Category Archives: Library

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 Protocols are not peer-reviewed or edited, but free to use or comment upon.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/.
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

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.

December 2015, Events for Students, Library, Library Events

Upcoming Library Events (December 2015)

Library Fun Labs: Wintry Crafts

Gingerbread House
Credit: Carrie Stevens on Flickr, CC BY 2.0

Date: Friday, December 11th

Time: 12 PM – Supplies run out!

Location: Library Service Desk, Sackler 4

Create your own gingerbread house, snowflakes and other crafts. All supplies will be provided, just bring your creativity!

New Library Website!

Hirsh Health Sciences Library

The Hirsh Health Sciences Library’s new website will launch on Sunday, December 20th, so be prepared for a new look. The beta version of the new site is currently available: https://beta.hirshlibrary.tufts.edu/. Provide feedback on the beta site for a chance to win a gift basket. Winner will be announced when the new website is officially launched.

Extended & Holiday Hours

See HHSL website: http://www.library.tufts.edu/hhsl/about/hours.html

December 2015, Library, On the Shelf

On the Shelf (December 2015)

For  work…

Electronic Resource: Journal of Visualized Experiments (JoVE)

Location: Search for ‘JoVE’ in the Tufts Catalog Journal of Visualized Experiments(http://library.tufts.edu/)

JoVE is a peer-reviewed scientific journal that publishes experimental techniques in video format. The 8-15 minute, professionally-produced videos show standard and novel methods and procedures in the fields of cellular and molecular biology, bioengineering, immunology, medicine, neuroscience and more. A written protocol, with complete list of materials, accompanies each video article. So next time you are looking for information on how to perform a technique, search or browse JoVE.

And leisure…

Making Nature: The History of a Scientific Journal, by Melinda Baldwin Making Nature: The History of a Scientific Journal

Location: Tisch Book Stacks (Click ‘Request Item’ link at top of catalog record for delivery to Hirsh Health Sciences Library: http://library.tufts.edu:80/record=b2807116~S1)

This cultural account examines how editors, contributors, subscribers, and events have shaped the 150-year history of the journal Nature. Authored by a lecturer in the History of Science Department at Harvard University.

December 2015, Library, PubMed Tip of the Month

PubMed Tip of the Month: Advanced Search Builder

The PubMed Advanced Search Builder allows you to view your search history, search specific fields (e.g. title, author, abstract, journal, etc.), and combine searches using Boolean operators (AND, OR, NOT). To access the Advanced Search Builder, click on the ‘Advanced’ link below the PubMed search box.

PubMed Advanced Search Builder
Use Advanced Search Builder to view search history and combine searches.
Library, November 2015, On the Shelf

On the Shelf (November 2015)

For work…

Electronic Resource: Knovel

Location: Search for ‘Knovel’ in E-Resources Finder (http://www.library.tufts.edu/hsl/CentralDatabase/centraldatabase.html)

Collection of engineering and applied science reference books and databases. While this collection is designed for engineers, it does cover biochemistry, biotechnology and pharmaceutical topics. A unique search feature of Knovel allows you to find data within tables, graphics and equations. Two particularly useful resources in this collection are Knovel Critical Tables and the Biology Data Book. Knovel Critical Tables are a set of interactive tables of constants and physical, electrical and thermodynamic properties. The Biology Data Book is an old, but indispensable resource that provides basic biomedical data for biological substances and hundreds of organisms, including humans and common laboratory species.

And leisure…

Room cover

Room, by Emma Donoghue

Location: HHSL Leisure Reading Fiction D687

This 2010 novel, told from the perspective of a 5-year boy, tells the story of a woman and her son held captive in a single room. This riveting and thought-provoking book has recently been made into a movie.

-Laura Pavlech

Events for Students, Library, Library Events, November 2015

Upcoming Library Events (November 2015)

Open Workshop: Using Images

Wednesday, November 4th & Thursday, November 5th, 12-1 PM

Sackler 510

Registration: http://www.library.tufts.edu/hsl/education/workshops.html

This workshop will survey image collections licensed by Tufts and show you how to find images available in the public domain. Options for storing, displaying and citing images will also be discussed.

 

Open Workshop: Basic PubMed

Wednesday, November 18th & Thursday, November 19th, 12-1 PM

Sackler 510

Registration: http://www.library.tufts.edu/hsl/education/workshops.html

This workshop will review: the structure of PubMed; planning and executing a search; narrowing search results; finding full text and exporting citations into citation management programs, such as EndNote and RefWorks.

 

Fun Fridays: Elementary School Throwback

Friday, November 20th, Time TBD

Library Service Desk, Sackler 4

Come make hand turkeys and other crafts that will remind you of your younger days!

