Category Archives: Library

Library, Notes from the library, November 2016

Notes from the Library…Finding Chemical & Drug Information: Part II

Last month, I wrote about methods and resources for finding chemical information; this month, I will do the same for drug information.  All the resources listed below are accessible from the ‘Find Chemical & Drug Information’ page in the Sackler School Biomedical Sciences Research Guide.

The following resources provide information on the clinical use of drugs (enter your Tufts username and password for off campus access):

AHFS Drug Information: From the American Society of Health-System Pharmacists, this book offers evidence-based information on the therapeutic use of drugs.  The entry for each drug covers topics ranging from dosage and administration to lab test interference, and provide pharmacokinetic and pharmacodynamic information.

DynaMed Plus: This point-of-care resource provides evidence-based summaries for thousands of clinical topics.  It includes drug monographs with detailed information on dosing, interactions, toxicology and pharmacokinetics.

Lexicomp Online: A point-of-care resource dedicated to drug information.  Monographs have information on: dosing and administration; warnings and precautions; pharmacogenomics; and pharmacology.  Lexi-Tox, a separate database within Lexicomp Online, provides information on the presentation, treatment and pharmacology of a variety of toxins.

For U.S. regulatory information:

U.S. Food and Drug Administration: The agency responsible for ensuring the safety and efficacy of drugs, vaccines and other biological products.  Search Drugs@FDA to find official information, such as active ingredients, marketing status and approval letters, about approved drugs and biological products.  The Orange Book, also known as Approved Drug Products with Therapeutic Equivalence, is an easy way to view a list of equivalent approved drugs.  Entries have a link to patent and exclusivity information.

For information on the toxicology of drugs and chemicals:

TOXNET: Collection of databases from the National Library of Medicine.  Two TOXNET databases, TOXLINE and Developmental and Reproductive Toxicology (DART), index the scientific literature on the biochemical, pharmacological, physiological and toxicological effects of drugs and chemicals.  The suite of TOXNET databases also includes the Hazardous Substances Data Bank and the Comparative Toxicogenomics Database.

Library, October 2016, PubMed Tip of the Month

PubMed Tip of the Month: Searching for Chemicals & Drugs

Use the common name: PubMed is not primarily a resource for chemical information, so forget what I said in my column about not searching by name. Enter the common name for a chemical, drug or other substance in the main search box.  Scroll down the results page to the ‘Search Details’ box in the right-hand column to check to see if the name you entered matched a MeSH term.

Use the standardized name: To search by standardized name in PubMed, replace any brackets or parentheses with a hyphen (if not already present). You can either spell out or enter the symbol for Greek characters such as β.

To search for: 1-[(3,5-dichloro)-2,6-dihydroxy-4-methoxyphenyl]-1-hexanone

Enter: 1-3,5-dichloro-2,6-dihydroxy-4-methoxyphenyl-1-hexanone

Search the MeSH database: Didn’t find what you were looking for when you searched by name? Try searching the MeSH database.  Select ‘MeSH’ from the dropdown menu to the left of the main search box.  Enter a component of the name.

To search for: alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid

Enter: isoxazolepropionic

Try a unique identifier: In either PubMed or the MeSH database, enter the CAS RN or FDA Unique Ingredient Identifier (UNII, identifier assigned by the FDA Substance Registration System to substances in drugs, biologics, foods and devices) for a substance. If searching PubMed, then enter the identification number, followed by the field tag ‘[RN]’.  For example: 69-93-2[RN].  I find this method of limited utility, partly because CAS RNs have not been added to MeSH since 1998.

Library, October 2016, On the Shelf

On the Shelf…

For work…

Lab Math

Lab Math, by Dany Spencer Adams

Location: HHSL Book Stacks, Sackler, 5th Floor, QA40.A34 2014

Authored by a Tufts biology professor, this is a handbook of measurements, calculations and quantitative skills for use at the bench. The book describes various mathematical principles, basic statistics, and tasks involving numbers, such as calibrating lab equipment and making solutions.

And leisure…

I Contain Multitudes

I Contain Multitudes: The Microbes Within Us and a Grander View of Life, by Ed Yong

Location: HHSL Book Stacks, Sackler, 5th Floor, QW 4 Y55 2016

This well-reviewed book, by the science writer Ed Yong, explores the relationships between animals and the microbes that live in, on, and around them.

Library, Notes from the library, October 2016

Notes from the Library…Finding Chemical & Drug Information: Part I

In the course of your research, you may need information about chemical properties, structures and reactions, and articles from the chemical, biochemical and drug literature.  In this month’s column, I will cover resources for finding chemical information.  Next month, I will discuss drug information resources.

First, a few tips on searching for chemical property or reaction information.  Different resources use different naming conventions for chemical substances.  Thus, searching by substance name is the least efficient way to find chemical information.  The following approach is recommended:

  1. Structure: Utilize structure editor in resource to draw substance. Most effective method of searching, but available in all resources.
  2. Chemical Abstracts Service Registry Number (CAS RN): The Chemical Abstracts Service (CAS) of the American Chemical Society assigns unique identification numbers to chemical substances, e.g. 1007-32-5. Highly accurate method of searching, but not 100%, particularly in databases not produced by CAS.
  3. Molecular Formula: Effective search method, but may retrieve a long list of results.

