Archive for the ‘Open Access’ Category
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
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.
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.
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/
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 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/
Monday, January 26th, 2015
In May 2014, the National Library of Medicine posted a Request for Information (RFI) asking for ideas on how the National Network of Libraries of Medicine (NN/LM) (http://nnlm.gov) can more effectively and efficiently provide equal access to biomedical information and improve an individual’s access to health information. Based on the feedback from nearly 50 respondents and a review of historical data related to the program, NLM will change the award mechanism for the 2016-2021 Regional Medical Libraries’ cycle from contracts to cooperative agreements. This type of funding mechanism will allow NLM to participate more fully in the work of the RMLs and better coordinate collaborative programs and projects. A Notice of Intent was published on the NIH Grants & Funding site on January 22, 2015.
Join NLM in a teleconference to hear about the responses to the RFI and learn about Cooperative Agreements:
- Tuesday, January 27, 2015 / 4 pm (ET)
- Teleconference Number: 1-888-450-5996
- Participant Passcode: 662939
The world’s largest biomedical library, the National Library of Medicine maintains and makes available a vast print collection and produces electronic information resources on a wide range of topics that are searched billions of times each year by millions of people around the globe. It also supports and conducts research, development and training in biomedical informatics and health information technology.
Thursday, January 22nd, 2015
SciENcv enhancements will include the new NIH biographical sketch format as a choice for creating SciENcv profiles. SciENcv will continue to support the current NIH biographical sketch format; however, NIH encourages researchers to use the new format with their grant submissions. Researchers will be required to employ the new NIH biographical sketch starting May 25, 2015. Users will be able to utilize their existing Science Experts Network Curriculum Vitae (SciENcv) profiles to create profiles in the new NIH biographical sketch format, as well as be able to select the new NIH biographical sketch format when creating profiles manually or through a data feed from an external source. The Personal Statement section of the NIH biographical sketch has been updated to include an option to list up to four peer-reviewed citations. A new section, Contribution to Science, replaces the former section Selected Peer-Reviewed Publications, and it aims to give researchers a place where they can describe five of their most significant contributions to science.
SciENcv users will also soon be able to create profiles in the National Science Foundation (NSF) biographical sketch format. This newly added format will be available to download in PDF, MS Word or XML, and users will be able to share their SciENcv NSF profiles through a public URL. In addition, by linking your NSF account to an NCBI account, you will be able to populate SciENcv profiles with information stored in your NSF account. The NSF biographical sketch is the official format used for grant submissions to the NSF and consists of five sections: Professional Preparation, Appointments, Products, Synergistic Activities, and Collaborators & Other Affiliations.
For more information visit the NLM Technical Bulletin articles: My NCBI – New NIH Biographical Sketch Available in SciENcv and My NCBI – National Science Foundation Biographical Sketch and Data Integration with SciENcv.
Thursday, January 22nd, 2015
The Public Access Compliance Monitor (PACM or “compliance monitor”) is a service from the National Library of Medicine that helps users at NIH-funded institutions locate and track the compliance of funded papers with the NIH Public Access Policy at an institutional level. Whether you are looking for a quick snapshot of your institution’s compliance rate or want to take an active role in helping your investigators comply with the policy, PACM can help you get the information you need.
To gain access to the compliance monitor, users must first be assigned a compliance reports role (“PACR”) role by an administrator at their institution who is authorized to assign roles in the NIH eRA Commons grants administration system. Users with a PACR role will then have access to the compliance reports for their institution.
PACM provides users with a list of all PubMed citations associated with an institution’s NIH funding and classifies the articles according to compliance status (i.e., Compliant, Non-Compliant, In Process). The compliance monitor also provides detailed information about each article including:
- a full citation including the PMID (PubMed ID) and link to the PubMed record
- associated grants and principal investigators
- NIHMSID (NIH Manuscript Submission Reference Number), where available
- PMCID (PubMed Central ID), where available
- key names and dates in the NIHMS, where available
- article compliance status
- method A status
- journal publisher
Compliance reports can be downloaded from these lists and the data filtered based on an institution’s needs.
For more information on the PACR role, the compliance monitor, and the available reports, see the User Guide. Additonally, an overview video of PACM from The NIH Public Access Policy for Librarians Webinar and a four-minute Look at the NIH Public Access Policy Compliance Monitor are available.
Thursday, January 22nd, 2015
Sunday, January 11th, 2015
Are you new to e-Science, unsure what it means, or interested in exploring possible roles for your library? The following resources are great starting points for understanding e-Science and research data management:
The New England e-Science Program offers the following e-Science resources, tools, and events for librarians:
- E-Science Portal for New England Librarians: “A librarians’ link to e-Science resources,” includes an e-Science Thesaurus, resources on data management, data literacy, data publishing, science primers, Science Boot Camp resources, research funders’ policies, and professional development opportunities.
