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Dispatches: Sources in biology and medicine

By Tim Vickers and Eubulides, June 30, 2008

In general, the most reliable sources in biology and medicine are peer-reviewed publications in scientific journals. An excellent starting point is PubMed, which is a database of publications in biology and medicine. Although this is a very comprehensive database, many of the journals it lists restrict on-line access, so there is the alternative of PubMed Central, where all the articles are free.

Types of sources

There are two main types of sources in the scientific literature: primary publications, which are papers describing novel research for the first time, and review articles, which try to summarize and integrate other people's work into an overall view of a topic. In medicine there are also clinical trials, which test new treatments, and meta-analyses that bring together the results from many clinical trials and try to get an overall view of how well a treatment works. It is usually best to use reviews and meta-analyses if you can, since these give a balanced and general view of a topic, and are usually a bit easier to understand!

Assessing the "quality" of a source is difficult. To know how much weight to give a particular publication you usually need to have a good grasp of what has been published before, and how this fits into other people's results – this is why reviews are so useful, since they do this for you. However, two general rules of thumb can be useful. First, if a biology/medicine journal is not listed in PubMed, it is of doubtful quality – the journal published by the Creation Research Society would be one example. Second, the impact factor of the journal can tell you how influential it is. This number measures how often a paper in this journal is usually cited by other papers – good journals publish papers that other people find useful, while bad work sinks into well-deserved obscurity.

Accessing sources

Other things being equal, it is better to cite a source whose full text is freely-readable, so that your readers can follow the link to the source. However, many top-quality journals, such as Nature and Science, require a fee or a subscription, and as these journals publish some of the best papers it can still be best to cite them.

Often an article's abstract is freely-available, even when its full text is not. When searching for sources, it good to read everything you can, including abstracts of papers you can't access, and use that to get a feel for what reliable sources are saying. When it comes to actually writing a Wikipedia article, though, it is generally not a good idea to cite a source after reading only its abstract, as the abstract necessarily presents a stripped-down version of the conclusions and omits the background that can be crucial for understanding exactly what the source says. You may need to visit a library in order to get the source, or ask somebody at Wikipedia:WikiProject Resource Exchange to either provide you with a copy or read the source for you and summarize what it says; if neither is possible you may need to regretfully cite some other, lower-quality source.

Some source are in the public domain. These include many U.S. government publications, such as the Morbidity and Mortality Weekly Report of the U.S. Centers for Disease Control and Prevention. You can incorporate public-domain text bodily into a Wikipedia article without infringing copyright, which can help you write an article on a new topic quickly. However, in such cases you should follow scholarly practice and cite the source, putting quote marks around direct quotations. Generally speaking it is better to summarize sources even when they are public domain, as they typically are not encyclopedias and are not written in an encyclopedic style.

Searching for sources

Each search engine has its own quirks, advantages, and disadvantages, and often searches do not return the results that you need. It typically takes some experience and practice to recognize when a search has not been effective; even if you find some useful sources, you may have missed some other sources that would have been more useful, or you may get pages and pages of less-than-useful material.

You should not rely solely on search engines to find sources, because they often miss sources. A good strategy is to find a few recent high-quality sources, and then follow their citations to see what your search engine missed. It can also be helpful to do a plain web search rather than one of scholarly articles only.

Searching PubMed

There are basic and advanced options for searching PubMed. In the basic option you enter some keywords, such as "breast cancer" – and will get over 180,000 results that include this specific phrase. Just above the list of hits there are two tabs, one labeled "All" and the other "Review". If you click on the "review" tab it will take you to a list of about 14,000 academic reviews.

To look at one of these in more detail, just click on the title – such as RE Coleman's review on Risks and benefits of bisphosphonates. This takes you to a summary (the abstract) of the review and gives you a list of authors and, on the right, a list of related articles. This "See all Related Articles" link is very useful for narrowing down searches. In the top right there can be a link to the journal website (here it is the British Journal of Cancer). At the bottom of the abstract is a number called the PubMed ID number, which is PMID 18506174 in this instance. To generate a {{cite journal}} template for Coleman's review, just copy the PMID number into Diberri's tool.

