All posts by Laura Pavlech

April 2016, Library, Notes from the library

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” (https://scholar.google.com/intl/us/scholar/citations.html – 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’: http://www.harzing.com/publications/white-papers/reflections-on-the-h-index.

April 2016, arts & culture, Library, On the Shelf

On the Shelf…

For work…

Essential Science Indicators

Electronic Resource: Essential Science Indicators

Location: Search for ‘Essential Science Indicators’ in Databases search box on the HHSL homepage (http://hirshlibrary.tufts.edu/).

This research analysis tool, integrated with Web of Science, provides performance statistics for authors, journals and articles for 22 subject fields.  Essential Science Indicators can answer questions like: who are the most-cited authors in my field; what journals publish the top papers in my field; what is the average number of citations per article in my field; or what is the minimum number of citations that my article needs to receive to be in the 10% percentile in my field?

And leisure…

All the Light We Cannot See

All the Light We Cannot See, by Anthony Doerr

Location: HHSL Leisure Reading, Sackler, 4th Floor, Fiction D652

Winner of the 2015 Pulitzer Prize for fiction and numerous other awards, this book tells the parallel, and eventually intersecting, stories of a girl in France and a boy in the German army during World War II.

April 2016, Library, PubMed Tip of the Month

PubMed Tip of the Month: Author Search

Go to the Advanced Search Builder by clicking the ‘Advanced’ link under the PubMed search box.

Choose Author from the All Fields drop-down menu (just Author, not Author – Last, Author – Full, or any of the other options). Enter the author’s last name, followed by 1 or 2 initials with no intervening punctuation (for example: Jones EA). If you are unsure about the inclusion of the second initial, then do not include it.

If the author has a common last name, then you probably want to narrow your search by including an affiliation. To do so, choose Affiliation from the All Fields drop-down menu below the boxes where you have entered the author’s name. Enter the name and/or location of the institution with which the author is associated. Affiliation can become complicated if the author has been (or is currently) associated with multiple institutions, or the name of the institution has several possible variations. If the author has an uncommon last name, then first try searching without an affiliation.

Check the results to ensure that they authored by the person in whom you are interested.

If you have searched for your own name, then you can send the results to the My Bibliography section of My NCBI by clicking ‘Send to:’ in the top right corner of the results page.

Author Search in PubMed Advanced Search Builder
Author Search in PubMed Advanced Search Builder
Library, March 2016, Notes from the library

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 (laura.pavlech@tufts.edu).

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: https://www.mendeley.com/.

RefWorks: Available to Tufts students, faculty and staff. Create account at: https://www.refworks.com/refworks2/default.aspx?r=authentication::init&groupcode=RWTuftsU

Zotero: Freely available to anyone. Create account and download at: https://www.zotero.org/

Library, March 2016, PubMed Tip of the Month

PubMed Tip of the Month: My NCBI

My NCBI is a personalized account for PubMed and other National Center for Biotechnology Information (NCBI) databases, such as Gene and Protein. This account allows you to:

  • Save searches and receive daily, weekly or monthly email alerts when new articles meeting your search criteria become available.
  • Save collections of references; in the My Bibliography section, you can save references to articles that you have authored. Collections, including My Bibliography, can be made publicly available, providing you with a URL to share with colleagues or use in grant applications.
  • Change preferences for how your results are displayed in PubMed, and select favorite filters.
  • Manage compliance with the NIH public access policy in the My Bibliography section.
  • Utilize Science Experts Network Curriculum Vitae (SciENcv) to help you create biosketches for NIH and NSF grants.

To create an NCBI account:

Click the ‘Sign in to NCBI’ link in the top-right hand corner of any PubMed page (or, click here).

Click ‘Register for an NCBI account’ link, or sign in with a 3rd party option, such as Google or eRA Commons (recommended for NIH-funded investigators who do not currently have an NCBI account). Note, you cannot user your Tufts username and password as a 3rd party sign in option.

My NCBI Sign In
My NCBI Sign In
Library, March 2016, On the Shelf

On the Shelf…

For work…

Career Options for Biomedical Scientists

Career Options for Biomedical Scientists, edited by Kaaren Janssen & Richard Sever

Location: HHSL Book Stacks, Sackler, 5th Floor, W21 J35 2015

This books begins with a brief introduction of why PhDs should consider careers beyond traditional academic positions and then delves into the alternatives, including teaching at an undergraduate or liberal arts institution, management consulting or science policy.  Each chapter, authored by an individual working in the field, provides a description of the job options, required qualifications, and advice on applying and interviewing for positions in the field.

And leisure…

The Short and Tragic Life of Robert Peace

The Short and Tragic Life of Robert Peace, by Jeff Hobbs

Location: Tisch Tower Café, Tisch Library (Medford) 1st Floor, or request through BLC WorldCat (http://tufts.worldcat.org/oclc/872653974)

Recipient of many accolades, this book tells the story of a man from East Orange, New Jersey who studied molecular biophysics and biochemistry at Yale, but never quite managed to move beyond the neighborhood of his youth, and ultimately met an untimely death.  Written by his roommate at Yale, this book provides an intimate and thought-provoking portrait of a life.

February 2016, Library, On the Shelf

On the Shelf…

For work…

Henry Stewart Talks

Electronic Resource: Henry Stewart Talks – Biomedical & Life Sciences Collection

Location: Search for ‘Henry Stewart Talks’ in Databases search box on the HHSL homepage (http://hirshlibrary.tufts.edu/)

Video collection of seminar style lectures by leading scientists on the fundamentals and latest research in a variety of areas, including: cancer, cell biology, immunology and pharmacology. Separate subject area devoted to methods.

