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Notes from the Library…Introducing JumboSearch

In June, Tufts Libraries launched a new iteration of our search platform, JumboSearch.  This means that the way you search for resources (books, journals, databases, articles, etc.) available through our libraries has changed.  This new search platform is part of our transition to a new integrated library system, which will improve how we manage our resources.

Here is a brief primer on how to use JumboSearch to find the resources you need.

How do I access JumboSearch?

The search box at the center of the Hirsh Health Sciences Library homepage (https://hirshlibrary.tufts.edu/) is for JumboSearch.

How do I find a book in JumboSearch?

Enter a title, author or keyword in the search box at the center of the Hirsh Health Sciences Library homepage.  Use the filters on the left side of the results page to limit your search to books.  Once you find the book that you need, click the title to view additional information, such as location and availability, and, if it is available electronically, access the full text.

What if the book I want is located at another Tufts library?

If the book is located at another Tufts library, then click the title of the book on the JumboSearch results page.  Select the ‘Log in’ link in the yellow bar at the center of the page.  Once you have signed in with your Tufts username and password, click the ‘Request item’ link to request delivery of the book to the Hirsh Health Sciences Library.  You will receive email notification when the book is ready for you to pick up at our Library Service Desk.

How do I find a journal? 

Enter the title of a journal in the JumboSearch box at the center of the Hirsh Health Sciences Library homepage.  If the journal is available through our libraries, then the title should appear at the top of the results.  Click the title of the journal to view print and electronic availability.

Another (and I find more efficient) method of finding a journal is to click the ‘Journals’ tab at the top of any JumboSearch page, which brings you to a page where you can search or browse our Journal list (versus all of our resources).

Can I use JumboSearch to find the full text of an article?

Yes!  If you have the title of a journal article and want to know whether or not the full text is available through Tufts, then copy and paste the title into JumboSearch.  If necessary, use the filters on the left side of the results page to narrow your results.  Once you find your article, click the ‘Full text available’ link.

How do I access my library account?

Use the ‘Log in’ link in the upper right-hand corner of any JumboSearch page, or in the yellow bar at the center of an item details page.  In your library account, you can see the items that you currently have checked out (including interlibrary loan books), requests, fines and blocks, as well as renew Tufts Libraries’ books.

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’

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: 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.

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

PubMed Tip of the Month: My Bibliography

As I mentioned in my March post, the My Bibliography section of My NCBI allows you to save citations to your journal articles, book chapters, presentations, meeting abstracts, etc.  This list of citations can be shared via a stable URL, exported to a text file, or saved as a PDF.  NIH recommends using My Bibliography if you wish to include a link to a complete list of published works in your biosketch.  My Bibliography is also used to demonstrate compliance with the NIH Public Access Policy on progress reports.

Access My Bibliography

Log in to your My NCBI account, find the My Bibliography box (note: you can drag and drop the boxes in My NCBI to change the order in which they appear) and click the ‘Manage My Bibliography’ link.

Add Citations

Once you are in My Bibliography, use the buttons in the right-hand column to add a citation from PubMed (preferred method), manually (use for articles not in PubMed, or other products, such as meeting abstracts, presentations or data sets), or from a file (must be in either MEDLINE or RIS format).

Citations can also be added to My Bibliography from any PubMed results page.  Click the boxes next to the citations you wish to add, then choose My Bibliography from the Send to dropdown menu at the top of page.

Add citations from PubMed results page

PubMed Send to

Make Publicly Available

Click the ‘Edit settings’ link at the top of the My Bibliography homepage.  This will bring you to a page where you can change your sharing settings from private to public.  Once you do so, the URL will appear at the top of your My Bibliography homepage.  Note: do not copy and paste the URL that appears in your browser when you are in My Bibliography because this is different than the unique URL generated for your collection.

Public URL and edit settings for My Bibliography

My Bibliography homepage

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.

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

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

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)

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.