To do an advanced search with the same keywords, go back to the search screen, enter "breast cancer", as before, and then click on the "Limits" tab just below the search box. This takes you to a set of options that allow you to limit your search to particular dates, types of articles or topic areas. To search for meta-analyses, for example, tick that box in the section on Type of Article and hit "search". You will now get a list of about 460 meta-analyses that deal with breast cancer.

If your Pubmed search finds a lot of sources, you can restrict yourself to the freely-readable ones by clicking on the "Limits" tab and checking the box labeled "Links to free full text".

Other indexes

Pubmed is not the only game in town for biomedical searching. There are alternatives.

Some search engines attempt to cover all scholarly sources. They are invaluable for topics not covered by the more-specialized indexes discussed above, and can provide useful sanity checks even for topics such as medicine that have more-specialized indexes. The best-known is Google Scholar; other engines include getCited and Scirus. A version of Google Scholar that automates generating citation templates is WikiScholar.

The Cochrane Library contains a database of systematic reviews and meta-analyses and is a key resource in evidence-based medicine. Its reviews are generally considered to be very high in quality.

EMBASE is a high-quality index that often generates better results than Pubmed. Unfortunately it is proprietary and requires a subscription.

CINAHL is a proprietary index on nursing and allied health care.

In order to be indexed in Pubmed, journals must meet editorial and content quality standards. When writing articles on non-mainstream topics it may be useful to search indexes that include journals not meeting these standards. Obviously, you must be careful not to misrepresent these publications as reflecting mainstream opinion. These indexes include AMED for allied professions and complementary medicine, Alt HealthWatch for complementary and alternative medicine, ICL for chiropractic, and MANTIS for manual medicine.

