Category Archives: Notes from the library

Notes from the Library…Approaching the Literature Review

Whether you are preparing a literature review for your thesis, a journal article, or grant application here are a few tips to help you get started and stay organized:

  1. Determine what information you need.

Why are you searching the literature?  Are you developing a research project and want to know what has been published about your topic?  Are you interested in literature on a particular method?  Are you preparing a grant application or manuscript to submit to a journal?  The answers to these questions will help you decide where to search, and whether or not the information that you find is what you need.

  1. Develop a focused question.

If you enter a few words, or a phrase, into a database, then you are likely to retrieve either a very large or very small number of results.  Developing a focused research question helps you construct a search strategy that will retrieve a precise set of results.  If you have a complex topic, then you may have multiple questions (and searches).

  1. Choose your resources.

Once you have determined what information you need and developed a focused question, then you are ready to choose your resources.  Choosing which resources to search can be overwhelming.  While PubMed is often a good place to start, think about where, and by whom, information about your topic is likely to be published, and what type of information you need (e.g. journal articles, conference proceedings, patents).  What disciplines might have a perspective on your topic?  What organizations, associations, institutes, companies or agencies investigate issues related to your topic?

Bibliographic databases, such as PubMed and Web of Science Core Collection, are organized collections of references to published literature (e.g. journal articles, conference abstracts, books).  When you are deciding which database(s) to search, consider the subjects, dates, and types of literature the database covers, as well as the search platform.  For example, MEDLINE, the database that is the principal component of PubMed, is also available through the Ovid search platform.  While PubMed and Ovid MEDLINE are similar, small differences in the content and search features of these two databases means that you will retrieve different results.  See the Sackler School Biomedical Sciences Research Guide for a list of biomedical database, or ask me!

  1. Create personal accounts.

You may think that you are finally ready to start searching.  Not quite.  Create a personal account with the databases, or platforms (e.g. Ovid, Web of Science), that you plan to search.  A personal account allows you to save searches and sets of results, and receive email notifications when new results matching your search criteria become available.  Unfortunately, you have to create a separate accounts for each database or platform, but it is a good idea to do so for the resources that you use frequently.  At the very least, I suggest that you create a My NCBI account, which is the personal account associated with PubMed and other National Center for Biotechnology Information (NCBI) databases, such as Gene and Protein.  See the March 2016, May 2016, summer 2016 and December 2016 PubMed Tip of the Month posts for more information on creating and using a My NCBI account.

  1. Use a citation manager.

Choose a citation manager before you embark on a literature review.  Citation managers allow you to organize and store your own collection of references, and insert formatted citations and bibliographies into documents.  Contact me ( if you need assistance selecting or using a citation manager.

  1. Document your search methods.

Get into the habit of documenting the parameters of your search, including: the databases that you searched; the platform on which you searched (e.g. Ovid, Web of Science, etc.); years covered by the database; complete search strategies; any limits applied, such as year, age, language; and the date on which you ran the searches.  While this information is not typically required for a manuscript (unless, of course, you are doing a systematic review, meta-analysis or scoping review), or grant application, a literature search is part of your research and should be recorded as you would any other experiment.  Doing so saves you considerable time and effort if you need to replicate the search in the future.

Notes from the Library…Software on Library & Personal Computers

We often get asked about what statistical and data analysis programs are installed on the library’s computers, or available for installation on personal computers.  Here is a summary of the computers available at the Hirsh Health Sciences Library, and a chart indicating which statistical and data analysis programs are installed on these computers and available to students:

  • Public Computers: Desktop computers on the 4th and 5th floors of the Sackler; available for anyone to use.
  • Computers labs: Desktop computers in Sackler 510 and 514; available for use when not reserved for a class (check schedule on white board behind Tufts Technology Service Desk on 5th floor of Sackler). All computers in both labs were recently replaced.
  • Laptops: Mac and PC laptops available for checkout at the Library Service Desk on the 4th floor of Sackler; available for students, faculty and staff to checkout for 4 hours.