- E-Science Community blog: a forum for thoughtful commentaries and articles by librarians and library students engaged in various aspects of research data support services, news announcements, and a calendar of upcoming events. (Follow the e-Science Community on Twitter @NERescience).
- Journal of eScience Librarianship (JeSLIB): an open access peer review journal dedicated to advancing the discipline of eScience librarianship. JESLIB explores the many roles of librarians in supporting eScience and features articles by contributors from all areas of the globe related to education, outreach, collaborations, policy, tools, and best practices.
- New England Collaborative Data Management Curriculum is an instructional tool for teaching data management best practices to undergraduates, graduate students, and researchers in the health sciences, sciences, and engineering disciplines. Each of the curriculum’s seven online instructional modules aligns with the National Science Foundation’s data management plan recommendations and addresses universal data management challenges.
- University of Massachusetts and New England Area e-Science Symposium, April 9, University of Massachusetts Medical School, Worcester, MA (Event is free, but due to limited space, advance registration is required.)
- Science Boot Camp for Librarians , June 17-19, Bowdoin College, Brunswick, Maine. Organized by a collaboration of New England STEM and health sciences librarians, each Science Boot Camp offers immersive sessions on three science subjects and a Capstone session on topics relevant to STEM and health sciences librarianship. Agenda for the 2015 science boot camp will be announced by the end of February. Registration opens April 9.
For further information about the e-Science Program, or if you would like to be added to the e-Science Community of Interest mailing list, contact Donna Kafel, Project Coordinator for the New England e-Science Program at Donna.Kafel@umassmed.edu
Monday, December 22nd, 2014
Interested participants from libraries, scholarly publishers, research funders, scholars, university departments of academic affairs, providers of alternative metrics data, and system providers are encouraged to contact NISO
The voting members of the National Information Standards Organization (NISO) have approved four new projects to develop standards for alternative assessment metrics (altmetrics). The NISO Alternative Assessment Metrics Initiative was begun in July 2013 with funding from the Alfred P. Sloan Foundation with a goal of building trust and adoption in new methods of assessing impact. Phase 1 of the project, which was completed this summer, gathered a large array of relevant stakeholder groups to identify what areas of alternative metrics would benefit most from standards-related developments. This input was distilled into a white paper published in June 2014, which was then presented to the NISO community to prioritize the action items as possible NISO work items. Phase 2 of the project will be to develop standards or recommended practices in the prioritized areas of definitions, calculation methodologies, improvement of data quality, and use of persistent identifiers in alternative metrics. As part of each project, relevant use cases and how they apply to different stakeholder groups will be developed.
“Assessment of scholarship is a critical component of the research process, impacting everything from which projects get funded to who gains promotion and tenure, and which publications gain prominence in their fields of inquiry,” explains Martin Fenner, Technical Lead, PLOS Article Level Metrics, and Chair of the NISO Alternative Metrics Initiative Steering Committee. “However, traditional metrics that have been primarily based on print processes are failing to keep pace with both the expanded range of research outputs produced by scholars, and the diverse usage of these research outputs in scholarly communication that is increasingly purely electronic. Altmetrics are increasingly being used and discussed as an expansion of the tools available for measuring the scholarly and social impact of research. For altmetrics to move out of its current pilot or proof-of-concept phase, we need to develop commonly used definitions and guidelines for appropriate collection and reporting of data, so that organizations who wish to utilize these metrics can adequately understand them and ensure their consistent application and meaning across the community.”
“The NISO Alternative Assessment Steering Committee will oversee several working groups that will be formed to develop the identified standards and recommended practices,” states Nettie Lagace, NISO Associate Director for Programs. “For participation on these working groups, we are seeking interested participants from all the affected stakeholders including libraries, scholarly publishers, research funders (governmental and non-governmental), scholars, university departments of academic affairs, providers of alternative metrics data, and system providers who incorporate different elements of alternative metrics in their services.”
“We expect this initiative will continue to be broadly inclusive, with contributions from a diverse set of voices, who will be reliant on these new metrics and resulting tools,” said Todd Carpenter, NISO Executive Director. “In addition to the working group members, we also will seek broader community feedback through stakeholder interest groups. In addition, draft documents will be made available for public comment and/or trial use before finalization and publication. NISO will also schedule public webinars for further discussion and training during the development process.”
The approved proposal for the Phase 2 projects as well as the Phase 1 White Paper are available on the NISO website at: www.niso.org/topics/tl/altmetrics_initiative/. Anyone interested in participating on one of the initiative’s working groups should use the online contact form (www.niso.org/contact/) and indicate in which of the four activity area(s) you are interested.
Technical Editor / Consultant
National Information Standards Organization