July 2019 Issue

Are you a biomedical researcher searching for information on genes related to a particular disease, pathway, or process? Are you overwhelmed by the vast quantity of associated literature? Have you considered that some genes are more highly investigated than others, which leads to an overabundance of literature to review for some genes as well as a scarcity of information on others?

Geneshot is a new search engine created to bridge this gap and highlight understudied genes by mining publications for mentions of any genes with the search term(s), then prioritizing the genes. Searching for a biomedical term returns two ranked gene lists. The first contains genes reported in the literature and the second contains predicted genes identified via data integration from multiple sources. The underlying data sets are from PubMed, GeneRIF, AutoRIF (more comprehensive than the former), gene-gene co-expression matrix data using ARCHS4, and gene-gene co-occurrence matrix Tagger and Enrichr data. Geneshot can also facilitate hypothesis generation by assessing gene set novelty and proposing additional relevant genes to augment gene sets. A detailed description of the mining and prediction methodology is available in the Geneshot publication.  Continue reading →

As the saying goes, “A picture is worth a thousand words.” While it can take hundreds or thousands of words to convey a complicated concept; a single image can easily do the same thing. OPEN-i® is the open access biomedical image search engine from the National Library of Medicine’s Lister Hill Center for Biomedical Communications. OPEN-i® is unique in its ability to index both the article’s text and images from the open source literature and biomedical image collections. OPEN-i® searches and retrieves both abstracts and images (including charts, graphs, clinical images, etc.)

You can conduct a search in OPEN-i® by typing your terms in the search box or by selecting a saved image. From the results display, hover your cursor over an image and a MEDLINE citation will pop-up.

The following limits can be applied to your searches:

• Rank By (Newest, Oldest, Diagnosis, Etiology, etc.)
• Article Type (Abstract, Book Review, Brief Report, etc.)
• Image Type (CT Scan, Graphics, MRI, etc.)
• Subsets (Basic Sciences, Clinical Journal, Ethics, etc.)
• Collections (PubMed Central, Indiana U. Chest X-rays, USC Orthopedic Surgical Anatomy, etc.)
• License Type (Attribution, Attribution noncommercial, Attribution noncommercial no derivatives, etc.)
• Specialties (Behavioral Sciences, Biochemistry, Cancer, etc.)
• Search In (Titles, Mentions, Abstracts, etc.)

OPEN-i® contains over 3.7 million images from about 1.2 million PubMed Central® articles; over 7,400 chest x-rays with over 3,900 radiology reports; 67,500 images from the NLM History of Medicine collection; and over 2,000 orthopedic illustrations, plus MedPix.

Images are obtained from the following sources:

• The Open Access Subset of PubMed Central (PMC)
• The Indiana University hospital network
• The Orthopedic Surgical Anatomy Teaching Collection at the USC Digital Library
• Images from the History of Medicine Division from the U.S. National Library of Medicine
• MedPix

Copyright for use of the images remains with the authors or the journal.

For more information about copyright, search help, and technical problems, see the OPEN-i® FAQ page.

*Parts of this article were derived from the OPEN-i® website.

~Jill Foust

The HSLS Staff News section includes recent HSLS presentations, publications, staff changes, staff promotions, degrees earned, etc.

Names in bold are HSLS-affiliated

News

Welcome to Anthony Harris, Assistant Learning Management System Developer. Anthony recently graduated from the University of Pittsburgh with a Bachelor of Science in Information Science and will be working with both the NNLM Web Services Office (NWSO) and the NLM All of Us Research Program Training and Education Center (TEC).

Tessa Zindren joined the staff of the National Network of Libraries of Medicine, Middle Atlantic Region, as Program and Outreach Assistant. Tessa will be responsible for maintaining outreach materials, responding to member and staff requests, and reporting to internal and external stakeholders. She has a Bachelor of Science in Business Administration with a major in Marketing from Pitt and was most recently Project Manager at AMG Research.

Publications

M.A. Bowman, D.J. Buysse, J.E. Foust, Research and Instruction Librarian, et al., published “Disturbed Sleep as a Mechanism of Race Differences in Nocturnal Blood Pressure Non-Dipping,” in Current Hypertension Reports, 21(7), May 22, 2019. Continue reading →

Painless PubMed, Tuesday, July 2, 9–10 a.m.

Single Cell Transcriptomics, Wednesday, July 10, 10 a.m.–12 p.m. (morning session) and 1–4 p.m. (afternoon session)

Reporting Guidelines: A Pathway to Transparent Writing Equals Better Results, Thursday, July 11, 10–10:30 a.m.

Basic EndNote, Monday, July 15, 9:30–10:30 a.m.

Painless PubMed, Tuesday, July 16, 9:30–10:30 a.m.

Bioinformatics Data Analysis: Options 4 Rigor, Tuesday, July 16, 12–1 p.m.

Gene Expression Visualization, Wednesday, July 17, 1–4 p.m.

Basic Python through Jupyter, Thursday, July 18, 1–4 p.m.

Advanced EndNote, Friday, July 19, 10–11 a.m.

Visualized Searches: VOSViewer for Literature Analysis, Friday, July 19, 12–1 p.m.

ChIP-Seq & Partek Flow, Tuesday, July 23, 1–4 p.m.

Introduction to Data Management, Wednesday, July 24, 10–11 a.m.

Research Metrics and Publication Reports: Showcasing Impact, Tuesday, July 30, 4–5 p.m. Continue reading →