July 25, 2014

From the GMR: NCBI Announcements

FYI: NCBI Upcoming events and honors
BLAST in the Cloud webinar July 30th

In one week, NCBI will offer a webinar entitled "BLAST in the Cloud". This presentation will show you how to log on to AWS and deploy the NCBI-BLAST Amazon Machine Image (AMI) quickly. Prior knowledge of using web and standalone BLAST is required.

To register, please go to this link:

* NCBI News:

NCBI webinar "Using the New NCBI Variation Viewer to Explore Human Genetic Variation" on August 13th

On August 13th, NCBI will host a webinar entitled "Using the New NCBI Variation Viewer to Explore Human Genetic Variation". This presentation will show you how to find human sequence variants by chromosome position, gene, disease names and database identifiers (RefSNP, Variant region IDs) using NCBI's new Variation Viewer.

You will learn how to browse the genome, navigate by gene or exon, filter results by one or more categories including allele frequencies from 1000 Genomes or GO-ESP, and link to related information in NCBI's molecular databases and medical genetic resources such as ClinVar, MedGen, and GTR. You will also be shown how to upload your own data to add to the display and download results.

Anyone who works with clinical or research variation data will find that the Variation Viewer provides a convenient and powerful way to access human variation data in a genomic context that is fully integrated with all other NCBI tools and databases.

To register, please go to this link

Related Links:
• Variation Viewer:
• 1000 Genomes:
• ClinVar:
• MedGen:
• GTR:

Announcing major revision of the NCBI genomes FTP site

Within the next two weeks, NCBI will make a major revision to the genomes FTP site. This redesign will expand available content and facilitate data access through an organized, predictable directory hierarchy. The updated site will also provide greater support for downloading assembled genome sequences and/or corresponding annotation data. To give those with automated tools time to update, we plan to maintain the older content and structure of the preexisting /genomes/ FTP site in parallel with the new structure for six months.

The new FTP site structure provides a single entry point to access content representing either GenBank or RefSeq data. Advantages of the updated genomes FTP site include the comprehensive provision of data through a single process flow that is reliant on content in NCBI's Assembly database (which excludes viruses at this time), integration of quality assurance regression tests, and provision of a consistent core set of files for all organisms and assemblies.

Stay tuned for more information about the changes to come and the official launch of the revamped genomes FTP site.

. Current Genomes FTP site:
. GenBank:
. RefSeq:
. Assembly:

NCBI/CDC/FDA/USDA collaboration using whole genome sequencing (WGS) to improve food safety is honored with an HHSinnovates award

A collaborative project between NCBI and several other Federal and state partners to reduce the time and improve the accuracy of detecting foodborne pathogens by using whole genome sequencing (WGS) techniques received an HHSinnovates award on July 21.

The HHSinnovates program was initiated in 2010 to recognize new ideas and solutions developed by HHS employees and their collaborators. Six finalist teams were recognized at the awards ceremony. The WGS Food Safety Project, which also involved the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA), the U.S. Department of Agriculture (USDA), and state public health laboratories, was one of three projects to be honored as "Secretary's Picks" by HHS Secretary Sylvia Mathews Burwell.

Presenting the award, HHS Deputy Secretary Bill Corr said: "Together all these folks engaged in a demonstration project to showcase the benefits of using whole genome sequencing for food surveillance and detection purposes. They showed that whole genome sequencing can produce faster detection of foodborne pathogens than the traditional method, helping us stop an outbreak of disease in its tracks, and for that we deeply appreciate your work." The award went to the specific individuals leading the project in the various agencies; in the case of NCBI, Senior Scientist William Klimke, Ph.D., was honored for his work in heading NCBI's part of the project.

WGS provides greater specificity than other techniques, such as the commonly used pulsed-field gel electrophoresis (PFGE), in identifying the DNA fingerprint of bacteria. It also can more rapidly determine whether isolates are related to a foodborne disease outbreak.

The demonstration project involves real-time sequencing of Listeria monocytogenes isolates from human DNA as well as the food supply chain. In the project, the whole genomes of isolates are sequenced and the sequencing data are sent to NCBI, which performs assembly, annotation, and analysis and then sends results back to CDC, FDA, USDA, and the labs.

