Archive for the 'databases' Category

Precision Medicine: Finally, it’s all about YOU!

At the January 2015 State of the Union Address, President Obama announced his Precision Medicine Initiative. This initiative would put $215 million dollars toward understanding how to personalize an individual’s medical treatment based on his or her genes, environment and lifestyle. While the concept of precision (also referred to as personalized or individualized) medicine isn’t new – think eyeglasses and blood transfusions – advances in science and technology will allow for the exploration of novel treatments and prevention strategies for complex diseases like coronary artery disease, COPD, and hypertension. One million citizens will be asked to volunteer their health data and numerous public and private entities will be collaborating to explore effective disease prevention and treatment.

Why Now?

Developments in basic science, genomics, proteomics, metabolomics, and advances in technology supporting mHealth, electronic health records, and the storage of big data have created the perfect environment to greatly expand precision medicine. If the past ten years is any indication of rapid change, the sky’s the limit for the next decade:

  • Amount of time to sequence the human genome: 2004-2 years, 2014-2 days
  • Cost of human sequencing: 2004-$22,000,000, 2014-$1,000-$5,000
  • Number of smart phones: 2004-1,000,000, 2014-160,000,000
  • Computing power: 2004-n, 2014-n16

Precision Medicine in Action

The Veteran’s Administration (VA) Office of Research and Development has been working to identify genes linked to post traumatic stress disorder (PTSD), high blood pressure, and heart disease. VA researchers have discovered that individuals with a certain form of the serotonin transporter gene 5-HTT are at a greater risk for PTSD and depression, information which helps individualize use and dosage of selective serotonin reuptake inhibitors (SSRI). They have also found that people with certain forms of angiotensin II receptor type-1 (AGTR1) may have an increased risk for high blood pressure, heart disease, and diabetes. This information can help clinicians develop a personalized preventative care program. Find out more on VA research.

Precision medicine can not only impact an individual, it can address health prevention in an entire community. In 2008, an OB/GYN began mapping children born into poverty in Gainesville, Florida. She was put in contact with a sheriff who was also interested in mapping, but her focus was the community’s incidence of crime. When the two women met, they discovered the maps matched exactly to a one square-mile area and further investigation showed the area also had the highest rate of domestic violence, child abuse and neglect. But why? A ride around the area revealed a lot about the environment and lifestyles of community members. There was poorly maintained housing and a complete lack of access to services like child care, healthy food and medical care – with the closest clinic a 2-hour bus ride away. Find out more about what happened to this community.

Resources for Genetic and Environmental Health


Community College and University

  • Environmental Health and Toxicology – portal links health professionals and consumers to many resources to understand the connection between the environment and human health and development.
  • GeneEd Web site – (Grades 9 -12+) Links to vetted genetic Web sites based on high school science curriculum. Includes lesson plans and current events.
  • Genetics Home Reference – Consumer-friendly information about genetic variation and human health.

Consumer and Patient Education

  • Environmental Health and Toxicology – portal links health professionals and consumers to many resources to understand the connection between the environment and human health and development.
  • Genetic Alliance – Nonprofit health advocacy organization committed to transforming health through genetics and promoting an environment of openness.
  • Genetics Home Reference – Consumer-friendly information about genetic variation and human health.
  • NHGRI Talking Glossary – Genetic terms, images and animation. (English/Spanish).
  • Office of Rare Diseases Research – Rare diseases information for patients, families, healthcare providers, researchers, educators and students.

Genetics Professionals


Public Health

  • Environmental Health and Toxicology – portal links health professionals and consumers to many resources to understand the connection between the environment and human health and development.
  • PHPartners – a collaboration of U.S. government agencies, public health organizations, and health sciences libraries which provides timely, convenient access to selected public health resources on the Internet.
  • Public Health Genomics – information on infectious diseases and noncommunicable diseases with a focus on human and pathogen genomics, genomic tests, family history, public health science, programs and practice, as well as policy and legislation.
  • National Information Center on Health Services Research and Heath Care Technology (NICHSR) – information and tools for the health services research community.

