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Archive for the ‘NLM Resources’ Category

Nucleic Acids Research Database 2015 Issue Features NCBI Databases

The 22nd annual edition of the Nucleic Acids Research Database Issue features nine free full-text papers from NCBI staff that present recent updates to the databases, including GenBank, Gene, and RefSeq. These papers describe the state of NCBI databases as well as future plans to improve their use, from new reference resources created to improve the usability of viral sequence data to in-house curation efforts in the Conserved Domain Database, and much more. The articles are all available from PubMed.

New Secondary Source ID (Databank) Search Value

A new PubMed search option “hasdatabanklist” has been created to retrieve citations that carry a value in the Secondary Source ID [SI] field regardless of what the specific value(s) may be. Typically, the SI field contains information about where additional data related to an article are deposited. Please see MEDLINE Databank Sources to view the list of repository values.

To limit a search to citations that may have deposited data in a repository and acknowledged that deposit in the full text of the article, search using AND hasdatabanklist; for example: randomized controlled trial [pt] AND hasdatabanklist.

National Library of Medicine Resource Update: LiverTox

The National Library of Medicine (NLM) LiverTox resource is a free website providing up-to-date, comprehensive and unbiased information about drug-induced liver injury caused by prescription and nonprescription drugs, herbals, and dietary supplements. LiverTox represents a collaborative effort by medical and scientific specialists to provide a central repository of clinical information in support of clinical and basic research on the prevention and control of drug-induced liver injury. The site also provides guidance to clinicians and healthcare providers on the diagnosis and management of this important cause of liver disease. LiverTox contains approximately 850 drug and herbal records. It is a joint effort of the Liver Disease Research Branch of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) and the Division of Specialized Information Services (SIS) of NLM.

Look for these LiverTox updates in the coming months:

  • Addition of about 100 new records.
  • New histopathologic imaging (microscopic structure of diseased tissue) from the National Cancer Institute (NCI) included in drug records.
  • Section  providing public access to reference cases, initially populated with clinical cases from the Drug-Induced Liver Injury Network, a consortium of eight academic medical centers throughout the United States. This repository will allow for statistical analyses of trends in drug-induced liver disease, as well as better characterization of clinical patterns of injury.

National Library of Medicine Resource Update: Alternatives to Animal Testing Portal

The National Library of Medicine’s (NLM) Alternatives to Animal Testing (ALTBIB) portal provides access to PubMed/MEDLINE citations relevant to alternatives to the use of live vertebrates in biomedical research and testing. The ALTBIB topics and subtopics are aligned with current U.S. and international approaches. For example, information is provided on in silico, in vitro, and refined or improved animal testing methods. Strategies that incorporate validated methods and other approaches are also covered. In addition to the topic areas for PubMed searches, the ALTBIB portal includes a searchable bibliographic collection of alternatives to animal testing, including citations from published articles, books, book chapters, and technical reports published from 1980 to 2000.

The Hazardous Substances Data Bank (HSDB), part of NLM’s Toxicology Data Network (TOXNET), now includes subheadings (“/alternative/ and /in vitro tests/”) in the Human and Non-Human Toxicity Excerpts fields. These subheadings allow users to locate data from in vitro and other alternative methods. For example, users can search “ALTERNATIVE IN VITRO TESTS” to locate records with this data. Coverage includes results from methods validated by the Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) and the European Union Reference Laboratory for Alternatives to Animal Testing (EURL-ECVAM).

SciENcv Enhancements: NIH and NSF Biographical Sketch Formats

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.

Public Access Compliance Monitor

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.

NLM HIV/AIDS Portal Now Offers Multilingual Content Search!

NLM’s HIV/AIDS Portal now offers the ability to search for multilingual content. The new Multilingual Search interface searches specifically for HIV/AIDS related topics from the multilingual and multicultural content of HealthReach (formerly RHIN). HealthReach offers easy access to quality health information to individuals for whom English is not the primary language. It is also an important resource for health professionals as well as public health administrators. Users can search by subject/topic, language, and format. The default for the search is always HIV/AIDS so there is no need for these terms to be included in the search. There is also an Advanced Search capability to further refine retrieval. The content is available in audio and video formats as well as text. For text documents there is a feature that allows viewing the document in a split screen with one side being English and the other being the language requested in the search.

NLM Selected as a Host Site for the 2015 National Digital Stewardship Residency

The National Library of Medicine (NLM) is pleased to announce its participation in the second year of the National Digital Stewardship Residency (NDSR), a significant partnership of the Library of Congress (LC) and the Institute of Museum and Library Services (IMLS), to build a dedicated community of stewards capable of managing, preserving and making accessible the nation’s digital assets. The NDSR enables recent Master’s program graduates in relevant fields to complete a paid 12-month residency at host institutions in the Washington DC area, where they work on significant digital stewardship projects. Similar NDSR programs are on-going in Boston and New York.

NLM’s NDSR project proposal, to select and preserve an NLM-produced software product, was chosen in a highly competitive process from about 15 other proposals. NLM will join the American Institute of Architects, the DC Public Library, the Government Publishing Office and the U.S. Senate, Historical Office as a host institution beginning in June, 2015. A detailed list of all five projects can be found at the NDSR website. This is the second year that NLM has been chosen as an NDSR host site, evidence of NLM’s commitment and support of digital stewardship.

NDSR is now accepting applications for qualified applicants for places in the five Washington DC host institutions. The residency application period is open from December 17 to January 30. The application instructions and list of requirements can be found on the NDSR website. Candidates may apply online for one of the five residencies.

TOXNET Provides Permalinks to Individual Records

Permanent links to National Library of Medicine (NLM) TOXNET records are now provided for the Hazardous Substances Data Bank (HSDB), TOXLINE, LactMed, Developmental and Reproductive Toxicology Database (DART), Toxics Release Inventory (TRI), Comparative Toxicogenomics Database (CTD), Integrated Risk Information System (IRIS), International Toxicity Estimates for Risk (ITER), Chemical Carcinogenesis Research Information System (CCRIS), and GENE-TOX.

To create a permanent link, click on the “Permalink” button found in the upper right of a TOXNET record. This provides a pop-up window with a URL to share or to save for retrieving the record at a later time.

12-18-2014 10-16-10 AM

2015 MeSH Now Available in PubMed!

As of December 15, PubMed/MEDLINE citations (including the backlog of citations indexed since November 19 with 2015 MeSH), the MeSH database, and the NLM Catalog were updated to reflect 2015 MeSH. The MeSH translation tables were also updated on December 15. Now that end-of-year activities are complete, MEDLINE/PubMed may be searched using 2015 MeSH vocabulary. Highlights of MEDLINE Data Changes for 2015 were previously published in the NN/LM PSR Latitudes blog. On December 16, NLM resumed daily MEDLINE updates to PubMed.