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Archive for the ‘Technology and Libraries’ Category

NCBI Webinar: The Next Generation of Access to Sequencing Data

Friday, February 20th, 2015

Next Wednesday, February 25, NCBI staff will present a webinar on the SRA Toolkit, a system for accessing the approximately 3.4 Petabases of next-generation genomic and expressed sequence data housed in the NCBI Sequence Read Archive (SRA). As data sets become larger, mining information and performing comparisons directly from structured databases becomes increasingly necessary. The SRA Toolkit is not only capable of dumping the data out as a fastq or sam file, but also provides direct analysis and comparison from specific genomics regions across hundreds or thousands of samples.

In the webinar, we will show examples of configuration and use of the Toolkit for both public SRA and controlled access data associated with studies in the Database of Genotypes and Phenotypes (dbGaP).

To register for this webinar: https://attendee.gotowebinar.com/register/2847950984085163009

Deadline Extended for Public Comments on Proposals to Enhance Transparency of Clinical Trial Results

Friday, February 20th, 2015

In November, the Department of Health and Human Services (HHS) and the National Institutes of Health (NIH) released for public comment two proposals to increase the transparency of clinical trials via information submitted to ClinicalTrials.gov, a publicly accessible database operated by the National Library of Medicine. One is a Notice of Proposed Rulemaking (NPRM) that describes proposed regulations for registering and submitting summary results of certain clinical trials to ClinicalTrials.gov in compliance with Title VIII of the Food and Drug Administration Amendments Act of 2007 (FDAAA). A major proposed change from current requirements is the expansion of the scope of clinical trials required to submit summary results to include trials of unapproved, unlicensed, and uncleared products. The second proposal is a draft NIH policy that would extend the similar registration and reporting requirements to all clinical trials funded by NIH, regardless of whether they are subject to FDAAA. Both proposals aim to improve public access to information about specified clinical trials, information that is not necessarily available from other public sources.

The public may comment on any aspect of the NPRM or proposed NIH Policy. Written comments on the NPRM should be submitted to docket number NIH-2011-0003. Commenters are asked to indicate the specific section of the NPRM to which each comment refers. Written comments on the proposed NIH Policy should be submitted electronically to the Office of Clinical Research and Bioethics Policy, Office of Science Policy, NIH, via email; mail at 6705 Rockledge Drive, Suite 750, Bethesda, MD 20892; or by fax at 301-496-9839, by March 23, 2015.

PubMed Subject Filter Strategies Updated for 2015

Friday, February 20th, 2015

PubMed subject filter strategies are reviewed each year to determine if modifications are necessary. Modifications may include revisions due to changes in Medical Subject Heading (MeSH) vocabulary or MEDLINE journals, adding or deleting terms, and changing parts of a strategy to optimize retrieval. The following subset strategies were recently revised:

Opportunity to Affect the Future of the National Library of Medicine

Friday, February 13th, 2015

You have a unique opportunity to affect the future of the National Library of Medicine. As Dr. Donald A.B. Lindberg retires after 30 years as director of NLM, Dr. Francis Collins, Director of the National Institutes of Health, has convened a “Working Group to Chart the Course for the NIH National Library of Medicine.” The group’s charge and members: http://www.nih.gov/about/director/02032015_working-group_nlm.htm.

Consider responding to this time-sensitive NIH Request for Information (RFI), soliciting input into the deliberations of the working group of the advisory committee to the NIH Director. This is a very important opportunity to contribute feedback of the value of the National Library of Medicine, and to directly influence the future of this organization.

Your response must be submitted electronically at http://grants.nih.gov/grants/rfi/rfi.cfm?ID=41, and will ONLY be accepted through March 13, 2015.

Please share this information with colleagues and friends who might wish to respond with thoughts about how the NLM, and especially the collections, programs, and resources, have contributed to their research, teaching, education, and professional development.

List of Serials Indexed for Online Users

Friday, February 13th, 2015

The List of Serials Indexed for Online Users (LSIOU), 2015 edition, is now available in XML format. The 2015 edition contains 14,856 serial titles, including titles currently indexed for MEDLINE as well as titles indexed over time which have ceased or changed titles. The titles are listed alphabetically by the journal title abbreviation. Tailored lists of indexed journals may be generated from the NLM Catalog. While the XML version of the LSIOU is a snapshot in time, the results of a search in the NLM Catalog will provide a “real time” list for the LSIOU.