Researcher Tools from NIH

  • GenBank – an annotated collection of all publicly available DNA sequences.
  • Gene – integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
  • Genes and Expressions – Tools to help users query and download experiments and curated gene expression profiles.
  • Human Genome Resources – integrated, one-stop, genomic information infrastructure for biomedical researchers from around the world so that they may use these data in their research efforts.
  • International HapMap Tool – partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals.
  • NCBI Webinars and Courses – a series of webinars and courses led by NCBI staff who explain and demonstrate the use of various NCBI web resources with particular emphasis on recent changes and improvements.
  • OMIM – comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily.


-Dana Abbey, Colorado/Health Information Literacy Coordinator

Health Information Resources for Limited English Proficient Persons

Numerous studies over the past 25 years have demonstrated a strong connection between language and health. Language can affect the accuracy of patient histories, the ability to engage in treatment decision-making, understanding a medical diagnosis or treatment, patient trust level with care providers, underuse of primary and preventative care, and lower use or misuse of medications. Culture also plays a significant role in health, healing and wellness belief systems – impacting how illness, disease, and their causes are perceived by the patient and the care provider.

The story of Mohammad Kochi illustrates how language and culture can impact health outcomes.  Mr. Kochi, a 63-year-old from Afghanistan, is diagnosed with stomach cancer. While he agrees to surgery, he declines chemotherapy due to religious beliefs, language barriers, and family conflict. Mr. Kochi is a Limited English Proficient (LEP) person.

An LEP person is defined as an individual who does not speak English as their primary language and have a limited ability to read, speak, write, or understand English. An LEP person’s national origin is based on ancestry, not citizenship. There are an estimated 25.3 million LEP individuals in the United States – up 81% since 1990.[1]

These persons are protected under Title VI of the Civil Rights Act of 1964, and all organizations receiving Federal financial assistance have a responsibility to take “reasonable” steps to ensure meaningful access to their programs and activities by persons with LEP. Title VI applies to many types of organizations including schools, hospitals, public health clinics, police departments, and social services.

Libraries can play a key role in supporting an organization’s ability to provide meaningful access, especially in the area of health information. The National Library of Medicine (NLM) has developed many no-cost LEP-friendly health information resources for a variety of age and language groups. In addition, there are government agencies and authoritative non-profit organizations creating free health information content to address the linguistic diversity of the communities you serve. (Resources)

Spanish is the predominant language – other than English – spoken in the MidContinental Region (MCR) though you may see communities with strong German, French, Vietnamese, Chinese, Navajo, or Algonquian populations[1]. The following table shows the LEP populations ages 5 and over in the MCR[2]:


Supporting LEP Person’s Access to Health Information

Public Libraries

Public libraries are highly focused on serving their local constituency, and continue to be an excellent conduit for transferring health information to community members with trained staff and technology infrastructure. For many citizens, the public library is the go-place for health information.


  1. What languages are represented in your community?
  2. What health information resources do you have access to in other languages?
  3. What organizations in your community might you work with to assist a non-English speaker with health information?


  • Local health departments, emergency responders, police and fire departments, clinics, hospitals, schools, churches.

K-12, Colleges, and Universities

Students whose first language is not English require language supports in order to meaningfully participate in school. Schools must also adequately communicate with limited-English-speaking parents about important school-related information in their preferred language.[1]

If you work in a K-12 setting, educators can utilize these resources in the classroom to help introduce, reinforce, and supplement health and science curricula; and school nurses can use them to enhance communication with students and parents. Here are the percentages of school-aged children of immigrants in the MCR[2]:

  • Colorado        24.30%
  • Kansas            28.52%
  • Missouri         29.67%
  • Nebraska        30.29%
  • Utah                29.06%
  • Wyoming        dataset too small for percentage

If you work with colleges or universities offering allied health or health sciences degrees, students would benefit from knowledge of these resources as future healthcare workers.