Collaborative projects using WGS for other pathogens related to food safety are also underway.

* HHSinnovates:

July 24, 2014

From the GMR: Save the Date announcement for "A Librarian's Guide to NCBI"

Some of you have been waiting for this class to come again.

The required online class will be offered:
January 12 - February 20, 2015
Registration opens September 29th
The in-person five-day class in Bethesda, MD runs:
March 9-13, 2015
Registration will be offered to those who complete the online class.

Enjoy - and be aware the class fills up quickly.


---------- Forwarded message ----------
From: Sharon E. Dennis
Date: Tue, Jul 15, 2014 at 11:12 AM
Subject: [NNLMout] Save the Date announcement for "A Librarian's Guide to NCBI"
To: ""

Hi everyone,

We have posted the "Save the Date" announcement for the 2015 session of "A Librarian's Guide to NCBI." You can see the announcement on NTC's blog:

Or in the NLM Technical Bulletin:

Let me know if you have questions. Thanks!

Best regards,

Sharon Dennis
Assistant Director
National Library of Medicine Training Center (NTC)
Spencer S. Eccles Health Sciences Library
University of Utah
10 North 1900 East
Salt Lake City, UT 84112

800-338-7657, press 2
Fax: 801-581-3632

May 14, 2013

From the GMR: NLM presentations at MLA available online

The NLM exhibit booth at the Annual Meeting of the Medical Library Association (NLM) featured theater presentations to bring users up-to-date on several NLM products and services. The presentation recordings are available at the link below and will soon be accessible from the NLM Distance Education Program Resources page.

Topics include: NLM apps and social media; History of Medicine Division exhibitions, programs, and resources; NIH Public Access compliance and PubMed My NCBI, MedlinePlus Connect and Meaningful Use; Resources for a multi-cultural world; and updates on PubMed, PubMed Central International, Health Services Research and Public Health, PubMed Health and

NLM Technical Bulletin, May-Jun 2013, MLA 2013: NLM Theater Presentations

Have a wonderful week everyone!


Holly Ann Burt, MLIS, AHIP
Outreach and Exhibits Coordinator
NN/LM-Greater Midwest Region
1750 W. Polk St. M/C 763
Chicago, IL 60612-4330
phone: 800-338-7657 (in the Region) or 312-996-2464
fax: 312-996-2226

September 4, 2012

From the GMR: New Genetics Education Resource

The National Library of Medicine (NLM) is pleased to announce the release of a new educational resource, GeneEd. Developed in collaboration with the National Human Genome Institute (NHGRI), teachers and experts in genetics and genetic counseling, GeneEd is a safe and useful resource for students and teachers in grades 9 - 12 to learn genetics.

GeneEd allows students and teachers to explore topics such as:

  • Cell Biology

  • DNA

  • Genes

  • Chromosomes

  • Heredity/Inheritance Patterns

  • Epigenetics/Inheritance and the Environment

  • Genetic Conditions

  • Evolution

  • Biostatistics

  • Biotechnology

  • DNA Forensics

  • Top Issues in Genetics

Teachers can use the site to introduce topics, supplement existing materials, and provide as a reliable source to students conducting research.

The site links to categories such as research articles, animation, games, videos, interactive tutorials, and labs and experiments. 3D images, illustrations and text from NHRGI help to enrich the user experience by providing vivid imagery to reinforce genetic concepts. Text varies from easy-to-read to advanced reading levels, which makes this a versatile tool both in and out of the classroom. Specialty pages including Teacher Resources and Labs and Experiments highlight those tools that teachers may find particularly helpful.

Other specialty pages such as Careers in Genetics and Highlights allow students to see what is new and noteworthy in the field of Genetics along with links to different careers related to the science of Genetics.

To stay up to date with all NLM's K-12 resources subscribe to the K12NLMRESOURCES email list, follow us on Twitter or like us on Facebook.

July 30, 2012

From the GMR: Online PubMed Class - There's Still Room for You!