@@ Line 11: / Line 11: @@
 Assessing the "quality" of a source is difficult. To know how much weight to give a particular publication you usually need to have a good grasp of what has been published before, and how this fits into other people's results – this is why reviews are so useful, since they do this for you. However, two general rules of thumb can be useful. First, if a biology/medicine journal is not listed in PubMed, it is of doubtful quality – the journal published by the [[Creation Research Society]] would be one example. Second, the [[impact factor]] of the journal can tell you how influential it is. This number measures how often a paper in this journal is usually cited by other papers – good journals publish papers that other people find useful, while bad work sinks into well-deserved obscurity.
-==Searching PubMed==
-There are basic and advanced options for searching PubMed. In the basic option you enter some keywords, such as ''"breast cancer"'' – and will get over 180,000 results that include this specific phrase. Just above the list of hits there are two tabs, one labeled "All" and the other "Review". If you click on the "review" tab it will take you to a list of about 14,000 academic reviews.
-To look at one of these in more detail, just click on the title – such as RE Coleman's review on ''Risks and benefits of bisphosphonates.'' This takes you to a summary (the ''abstract'') of the review and gives you a list of authors and, on the right, a list of related articles. This "See all Related Articles" link is very useful for narrowing down searches. In the top right there can be a link to the journal website (here it is the ''British Journal of Cancer''). At the bottom of the abstract is a number called the PubMed ID number, which is PMID 18506174 in this instance. To generate a {{t1|cite journal}} template for Coleman's review, just copy the PMID number into [http://diberri.dyndns.org/cgi-bin/templatefiller/?type=pubmed_id&id= Diberri's tool.]
-To do an advanced search with the same keywords, go back to the search screen, enter ''"breast cancer"'', as before, and then click on the "Limits" tab just below the search box. This takes you to a set of options that allow you to limit your search to particular dates, types of articles or topic areas. To search for meta-analyses, for example, tick that box in the section on Type of Article and hit "search". You will now get a list of about 460 meta-analyses that deal with breast cancer.
 == Accessing sources ==
-Other things being equal, it is better to cite a source whose full text is freely-readable, so that your readers can follow the link to the source. If your Pubmed search finds a lot of sources, you can restrict yourself to the freely-readable ones by clicking on the "Limits" tab and checking the box labeled "Links to free full text". However, many top-quality journals, such as [[Nature (journal)|''Nature'']] and [[Science (journal)|''Science'']], require a fee or a subscription, and as these journals publish some of the best papers it can still be best to cite them.
+Other things being equal, it is better to cite a source whose full text is freely-readable, so that your readers can follow the link to the source. However, many top-quality journals, such as [[Nature (journal)|''Nature'']] and [[Science (journal)|''Science'']], require a fee or a subscription, and as these journals publish some of the best papers it can still be best to cite them.
-=== Abstracts versus full text ===
 Often an article's abstract is freely-available, even when its full text is not. When searching for sources, it good to read everything you can, including abstracts of papers you can't access, and use that to get a feel for what reliable sources are saying.
+When it comes to actually writing a Wikipedia article, though, it is generally not a good idea to cite a source after reading only its abstract, as the abstract necessarily presents a stripped-down version of the conclusions and omits the background that can be crucial for understanding exactly what the source says. You may need to visit a library in order to get the source, or ask somebody at [[Wikipedia:WikiProject Resource Exchange]] to either provide you with a copy or read the source for you and summarize what it says; if neither is possible you may need to regretfully cite some other, lower-quality source.
+Some source are in the [[public domain]]. These include many U.S. government publications, such as the ''[[Morbidity and Mortality Weekly Report]]'' of the U.S. [[Centers for Disease Control and Prevention]]. You can incorporate public-domain text bodily into a Wikipedia article without infringing copyright, which can help you write an article on a new topic quickly. However, in such cases you should follow scholarly practice and cite the source, putting quote marks around direct quotations. Generally speaking it is better to summarize sources even when they are public domain, as they typically are not encyclopedias and are not written in an encyclopedic style.
-When it comes to actually writing a Wikipedia article, it is generally not a good idea to cite a source after reading only its abstract, as the abstract necessarily presents a stripped-down version of the conclusions and omits the background that can be crucial for understanding exactly what the source says. You may need to visit a library in order to get the source, or ask somebody at [[Wikipedia:WikiProject Resource Exchange]] to either provide you with a copy or read the source for you and summarize what it says; if neither is possible you may need to regretfully cite some other, lower-quality source.
-=== Public domain sources ===
+==Searching for sources==
+Each search engine has its own quirks, advantages, and disadvantages, and often searches do not return the results that you need. It typically takes some experience and practice to recognize when a search has not been effective; even if you find some useful sources, you may have missed some other sources that would have been more useful, or you may get pages and pages of less-than-useful material.
