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Archive for the ‘Informatics’ Category

Save the Dates: 2015 “A Librarian’s Guide to NCBI” Course

Thursday, July 10th, 2014
“This course was a great idea and very well executed! I learned a lot and am much more confident going back to my institution and teaching these resources as well as starting an information service. It’ll take time to become proficient but this was a great start!”
“The singularly most useful and interesting class I’ve taken in years.”
               — Comments from recent class participants

Attention health science librarians in the United States who wish to initiate and/or extend bioinformatics services at your institution! The National Center for Biotechnology Information (NCBI) and the NLM Training Center (NTC) will be offering “A Librarian’s Guide to NCBI” course in 2015. Participants who complete the class will be eligible for Medical Library Association (MLA) Continuing Education credits. The course is free, but travel costs are at the expense of the participant.

There are two parts to the course, and applicants must take both parts:

  • Part 1: “Fundamentals in Bioinformatics and Searching” is a six-week, online (asynchronous) pre-course.
  • Part 2: A five-day in-person course offered on-site at the National Library of Medicine in Bethesda, Maryland.

Important Dates:
Monday, September 29, 2014 – Watch for a detailed announcement about the course and application process here in the NLM Technical Bulletin.
Monday, November 17, 2014 – Application deadline
Monday, December 15, 2014 – Acceptance notifications e-mailed
Monday, January 12, 2015 – “Fundamentals in Bioinformatics and Searching” pre-course begins
Monday, March 9, 2015 – “A Librarian’s Guide to NCBI” five-day in-person class begins at NLM

Mark your calendars for this training opportunity.

Questions?  E-mail

NCBI turns 25!

Wednesday, November 6th, 2013

On November 4, 1988 Congress established the National Center for Biotechnology Information (NCBI) to develop new information technologies to aid in the understanding of the molecular processes that control health and disease. Since then, the number of tools and databases at NCBI has grown enormously. It can be difficult to keep track of which database does what, so NCBI provides a handy overview of selected NCBI databases. You can download the printable factsheet with short descriptions of each resource or database.

If you’d like to learn more about NCBI resources, check out their Educational Resources page and YouTube videos.  They have a wealth of resources, but you don’t have to learn them all at once! Maybe you’d like to challenge yourself to take 30 minutes a week to discover and explore one of their resources. You can learn a lot in just a few minutes. For example, the short video below describes how to locate all of the genetic sequences of an organism.

Send in Your Application to Participate in a New Bioinformatics Training Course: “A Librarian’s Guide to NCBI”

Thursday, December 13th, 2012

In sponsored partnership, the National Center for Biotechnology Information (NCBI) and the National Network of Libraries of Medicine (NN/LM) National Library of Medicine Training Center (NTC), are pleased to invite participation of health sciences librarians in a new bioinformatics training course: “A Librarian’s Guide to NCBI.” 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 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 bioinformatics services at your institution and/or extend current initiatives. Prior knowledge of molecular biology and genetics is not required. Participants who complete the class will be eligible for MLA Continuing Education credits. The course is free but travel costs are at the expense of the participant.

For more information and a link to the application, visit the Technical Bulletin article dated December 13, 2012 here:

E-Science Part 2: Translational Librarianship

Monday, January 9th, 2012

It seems to me in an attempt to justification and rationalization every and any thing using a business model to define and describe behavior has become the modus operandi for most enterprises, including library management. This exercise serves as an aid for budgeting, accounting, public reporting and has become our raison d’être.

Remember the days when libraries consider it an accomplishment to collect? When a subject specialist was free to direct purchasing in order to build an empire within the structure and confines of their institution and its mission?

Since no one is allowed to exist in a vacuum except seemingly McArthur fellows who are uncovered in deep pockets of individualistic enterprise and intellectual pursuit, everything that anyone does has to be translational.

By that I mean we have to place our work in context, state and publish objectives and strategies, and use a revolving evaluative tool to measure our output and outcome.

Librarians have always dealt with knowledge objects. Now we must deal with knowledge management vaguely named data.

And that is where the e-science issue looms so large.