Summer School? YES! If you haven't taken it yet, join us for this popular (and free) online class in PubMed.

Making PubMed Work for You is three-week course which covers the same materials as the in-person class. Spend about one hour a week, taking this course at your own pace via Moodle. This class is intended to hone basic searching techniques and the ability to develop search strategies that takes advantage of the PubMed interface to MEDLINE. Topics covered include Automatic Term Mapping, Search Results, Details, Related citations, My NCBI, Searching with MeSH, and the Single Citation Matcher.

Join us from July 30th through August 17, 2012. Register online with the GMR registration system at:

See you online and feel free to email me directly with any questions.

P.S. More online PubMed courses coming soon.


Holly Ann Burt, MLIS
Outreach and Exhibits Coordinator
NN/LM-Greater Midwest Region
1750 W. Polk St. M/C 763
Chicago, IL 60612-4330
phone: 800-338-7657 (in the Region) or
fax: 312-996-2226

July 2, 2012

Regions Hospital hosting NLM traveling exhibit in July

Regions Hospital Medical Library is hosting the NLM exhibit, Binding Wounds, Pushing Boundaries: African Americans in Civil War Medicine. The exhibit will be in the library from July 2nd - Aug. 3rd. The library is open to the public M,Tu,W,F 8am - 4:30pm and Thursdays 8am - 7:30pm. The exhibit will also be hosted at the HealthPartners building in Bloomington the week of Aug. 6th. There it will be in the conference center and be available to the public from 6am-6pm. HealthPartners is on the LRT line at the Bloomington Central stop.

Dr. Jennifer Gunn from the U of M will also come speak at Regions Hospital atrium on July 18th at 12:30pm. Her talk is titled, "Disease and Debility: Minnesotans' experience of medicine in the Civil War". Refreshments will be served.

Please stop by and check out the exhibit, or visit on July 18th for the speaker! If you have any questions, feel free to contact Jennifer Feeken 651-254-3608 or

March 12, 2012

From the GMR: NIH & NCBI launch the Genetic Testing Registry (GTR) - plus other genetic resources

If you haven't seen this:

The Genetic Testing Registry (GTR) is a new resource for finding information about genetic tests and test providers. For more information, please see the GTR homepage ( & the NIH Press Release (

Additional National Library of Medicine (NLM) information and databases related to genetics include:

  • Genetics Home Reference provides consumer-friendly information about the effects of genetic variations on human health.
  • Human Genome Resources works to piece together and analyze the plethora of data being generated through the Human Genome Project
  • NCBI Educational Resources include tutorials, workshops, manuals and guides
  • Bookshelf provides free access to books and documents in life science and healthcare including GeneReviews - and can be added to a Library's Linkout program

Linked from and searchable through NLM:

January 11, 2012

From the GMR: NLM's Tox Town Introduces New US Southwest Neighborhood

FYI. Interesting section on fracking available - with links to a variety of other resources!

Tox Town Introduces New US Southwest Neighborhood in both English and Spanish

What is fracking? What are uranium tailings and how can they affect my health? Answers to these questions can be found in Tox Town's new US Southwest Scene. (English) (Spanish)

This scene, developed in conjunction with Diné College in New Mexico, highlights locations associated with environmental health concerns impacting the Navajo and others living in the Southwest region of the United States. New Tox Town locations found in this scene include:

Abandoned Mines
Coal-Fired Power Plants
Dust Storms
Hydraulic Fracturing
Irrigation Canals and Ditches
Oil and Gas Fields
Sheep Ranching
Uranium Tailings
Water Wells

Regardless of where you live, you will definitely want to visit this new neighborhood and learn about possible environmental health risks in this part of the country.

September 27, 2011

From the GMR: Enhanced Access to Herb and Supplement Information on MedlinePlus

Very cool update!



The National Library of Medicine enhanced access to herb and supplement information on MedlinePlus. On the English and Spanish supplements index pages, links to external sources of herb and supplement information now appear along with the information that we license from National Medicines Comprehensive Database. These links also appear on MedlinePlus search results pages in the Drugs & Supplements collection.