+You should not rely solely on search engines to find sources, because they often miss sources. A good strategy is to find a few recent high-quality sources, and then follow their citations to see what your search engine missed. It can also be helpful to do a plain web search rather than one of scholarly articles only.
-Some source are in the [[public domain]]. These include many U.S. government publications, such as the ''[[Morbidity and Mortality Weekly Report]]'' of the U.S. [[Centers for Disease Control and Prevention]]. You can incorporate public-domain text bodily into a Wikipedia article without infringing copyright, which can help you write an article on a new topic quickly. However, in such cases you should follow scholarly practice and cite the source, putting quote marks around direct quotations. Generally speaking it is better to summarize sources even when they are public domain, as they typically are not encyclopedias and are not written in an encyclopedic style.
-==General databases==
+==Searching PubMed==
+There are basic and advanced options for searching PubMed. In the basic option you enter some keywords, such as ''"breast cancer"'' – and will get over 180,000 results that include this specific phrase. Just above the list of hits there are two tabs, one labeled "All" and the other "Review". If you click on the "review" tab it will take you to a list of about 14,000 academic reviews.
-Some search engines attempt to cover all scholarly sources. They are invaluable for topics not covered by the more-specialized indexes discussed above, and can provide useful sanity checks even for topics such as medicine that have more-specialized indexes. The best-known is [[Google Scholar]]; other engines include [[getCited]] and [[Scirus]]. A version of Google Scholar that automates generating citation templates is [http://www.srcf.ucam.org/~ms609/Wiki/Scholar WikiScholar].
+To look at one of these in more detail, just click on the title – such as RE Coleman's review on ''Risks and benefits of bisphosphonates.'' This takes you to a summary (the ''abstract'') of the review and gives you a list of authors and, on the right, a list of related articles. This "See all Related Articles" link is very useful for narrowing down searches. In the top right there can be a link to the journal website (here it is the ''British Journal of Cancer''). At the bottom of the abstract is a number called the PubMed ID number, which is PMID 18506174 in this instance. To generate a {{t1|cite journal}} template for Coleman's review, just copy the PMID number into [http://diberri.dyndns.org/cgi-bin/templatefiller/?type=pubmed_id&id= Diberri's tool.]
-Each search engine has its own quirks, advantages, and disadvantages, and often searches do not return the results that you need. It typically takes some experience and practice to recognize when a search has not been effective; even if you find some useful sources, you may have missed some other sources that would have been more useful, or you may get pages and pages of less-than-useful material.
+To do an advanced search with the same keywords, go back to the search screen, enter ''"breast cancer"'', as before, and then click on the "Limits" tab just below the search box. This takes you to a set of options that allow you to limit your search to particular dates, types of articles or topic areas. To search for meta-analyses, for example, tick that box in the section on Type of Article and hit "search". You will now get a list of about 460 meta-analyses that deal with breast cancer.
-Here is an example of how a query might work with Google Scholar. Suppose you are interested in the history of [[daylight saving time]]. As of this writing, the Google Scholar query ''[http://scholar.google.com/scholar?q=history+of+daylight+saving+time history of daylight saving time]'' returns about 31,100 sources; in the first page listing ten sources, only two are relevant. The better query ''[http://scholar.google.com/scholar?q=history+daylight-saving history daylight-saving]'' returns only 2,400 sources, but again, only two of the first ten sources are relevant. Clicking on "Recent articles" narrows [http://scholar.google.com/scholar?q=history+daylight-saving&as_ylo=2003 the search]'s results to 491 total articles published since 2003, where four of the first ten sources are relevant. Of these four sources, two are books and are not freely readable; one is freely readable and on the net; the other is also freely readable but you'll need a further web search to find it.
+If your Pubmed search finds a lot of sources, you can restrict yourself to the freely-readable ones by clicking on the "Limits" tab and checking the box labeled "Links to free full text".
-You should not rely solely on search engines to find sources, because they often miss sources. For example, the last-mentioned Google Scholar query missed many of the sources used in the Wikipedia section on the [[Daylight saving time #Origin|history of daylight saving time]], ranging from [[Berthold Ullman]]'s article "Daylight saving in ancient Rome" published in the ''Classical Journal'' in 1918, to Joseph Myers's "History of legal time in Britain", self-published at Cambridge University in 2007. A good strategy is to find a few recent high-quality sources, and then follow their citations to see what your search engine missed. It can also be helpful to do a plain web search rather than one of scholarly articles only.
-== Other biomedical databases ==
+== Other indexes ==
 Pubmed is not the only game in town for biomedical searching. There are alternatives.
+*Some search engines attempt to cover all scholarly sources. They are invaluable for topics not covered by the more-specialized indexes discussed above, and can provide useful sanity checks even for topics such as medicine that have more-specialized indexes. The best-known is [[Google Scholar]]; other engines include [[getCited]] and [[Scirus]]. A version of Google Scholar that automates generating citation templates is [http://www.srcf.ucam.org/~ms609/Wiki/Scholar WikiScholar].
 *The [[Cochrane Library]] contains a database of systematic reviews and meta-analyses and is a key resource in [[evidence-based medicine]]. Its reviews are generally considered to be very high in quality.