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.

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:

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.

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:

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.

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 (  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 (

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:  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:

Notes From the Library…Measuring Research Impact: Altmetrics

What are altmetrics?

The graduate student who coined the term ‘altmetrics’ in a 2010 tweet has defined altmetrics as “the study and use of scholarly impact measures based on activity in online tools and environments” (Priem, 2012).  The term is often used to describe any alternative, non-citation based measure of research impact, such as:

  • Number of times an article has been viewed or downloaded from a journal website, or database
  • Number of times an article has been exported to a citation manager
  • Number of times an article has been shared via email or on Twitter, Facebook or other social media sites
  • Mentions in the mainstream media

How are altmetrics different from traditional citation metrics?

Altmetrics are generated rapidly, as opposed to citations which take time to accumulate.  Altmetrics capture data from a variety of sources, both within and beyond the scholarly community, versus traditional citations, which only capture information from published scholarly works.  Altmetrics also recognize research products beyond the peer-reviewed journal article, such as data sets and code (Khodiyar, Rowlett and Lawrence, 2014).

Where can I find altmetrics? 

Look for altmetrics when viewing an article on a journal’s website:  Many publishers, such as PLoS, provide the number of times an article has been viewed, shared, saved or download from their site.

Look for an Altmetric score: Altmetric ( monitors online activity for mentions of scholarly articles.  The collected data is used to calculate an Altmetric score, a measure of the quality and quantity of attention that an article receives.  A recent article in the Annals of Emergency Medicine describes how the Altmetric score is calculated, and the potential impact and limitations of this score.

Install the free Altmetric bookmarklet to get stats for an article you are reading online, or look for an Altmetric score Altmetric Score when viewing articles on:

  • A journal’s website
  • JumboSearch: Copy and paste the title of an article into our library’s search tool, JumboSearch ( If an Altmetric score is available for the article, then you will see an Altmetric Box icon  below the abstract.
  • Scopus: Scopus is a database that indexes journal articles, conference proceedings and books from the sciences, social sciences, art and humanities. When viewing an article abstract in Scopus, look for the Metrics box in the right-hand column.

Impactstory: Impactstory ( is a web-based tool that gathers metrics on research products (articles, data sets, etc.) from a variety of sources, including Facebook, Google+, Twitter and PubMed Central.  Impactstory profiles display raw numbers as well as badges that indicate how a product has performed compared to similar products in the same discipline.  Individuals with an ORCID (Open Researcher and Contributor ID) can create an Impactstory profile for free.

So, what do these all this mean?

Altmetrics are an evolving area of use and study.  Altmetrics provide a more nuanced picture of how articles are being used, and therefore compliment, not replace, traditional measures of research impact.  For more on altmetrics, see ‘Research Impact: Altmetrics Make their Mark’ from Nature, and ‘Rise of “Altmetrics” Revives Questions about How to Measure Impact of Research’ from The Chronicle of Higher Education.

Notes from the Library…Measuring Research Impact: Author Metrics

At some point in your career, you will be asked to demonstrate the impact of your work.  You may be asked to do this for a grant application, progress report or renewal, or on a CV for a job application, promotion, tenure or performance review.  Traditionally, this has meant providing a list of publications you have authored, and perhaps the number of citations that those publications have received.  Alternative methods of demonstrating research impact will be discussed in a later post.

How can I create a list of publications that I have authored?

You can do an author search in any bibliographic database, such as PubMed (see this month’s PubMed tip), Web of Science, or Scopus.  It may be necessary to search more than one database to generate a complete list.  Once you have run the search, you can save the results within the database (for example, send results to the My Bibliography section of My NCBI in PubMed) or export them to a citation manager.

Where can I find how many times my articles have been cited?