To summarize the e-science events I have attended in the recent past, especially, the University of California Davis E-Science Day: An opportunity for education and networking (held on December 6, 2011 and funded by the NNLM PSR).  This E Science presenters consisted of Michael Conlon, a biostatistician from academia, Michael Hogarth, Director of Pathology Informatics Core at UC Davis, a bioinformaticist, several health science librarians, a Burn Center Data coordinator and an implementer of REDCap (Research Electronic Data Capture)

Conlon covered issues such as:

  • Broad views of the entity known as data
  • What data look like?
  • Data processes and flows
  • Sharing of data repositories
  • Controlled vocabulary required for data sharing and processing
  • The application of the principle of “triples”, subjects, predicates and objects
  • The connective tissue of data.

Hogarth’s presentation via Slide Rocket was a thing of beauty. He introduced resources such as:

If we begin to offer data support services librarians could go full circle and return to what we started out doing, curating, organizing and disseminating. What have changed are the nature of content, the technology useful to get the job done and the size of the voice with which we claim our appropriate role.

The NN/LM New England Region’s Elaine Martin has shown leadership since the CTSA E science symposium that was held in April 2009. Since then they have held E-Science boot camps, workshops, and annual Symposium. The emphasis is on partnership with the science community, creating an e-science knowledge domain for librarians.

The E-Science event in Davis, CA included Elaine Martin and her discussion about their pioneering work with e-science to demonstrate a useful approach for librarians in how to translate theory into local practice. Other regions need to follow the example being set in Massachusetts.

New England Region 2012 planned events:

In 2012 I am sure we will continue to see and hear more about out of control data production and the ongoing need to wrangle with the data being produced and yet to be conceived, including visuals, 3D, maps, RFID with 3-D thermal imaging, etc.

My visual image is a huge reel of film unwinding from its spool onto the viewing booth floor.

E-Science Events

Wednesday, January 4th, 2012

Looking back at 2011 the term E-Science is my nomination for one of the health science librarianship buzzwords for the year.

The term “E-Science” is almost as vague in meaning and purpose as the word “outreach”. It is tells us little and leaves us scratching our heads hoping for something a little more specific.

Especially when we find out that E-Science scientists say, “Just call it Science”.

Perhaps health science librarians add the E to emphasize the involvement of technology by referring to the digital involvement?

Here is a list of recent E Science events on my small radar screen:

The Association of American Medical Colleges (AAMC)
Informatics and the future healthcare Workforce Webinar
September 22, 2011

MLA webcast
Connecting E-science and team science: the changing nature of research
November 18, 2011

University of California Davis funded by the NNLM PSR
E-Science Day: An opportunity for education and networking
December 6, 2011

Coming up: February 22, 2012 Priscilla M. Mayden Lecture at the University of Utah Spencer S. Eccles Health Sciences Library: “eScience and the Evolution of Library Services” featuring Bart Ragon as the keynote speaker and a Meet the Experts panel.

And in December, 2011
Bart Ragon and Andrea S. Horn released “E-Science and Data Support Services among Academic Health Sciences Libraries” providing a summary of surveys amongst academic libraries that have begun to provide e-science support.

Next week, I will discuss “translational librarianship.”

“Bringing Scientific Evidence into Clinical Practice” Lecture

Tuesday, November 8th, 2011

I received the link below in June 2011.  It took only four months until I “found my way” to view this 67 minute archived videocast.  I found it well worth the investment of time.

NLM’s Extramural Programs (EP) hosted a lecture by one of their Biomedical Library and Informatics Review Committee  (BLIRC) member, Dr. Eneida Mendonca on Wednesday, June 8, 2011.  The lecture was entitled, “Bringing scientific evidence into clinical practice: challenges, successes and failures.”  It is available from

According to the University of Wisconsin Madison Biostatistics and Medical Informatics website Dr. Mendonca focuses on the “investigation of the use of natural language processing in both biomedical literature and in electronic medical record narratives in order to identify knowledge relevant to medical decision making in the context of patient care.”

This presentation addresses Dr. Mendonca’s study of the use of speech recognition software at the point of care to avoid disruption of patient care but to allow for the communication of clinical questions to promote treatment based on informed decisions.

The goal of the study is analyze the efforts to translate high-level information needs into an effective search strategy using the most appropriate biomedical electronic resources.

What makes it particularly pertinent to medical librarians is the conversation about the cognitive study of librarians as they formulate queries.  The study analyzes and evaluates the search results found using PubMed and other electronic resources such as UptoDate, STAT!Ref, etc.

As in most initial studies there are more questions posed than answers given.