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Archive for the ‘Search Tools’ Category

Upcoming NCBI Webinars: Eukaryotic Genome Data Curation and NCBI Graphical Viewers

Join NCBI staff for the upcoming webinars on RefSeq and NCBI Graphical Viewers (including Sequence Viewer and Variation Viewer):

Eukaryotic Genome Data Curation at NCBI
Tuesday, January 5, 2016, 10:00-11:00 am PST
What do a fish, a plant, and a protozoan have in common? These are all example organisms for which NCBI Reference Sequence (RefSeq) staff manually examine and improve the scientific data in NCBI Assembly, Gene, Genome, and RefSeq (among other) databases. The RefSeq project spans viruses to human and in this webinar, three RefSeq biocurators will focus on aspects of data curation for eukaryotic organisms. We will discuss several aspects of manual curation including sequence analysis, functional annotation, data validation and community collaboration. We will also highlight how these curation efforts improve the programmatic approaches used by RefSeq genome annotation pipelines, which allow NCBI to handle the ever-increasing amount of data generated by researchers.

NCBI Minute: New track options for getting the most out of NCBI Graphical Viewers
Thursday, January 7, 2016, 9:00-9:15 am PST
New track options in the NCBI graphical viewers and genome browsers provide powerful features including seven different NCBI Recommended Track Sets, the ability to create, save and share custom track sets as a collection in My NCBI. You will learn how to use these new features as well see how to search and quickly find relevant tracks and to upload your own custom data. This webinar will help you get the most out of the NCBI Graphical Sequence Viewer, Variation Viewer and other NCBI graphical browsers.

Visit the NCBI Webinars and Courses webpage to view archived webinars and materials, and to learn about future webinars. Archived webinars can also be accessed on the NCBI YouTube channel.

MedlinePlus Health Topics Subcategories Changes!

MedlinePlus and MedlinePlus en español currently have over 950 health topics in both English and Spanish. These health topic pages contain collections of vetted links to consumer health resources, which are organized into subcategories. On January 12, 2016, in an effort to simplify and streamline the subcategories schema, the following changes were made to both MedlinePlus and MedlinePlus en español:

Deleted Subcategories:

  • “Diagnosis/Symptoms”
  • “Prevention/Screening”
  • “Finance and Policy”

New Subcategories:

  • “Symptoms”
  • “Diagnosis and Tests”
  • “Prevention and Risks Factors”

Merged Subcategories:

  • Videos and Tutorials into “Videos and Tutorials”

Changed Subcategory

  • Specific Conditions to “Specifics”

Search PubMed with 2016 MeSH!

As of December 15, PubMed/MEDLINE citations (including the backlog of citations indexed since November 18 with 2016 MeSH), the MeSH database, and the NLM Catalog were updated to reflect 2016 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 2016 MeSH vocabulary. See MEDLINE Data Changes — 2016 for details on the data changes. On December 16, NLM resumed daily MEDLINE updates to PubMed.

New PubMed Health Resources!

Earlier this year PubMed Health was expanded with research on research methods. These are studies and guidance for doing systematic reviews and helping them make an impact. A new resource takes this process a step further; the PubMed Systematic Review Methods Filter, as well as a new section at PubMed Health “For Researchers.” Also available are new glossary pages especially for research methods for anyone who wants to understand more about the mechanics of health research. The glossary will grow to cover the most common research terms used in PubMed Health.

Whenever you search in PubMed Health, you also get results from PubMed using the new filter. They will appear to the right of the main search results, in a box called “Systematic Review Methods in PubMed.” It’s below a box called “Systematic Reviews in PubMed,” which is a search for systematic reviews themselves. The filter searches through a subset of PubMed records that are either research or guidance on systematic review methods. The publications could relate to the development or evaluation of any step in doing or using systematic reviews. To use the filter in PubMed, enter sysrev_methods [sb] in the search box. You can use it like any search term, for example, sysrev_methods [sb] AND “network meta-analysis.”

The methods filter is a result of collaboration between the PubMed Health team and the Scientific Resource Center (SRC) for the U.S. Agency for Healthcare Research and Quality (AHRQ). The SRC team selects the publications, after scanning widely every day looking for new candidates. When you see a systematic review at PubMed Health, there will often be a methods box to the right. That links to the relevant methods guide from the organization behind the review. Six groups so far have started contributing their methods guidance and research to PubMed Health. You can see the list on the new “For Researchers” page.

Navigation isn’t the only part of PubMed Health with a new look. The homepage also has a new design. For further details, visit the PubMed Health Blog.

Check Out What’s New for 2016 MeSH!

MeSH, the National Library of Medicine’s controlled vocabulary thesaurus, is updated annually. It is used to index articles from thousands of biomedical journals for the MEDLINE/PubMed database and for the cataloging of books, documents, and audiovisuals acquired by NLM. Changes for 2016 MeSH include: 438 new Descriptors, 17 Descriptor terms replaced with more up-to-date terminology, 9 deleted Descriptors, and deletion of the Subheading “diagnostic use.” Content of MeSH now includes 27,883 Descriptors; 87,028 Descriptor entry terms; 82 Qualifiers (Subheadings); and 230,872 Supplementary Concept Records. Three new Publication Types were added for catalogers; Blogs, Graphic Novels, and Public Service Announcements. The Publication Type Clinical Study was added mainly for use by indexers. Additional changes involve the MeSH Trees and Scope Notes. For a complete list of changes, visit the NLM Technical Bulletin.

