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SEA Currents

Newsletter of the NN/LM Southeastern/Atlantic Region

NIH Requests Information on Processes for database of Genotypes and Phenotypes (dbGaP) Data Submission, Access, and Management

Today, in the NIH Guide to Grants and Contracts, NIH published a Request for Information (RFI) that seeks public comment on the data submission and access processes for the NIH National Center for Biotechnology (NCBI) database of Genotypes and Phenotypes (dbGaP).  The RFI also seeks comment on the management of data in dbGaP in order to consider options to improve and streamline these processes and to maximize the use and utility of dbGaP.

The complete RFI, as well as instructions on how to comment, can be found by clicking here.  Electronic responses will be accepted through April 7, 2017. NIH will consider all public comments before taking next steps. No proprietary, classified, confidential, or sensitive information should be included in your response. Comments received, including any personal information, will be posted without change after the close of the comment period to the following website: https://gds.nih.gov/

Comments may also be mailed to: Office of Science Policy, National Institutes of Health, 6705 Rockledge Drive, Suite 750, Bethesda, MD 20892. Mailed comments must be postmarked by April 7, 2017, to be considered.

Additional information about the importance of this RFI can be found in an “Under the Poliscope” blog published today by Dr. Carrie D. Wolinetz.

For more information or additional questions, please contact the NIH Office of Science Policy, by email at SciencePolicy@od.nih.gov or by telephone at 301-496-9838.

Free Gene Database Webinar – 5 Questions you can answer using Gene

The Gene resource from NCBI is a central hub for accessing nearly all molecular and literature resources for a particular gene. You can easily answer the most common questions and perform the most common tasks by starting in Gene.

In this webinar you will learn about the structure and contents of the Gene resource and how to use Gene to answer the following questions about a gene:

  • Where is the gene located (chromosome and position) in the genome assembly?
  • What are the Reference genomic, transcript and protein sequences for the gene?
  • What variations are present in the gene and are they associated with disease?
  • In what tissues and under what conditions is the gene expressed?
  • What are the equivalent genes (homologs) in other species?

Presenters: Peter Cooper and Bonnie Maidak, NCBI

Class Details:

Mar 9, 2017

1:00PM – 2:00PM ET

1 MLA CE credit

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

Data Science Research: Personal Health Libraries for Consumers and Patients (R01) (PAR-17-159)

https://grants.nih.gov/grants/guide/pa-files/PAR-17-159.html

Purpose

The National Library of Medicine seeks applications for novel informatics and data science approaches that can help individuals gather, manage and use data and information about their personal health. A goal of this program is to advance research and application by patients and the research community through broadly sharing the results via publication, and through open source mechanisms for data or resource sharing. To bring the benefits of big data research to consumers and patients, new biomedical informatics and data science approaches are needed, shaped to meet the needs of consumers and patients, whose health literacy, language skills, technical sophistication, education and cultural traditions affect how they find, understand and use personal health information. Novel data science approaches are needed to help individuals at every step, from harvesting to storing to using data and information in a personal health library.

Applicants must base their proposed work on an informed profile of the intended users, and, the work should be developed through interaction with the user. The strongest projects will provide approaches that incorporate health data and information from more than one source, such as diagnostic images and links to full-text articles or genome sequence data linked to a family health history. An application should be centered on the problem area being addressed and the intended audience, propose a possible solution that employs novel data science or informatics, and undertake a pilot that will result in evidence of the degree of success and/or needed next steps. Applicants should expect to involve the intended users in their work.

This program expires March 20, 2018 unless reissued. Only electronic applications are accepted.

NLM Contact

Dr. Alan VanBiervliet alan.vanbiervliet@nih.gov

Deadlines

Deadlines for New Applications: May 1, 2017 and March 19, 2018

 

Pilot Project: Join our Consumer Health Information Specialization (CHIS) Facebook Group and your CHIS Fee is on Us!

Are you currently taking classes to earn your CHIS from the Medical Library Association? Are you passionate about consumer health? Would you like to connect with like-minded health information professionals?