For a “real time” list for the LSIOU, enter reportedmedline in the search box and click “Search.” For a list of only the currently indexed MEDLINE journals, enter currentlyindexed in the search box and click “Search.” Display and sort formats are selected from the results page; click on the Display Settings pull-down menu to choose a display format (for example, the Journal display) and an appropriate sort (for example, Title or Title Abbreviation). To save the entire list as one document, click on the “Send to” pull-down menu, with “File” as the destination, choose a format and sort order, and then click “Create File.” Click “Save” in the File Download pop-up box. Provide your directory location and desired file name.

Additional information about journals indexed for MEDLINE can be found via the links from the MEDLINE/PubMed Resources web page. This page includes Journals Recently Accepted by NLM for Inclusion in MEDLINE, a list of titles selected by the Literature Selection Technical Review Committee (LSTRC) that meets three times per year in February, June, and October. Results from those meetings appear online about six weeks after each meeting, both on the web page and in the NLM Catalog. For additional details about searching the NLM Catalog, visit NLM Catalog Quick Tours and Searching for Journals in the NLM Catalog.

AHRQ and NASA Release Their Public Access Plans

Friday, February 13th, 2015

Both AHRQ and NASA have released their public access plans (response to the “OSTP Memo”). Both intend to use PMC as a repository for publications written by investigators/researchers they fund.

Links to their plans are below. The HHS plan (which will include NIH) should be released very soon.

AHRQ: http://www.ahrq.gov/funding/policies/publicaccess/index.html

NASA: http://science.nasa.gov/media/medialibrary/2014/12/05/NASA_Plan_for_increasing_access_to_results_of_federally_funded_research.pdf

Is Granularity the Next Discovery Frontier?

Friday, February 13th, 2015

NISO Two-Part March Webinar: Is Granularity the Next Discovery Frontier?

Part 1: Supporting Direct Access to Increasingly Granular Chunks of Content

Date: March 11, 2015

Time: 1:00 – 2:30 p.m. Eastern time

Event webpage: http://www.niso.org/news/events/2015/webinars/granularity_pt1/

 

Part 2:  The Business Complexities of Granular Discovery

Date: March 18, 2015

Time: 1:00 – 2:30 p.m. Eastern time

Event webpage: http://www.niso.org/news/events/2015/webinars/granularity_pt2/

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NISO will be holding a two-part webinar on March 11 and 18 to explore the question, Is Granularity the Next Discovery Frontier?

The rise of the Discovery System in the library world has helped to streamline searching for end users by providing them with search functionality that more closely resembles search engines like Google than traditional database searches. But with this streamlined search comes added expectations from users about their ability to drill down into content and retrieve more granular pieces of information—anything from book chapters and individual letters to the editor to specific graphs and images could conceivably be retrieved in a more granular search.

Users are beginning to expect more granular search and access in Discovery System searches — encyclopedia articles, images, tables, book chapters. The implications for discovery system providers, content providers, and libraries to realize this vision are significant. These granular “objects” each have to be retrievable separately from the parent object and each has to have its own metadata and indexing. What is needed to ensure that discovery systems can retrieve and display information below the publication or article level? What is the role of the content provider and the library in this scenario? How do libraries help end users find and use this content?

This two-part NISO Webinar for March will examine the many implications of an increasingly granular discovery environment.

ABOUT PART 1: Supporting Direct Access to Increasingly Granular Chunks of Content

In Part 1: Supporting Direct Access to Increasingly Granular Chunks of Content, this webinar will discuss the implications of granular content for user search interfaces and discovery engines.

Topics and speakers are:

  • Working with Metadata Challenges to Support Granular Levels of Access and Descriptions – Myung-Ja Han, Assistant Professor/Metadata Librarian, University of Illinois at Urbana-Champaign Urbana, Illinois
  • How Discovery Services are Meeting Evolving Granular Discovery User Needs – Tito Sierra, Director of Product Management, EBSCO Information Services

ABOUT PART 2: The Business Complexities of Granular Discovery

Part 2 will look at The Business Complexities of Granular Discovery, and presenters will discuss the implications of granular content​ discovery for the business side of the equation.

