“Pharmacological Action” in PubMed has no True Equivalent in OVID MEDLINE

11 01 2012

Searching for EMBASE Subject Headings (the EMBASE index terms) for drugs is relatively straight forward in EMBASE.

When you want to search for aromatase inhibitors you first search for the Subject Heading mapping to aromatase inhibitors (aromatase inhibitor). Next you explode aromatase inhibitor/ if you are interested in all its narrower terms. If not, you search both for the general term aromatase inhibitor and those specific narrower terms you want to include.
Exploding aromatase inhibitor (exp aromatase inhibitor/) yields 15938 results. That is approximately twice what you get by searching aromatase inhibitor/ alone (not exploded). This yields 7434 hits.

It is different in MEDLINE. If you search for aromatase inhibitors in the MeSH database you get two suggestions.

The first index term “Aromatase Inhibitors” is a Mesh. It has no narrower terms.
Drug-Mesh are generally not arranged by working mechanism, but by chemical structure/type of compound. That is often confusing. Spironolactone for instance belongs to the MeSH Lactones (and Pregnenes) not to the MeSH Aldosterone Antagonists or Androgen Antagonist. Most Clinicians want to search for a group of compounds with the same mechanism of action, not the same biochemical family

The second term “Aromatase Inhibitors” [Pharmacological Action]  however does stand for the working mechanism. It does have narrower terms, including 2 MeSH terms (highlighted) and various substance names, also called Supplementary Concepts. 

For complete results you have to search for both MeSH and Pharmacological action: “Aromatase Inhibitors”[Mesh] yields 3930 records, whereas (“Aromatase Inhibitors”[Mesh]) OR “Aromatase Inhibitors” [Pharmacological Action] yields 6045. That is a lot more.

I usually don’t search PubMed, but OVID MEDLINE.

I know that Pharmacological Action-subheadings are important, so I tried to find the equivalent in OVID .

I found the MeSH Aromatase Inhibitors, but -unlike PubMed- OVID showed only two narrower Drug Terms (called Non-MeSH here versus MeSH in PubMed).

I found that odd.

I reasoned “Pharmacological action” might perhaps be combined with the MESH in OVID MEDLINE. This was later confirmed by Melissa Rethlefsen (see Twitter discussion below)

In Ovid MEDLINE I got 3937 hits with Aromatase Inhibitors/ and 5219 with exp Aromatase Inhibitors/ (thus including aminogluthemide or Fadrozole)

At this point I checked PubMed (shown above). Here I found  that “Aromatase Inhibitors”[Mesh] OR “Aromatase Inhibitors” [Pharmacological Action] yielded 6045 hits in PubMed, against 5219 in OVID MEDLINE for exp Aromatase Inhibitors/

The specific aromatase inhibitors Aminogluthemide/and Fadrozole/ [set 60] accounted fully for the difference  between exploded [set 59] and non-exploded Aromatase Inhibitors[set 58].

But what explained the gap of approximately 800 records between “Aromatase Inhibitors”[Mesh] OR “Aromatase Inhibitors”[Pharmacological Action]* in PubMed and exp aromatase inhibitors/ in OVID MEDLINE?

Could it be the substance names, mentioned under “Aromatase Inhibitors”[Pharmacological Action], I wondered?

Thus I added all the individual substance names in OVID MEDLINE (code= .rn.). See search set 61 below.

Indeed these accounted fully for the difference (set 62= 59 or 61 : the total number of hits in PubMed is similar)

It obviously is a mistake of OVID MEDLINE and I will inform them.

For the meanwhile, take care to add the individual substance names when you search for drug terms that have a pharmacological action-equivalent in PubMed. The substance names are not automatically searched when exploding the MeSH-term in OVID MEDLINE.

——–

For more info on Pharmacological action, see: http://www.nlm.nih.gov/bsd/disted/mesh/paterms.html

Twitter Discussion between me and Melissa Rethlefsen about the discrepancy between PubMed and OVID MEDLINE (again showing how helpful Twitter can be for immediate discussions and exchange of thoughts)

[read from bottom to top]

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Search OVID EMBASE and Get MEDLINE for Free…. without knowing it

19 10 2010

I have the impression that OVIDSP listens more to librarians than the NLM, who considers the end users of databases like PubMed more important, mainly because there are more of them. On the other hand NLM communicates PubMed’s changes better (NLM Technical Bulletin) and has easier to find tutorials & FAQs, namely at the PubMed homepage.

I gather that the new changes to the OVIDSP interface are the reason why two older OVID posts are the recent number 2 and 3 hits on my blog. My guess is that people are looking for some specific information on OVID’s interface changes that they can’t easily access otherwise.

But this post won’t address the technical changes. I will write about this later.