The screen capture below shows the top of the index page. The producing organization (Natural Medicines Comprehensive Database, National Center for Complementary and Alternative Medicine, National Toxicology Program, etc.) appears next to each link to distinguish different pages on the same herb. For example, MedlinePlus provides links to Acai information from both the National Center for Complementary and Alternative Medicine and Natural Medicines Comprehensive Database.

Natural Medicines Medline Plus screenshot

If you have any questions, contact the MedlinePlus team by clicking the "Contact Us" link that appears at the top of every MedlinePlus page.

Thank you!

September 7, 2011

From the GMR: New NLM Enviro-Health Links: Developing and Using Medicines for Children

The National Library of Medicine (NLM) Division of Specialized Information Services (SIS) has released an Enviro-Health Links page on Developing and Using Medicines for Children.

In regards to medications, it is important to remember that children are not small adults. Developing and Using Medicines for Children provides links to resources that can help researchers, medical professionals and parents provide effective medicines and administer them safely. The links include information about pediatric drug development, clinical trials, and existing laws and regulations.

NLM also offers other Enviro-Health Links on topics, including:

Children's Environmental Health

Education, Careers, and Outreach in Toxicology and Environmental Health

Indoor Air Pollution

Keeping the Artist Safe: Hazards of Arts and Crafts Materials

Lead and Human Health

Mercury and Human Health

Water Pollution

Women's Health Resources

NLM Enviro-Health Links

July 13, 2011

From the GMR: NLM releases Chemical Hazards Emergency Medical Management (CHEMM)

The National Library of Medicine has released Chemical Hazards Emergency Medical Management (CHEMM) .

Chemical emergencies are high risk events that require first responders to quickly make a series of complex decisions to minimize the risk of injury to their patients and themselves. The tools in CHEMM provide a comprehensive resource to help responders make safer decisions and provide them with the right information when it is needed most.

CHEMM enables first responders and other healthcare providers and planners to plan for, respond to, recover from, and mitigate the effects of mass-casualty incidents involving accidental or terrorist chemical releases.

CHEMM enhances and builds on the successes of the suite of Emergency Medical Management tools that began with the Radiation Emergency Medical Management (REMM; web-based resource, which provides information for health care providers about clinical diagnosis and treatment of radiation and other injuries anticipated following radiological and nuclear emergencies.

CHEMM is a web-based resource that is downloadable in advance so that it is available during an event if the Internet is not accessible. It provides evidence-based information and guidance on a wide variety of topics, including quick chemical identification, acute patient care guidelines, and initial event activities.

CHEMM and REMM are the result of collaborative efforts between the United States Department of Health and Human Services, the Office of the Assistant Secretary for Preparedness and Response (ASPR) - Office of Preparedness and Emergency Operations (OPEO), the National Library of Medicine - Division of Specialized Information Services (NLM/SIS), as well as many medical, emergency response, toxicology, industrial hygiene, and other experts.

July 6, 2011

From the GMR: NLM LactMed now contains CAM products

The National Library of Medicine Drugs and Lactation Database (LactMed) has added complementary and alternative medicine (CAM) products. CAM products generally consist of dietary supplements derived from botanicals (herbals), "nutraceuticals" (natural and synthetic nonherbals, such as coenzyme Q10), and related products.

The LactMed CAM product records bring together research on these products relevant to breastfeeding. Special emphasis is placed on potential side effects in mothers and infants and on other problems associated with the products. The CAM product records feature a new field for the products' scientific genus and species names.

LactMed currently contains 19 of an expected 100 CAM products (cabbage, comfrey, lecithin, milk thistle, blessed thistle, stinging nettle, St. John's wort, garlic, fenugreek, blue cohosh, black cohosh, raspberry leaf, ginger, coenzyme Q10, borage, caraway, coriander, fennel, anise). These records focus on supplements that are frequently used by nursing mothers, including those claiming to stimulate lactation. Future products will include the most common supplements sold in the United States. A complete list of CAM records in the database can be found by using the search term "complementary therapies" in the main LactMed search box.