  1. What languages are represented in your school district, college, or university?
  2. What health information resources do you have in other languages?
  3. Who in your institution or community would benefit from these resources?
  4. Do you have access to trained interpreters? If so, what languages?


  • Teachers, faculty, school nurses, students, parents, administrators.

Medical Care and Public Health

Communication problems are the most common cause of serious adverse events with LEP patients and clients. They are at higher risk for longer hospital stays, readmission, misdiagnosis, and inappropriate treatment.


  1. What languages are represented in communities served by the medical care or public health staff?
  2. What health information resources do you have in other languages?
  3. Who in your institution or community would benefit from these resources?
  4. Do you have access to trained interpreters? If so, what languages?


  • Clinical staff, compliance staff, volunteers, case workers, patient navigators.

[1] U.S. Department of Education, Office for Civil Rights. Title VI Enforcement Highlights, July 2012, p. 13. Accessed July 18, 2014.

[2] Urban Institute, Children of Immigrants Data Tool, 2011. Accessed July 21, 2014.

[1] See the Resources section for multi-language and language identification tools.

[2] Authors’ tabulations from the US Census Bureau’s 2010 American Community Survey (Table B16001. Language Spoken at Home by Ability to Speak English for the Population 5 Years and Over). Accessed July 18, 2014.

[1]Migration Policy Institute, Limited English Proficient Population of the United States. Accessed July 18, 2014.

Announcing new service: Lynx

By now, many Colorado libraries are taking advantage of a new package of EBSCO databases. The package contains a diverse range of electronic resources (including full-text and multimedia assets) to suit school, public library and academic library needs.
This new package represents a good value for libraries. But databases alone are insufficient. This is why the State Library and the Colorado Library Consortium (CLiC) are pleased to formally announce a new joint SERVICE named Lynx. Continue reading ‘Announcing new service: Lynx’

New CVL Is Right Around The Corner

After more than a year of hard work by the Networking & Resource Sharing team of the State Library, the new Colorado Virtual Library (CVL) will be launched sometime during the week of 10/10 with 3 content collections (and more to come):

  • Colorado Histories
  • Tech Help
  • Tools for Tough Times

There is much more work to be done, because the CVL will never truly be done. It is designed to be ever-changing, evolving, and improving. We hope you love it, but of course are open to constructive criticism.

Stay tuned!

AIRS Announces 2011-12 Statewide Package

Posted on behalf of Linda Sturgeon, AIRS Chair—–
The AIRS Committee (Acquisition of Information Resources Statewide) has negotiated with OCLC and EBSCO to provide selected databases covering general, business and K-12 information at a special Colorado statewide rate.
For the coming fiscal year (July 1, 2011 – June 30, 2012), the statewide package of databases has been finalized. Details about the FY11-12 program are available on the AIRS web site. The AIRS Committee was able to keep pricing stable for FY2011-2012 even while many libraries with shrinking budgets were forced to drop out last year and may be dropping out during the coming year.

Online Twitter Directory for Libraries – Add Your Name!

The State Library has put together a Twitter directory for the Colorado library and education community, and we invite you to add your Twitter username to the list.

This directory is an online version of the content that was previously kept in an ever-growing spreadsheet, for those of you who remember it. Anyone on that spreadsheet has automatically been added to the new directory.

Please check out the directory and look for your Twitter username. If you don’t see it, you may add it by following the Submit an Account link at the top of the page. To edit or remove your information from this directory or to pass on any comments or suggestions, please email Michelle Gebhart. And don’t forget to search for colleagues; this new site makes it easy to search by username or category.Twitter-Icon

More resources on Twitter can be found on the Colorado State Library website, and for “newbies,” the Colorado Libraries 2.0 website offers a Twitter tutorial.