Now that you know a little about how to search for chemical information, you need to know where search.  All the resources listed below are accessible from the ‘Find Chemical & Drug Information’ page in the Sackler School Biomedical Sciences Research Guide: http://researchguides.library.tufts.edu/c.php?g=275784&p=2706564.

Here are a few resources for finding property information:

CRC Handbook of Chemistry & Physics: The electronic version of this classic reference book provides tables of property data for organic, inorganic and biochemical compounds.  To search by structure, property, or molecular formula, click the flask icon in the upper right corner of the homepage.

Knovel Critical Tables: Collection of interactive tables that provide physical, thermal and electrical properties of chemicals compounds and solvents.  Good for approximate values, but tables do not include information about conditions under which properties were measured.  Search by CAS RN; structure search not available.

Merck Index Online: Encyclopedia of chemicals, drugs and biologicals with links to reference articles in PubMed.  Good for quickly finding structure, property and toxicity information.  Search by structure, CAS RN, molecular formula or name.

For chemical literature, as well as property and reaction information, try these databases:

Reaxys: Database of references to chemical journals, books, conference proceedings and patents.  Comprehensive indexing that extracts property, bioactivity, reaction and synthesis data from the literature means you can get experimentally-derived property data for organic, inorganic and organometallic substances without having to sift through the studies yourself.  Good for detailed information culled from the chemical literature.  To find property information, select the ‘Substances, Names, Formulas’ box on the Reaxys homepage.  Search by structure, CAS RN or molecular formula.

SciFinder: This Chemical Abstracts Service (CAS) database offers property data on organic and inorganic molecules, proteins and polymers as well as experimental procedures, conditions, yields and solvents for chemical reactions.  SciFinder also provides references to the chemical, biochemical and chemical engineering literature from the CAplus and MEDLINE databases.  Registration required to use this database.  To register, follow instructions on the page that opens from the link above.

Library, Notes from the library, September 2016

Notes from the Library…New & Noteworthy

A warm welcome to all students! Over the summer, a few changes occurred at the library, notably…

New study spaces: In an ongoing effort to make the library a functional space for all students, the lounge behind the café on Sackler 4 (adjacent to the bathrooms and bridge to the dental school building) has been converted into the Hirsh Library Reading Room. The construction of a glass wall with a sliding door, and installation of new furniture and a wall monitor, have transformed this space into a semi-quiet, semi-private place available to anyone for individual or group study. Standing desks have been added to the 5th and 6th floors of Sackler, and new study carrels have been added to the existing carrels on the 6th and 7th floors.

Business & Careers Collection: In response to a request from the Biomedical Business Club, we have created a special place for our business and career books. Located behind the seating section next to the Library Service Desk on Sackler 4, the Business & Careers Collection features books on life after grad school, scientific communication and leadership. Can’t find what you’re looking for? Take a look at the Biomedical Business & Career Resources guide for e-books and print books located at other Tufts libraries, or recommend a purchase.

Business and Careers Collection
Business & Careers Collection on the 4th floor of the Hirsh Health Sciences Library.

Software: Sometime in the upcoming months, the Prism software that is currently on the computers in Sackler 514 will be removed from those computers and installed on the computers in Sackler 510 and the PC laptops available for checkout at the Library Service Desk. Hopefully, this will provide more options for using this program. As long as a class is not in session, the library computer labs (Sackler 510 and 514) are open for anyone to use. Check the white board behind the IT Service Desk on Sackler 5 for the weekly class schedule. A complete list of available on the library’s computers and laptops is available at: http://hirshlibrary.tufts.edu/it-support/software.

Printing: New laser printers have been installed at the printing stations on the 4th and 5th floors of Sackler. New swipe stations will be installed in the upcoming weeks. More importantly, there has been a change in how you send documents to the printers. The box that appears when you print looks the same, but instead of entering a name and password for your print job, you enter your Tufts username (e.g. jsmith01) and a name for the print job. This subtle change means that now when you swipe your card at the printer, you will see only your own documents. If you have questions about printing, then ask for help at the Library Service Desk on Sackler 4.

Library, PubMed Tip of the Month, September 2016

PubMed Tip of the Month: PubMed Labs

PubMed Journals

PubMed Labs is the National Center for Biotechnology Information’s (NCBI) innovation incubator. PubMed Labs releases early versions of tools, features and content for anyone to experiment with and comment on. One recent development is PubMed Journals, a site where you can browse and follow journals, see ahead of print articles, and view trending articles and updates, such as retractions. NCBI is considering how to push content from the site to users. The news feed in PubMed Journals links studies mentioned in the mainstream media directly to the reference article. I have not really explored the site (it was just announced on September 7th), but it may develop into a nice way to monitor journals contents and news via your My NCBI account.

