Monday, December 30, 2019

Looking up research on the European version of PubMed, called EuropePMC

Sample of EuropePMC search bar


A friend recommended using EuropePMC, https://europepmc.org/  as an alternative to PubMed (thank you, Chris).  This repository describes themselves as:
  • Europe PMC is an open science platform that enables access to a worldwide collection of life science publications and preprints from trusted sources around the globe.
  • Europe PMC is developed by EMBL-EBI. It is a partner of PubMed Central and a repository of choice for many international science funders.
  • Free, transparent, and community-driven, Europe PMC is your gateway to life science research.
Doing a search on EuropePMC is similar to doing a search on PubMed (which works much like a Google search; see this recent blog post), but the search results can be quite different.  Hmm.  Why?

Many things are the same with PubMed and EuropePMC. There are Basic (like a Google search) and Advanced search available in both (for searches by journal, for example).  You can also sort the results by date or by "relevance"/"best match."  Further, you can limit results for a particular date range and whether there is a free article available for both, and you can search by article type, but each repository does it differently (advanced search in EuropePMC, filters in PubMed).  The way the two identify free articles (full articles available to all) is a bit different, but both seem to have the same access.  In addition, both have ways to tell about other research that cites this article (a real-world measure of influence), show links to similar articles, and highlight keywords.  Here is an excerpt from a sample EuropePMC search:

The more restrictive your keywords are, the more similarities you find between the two tools.  When I used the keywords (example: Parkinson's dementia rivastigmine) and sorted by recent date, the first article is the same - but many of the rest of the citations/abstracts are not.

But what causes the differences?   Partly different journals are available (there are more in EuropePMC), but partly, I suspect, because of different indexing (selection of keywords for each article).  Here's a recording of a webinar about how to do search on EuropePMC:

Another difference is that PubMed will let you email a search to yourself, which is handy if you use multiple computers;  you can email just the citations in EuropePMC, but since EuropePMC saves your previous searches - and you can sign in to the system - the email may not be as important.  Also, some features in filters on both platforms don't seem to work, but I can't tell if this is a limitation based on indexing that just hasn't been done.

I happen to prefer PubMed, probably because I'm used to it.  But I use both repositories to search research.  When I don't find results in one, I often can find results in the other (one of the reasons I suspect the indexing is different).

See which one you prefer.

Monday, December 23, 2019

Suppose you want a complete research paper but you only have the abstract

Sometimes the abstract is so brief that you want to know more.  Sometimes it doesn't summarize anything including the conclusions (grrr).  Or maybe people are talking about it and you want to know what they are talking about.

What are some ways to get the paper?

1.  The NIH requires that any study it funds must open their research results to all; some foundations do this, too.  (But not enough of them.)  Some journals only publish as "open access," so all their papers are available, too.  For these, you will see some variant of this, over on the PubMed abstract, upper right side:

2.  If you click on the DOI number on the PubMed abstract (right under the authors' names), sometimes that will give you a full version of the paper, even though the official link (see #1)  does not.
3.  If there is a corresponding author and email available on the abstract, you can email this person asking for the paper (give the precise title because they may be involved with a lot of papers and projects).  Most will give it to you.  Quickly, too.

4.  Google the exact title.  Some researchers have placed their paper on a university website.

5.  Ask a friend/family member who may have access to bio-medical journals on-line at work.  Know anybody who works for a college or university?  (Just don't wear out your welcome.)

6.  Rent the article (available for a fee from some publishers, but much less than the $35/article that many publishers charge for purchasing the article.)  Some publishers offer this.  Copy and paste the article into your word processor so that you have time to read it without worrying about the limited rental period.

7.  Then there is the illegal way.  A Russian maintains a website for access to full papers - sometimes an early version of the paper is available.  https://sci-hub.tw/   
Here's the rationale behind Sci Hub:
Donations are accepted in Bitcoin which means they're untraceable.  The Russian internet seems to be the Wild West, so Sci-Hub operates there without benefit of a government enforcing copyright law (that's the illegal part). There is probably some risk because this is Russia.

Sometimes on Sci-Hub instead of the paper, first there will be incomprehensible directions in Russian.  This is very like Captcha.  Type in the English letters that are shown and click the Russian word below.  Sometimes this works and sometimes it doesn't.

Lots of different ways to get the full paper if you really want to read the whole thing.  

I find that the particularly useful parts of the paper are:  # of patients who participated in the study, and # of participants by gender, if it's a clinical trial; Discussion; Conclusion.  

What do you want to find out?

Monday, December 16, 2019

Using the new PubMed


PubMed is a free database that has more than 30 million abstracts (summaries) of biological/medical and life sciences research, from MEDLINE, life science journals, and online books, and is located in NIH.  Sometimes there are links to the full-text research as well, not just the abstracts.


Why would you want to use PubMed instead of Google (or even Google Scholar)?  Because much of this research isn't available on Google/Google Scholar, and PubMed has terrific tools that make its use really easy and useful.
While you can search it just like you do Google, there are many additional filters that make PubMed more useful.  (And by the way, it says "Log In" but for looking up research, that's not required.)  Let's look at an example of search results to see some of PubMed's useful features:
The default sort is Best Match, that is the abstracts that best meet your search.  But if you prefer, you can change this to Most Recent, the abstracts in date order, with most recent first.  Any restrictions using the filters are highlighted in pink in the center of the page.  You can see that I've used the Article Type Review to limit abstracts to just Reviews, since Reviews are often evaluations of many related pieces of research.  Also notice that the search terms are shown in bold in the search results.

These are not all the possible filters, but seem to be frequently used - such as only "full text," or only published in the past "5 years."

If you look at an Abstract (PubMed calls these citations, but virtually all are abstracts), you can see information such as the authors - and if you click on Expand next to the authors' names, you can learn an email for correspondence, and what institutions the authors work for.
Also, you can see the full-text link, in the upper right (which will say "free" if anybody can see the article), and also the DOI number, under the authors' names - a clickable link that will occasionally take you to the full article, even if the full-text link will not.  (Each article has a unique DOI number - Digital Object Identifier - which can be handy.)

Also handy are "Similar articles," and "Citations" (other papers that cited this article).  Citations won't be that helpful for a just-published article because it is just too new to be cited yet;  but journals and others base quality measures on how often an author/ article/ journal is cited.

Now, why would the article not be available - this is called putting articles behind a paywall?  Well, publishers make money from subscriptions, and while universities and drug companies pay for subscriptions, private citizens usually don't.  But few of us want to pay $35.00 for each article we want to read in detail.  We'll talk about ways to get around this in another blog post.

Besides looking up abstracts, you can email the search results or abstracts to yourself (handy if you are working in more that one place), and even have the system send you Alerts whenever there are new articles that meet your criteria.  This requires you to Log In (see the first image).  Usually, you don't need to log in, but for Alerts you must.  One of the choices for logging in is your Google account, but this was not working when I tried it.

PubMed is added to daily, is indexed, and is free.  It's a tool I use every day.  You can, too.

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