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Archive for the ‘NCBI Databases’ Category

The NCBI Gene Database: a librarian’s unknown known for genetic questions

Monday, February 27th, 2017

Stop me if you’ve heard this one before.

A student walks into a library looking for breast cancer information for a class project. All they know is their teacher asked for a report on the genetics of breast cancer. The teacher wants to know the location of the chromosome in the gene assembly where the breast cancer gene mutation occurs, variations in the gene and if  they are associated with other disease, and genetic testing options. The project is due tomorrow. Can you help?

Before you start thinking the joke is on you, consider the NCBI Gene  database.

NCBI Gene is one of those databases you don’t know you need to know until you need to know and you don’t know.

Basically, it’s like a Wikipedia for gene related information.

I draw that similarity because  NCBI Gene centralizes gene related information into individual records. All kinds of gene-specific data are connected, from gene symbols to PubMed citations to 3D gene visualization. Much like a long Wikipedia entry, the gene-specific data are presented in an expandable outline format, so getting to a particular piece of the gene-specific data is fairly painless. It also bears mentioning that much of the data in NCBI Gene is user-submitted, so in that respect, like Wikipedia, NCBI Gene is crowd-sourced.

So the next time a last minute request for genetic information comes your way, don’t panic. Head to NCBI Gene and try searching the keyword. It helps to know the organism (ex: homo sapiens), or you can filter results by Top Organisms. (For the record, the breast cancer gene – BRCA1 is located in Chromosome 17 of the human genome.)

Learn more about how to search NCBI Gene at our bioinformatics webinar next Thursday, March 9 at 10 am PT/ 11 am MT/ Noon CT/ 1pm ET

Can’t make it? Register anyway & we’ll send you a recording. Registration info below.

Five questions you can answer using the NCBI Gene database

Mar 9, 2017
1:00PM – 2:00PM ET

Register: https://nnlm.gov/class/five-questions-you-can-answer-using-ncbi-gene-database/7094 

 

 

 

 

Apply Now for “A Librarian’s Guide to NCBI” Bioinformatics Course

Thursday, August 13th, 2015

Group of approximately 20 people standing in front of the National Library of Medicine

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.

Online Pre-Course and In-Person Course Components
The two parts to “A Librarian’s Guide to NCBI” are listed below. 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).

  • Part 1: “Fundamentals in Bioinformatics and Searching,” an online (asynchronous) course, October 26-December 11, 2015.

The major goal of Part 1 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. The course encompasses visualizing bioinformatics end-user practice. It places a strong emphasis on hands-on acquisition of NCBI search competencies, and developing a working molecular biology vocabulary through self-paced hands-on exercises.

Other option: Interested in taking only the online version of the “Fundamentals in Bioinformatics and Searching” course? Watch for an upcoming second announcement of an offering in January-February 2016.

  • Part 2: A 5-day in-person course offered on-site at the National Library of Medicine in Bethesda, Maryland, March 7-11, 2016.

The focus of the in-person course is on using the BLAST sequence similarity search and Entrez text search systems to find relevant molecular data. The course describes the various kinds of molecular data available and explain how these are generated and used in modern biomedical research. The course is a combination of instruction, demonstration, discussions, and hands-on exercises (both individual and group).

Who can apply?

  • 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.

What does it cost?

  • There is no charge for the classes. Travel, lodging and meal costs for the in-person class are at the expense of the participant.

Important Application Dates

  • Application deadline: September 14, 2015
  • Acceptance notification: On or about October 5, 2015

How to Apply

  1. Please fill out the Application Form at https://www.surveymonkey.com/s/guide_2016_app.
  2. Once you complete the Application Form, you will be directed to download the Supervisor Support Statement (ftp://ftp.ncbi.nih.gov/pub/education/librarian_guide/Forms/Supervisor_Supportv2.pdf). 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.
  3. Provide your current curriculum vitae (CV). Please use the suggested CV model as a guideline for the type of information desired (ftp://ftp.ncbi.nih.gov/pub/education/librarian_guide/Forms/LibGuide_CV_model.pdf).Your application is not complete until we receive both your CV and the Supervisor Support Statement in addition to the Application Form.

Course Page
The course page with additional information is at: http://www.ncbi.nlm.nih.gov/education/librarian/

Questions?
Please direct any questions to: ncbi_course@utah.edu

Save the Dates: 2015-2016 “A Librarian’s Guide to NCBI” Course

Tuesday, July 28th, 2015

“…by far the best educational experience I have had in my years of being a librarian.”

“I don’t think I’ve ever had such a comprehensive professional development opportunity.”

[I am] “confident going back to my institution and teaching these resources as well as starting an information service.”

— Comments from recent class participants

Are you a health science librarian in the United States who offers (or wants to offer) bioinformatics services at your institution? The National Center for Biotechnology Information (NCBI) and the NLM Training Center will be offering “A Librarian’s Guide to NCBI” course in 2015-2016. Participants who complete the class will be eligible for Medical Library Association Continuing Education credits. The course is free, but travel, lodging and related 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. Successful completion of this pre-course is required to continue to Part 2.

Part 2: A five-day in-person course offered on-site at the National Library of Medicine in Bethesda, Maryland.
Previous graduates of the “Fundamentals in Bioinformatics and Searching” online course are encouraged to apply and may audit Part 1 in preparation for Part 2.

Interested in taking only the online version of the “Fundamentals in Bioinformatics and Searching” course? Watch for an upcoming second announcement of an offering in January – February, 2016.

Important Dates:
Monday, August 10, 2015 – Application materials will be posted, linked from a detailed announcement here in the NLM Technical Bulletin.
Monday, September 14, 2015 – Application deadline.
Monday, October 5, 2015 – Acceptance notifications e-mailed.
Monday, October 26, 2015 – “Fundamentals in Bioinformatics and Searching” pre-course begins.
Monday, March 7, 2016 – “A Librarian’s Guide to NCBI” five-day in-person class begins at NLM.

Mark your calendars for this extraordinary training opportunity!

Genetic Testing Registry

Wednesday, February 11th, 2015

Have you used the Genetic Testing Registry? Here’s your chance to learn about another resource from NCBI in just 4 minutes. The GTR “provides a central location for voluntary submission of genetic test information by providers. The scope includes the test’s purpose, methodology, validity, evidence of the test’s usefulness, and laboratory contacts and credentials.”

 

In Case You Missed It

Wednesday, February 4th, 2015

Here are some of the most popular links we shared on Twitter in the last few months. You can follow us on Twitter (@nnlmntc) for even more tips on NLM resources, teaching or training, presentations, and more.