Tag Archives: Pubmed

December 2017, Library, Notes from the library

Notes from the Library…Finding Gene Information in PubMed

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PubMed is just one database from the National Library of Medicine (NLM).  The National Center for Biotechnology Information (NCBI), a division of the NLM, maintains several molecular biology databases.  These databases link to one another and to PubMed.  This month, I’ll describe how to find information about a gene in PubMed and the Gene database.

Which NCBI resource(s) should I use to find information on a gene?

You can start in either PubMed or Gene, a database of known and predicted genes for a several species.  Each record is devoted to a single gene and may provide information on nomenclature, chromosomal location, gene products, phenotypes, and interactions, as well as links to literature, sequences, and other NCBI and external databases.  Consider a Gene record a gene’s homepage in NCBI.

I’ll begin in PubMed because it is the database with which you are likely most familiar.  In the PubMed search box, you can enter either a gene’s name or symbol.  To activate the Gene Sensor (see next question), use the official gene symbol, which can be found at genenames.org, the site for the HUGO Gene Nomenclature Committee (HGNC).  The HGNC assigns standardized names to human genes.

What is the PubMed Gene Sensor?

Gene Sensor checks the gene symbol that you enter against symbols in the Gene database and, if a match is found, displays links to information about the gene in NCBI databases at the top of your PubMed search results.  These links include: the records(s) for the gene in the Gene database; articles on the gene’s function (GeneRIF; see below); and tests in the Genetic Testing Registry.

Choose the link to the gene’s record in the Gene database.  The first option will be for the human gene, with links for other species, if available, following.

Gene Sensor results in PubMed
Gene Sensor results in PubMed

What if my initial PubMed search does not activate the Gene Sensor?

If you do not see the Gene Sensor box at the top of your PubMed results, then you can search the Gene database directly by selecting ‘Gene’ from the drop-down menu next to the search box.  Enter a gene name or symbol, species, or disease.

Gene database in drop-down menu
Choose Gene database from drop-down menu

How do I find information once I am in a Gene record?

Use the Table of Contents in the right-hand column of the record to navigate to specific information about the gene.  Scroll down to the ‘Related information’ section of the right-hand column for links to information about the gene in other NCBI databases.

Record in Gene database
Record in Gene database, with Table of Contents in right-hand column

So how does this help me find PubMed articles about a gene?

In the Related information section of a Gene record, you will notice several links to PubMed.  Each of these links retrieves a specific set of articles in PubMed:

  • PubMed: Articles that have been indexed with the Medical Subject Heading (MeSH) of the protein that the gene codes for, combined with the subheading ‘genetics’. For example: ‘Hemochromatosis Protein/genetics’[MeSH].
  • PubMed (GeneRIF): Articles that focus on the function of a gene. GeneRIFs (reference into function) are identified in three ways: by National Library of Medicine staff; by volunteer collaborators who submit a function, and article(s) describing that function (if you know of, or have authored, an article about a gene’s function, then you can submit a GeneRIF); through reports from HuGE Navigator, a human genome epidemiology knowledge base from the Centers for Disease Control and Prevention.  PubMed (GeneRIF) also includes articles that describes a gene’s interactions.
  • PubMed (OMIM): Articles cited in Online Mendelian Inheritance in Man (OMIM) records. OMIM is a compendium of human genes and phenotypes.
  • PubMed (nucleotide/PMC): Articles identified from shared sequence and PubMed Central links.

Each set of articles is continuously updated.  Use these links to retrieve the set of articles that best describes the type of literature you are seeking.

PubMed links in Gene record
PubMed links under ‘Related information’ in Gene record

What if I want to find all the literature on a particular gene in PubMed?

If you want to do a comprehensive PubMed search for literature on a gene, then use the Gene record and HGNC (genenames.org) to identify the gene’s current and past names, symbols, and synonyms.  Use ‘OR’ to combine these keywords with the MeSH term for the protein that the gene codes for, with the subheading ‘genetics’.  Some genes, but not all, genes also have a MeSH term for the gene itself.

For example:

“BRCA1” OR “BRCC1” OR “FANCS” OR “BROVCA1” OR “PPP1R53” OR “breast cancer 1” OR “Genes, BRCA1″[MeSH] OR “BRCA1 Protein/genetics”[MeSH]

You may get a lot of irrelevant results with a comprehensive search because many gene symbols are not unique.  Therefore, this search would likely have to be combined with another concept, using ‘AND’.