And leisure…

The Marriage of Opposites

The Marriage of Opposites, by Alice Hoffman

Location: HHSL Leisure Reading, Sackler, 4th Floor (http://library.tufts.edu:80/record=b2798246~S1)

Novel based on the life of Rachel Pissarro, mother of the Impressionist painter Camille Pissarro.

February 2016, Library, PubMed Tip of the Month

PubMed Tip of the Month: Searching for Methods

There are several techniques that can help you find methodology articles in PubMed:

  • MeSH Headings for Methodology: “Methods” and “Research Design” are MeSH headings. You can try combining these terms with MeSH headings or keywords for your topic.
  • MeSH Headings for Particular Technique(s): Depending on your area of research, there may be a specific MeSH term for the category of techniques in which you are interested, e.g. “Cell Culture Techniques”.
  • Subheadings: Subheadings are used in conjunction with MeSH terms to further describe a particular aspect of that term. Subheadings follow a MeSH term, e.g. “Polymerase Chain Reaction/methods”[MeSH].  Subheadings can also be free-floated in a search, e.g. “DNA Replication”[MeSH] AND “Methods”[Subheading]. Two useful subheadings for methodology searches are “Isolation and Purification” and “Methods” (yes, Methods is both a heading and subheading).
  • Search Particular Journal(s): You may wish to narrow your search to one or more journals devoted to methodology. To do so, open the Advanced Search Builder by clicking the Advanced link below the PubMed search box. Select Journal from the dropdown menu and start typing the title of the journal in the adjacent search box. Choose the journal from the list of titles that appear. Enter a search term in the next search box to search the journal for articles on a specific topic, e.g. “Methods in molecular biology”[Journal] AND CRISPR.

PubMed Journal Search

February 2016, Library, Notes from the library

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: http://www.bio-protocol.org/.
  • 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: https://library.tufts.edu:443/record=b2164037~S1.
  • 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: https://library.tufts.edu:443/record=b2180868~S10.
  • 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: http://www.nature.com/protocolexchange/.
December 2015, Library, Notes from the library

Notes from the Library…Searching a Literature Database

What is a structured search?

A structured search is a systematic approach to finding references in a literature database using Boolean operators (AND, OR, NOT), keywords and controlled vocabulary terms, such Medical Subject Headings (MeSH). The goal of a structured search strategy is to balance recall and relevance (sensitivity and specificity).

How do I create a structured search?

The key to creating a good structured search is doing a little work before you go to a database.

Step 1: Develop a focused question

Like all research, a good search begins with a good question. Health professional students are taught to use the acronym PICO to construct clinical questions, where ‘P’ stands for patient or problem, ‘I’ for intervention, exposure or prognostic factor, ‘C’ for comparison, and ‘O’ for outcome. The idea is to create a well-defined question with multiple concepts, which helps you build a search strategy and evaluate the relevance of your search results. You may need to modify your question once you conduct a few searches.

Example: How do genetic variants in the vitamin D pathway affect breast cancer risk?

Step 2: Identify the key concepts of your questions.

Break down your question into its components. You can use the PICO acronym, or simply think: who, what, when, where, how.

Example: How do genetic variants in the vitamin D pathway affect breast cancer risk?

Breast cancer (concept 1)

Vitamin D (concept 2)

Genetic variants (concept 3)

Step 3: Choose keywords and standardized (controlled vocabulary) terms to describe each concept.

The goal of this step is to think of different ways to describe each concept. Keywords are natural language, the terms you use when discussing the concept with a colleague; consider acronyms, abbreviations and close synonyms. Standardized terms are from a controlled vocabulary, such as MeSH in PubMed; not all databases have a controlled vocabulary. The inclusion of multiple keywords and standardized terms ensures that you do not miss relevant articles on your topic, regardless of how an author or indexer described the topic.

Example: How do genetic variants in the vitamin D pathway affect breast cancer risk?

Breast cancer (concept 1): Breast neoplasms, mammary carcinoma…

Vitamin D (concept 2): Calcitriol, 1,25-dihydroxycholecalciferol…

Step 4: Using Boolean operators, search each concept separately then combine.

Boolean operators (AND, OR, NOT) are used to combine words and phrases in a search strategy. Use ‘OR’ to combine all keywords and standardized terms for one concept and run this search in a database. Once you have searched each concept separately, then combine different concepts using ‘AND’. Searching each concept separately allows you to identify any problems with particular terms before you build a complicated search, and gives you the flexibility of combining your concepts in different ways.

Example: (Breast cancer OR Breast neoplasm OR Mammary Carcinoma) AND (Vitamin D OR Calcitriol OR 1,25-Dihydroxycholecalciferol) AND (Genetic variant OR Polymorphism OR Gene frequency)

OPERATOR SEARCH RESULTS VENN DIAGRAM
AND Heart disease AND hypertension Articles containing BOTH heart disease and hypertension   boolean_and
OR Heart disease OR Hypertension Articles containing EITHER heart disease, hypertension, or both  boolean_or
NOT Heart disease NOT hypertension Articles containing ONLY heart disease, not hypertension  boolean_not

Step 5: Use filters to limit results.

Most databases have filters, such as date, language and publication type, that allow you to further narrow your results. Be judicious when using filters. If you have too many irrelevant results, then you need to modify your search, not apply more filters.

This sounds complicated and time-consuming, do I really need to construct a structured search each time I need to find articles?

Not necessarily. If you just need a few good articles, then you can enter a couple terms in a database and scan the results. However, if you are doing a literature search for your dissertation, qualifiers, or grant proposal, then it is a good idea to do a structured search. This strategy may require an initial investment of time, but it will (hopefully) save you the frustration of scrolling through hundreds of irrelevant results, or missing an important article. Of course, I am always available to help you construct a search strategy.