If you answered yes to any of these questions, the National Network of Libraries of Medicine (NNLM), Southeastern Atlantic Region (SEA), has an offer exclusively for members of the SEA Region that we hope you can’t resist:

Join our brand new NNLM Southeastern/Atlantic Region Consumer Health Information Specialists Facebook group and we’ll pay the CHIS application fee for those within the Southeastern/Atlantic Region. You’re eligible once you’ve completed the courses needed to earn either the Level I or Level II Consumer Health Information Specialization and the offer applies whether or not you are a member of the Medical Library Association. The application fee is $55 for members and $75 for non-members.

We’re excited about our new Facebook group and hope you’ll join in to make it a great way to connect with others in the Region who are interested in consumer health and share information and items of interest with the group. The group will revolve around communication, sharing and interaction and we encourage everyone to chime in about how best to use it in serving the needs of the SEA Region.

If you’ve already earned your CHIS, you are welcome to join this group as well. Terri Ottosen and Nancy Patterson, Outreach and Education Coordinators, will be facilitating and administering the group on Facebook and will add people requesting to join, provided you are earning or have earned your CHIS certification. We envision the group page as a place to comment on and “like” posts, discuss issues surrounding providing consumer health services, coordinate with others, and collaborate to share projects and ideas.

This pilot project is an experiment, so we will seek your feedback to improve and modify the project as we go along. We hope this group will serve as a “meeting place” for those interested in and passionate about consumer health. We also hope this project allows for better sharing and collaboration throughout the Region, as well as to promote partnerships and comradery amongst those in the group.

For more information on the Medical Library Association’s Consumer Health Information Specialization, please visit: <http://www.mlanet.org/p/cm/ld/fid=329>

For questions, please contact Terri Ottosen (tottosen@hshsl.umaryland.edu) or Nancy Patterson (npatters@hshsl.umaryland.edu)

NLM Webinar series: “Insider’s Guide to Accessing NLM Data: EDirect for PubMed”

Beginning February 21, 2017, the National Library of Medicine (NLM) will present the three-part webinar series “Insider’s Guide to Accessing NLM Data: EDirect for PubMed.”

This series of workshops will introduce new users to the basics of using EDirect to access exactly the PubMed data you need, in the format you need. Over the course of three 90-minute sessions, students will learn how to use EDirect commands in a Unix environment to access PubMed, design custom output formats, create basic data pipelines to get data quickly and efficiently, and develop simple strategies for solving real-world PubMed data-gathering challenges. No prior Unix knowledge is required; novice users are welcome!

This series of classes involves hands-on demonstrations and exercises, and we encourage students to follow along. Before registering for these classes, we strongly recommend that you:

*             Watch the first Insider’s Guide class “Welcome to E-utilities for PubMed”, or be familiar with the basic concepts of APIs and E-utilities.

*             Be familiar with structured XML data (basic syntax, elements, attributes, etc.)

*             Have access to a Unix command-line environment on your computer (for more information, see our Installing EDirect page: https://dataguide.nlm.nih.gov/edirect/install.html#unix-command-line-environment).

*             Install the EDirect software (for more information, see our Installing EDirect page: https://dataguide.nlm.nih.gov/edirect/install.html#edirect-installation).

Due to the nature of this class, registration will be limited to 50 students per offering.

Registration is currently open for the February/March 2017 series:

  • Part 1: Getting PubMed Data: Tuesday, February 21, 1-2:30 PM ET
  • Part 2: Extracting Data from XML: Tuesday, February 28, 1-2:30 PM ET
  • Part 3: Building Practical Solutions: Tuesday, March 7, 1-2:30 PM ET

Students are expected to attend Part 1, Part 2, and Part 3 in a single series.

To register, and for more information, visit https://goo.gl/qgClZn.

Last updated on Tuesday, Nov 8, 2016

Funded under cooperative agreement number UG4LM012340 with the University of Maryland, Health Sciences and Human Services Library, and awarded by the DHHS, NIH, National Library of Medicine.