-Laura Pavlech

Library, November 2015, PubMed Tip of the Month

PubMed Tip of the Month: Clipboard (November 2015)

The Clipboard feature in PubMed allows you to temporarily store citations for review; items are deleted after 8 hours of inactivity. To place citations on the Clipboard, check the box to the left of an article title on the results page. Choose Clipboard from the Send to menu at the top of the page. Click Add to Clipboard. An icon will appear at the top of the page with a link showing the number of items on your Clipboard. I use this feature in a two-step review process. When I am satisfied that I have a good search, I do a first pass through the results, quickly scanning the title of each article and checking the box for any citation that may be relevant. I send these items to the Clipboard. Once I have completed the initial review, I go to the Clipboard, change the view from Summary to Abstract (menu at the top of the page) and read the abstract of each article to decide whether or not it is truly relevant.

-Laura Pavlech

Library, November 2015

Notes from the Library…Finding Journal Articles (November 2015)

How do I find journal articles about…?

The best place to search for journal articles is a bibliographic database, such as PubMed or Web of Science. Bibliographic databases index and organize citations to published literature, such as journal, newspaper and magazine articles or books and book chapters. Databases are often devoted to specific subjects, such as life sciences or engineering, and have sophisticated search features that allow you to retrieve relevant results.

How do I choose which database to search?

Tufts subscribes, or otherwise provides access to, hundreds of databases. When choosing a database, consider the subjects, dates and types of material (journal articles, books, conference proceedings, patents, etc.) that the database covers. The Find Articles page of the Biomedical Sciences Resource Guide (http://researchguides.library.tufts.edu/biomedical_research) provides a brief list of databases. A complete list of biomedical databases available at Tufts can be found here: http://www.library.tufts.edu/hsl/resources/dbases.html. Depending on your topic and purpose, you many need to search more than one database. When in doubt, just ask!

What about Google Scholar?

Google Scholar uses an algorithm to search scholarly literature available on the web. Like Google, results in Google Scholar are ranked and displayed according to relevance, with few options to filter the results. The careful selection of materials, indexing, and search capabilities of databases mean that you will usually get more precise results than a search in Google Scholar. I use Google Scholar to: supplement searches that I have done in databases; find grey literature (literature produced by government, academia, business or organizations and made available by means other than commercial publishers, for example, reports or white papers); find the full text of an article.

How do I find the full text of an article?

If you have found the article in a database, then look for the blue ‘Find It@Tufts’ button, which should take you directly to the full text if it is available through Tufts. Remember, you must access PubMed via the library homepage to see this button.

If you access Google Scholar from the library homepage, then you will see a ‘Get This Item at Tufts’ link if the article is available electronically through Tufts Libraries.

If you have the title of a journal article and want to know whether or not the full text is available through Tufts, simply copy and paste the title into JumboSearch (http://tufts.summon.serialssolutions.com/#!/; also accessible from the library homepage).

An article that I want is only available in print at a Tufts library. Does this mean that I have to go to the library to retrieve it?

No! If an article is available in print at any Tufts library (including Hirsh Health Sciences Library), then you can request that it be scanned and delivered to you electronically. This service is free and there is no limit to the number of requests that you may submit. Submit requests via ILLiad (https://illiad.library.tufts.edu/illiad/TFH/logon.html).

What if the full text of an article that I need is not available either in print or electronically at Tufts?

If an article is not available at Tufts, then you can submit a request for the article to be retrieved from another library and delivered to you electronically. Students have 20 free requests per academic year for items from non-Tufts libraries. A $4 fee per request will be charged once the 20 request limit has been surpassed (for more information, see: http://www.library.tufts.edu/hsl/services/docDelPolProc.html). Submit requests via ILLiad (https://illiad.library.tufts.edu/illiad/TFH/logon.html).

What if I want to browse the contents of specific journals?

The easiest way to browse and read journals available through Tufts is to use BrowZine, a mobile app that provides direct access to (most) of the journals that Tufts receives electronically. Available for free for both Apple and Android devices, this app allows you to: view current and past journal issues; create a bookshelf of journals of interest to you; and save articles for later reading. BrowZine recently released a web version of their service (http://www.browzine.com/). If you access this site from on campus, then you will be brought directly to the Tufts BrowZine Library. If you access the site from off campus, then select Tufts University and log in with your Tufts username and password. Eventually, you will be able to sync your bookshelf and reading lists between the web version and app. The library does receive some journals in print; current print issues can be found on the 4th floor of Sackler, older issues on the 7th floor.

-Laura Pavlech