Understanding Genetic Conditions

“If one of my parents or another close family member has cancer, does that mean I will eventually inherit that diagnosis too? That is a common question and to assist with answering that and many other questions about genetics and cancer, I recommend an excellent resource.  Genetics Home Reference (GHR) is a free product created and managed by the U.S. National Library of Medicine (the world’s largest medical library,) Bethesda, MD and is a consumer-friendly online resource to genetic conditions.  The user may browse more than 500 genetic conditions, diseases and syndromes.  They also may search in Genes by symbol, full name, group or classification in its databank of more than 700 genes.  Information about the 23 pairs of chromosomes may be found and for each specific one they provide content to answer such questions as  “What is that chromosome and how are changes in it related to health conditions;  is there a standard way to diagram that chromosome?” They present a diagram beneath to illustrate.  They also provide answers to questions such as “What is DNA; what is a chromosome; what is mitochondrial DNA and can changes in chromosomes affect health and development?”

Other features in GHR include a handbook with sections such as Cells and DNA, How Genes Work, Gene Therapy and many more.  The Glossary contains an alphabetical directory of hundreds of definitions related to genetic conditions.  In addition they feature a Resource and Patient Support web page that has general interest links to websites including genetics education, Human Genome Project, policy/ethics and health literacy.  Health professionals may find links under Resources to the NCI’s PDQ: Cancer Genetics Overview, Gene Tests, Online Mendelian Inheritance in Man (OMIM), PubMed Medical Genetics Searches, and much more.  Patients and families may click on links to websites such as Ask the Geneticist and the Genetic Alliance’s Understanding Genetics: A Guide for Patients and Professionals.

If one does a simple search of the alphabetical list under “Conditions” and click on “breast cancer,” they will find a description of the disease, its frequency, specific genes related to the disease such as BRCA1, BRCA2, PTEN, STK11, TP53 and others, with a direct link from each gene symbol to its web page with detailed information.  They also provide information on breast cancer inheritance and links for web pages on the diagnosis, management or treatment of breast cancer.  A simple search, in the search box at the top, on “cancer,” brings up 695 results including condition summaries, specific genes, definitions, chromosome summaries, and gene summaries all related to cancers.  Clicking on the “Genetic Conditions” tab at the top on the home page and then clicking on “Cancers” in their list of diseases by categories, results in a large list of genetic related cancers.

Patients, consumers and health professionals will find this a rich resource for learning about genetic conditions. The National Library of Medicine has a wealth of databases and electronic resources (All Free!) for health professionals and the public: .  For questions about Genetics Home Reference (GHR) or NLM’s other biomedical resources, contact Dana Abbey at 303-724-2110 or

NoveList meets VuFind at Marmot

We’ve done a nice job integrating NoveList content with the new “VuFind at Marmot” OPAC. Take a look at Ender’s Game by Orson Scott Card.
“Similar Titles” in the upper right is NoveList content in the OPAC, right where readers can use it, instead of parked off on the side in some database of titles that may or may not be in this library catalog.
“Also in this series” shows this title’s position in a series. Most importantly, this is a proper series list from the NoveList database rather than an attempt by OPAC software to make the best of series data which is typically dicey in even the best bibliographic records.
“Similar authors”, under jacket art on the upper left, is more NoveList content.
These NoveList features are now available to open source developers like us as the “NoveList Select” add-on product. We’re still working on the print function, so a page like this will print nice instead of goofy. Watch for that improvement in a couple weeks.

The State Library at CAL

The Colorado State Library will have a variety of pre-conferences and workshops at the 2009 CAL Conference.  Don’t forget to stop by our booth on Friday and Saturday in the Exhibits Area. We would love to:

  • * Share with you the latest services and resources we can offer Colorado libraries
  • * Hear how libraries have transformed your lives

CSL at CAL 2009 – Schedule (PDF)

Track your meds – online

Posted on behalf of Dana Abbey.

Did you know that adults in the U.S. average 11.5 prescriptions per year, and persons over 60 average 15.6? Pillboxbeta, provides an easy way to visually identify an unknown tablet or capsule medication based on imprint, shape or color.

The National Library of Medicine (NLM) is developing two free online tools to assist in identifying and tracking prescriptions and over-the-counter medications. Continue reading ‘Track your meds – online’