LactMed, part of the National Library of Medicine's (NLM) Toxicology Data
(TOXNET(r)), is a database of drugs and other chemicals to which breastfeeding mothers may be exposed. It includes information on the levels of such substances in breast milk and infant blood, and the possible adverse effects in the nursing infant.

June 23, 2011

From the GMR: MedlinePlus RSS & Content Sharing Enhancements

NLM released several exciting enhancements that improve users' ability to share and consume MedlinePlus content:

RSS feeds are now available for every health topic page on MedlinePlus and MedlinePlus en español. This means that MedlinePlus now offers nearly 1,800 feeds for English and Spanish combined that are customizable to your specific interests. Whenever we add a new link to a MedlinePlus topic page, the item appears as a new entry on the corresponding health topic RSS feed. You can subscribe to the health topic RSS feeds using the RSS reader/aggregator of your choice. Links to the feeds are available on all health topic pages, the MedlinePlus RSS Feeds page, and via your browser's RSS auto-detect feature.

In addition to the new health topic feeds, MedlinePlus now offers two new English RSS feeds allowing you to subscribe to all new links added to MedlinePlus and all new NIH links added to MedlinePlus. These new feeds are available on the RSS Feeds page under the heading "General Interest RSS Feeds." For Spanish-language users, there is a new RSS feed that contains all new links added to MedlinePlus en español. This new feed is available from the Spanish RSS Feeds page.

NLM also unveiled enhancements to the print, email, and AddThis share icons on MedlinePlus and MedlinePlus en español health topic pages. These icons are now located above the topic summary, and the Facebook and Twitter sharing options are more prominent, making it easier for you to share content in these very popular social networks.

Examples of the new RSS feeds and the improved sharing features can be seen on the health topic pages listed below:

-Food Allergy (English):
-Alergia a las comidas (Spanish):

If you have any questions about these enhancements, please use the "Contact Us" link that appears at the top of every MedlinePlus page.

June 21, 2011

From the GMR: New NLM Resource: Come On, Mom, Dad, Get Healthy!

FYI. New Resources from NLM's Specialized Information Services (SIS) focused for public and school librarians:

Come on, Mom, Dad, Get Healthy! The TAPAS (Teens Against Parent Addiction Squad) Take Action is a new book authored by Marti Szczur and is now available in PDF form on our K-12 Web page:

This story explores the issue of parental addictions and what kids can do to educate themselves (and their parents) on the health consequences of these addictions.

May 31, 2011

From the GMR: NLM Releases Medicine in the America

NLM is pleased to announce that the first books digitized for the MHL collection are publicly available in our Repository "Digital Collections".

For more information about the collection "Medicine in the Americas" see the news announcement at:

Digital Collections homepage:

April 12, 2011

From the GMR: New Radiation Emergency Medical Management (REMM) version released today

REMM (Radiation Emergency Medical Management) has just released new online and Mobile versions.

What's new on REMM lists some of the key updates, but there are many, many more.

We call your attention specifically to the following:

1. Mobile REMM: updated content for Android (new), iPhone, Blackberry, and Windows Mobile.

2. Nuclear Reactor Accidents: new content and references

3. Potassium Iodide: new content and references

4. Personal Protective Equipment (PPE): 14 new pages with photos

5. Seven new video screencast tutorials: explaining key REMM interactive clinical tools

6. Nuclear detonation clinical triage tool: for use if medical response resources are scarce

7. Simplified clinical algorithm for managing radiation exposure: new format and content

Thanks for your continued support! Contact us with questions or comments.

With appreciation for your support,
The REMM Team
Radiation Emergency Medical Management (REMM)

Guidance on diagnosis and treatment for health care providers

From the GMR: National Library of Medicine chemical structure images now available

FYI to all you chemists!

---------------------------- Original Message ----------------------------
Subject: National Library of Medicine chemical structure images now
available From: "NLM TOXENVLIST"
Date: Thu, April 7, 2011 8:10 am

The National Library of Medicine (NLM) Division of Specialized Information Services (SIS) has added chemical structure images from the NLM ChemIDplus database to Hazardous Substances Databank (HSDB) records.