Topics and speakers are:

  • Enabling discoverability into specific segments of multimedia– Andrea Eastman-Mullins, Chief Operating Officer, Alexander Street Press
  • The Business side of Making Granular Discovery Work  – Dan Valen, Product Specialist, figshare

REGISTRATION

Registration is per site (access for one computer) and closes at 12:00 pm Eastern on March 11 for Part 1 and March 18 for Part 2 (the days of the webinars). Discounts are available for NISO and NASIG members and students.

NISO Library Standards Alliance (LSA) members receive one free connection as part of membership and do not need to register. (The LSA member webinar contact will automatically receive the login information. Members are listed here:www.niso.org/about/roster/#library_standards_alliance. If you would like to become an LSA member and receive the entire year’s webinars as part of membership, information on joining is listed here: www.niso.org/about/join/alliance/.)

All webinar registrants and LSA webinar contacts receive access to the recorded version for one year. You can register for either or both parts. There is a 25% discount if registering for both. Visit the event webpages to register and for more information:
Part 1: http://www.niso.org/news/events/2015/webinars/granularity_pt1/
Part 2: http://www.niso.org/news/events/2015/webinars/granularity_pt2/

NIH Manuscript Submission System Refresh

Monday, February 9th, 2015

The NIH Manuscript Submission System (NIHMS) got a refresh this week. The NIHMS system supports the deposit of manuscripts into PubMed Central (PMC), as required by the NIH Public Access Policy and other participating funder (Howard Hughes Medical Institute). Are you a librarian who serves an NIH funded investigator or project? If so consider skimming through the NIHMS FAQStep-by-Step Tutorials, and Glossary.

From its Overview page:

The National Institutes of Health (NIH) developed the NIH Manuscript Submission (NIHMS) system to facilitate the submission of peer-reviewed manuscripts for inclusion in PubMed Central (PMC) in support of the NIH Public Access Policy. Since its inception in 2005, NIHMS has expanded to support the public access policies of other organizations and government agencies (for more details, see the Funders List). The NIHMS system allows users, such as authors, principal investigators, and publishers to supply material for conversion to XML documents in a format that can be ingested by PMC. Depositing a manuscript in NIHMS for inclusion in PMC is a multi-step process, requiring an author to approve the deposited files and associated funding before conversion and the PMC-ready version after conversion.

Librarians Talk about Using Altmetrics

Monday, February 9th, 2015

Library Journal and Plum Analytics are hosting a webinar about modern metrics.  There is growing interest in altmetrics and people are hungry for stories about how people are using them.  Many institutions are utilizing new metrics to help showcase research, do analysis, bring value to their institutional repositories and more.  This webinar features users telling their stories about what they are doing with these modern metrics.

Topic:  Practical Uses of Altmetrics

Date:  Wednesday, February 11

Time:  1:00 pm (ET)

The speakers for this webinar are:

  • Robin Champieux – Scholarly Communication Librarian, Oregon Health & Science University
  • Tim Deliyannides – Director, Office of Scholarly Communication and Publishing and Head, Information Technology, University of Pittsburgh
  • Andrea Michalek – President & Co-Founder, Plum Analytics

For more information go here.

Another Coffee Break: Word and Excel Templates

Monday, February 9th, 2015

Here at the Outreach Evaluation Resource Center (OERC) we began 2015 blogging about the CDC Coffee Breaks. For February we’re offering a refill by featuring some notes from a recent American Evaluation Association (AEA) coffee break webcast. Unlike the CDC, the 20 minute AEA coffee break webcasts are not freely available to the public but are an included benefit of AEA membership. The webcast briefly covered best practices in data visualization using two commonly available resources (Microsoft Word and Excel) and how to automate use of them by creating templates for report format consistency and easier workflow.

Some great resources to learn more how to do this and bookmark for future reference include

Specific for Word

Specific for Excel