New resource for Alaska Natives and American Indians: NativeOneStop.gov

The White House, in collaboration with the Department of the Interior and the Bureau of Indian Affairs, has announced a new resource for American Indians and Alaska Natives. NativeOneStop.gov was launched in an effort to provide American Indians and Alaska Natives with easy, online access to Federal resources and programs. It is a partnership of many Federal agencies and organizations with a shared vision – to provide improved, personalized access to Federal resources and programs for American Indians and Alaska Natives. NativeOneStop.gov will make it easier for tribes, Alaska Natives, and American Indians to find services, receive consistent information, and streamline outreach and services by Federal agencies.

Upcoming NCBI Webinars: Advanced Search in dbGaP and 1000 Genomes Project Data

Join NCBI staff for the upcoming webinars on dbGaP and the 1000 Genomes Project Data.

NCBI Minute: New Advanced Search in dbGaP Provides Easy Access to Relevant Data
Wednesday, December 16, 2015, 9:00-9:15 am PST
The new advanced search interface to dbGaP makes finding relevant data much easier. In this webinar you will learn how to access the new faceted search and to quickly find human subject data by study, variables, datasets, documents, and genotypes.

Accessing the 1000 Genomes Project Data at the NCBI
Thursday, December 17, 2015, 10:00-11:00 am PST
The 1000 Genomes Project data now include small-scale and structural variant calls from 2,504 individuals representing 26 human populations. In this webinar you will see how to access 1000 Genomes data through the SRA, dbVar, SNP and BioProject resources, as well as through tracks on annotated human sequences in the Graphical sequence viewer and the Variation Viewer. Most important you will learn how to display, search, and download individual and genotype level data through the dedicated 1000 Genomes Browser that allows searching by chromosomal position, gene names and other genome markers.

Visit the NCBI Webinars and Courses webpage to view archived webinars and materials, and to learn about future webinars. Archived webinars can also be accessed on the NCBI YouTube channel.

NLM Releases New Health Literacy Tool Shed Website

Health Literacy Tool Shed HomepageThe U.S. National Library of Medicine (NLM), in collaboration with Boston University School of Medicine is pleased to announce the launch of the Health Literacy Tool Shed. The Health Literacy Tool Shed is a free, user-friendly, unique, curated online database of more than 100 empirically validated health literacy instruments. The Tool Shed serves as an interactive, one-stop shop where researchers use provided filters to select a health literacy research instrument. The website was developed following user-centered design methods to ensure the site’s relevance and ease of use.

The Health Literacy Tool Shed provides background information about each instrument and enables users to compare them. Each instrument within the Health Literacy Tool Shed is peer reviewed by health literacy research experts including: Michael Paasche-Orlow, M.D., M.P.H., Boston University School of Medicine; and Lauren McCormack, Ph.D., M.S.P.H., RTI International. The selected instruments vary in terms of user accessibility and cost, as mandated by the original investigator.

NIH Manuscript Collection Optimized for Text-Mining and More

NIH-supported scientists have made over 300,000 author manuscripts available on PubMedCentral (PMC) since 2008. Now, NIH is making these papers accessible to the public in a format that will allow robust text analyses. You can download the entire PMC collection of NIH-supported author manuscripts as a package in either XML or plain text formats. The collection will encompass all NIH manuscripts posted to PMC since July 2008. While the public can access the articles’ full text and accompanying figures, tables, and multimedia on the PMC website, the newly available article packages include full-text only, in a form that facilitates text-mining. This resource was developed to increase the impact of NIH funding. Through this collection, scientists will be able to analyze these manuscripts, further apply the findings of NIH research, and generate new discoveries. For more information visit the PMC author manuscript collection web site.

December Webinar Opportunities Hosted by NN/LM Middle Atlantic Region

The NN/LM Middle Atlantic Region has announced two webinar opportunities that are open to anyone wishing to attend:

Tuesday, December 8: Hospital Libraries: Challenges and Opportunities – This session will include discussion of the current state of hospital libraries and consider their future in light of the Affordable Care Act, Meaningful Use, and budget cuts. It will also consider the role the librarian plays and their effect on these changes, as well as ways the library’s resources (including the librarian) can help offset the expenses hospitals are facing. Speaker: Heather N. Holmes, MLIS, AHIP, Clinical Informationist, Summa Health System, Akron, OH.
When: December 8, 2015, 9:00-10:00am PST
Where: https://webmeeting.nih.gov/boost2/
No Registration Required
Eligible for 1 MLA CEU

Thursday, December 17: Saving time with PubMed Subject-specific Queries – Want to boost your PubMed prowess? Looking for preformulated searches on drugs, health information technology, public health and other topics? Spend an hour with NN/LM MAR Outreach Coordinator, Kate Flewelling, to save hours on your searches!
When: December 17, 2015, 9:00-10:00am PST
Where: https://webmeeting.nih.gov/nlmfocus/
No Registration Required
Eligible for 1 MLA CE