Several databases provide the number of times an article has been cited.  Traditionally, Web of Science has been used to obtain citations counts; recently, Scopus and Google Scholar have emerged as alternatives to Web of Science.  Each resource provides a different citation count because each indexes (or, in the case of Google Scholar searches) a different set of journals over a different period of time.  Web of Science remains the best choice for authors with a long publishing history because Scopus indexes articles published from 1996 to the present (although older content is being added).  Google Scholar is a moving target because it “generally reflects the state of the web as it is currently visible to our search robots and the majority of users” ( – citations).  Regardless of the source that you choose, it is important to always cite that source.

How can I create a citation report in Web of Science or Scopus?

A Web of Science or Scopus citation report provides aggregate statistics for a set of search results.  See the library’s ‘Measuring your Research Impact’ guide for step-by-step instructions on generating a citation report in Web of Science and Scopus.

What is the h-index? 

You may have heard of, or noticed on your citation report, a metric called the h-index.  The h-index is the number of papers (h) in a set of results that have received h or more citations.  For example, an author with an h-index of 10 has 10 articles that have each received 10 or more citations.  This metric is an attempt to measure both quantity (number of publications) and quality (number of citations).  Therefore, it is considered a measure of the cumulative impact of an author’s work.  For a recent discussion of the h-index and other measures of academic impact, see Anne-Wil Harzing’s ‘Reflections on the h-index’:

Notes From the Library…Citation Managers

What is a citation manager?

At their most basic, citation managers are software programs that allow you to store and organize your references, and insert formatted citations and bibliographies into documents.

What citation managers are available?

There are several citation managers available; the library supports EndNote (and EndNote online), Mendeley, RefWorks and Zotero, which are all popular and well-established programs. Other available programs include Papers, Sente and Paperpile.

Which citation manager do you recommend?

It depends! While all citation managers have the same basic features, some citation managers are better for storing and annotating PDFs, working on multiple devices or computers, and collaborating with others. If I had to choose one, then I would recommend EndNote. This robust, widely-used citation manager has a bit of a steeper learning curve but several nice features such as automatically finding full text for references, annotating PDFs on your computer or mobile device, and thousands of citations styles.  If you need help choosing a citation manager, then ask your colleagues what they are using, or ask me (

How can I get a citation manager?

I will focus on the four programs that the library supports: EndNote, Mendeley, RefWorks and Zotero. All of these programs works on both Macs and PCs. An EndNote app is available for iPads; a Mendeley app is available for both Android and iOS devices.

EndNote: Available for installation on Tufts-owned or personal computer for anyone with a primary affiliation of student, faculty or staff in the Tufts White Pages. Bring your laptop to the Tufts Technology Services desk on the 5th floor of Sackler (Monday-Thursday 9AM-6 PM, Friday 9AM-7PM) or call 617-627-3376 for remote installation.

Mendeley: Freely available to anyone. Create account and download at:

RefWorks: Available to Tufts students, faculty and staff. Create account at:

Zotero: Freely available to anyone. Create account and download at:

Notes from the Library…Finding Protocols & Methods

Methods CoverIn December, I mentioned Journal of Visualized Experiments (JoVE), a journal that publishes experimental techniques in video format. In addition to JoVE, there are several resources for techniques, protocols and methods:

  • Bio-Protocol: Open-access, peer-reviewed e-journal established by a group of Stanford researchers. Publishes detailed biomedical protocols for cancer biology, immunology, molecular biology, neuroscience and more. Freely available at:
  • Cold Spring Harbor Protocols: Publishes both well-established and cutting-edge research methods in cell, developmental and molecular biology, genetics, protein science, immunology, etc. Available online through Tufts Libraries:
  • Methods: Journal that focuses on developing techniques in the biomedical sciences. Each topical issue is comprised of invited articles by specialist authors. Available online through Tufts Libraries:
  • Protocol Exchange: Open repository for the deposition and sharing of protocols, from Nature Protocols. Protocols are not peer-reviewed or edited, but free to use or comment upon. Freely available at: