Category Archives: Library

Library, March 2017, PubMed Tip of the Month

PubMed Tip of the Month…Topic-Specific Queries

Topic-specific queries in PubMed are carefully constructed search strategies that can either be applied to a set of results as a filter or added to a search using ‘AND’.  Each of these searches has been created by an expert, tested to optimize sensitivity and specificity, and is periodically updated.  To view a complete list of the available searches, click the ‘Topic-Specific Queries’ link under PubMed Tools on the PubMed homepage.  This will bring you to the Directory of Topic-Specific PubMed Queries, where you can view the available subject searches, which include: AIDS, bioethics, cancer, health disparities, toxicology and veterinary medicine.  Clicking the link for a subject either limits your PubMed search to that subject area (i.e. applies a filter) or brings you to a page with the search strategy and additional resources.

Topic-Specific Queries
Topic-Specific Queries link on PubMed homepage.

Some of the searches can also be applied as filters from a search results page.  To do so, click the ‘Show additional filters’ link in the left-hand column of a PubMed search results page.  Check the box next to Subjects and click the Show button.  Select a link under Subjects to narrow your results.  If you do not see a particular filter, then click the ‘Customize’ link under Subjects to choose additional filters.  I don’t use topic-specific queries too often, but they can save you a lot of work if an appropriate search filter has been constructed for your topic.

Library, March 2017, Notes from the library

Notes from the Library…Copyright

As both creators and users of copyrighted works, it is good to know a little about this topic.  Below, you will find a brief copyright primer.  For answers to copyright questions pertaining to your thesis, see FAQs for Dissertation & Thesis Writers from the Tufts University Libraries Scholarly Communications Team, where you will find answers to questions such as: Can I delay the release of my thesis?  What if I have already published part of my thesis as an article?  What if I want to reuse a graph created by someone else in my thesis?  What is open access?

What is copyright?

Copyright is a set of rights, which give the owner the exclusive right to do or authorize any of the following: reproduce the copyrighted work; prepare derivative works based on the copyrighted work; sell, transfer ownership of, rent, lease or lend copies of the work; publicly display or perform the work (17 U.S. Code § 106).

The authorization for copyright legislation goes back to Article 1, Section 8, Clause 8 of the United States Constitution.  The Copyright Act of 1976 provides the framework for today’s copyright law, which can be found in Title 17 of the U.S. Code.

What does copyright apply to?

Copyright applies to “original works of authorship fixed in any tangible medium of expression” (17 U.S. Code § 102).  This includes literary, pictorial, graphic, and audiovisual works.  Copyright does not extend to ideas, procedures, processes, methods of operation, concepts, principles or discoveries.  Patent, trademark or trade secret policy may apply to these forms of intellectual property.  For more information on these types of IP protection, see What Are Patents, Trademarks, Servicemarks, and Copyrights? and Trade Secret Policy on the U.S Patent and Trademark Office website.

How long does copyright last?

In general, for works created on or after January 1, 1978, copyright lasts for the life of the author plus 70 years (17 U.S. Code § 302).

Who owns the copyright to my thesis?

You do!  According to the Tufts Policy on Rights and Responsibilities with Respect to Intellectual Property: “Students generally own the copyright to the academic work they produce.  Academic work can include class papers, theses, dissertations…”.

February 2017, Library, On the Shelf

On the Shelf…

For Work

ontheshelf_fisher_enjoywriting_2017_02

Enjoy Writing your Science Dissertation or Thesis!, Elizabeth Fisher & Richard Thompson

Location: HHSL Book Stacks, Sackler 5, WZ 345 F533e 2014

I am not quite sure whether the title of this book (and exclamatory punctuation) is a command or a promise, but the book does provide advice on all aspects of thesis writing.

For Leisure

ontheshelf_marchant_cure_2017_02

Cure: A Journey into the Science of Mind Over Body, Jo Marchant

Location: HHSL Book Stacks, Sackler 5, WB885 M315 2016

Science writer Jo Marchant explores stories and research about the mind-body connection.

February 2017, Library, 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 (laura.pavlech@tufts.edu) 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.

February 2017, Library, PubMed Tip of the Month

PubMed Tip of the Month: Single Citation Matcher

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If you have limited information about a journal article (e.g. author name and year of publication), then PubMed’s Single Citation Matcher may help you locate the article.  Accessible from the PubMed homepage, this tool does exactly what its name implies: it matches citation information to PubMed records.  Single Citation Matcher can quickly narrow your search to records that match the information you have.

Single Citation Matcher in PubMed
Single Citation Matcher in PubMed

 

December 2016, Library, PubMed Tip of the Month

PubMed Tip of the Month: My NCBI Preferences

You can customize your preferences to make searching PubMed and other NCBI databases easier.  Log in to your My NCBI account (see Insight March 2016 for details on creating a My NCBI account) and click the ‘NCBI Site Preferences’ link in the top right corner of the homepage.

Here are a few preferences that you may want to adjust:

  • Highlighting: Highlights your search terms in a set of results, making scanning for relevant articles more efficient.
  • Filters & Icons: Personalized filters displayed in the right-hand column on results page. I recommend adding the MEDLINE filter, which limits results to articles that have had MeSH terms applied to them.  To do so, click on the ‘Filters & Icons’ link on the Preferences page, and on the page that opens, select the ‘Properties’ radio button.  Enter ‘MEDLINE’ in the search with terms box, then check the box next to MEDLINE.  You can also add the ‘Find it @Tufts’ button, which enables you to access the full text of an article through Tufts Libraries.  Adding this button to your NCBI account would obviate the need to access PubMed through the Hirsh Health Sciences Library website.  To add the ‘Find it @Tufts’ button, select the ‘LinkOut’ radio button on the Filters & Icons page.  Then, enter ‘Tufts University’ in the search box and check the link icon box next to Tufts University Hirsh Health Sciences and Veterinary Libraries.
  • Outside Tool: A simpler method of adding the ‘Find it @Tufts’ button to your account preferences. Click the ‘Outside Tool’ link on the Preferences page.  On the page that opens, select the radio button next to ‘Tufts’.
  • Result Display Settings: You can choose the format (summary or abstract) in which results are displayed, how results are sorted (I do not recommend changing this from the default, recently added), and the number of items per page (I prefer 200, so I don’t have to click through multiple pages).

These are just a few of the preferences that you can adjust in your My NCBI account.  You can also explore customized settings for other NCBI databases, such as Gene.

Preferences page in My NCBI

Preferences page in My NCBI

December 2016, Library, On the Shelf

On the Shelf…

For Work…

 naturemicro_work_2016_12

Electronic resource: Nature Microbiology

Location: https://library.tufts.edu:443/record=b3035776~S1

One of the latest titles from Nature Publishing Group, this exclusively online journal is dedicated to research in the field of microbiology.

And leisure…

 jahrens_labgirl_leisure_2016_12

Lab Girl, Hope Jahren

Location: HHSL Leisure Reading, Sackler, 4th Floor, Non-Fiction J25 2016

Geobiologist’s memoir of her life in scientific research.

December 2016, Library, Notes from the library

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.

HHSLcomputers_statistics_software-ie-or8

Library, November 2016, PubMed Tip of the Month

PubMed Tip of the Month: Finding Information on Drug Action

The Medical Subject Heading (MeSH) vocabulary includes headings for the pharmacologic actions of drugs.  Each drug and chemical in the MeSH vocabulary is assigned one or more of these headings.  The pharmacologic action headings can be used to find information on the action of a drug or class of drugs.

  1. Find articles in which a specific action of a drug is discussed: Combine the MeSH heading for the drug or chemical with the MeSH heading for the pharmacologic action of interest.

For example, to find articles on the antipyretic action of acetaminophen, enter: “Acetominophen”[MeSH] AND “Antipyretics”[MeSH]

In order to use this method, you need to know which pharmacologic action headings have been assigned to the drug or chemical.  This information can be found in the MeSH record for the drug.  To search the MeSH database, choose ‘MeSH’ from the dropdown menu to the left of the PubMed search box.

MeSH record for cyclosporine
MeSH record for cyclosporine, showing pharmocologic action terms
  1. Find articles in which any drug or chemical exhibiting a certain action is discussed: Use the pharmacologic action field tag, [Pharmacologic Action] or [pa]. This search would likely be added to another, using ‘AND’.

For example, to find articles on platelet aggregation inhibitors and heart attack, enter: “Platelet aggregation inhibitors”[pa] AND “Myocardial infarction”[MeSH]

  1. View a list of drugs and chemicals identified as having a certain pharmacologic action: Find the record for the term, labeled [Pharmacologic Action], in the MeSH database.

For example: “Antirheumatic agents”[Pharmacologic Action]

MeSH records for 'antirheumatic agents'
MeSH records for ‘antirheumatic agents’
Library, November 2016, On the Shelf

On the Shelf

Two for one this month…

Natural Medicines

Electronic resource: Natural Medicines

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

Natural Medicines is a collection of databases and tools that provide evidence-based information on dietary supplements, natural medicines, and complementary and alternative therapies.  Databases in this collection include: Food, Herbs & Supplements, which has monographs for vitamins, herbs, minerals, non-herbal supplements, naturally sourced chemical compounds, and foods; Health & Wellness, which has monographs for complementary and alternative therapies; Sports Medicine, which has monographs for substances or exercises that may affect athletic performance; and Commercial Products, a comprehensive list of manufacturers and the products they make.  You can search across all databases, or choose to search a particular database.  Monographs have sections on safety, effectiveness, dosing and administration, and adverse effects, with links to published literature.  Natural Medicines also has tools for evaluating interactions, nutrient depletion, and effectiveness.