
Librarians in the United States who specialize in health and related sciences are invited to participate in the next offering of the bioinformatics training course, A Librarian’s Guide to NCBI, sponsored by the National Library of Medicine (NLM), the National Center for Biotechnology Information (NCBI), and the National Network of Libraries of Medicine, NLM Training Center (NTC). The course provides knowledge and skills for librarians interested in helping patrons use online molecular databases and tools from the NCBI. Prior knowledge of molecular biology and genetics is not required. Participating in the Librarian’s Guide course will improve your ability to initiate or extend bioinformatics services at your institution. Instructors will be NCBI staff and Diane Rein, Ph.D., MLS, Bioinformatics and Molecular Biology Liaison from the Health Science Library, University at Buffalo.
The two parts to A Librarian’s Guide to NCBI are Part 1: Fundamentals in Bioinformatics and Searching, an online (asynchronous) course, October 26-December 11, 2015, and Part 2: A 5-day in-person course offered on-site at the National Library of Medicine in Bethesda, MD, March 7-11, 2016. Applicants must complete both parts. Participants must complete the pre-course with full CE credit (Part 1) in order to advance to attend the 5-day in-person course (Part 2).
Applications are open to librarians in the United States who specialize in health science or related sciences. Applications will be accepted both from librarians currently providing bioinformatics services as well as from those desiring to implement services. Enrollment is limited 25 participants. There is no charge for the classes. Travel, lodging and meal costs for the in-person class are at the expense of the participant. The application deadline is September 14, 2015 and acceptance notification will be on or about October 5, 2015. Once you complete the Application Form, you will be directed to download the Supervisor Support Statement. This is to be filled out and signed by your immediate supervisor. This statement describes your current and/or future role in bioinformatics support at your institution and confirms your availability to attend the course if selected. Provide your current curriculum vitae (CV). Please use the suggested CV model as a guideline for the type of information desired. Your application is not complete until both your CV and the Supervisor Support Statement are received, in addition to the Application Form.
NLM is announcing on behalf of the IHTSDO (International Health Terminology Standards Development Organization) the formation of seven new IHTSDO Advisory Groups (AGs). The AGs are the successors of the IHTSDO Standing Committees, which will allow for a more agile and flexible structure. The AGs will conduct specific activities that will contribute to the fulfillment of the IHTSDO Management Team’s responsibilities or the organization’s mandate.
The IHTSDO is seeking volunteers to serve on the following AGs:
- Content Managers Advisory Group
- E-Learning Advisory Group
- Modeling Advisory Group
- SNOMED CT Editorial Advisory Group
- Software Developers Advisory Group
- Terminology Release Advisory Group
- Tooling User Advisory Group
For additional information on the different Advisory Groups as well as the nomination and application process, please see the IHTSDO news note, Join an Advisory Group. The nomination period is open until August 14, 2015.
On May 7th, the Health Information Technology section of AHRQ (Agency for Healthcare Research and Quality) sponsored the presentation A National Web Conference on Assessing Patient Health Information Needs for Developing Consumer Health IT Tools. Featured speakers included:
- Wanda Pratt, Ph.D., Professor, Information School, University of Washington
- James Ralston, M.D., Associate Investigator/Physician, Internal Medicine, Group Health Research Institute
- Patricia Flatley Brennan, Ph.D., Moehlman Bascom Professor, College of Engineering, University of Wisconsin- Madison
The presenters described projects to improve communication of safety concerns among hospitalized patients, promote effective management of patients with diabetes, and improve asthma care in children. Presentation slides from the talks are now available on the Health Information Technology website.
The 22nd annual edition of the Nucleic Acids Research Database Issue features nine free full-text papers from NCBI staff that present recent updates to the databases, including GenBank, Gene, and RefSeq. These papers describe the state of NCBI databases as well as future plans to improve their use, from new reference resources created to improve the usability of viral sequence data to in-house curation efforts in the Conserved Domain Database, and much more. The articles are all available from PubMed.
The Robert B. Greenblatt, M.D. Library, Georgia Regents University, has announced that applications are now being accepted for the Spring and Fall 2015 sessions of the NLM Georgia Biomedical Informatics Course, to be held April 12-18 and September 27-October 3, 2015, at the Brasstown Valley Resort & Spa in Young Harris, GA. The course, previously held at the Marine Biological Laboratory in Woods Hole, MA, offers participants a week-long immersive experience in biomedical informatics and provides continuing education to health care professionals interested in the application of computer technologies to medicine. The application deadline for both sessions is December 15, 2014.
Biomedical administrators, faculty, and others who can become change agents for their institutions are strongly encouraged to apply. All costs for the course including travel, housing, and per diem are supported by NLM. The application is open to US citizens and US permanent residents. Enrollment is limited to 30 attendees. The course will provide attendees a diverse set of skills and experiences incorporating concepts, theories and building blocks of biomedical informatics; ability to use informatics for solving current health care challenges; application and policies related to computer technologies and information science; hands-on experience during evening workshops; and networking with nationally known bioinformatics educators and thought leaders.
The National Library of Medicine is saddened at the passing of Dr. Morris F. Collen, known around the world as “Mr. Medical Informatics,” on September 27, 2014. He was 100 years old. In addition to his wide-ranging contributions to medical informatics, Dr. Collen was a valued advisor to NLM. He was a member of the Lister Hill Board of Scientific Counselors from 1984 to 1987. He served on the Literature Selection Technical Review Committee, which advises NLM on the journals to be indexed in MEDLINE/PubMed, from 1997 to 2002, chairing the Committee from 2000 to 2002. He also contributed to NLM Long Range planning.
Morris Collen earned his bachelor’s degree in electrical engineering from the University of Minnesota and graduated from the University of Minnesota School of Medicine in 1938. His residency at the University of Southern California/Los Angeles County General Hospital took him to California, where he started what would become a legendary career at Kaiser (later Kaiser Permanente). He served as chief of medical services at Kaiser’s Oakland hospital from 1942 to 1952, and medical director the following year. From 1953 to 1961, Dr. Collen served as physician-in-chief at Kaiser Permanente (KP) in San Francisco.
During World War II, Dr. Collen was one of the first doctors to experiment with the use of a new wonder drug–penicillin–for the treatment of pneumonia in shipyard workers, at a time when most of the drug was shipped overseas for members of the armed forces. Dr. Collen’s interest in the use of computers as a way to improve medical care developed during a 1961 conference on biomedical electronics. Soon afterward, he founded Kaiser Permanente’s research division and created a prototype electronic health record fed by punch card into a huge IBM mainframe computer. The record included information from patient screenings and lab results. One of Dr. Collen’s major achievements at KP was the development of the multiphasic health checkup, which addressed the physician shortage of the 1950s, post-World War II. This series of procedures and tests, given to thousands of KP members, screened for conditions such as heart disease, diabetes, and cancer. Not only did these revolutionary tests save physicians’ time; they constituted a significant experiment in preventive care. Dr. Collen eventually automated the multiphasic health checkups, moving them onto a punch card system in 1964.
Electronic health records are in the headlines today, but their bloodlines run back to Dr. Collen. Kaiser Permanente’s early EHR system became internationally known because of his groundbreaking efforts. In fact, he predicted that the computer would have “the greatest technological impact on medical science since the invention of the microscope,” as noted in a 2008 Kaiser Permanente publication.