I just want to mention a few changes to the OVIDSP databases MEDLINE and EMBASE, some of them temporary, that could have been easily missed.

[1] First, somewhere in August, OVID MEDLINE contained only indexed PubMed articles. I know that OVID MEDLINE misses some papers PubMed already has -namely the “as supplied by publisher” subset-, but this time the difference was dramatic: “in data review” and “in process” papers weren’t found as well. I almost panicked, because if I missed that much in OVID MEDLINE, I would have to search PubMed as well, and adapt the search strategy…. and, since I already lost hours because of OVID’s extreme slowness at that time, I wasn’t looking forward to this.

According to an OVID-representative this change was not new, but was already there since (many) months. Had I been blind? I checked the printed search results of a search I performed in June. It was clear that the newer update found less records, meaning that some records were missed in the current (August) update. Furthermore the old Reference Manager database contained non-indexed records. So no problems then.

But to make a long story short. Don’t worry: this change disappeared as quickly as it came.
I would have doubted my own eyes, if my colleague hadn’t seen it too.

If you have done a MEDLINE OVID search in the second half of August you might like to check the results.

[2] Simultaneously there was another change. A change that is still there.

Did you know that OVID EMBASE contains MEDLINE records as well? I knew that you could search EMBASE.com for MEDLINE and EMBASE records using the “highly praised EMTREE“, but not that OVID EMBASE recently added these records too.

They are automatic found by the text-word searches and by the EMTREE already includes all of MeSH.

Should I be happy that I get these records for free?

No, I am not.

I always start with a MEDLINE search, which is optimized for MEDLINE (with regard to the MeSH).

Since indexing by  EMTREE is deep, I usually have (much) more noise (irrelevant hits) in EMBASE.

I do not want to have an extra number of MEDLINE-records in an uncontrolled way.

I can imagine though, that it would be worthwhile in case of a quick search in EMBASE alone: that could save time.
In my case, doing extensive searches for systematic reviews I want to be in control. I also want to show the number of articles from MEDLINE and the number of extra hits from EMBASE.

(Later I realized that a figure shown by the OVID representative wasn’t fair: they showed the hits obtained when searching EMBASE, MEDLINE and other databases in Venn diagrams: MEDLINE offered little extra beyond EMBASE, which is self-evident, considering that EMBASE includes almost all MEDLINE records.- But I only learned this later.)

It is no problem if you want to include these MEDLINE records, but it is easy to exclude them.

You can limit for MEDLINE or EMBASE records.

Suppose your last search set is 26.

Click Limits > Additional Limits > EMBASE (or MEDLINE)

Alternatively type: limit 26 to embase (resp limit 26 to medline) Added together they make 100%

If only they would have told us….


3. EMBASE OVID now also adds conference abstracts.

A good thing if you do an exhaustive search and want to include unpublished material as well (50% of the conference abstracts don’t get published).

You can still exclude them if you like  (see publication types to the right)

Here is what is written at EMBASE.com

Embase now contains almost 800 conferences and more than 260,000 conference abstracts, primarily from journals and journal supplements published in 2009 and 2010. Currently, conference abstracts are being added to Embase at the rate of 1,000 records per working day, each indexed with Emtree.
Conference information is not available from PubMed, and is significantly greater than BIOSIS conference coverage. (…)

4. And did you know that OVID has eliminated StopWords from MEDLINE and EMBASE? Since  a few years you can now search for words or phrases like is there hope.tw. Which is a very good thing, because it broadens the possibility to search for certain word strings. However, it isn’t generally known.

OVID changed it after complaints by many, including me and a few Cochrane colleagues. I thought I had written a post on it before, but I apparently I haven’t ;).

Credits

Thanks to Joost Daams who always has the latest news on OVID.

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Temporary Wrong OVID EMBASE Source Field.

10 12 2008

This post is only of interest to those who regularly search the EMBASE database from OVIDSP and load the records into Reference Manager or other reference management software, like Procite.

My colleague, Arnold, noticed that off half November the EMBASE records wouldn’t load properly into Reference Manager. This was due to the inclusion of the Publisher in the Source field.

New:
Source European Journal of Surgical Oncology. W.B. Saunders Ltd. 34(12)(pp 1285-1288), 2008. Date of Publication: December 2008.

Old:
Source European Journal of Surgical Oncology. 33(4)(pp 524-527), 2007. Date of Publication: May 2007.

Unfortunately it was not possible to make a new, completely working EMBASE-import filter.

Meanwhile our library has contacted OVID and they have restored the problem quite smoothly. The problem was apparently caused by the EMBASE reload of November 17th.

If you have loaded EMBASE records during the last 3 weeks it might be worthwhile to reload them in your reference manager software. Old EMBASE-filters should do the thing.