The chemical structures can be viewed in the HSDB record header with the chemical name and registry number. Users can save the chemical structure as a ".png" file (right mouse click). It is not available via the HSDB document download feature.

These structures are also available in:

* Chemical Carcinogenesis Research Information System (CCRIS):
Carcinogenicity, mutagenicity, tumor promotion, and tumor inhibition data from the National Cancer Institute (NCI)

* Comparative Toxicogenomics Database (CTD)(tm):
Molecular mechanisms by which environmental chemicals affect human disease

Peer-reviewed mutagenicity test data from the Environmental Protection Agency (EPA)

* Integrated Risk Information System (IRIS):
Data from the Environmental Protection Agency (EPA) supporting human health risk assessment and focusing on hazard identification and dose-response assessment

* International Toxicity Estimates for Risk (ITER):
Chemical risk information from authoritative groups worldwide

March 16, 2011

From the GMR: NLM resources related to earthquakes, tsunamis, radiation emergencies

The National Library of Medicine has resources that may help with understanding the health issues related to the devastating Japan earthquake, tsunami and possible nuclear power plant disruptions. Resources from NLM, US federal agencies, and other key resources are listed on the new topic page "Disasters in Japan 2011" at

For earthquake information for responders and health professionals, see the "Earthquakes-Resources for Response and Recovery" page at

MedlinePlus has topic pages on earthquakes and tsunamis in English and Spanish. Although not intended to be specific to the current events in Japan, these pages give background information for a general audience:



Clinicians who need to learn more about assessing and managing radiation emergencies can turn to the Radiation Emergency Medical Management (REMM) web site. Selected, key files from REMM are also available for downloading on mobile devices from

For a general audience, see the MedlinePlus pages on:
Radiation Emergencies

Radiation Exposure

September 30, 2010

From the GMR: New Herb and Supplement Information on MedlinePlus

Dear GMR Members,

Today, MedlinePlus released 100 new English and Spanish monographs on a broad range of dietary supplements and herbal remedies. The new content is provided by Natural Medicines Comprehensive Database Consumer Version (NMCD). Some of the highlights of the new monographs include:

  • Descriptions of herbal remedies, dietary supplements, and how they work
  • Effectiveness ratings for different indications
  • Safety concerns, including special precautions and warnings
  • Information on interactions with medications, foods, and other herbs and supplements
  • Dosages that have been studied in scientific research
  • Extensive lists of references, with links to PubMed
  • A "Share" button on each monograph that allows users to easily share the content with friends and family
The content from NMCD replaces the Natural Standard monographs that were previously on MedlinePlus. If you bookmarked any monographs from Natural Standard, MedlinePlus will automatically redirect you to the new information when equivalent content is available. Please review and update your bookmarks.

If you have questions or comments about the new content, please contact the MedlinePlus team by using the "Contact Us" link that appears at the top of every MedlinePlus page.

Samanthi Hewakapuge, MA, MLS
Consumer Health Coordinator
National Network of Libraries of Medicine
Greater Midwest Region
Library of Health Sciences - UIC
1750 W. Polk St. M/C 763
Chicago, IL 60612-4330
(312) 996-7791
(312) 996-2226 Fax

September 1, 2010

From the GMR: NLM Resource Update: crude oil and dispersants added to the Hazardous Substances Data Bank

The National Library of Medicine (NLM) Division of Specialized Information Services has added crude oil and dispersant records to the Hazardous Substances Data Bank (HSDB).

In response to the 2010 Deep Water Horizon oil spill, the HSDB development team and the HSDB Scientific Review Panel (SRP) compiled and reviewed data for crude oil, Corexit 9500, and Corexit 9527 records. Although many dispersants exist, the two selected were most widely used during recent oil clean up efforts in the United States Gulf area and are on the U.S. Environmental Protection Agency (EPA) list of authorized dispersants for use on the National Contingency Plan (NCP) Product Schedule.

The HSDB records include data on human health effects, animal toxicity studies, environmental fate and exposure, and hazard information.