For example:

(“BRCA1” OR “BRCC1” OR “FANCS” OR “BROVCA1” OR “PPP1R53” OR “breast cancer 1” OR “Genes, BRCA1″[MeSH] OR “BRCA1 Protein/genetics”[MeSH]) AND (“ovarian neoplasms”[MeSH] OR “ovarian neoplasms” OR “ovarian cancer”)

Library, October 2017, PubMed Tip of the Month

PubMed Tip of the Month…PubMed vs. PubMed Central

I often see people confuse PubMed and PubMed Central.  While these two resources are linked to one another, they are separate and distinct.  Here is a summary of the two:

 

PubMed

PubMed Central (PMC)
What is it? Citation & abstract database Full text repository
What am I searching? ·        Citations to journals indexed for MEDLINE, including out-of-scope articles (e.g. Nature article on plate tectonics) and articles not yet indexed for MEDLINE

·        Citations to articles in PubMed Central

·        Citations to books available on NCBI Bookshelf

 ·        Articles/manuscripts deposited by publishers or authors to comply with funder public access policies

·        Complete issues of journals that choose to deposit their full contents in PMC

 
How should I access & use? ·        Freely available

·        For links to full text articles through Tufts Libraries, access PubMed via the Hirsh Health Sciences Library website (‘PubMed @ Tufts’ from Databases tab, or under Quick Links)

·        While at Tufts (or any other institution that purchases journal subscriptions), do not use the ‘Free full text’ filter on a PubMed results page because this limits results to only those articles that are freely available to the public

 ·        Freely available

·        Can access directly, but usually no reason to do so

·        Look for ‘Free PMC Article’ link below article in PubMed list of results, or PMC button in PubMed abstract view

·        NIH Public Access Policy: all peer-reviewed journal articles that arise from NIH grant or cooperative agreement must be deposited in PMC & made publicly available no later than 12 months after publication

 

April 2017, Library, PubMed Tip of the Month

PubMed Tip of the Month…Search or Filter by Funder

Funding information is recorded in two fields in a PubMed record: Grant Number and Publication Type. Limiting a search to these fields can help you find articles that were supported by a specific grant, funder or type of funder (e.g. non-U.S. government).

  • Grant Number: The Grant Number field records grant or contract numbers as published in the article, or derived from PubMed Central as a result of the NIH Public Access Policy. To find articles funded by a particular organization, search the Grant Number field for the organization’s name, acronym or 2-letter code (click on link above for complete list funding agency names, acronyms and codes). For example, to find studies supported by the National Institute on Aging, search PubMed for: AA[gr].
  • Publication Type: Medical Subject Headings (MeSH), the standardized terms used to describe articles for MEDLINE, include Publication Types to identify financial support when that support is mentioned in the article. A list of publication types, including those for Research Support, can be viewed from the link above. To filter a search by one of the funding Publication Types: in the left-hand column of a results page, click ‘Customize’ under Article types. Scroll down and check the box next to the types of Research Support you would like to view. Click ‘Show’. The types of research support that you selected should now be visible under Article types. Click the research support type to filter your results.
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.

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

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, October 2016, PubMed Tip of the Month

PubMed Tip of the Month: Searching for Chemicals & Drugs

Use the common name: PubMed is not primarily a resource for chemical information, so forget what I said in my column about not searching by name. Enter the common name for a chemical, drug or other substance in the main search box.  Scroll down the results page to the ‘Search Details’ box in the right-hand column to check to see if the name you entered matched a MeSH term.

Use the standardized name: To search by standardized name in PubMed, replace any brackets or parentheses with a hyphen (if not already present). You can either spell out or enter the symbol for Greek characters such as β.

To search for: 1-[(3,5-dichloro)-2,6-dihydroxy-4-methoxyphenyl]-1-hexanone

Enter: 1-3,5-dichloro-2,6-dihydroxy-4-methoxyphenyl-1-hexanone

Search the MeSH database: Didn’t find what you were looking for when you searched by name? Try searching the MeSH database.  Select ‘MeSH’ from the dropdown menu to the left of the main search box.  Enter a component of the name.

To search for: alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid

Enter: isoxazolepropionic

Try a unique identifier: In either PubMed or the MeSH database, enter the CAS RN or FDA Unique Ingredient Identifier (UNII, identifier assigned by the FDA Substance Registration System to substances in drugs, biologics, foods and devices) for a substance. If searching PubMed, then enter the identification number, followed by the field tag ‘[RN]’.  For example: 69-93-2[RN].  I find this method of limited utility, partly because CAS RNs have not been added to MeSH since 1998.

Library, PubMed Tip of the Month, September 2016

PubMed Tip of the Month: PubMed Labs

PubMed Journals

PubMed Labs is the National Center for Biotechnology Information’s (NCBI) innovation incubator. PubMed Labs releases early versions of tools, features and content for anyone to experiment with and comment on. One recent development is PubMed Journals, a site where you can browse and follow journals, see ahead of print articles, and view trending articles and updates, such as retractions. NCBI is considering how to push content from the site to users. The news feed in PubMed Journals links studies mentioned in the mainstream media directly to the reference article. I have not really explored the site (it was just announced on September 7th), but it may develop into a nice way to monitor journals contents and news via your My NCBI account.

 

Library, PubMed Tip of the Month, Summer 2016

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