 

Library, On the Shelf, September 2016

On the Shelf…

For work…

BrowZine

Electronic resource: BrowZine

Location: Download from Apple or Android app store, or access online at: https://browzine.com/

BrowZine provides direct access to the library’s electronic journals, allowing you to browse full contents of current and older issues, create a personal bookshelf, and save and download articles for offline reading.

To get started:

  1. Download and open the app on your Apple, Android or Kindle Fire device, or go to https://browzine.com/.
  2. Choose Tufts University from the list of available libraries.
  3. Enter your Tufts username and password.

And leisure…

Stories from the Shadows

Stories from the Shadows: Reflections from a Street Doctor, by James J. O’Connell

Location: HHSL Book Stacks, Sackler, 5th Floor, WA 300 O18s 2015

A collection of stories and essays by the president of Boston Healthcare for the Homeless Program; this year’s common reading book for the School of Medicine. The author will speak at 4 PM on Monday, September 12th in the Sackler Auditorium.

Library, On the Shelf, Summer 2016

On the Shelf…

For work…

Experimental Design for Biologists

Experimental Design for Biologists, by David Glass

Location: HHSL Book Stacks, Sackler, 5th Floor, QH 323.5 G549e 2014

This handbook is designed to teach the fundamentals of experimental design.  The author, who is the executive director of the Muscle Diseases and Aging Initiative at the Novartis Institute for Biomedical Research, held a workshop on campus in May.

And leisure…

The Summer Before the War

The Summer Before the War, by Helen Simonson

Location: HHSL Leisure Reading, Sackler, 4th Floor, Fiction S611s 2016

Set in an English village on the cusp of World War I, this novel tells the story of a woman selected to be the first female Latin teacher in the local school.  A little ponderous and predictable, but an easy summer read.

Library, Notes from the library, Summer 2016

Notes From the Library…Author Identifiers

What are author identifiers?

An author identifier is a unique identifier that distinguishes one researcher from another, eliminating confusion in scholarly publication and grant funding.

Why do we need author identifiers?

If you have ever tried to do an author search a database, then you know how difficult it can be to find all articles by a particular author.  An author may have a common surname, publish under variations of the same name, change their name, or different geographical/cultural conventions for reporting their name.  Affiliation and field of study relieve some of the ambiguity associated with author names, but inclusion of this information in a search does completely eliminate the problem.  Two authors with the same name may work in the same field.  Like author names, there are often multiple ways to list the name of a department, school or university, and affiliations change as an author moves from one institution to another.  Moreover, some databases only provide the affiliation of the first author, or allow an author to list only one affiliation.  PubMed/MEDLINE did not include affiliation for all authors until 2014.  For these reasons, a simple search for articles by one author can easily become complicated.

What options exist for author identifiers? 

Over the past few years, one author identifier system has emerged as the frontrunner: Open Researcher and Contributor ID, or ORCID (http://orcid.org/).  ORCID is an open, non-profit community effort that provides unique persistent digital identifiers for researchers.  ORCID partners and members include universities, commercial research organizations, publishers, professional societies and funders, such as Nature Publishing Group and the National Institutes of Health (NIH).  Several publishers offer the option of including an ORCID ID when submitting an article, and some plan to make an ORCID ID mandatory for corresponding authors (http://blogs.plos.org/plos/2016/01/author-credit-plos-orcid-update/).

A few publishers have their own author identifier system.  For example, when researchers register for Thomson Reuters free online community, ResearcherID, they are assigned a unique alphanumeric identifier that can be used to track their publications and get citation metrics in Web of Science.  Authors of articles indexed in Scopus, an Elsevier database, are automatically assigned a unique identification number.

This sounds like one more account to maintain, do I really need an author identifier?

Yes, an ORCID ID is another account to create and maintain.  However, ORCID has gained traction amongst universities, publishers and funders, and if this pattern continues, then hopefully it will alleviate author ambiguity.

Any researcher can register for a free ORCID ID.  You can use your Tufts username and password to register for, or link to an existing, ORCID ID.  To get started, go to this page: https://orcid.org/signin.  Choose to sign in using your institutional account and search for Tufts.  You will be prompted to enter your Tufts username and password.  Once you do so, select the ‘Register for an ORCID ID’ link.  For more information about creating and managing your ORCID account, see: http://support.orcid.org/knowledgebase/topics/32827-using-the-orcid-registry.

Library, PubMed Tip of the Month, Summer 2016

PubMed Tip of the Month: Saving Searches and Creating Alerts

You can save searches to your My NCBI account (see PubMed Tip of the Month for March 2016), and choose to receive daily, weekly or monthly emails when new articles meeting your search criteria become available.  To save a search, simply click the ‘Create alert’ link under the PubMed search box on any results page.  If you are not already signed in to your My NCBI account, then you will be prompted to do so.  Name your search and select whether or not you wish to receive email alerts.  Once you have saved a search, it will appear in the Saved Searches box in My NCBI, where you can see a list of your searches, the last time you ran a search and any new articles that have been added to PubMed since you last ran the search.  Saving searches saves time and frustration, and allows you to remain current on articles in your area of research.

Create alert link on PubMed results page
PubMed Create Alert