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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Advanced Neuritis in PubMed

8 03 2009

pubmed-logoAlmost a year ago (June 2008) I discussed PubMed’s Advanced Search Beta in a series entitled PubMed: Past, Present and Future. At that time I was not particularly impressed by disliked Advanced Search Beta and I still do.

November last year some of its features have improved: like the addition of a Clear Button, Focused Queries, providing links to the Clinical Queries and Special Queries pages, and the author/journal search has been extended with optional fields so that it looks more like the valuable Single Citation Mapper in the blue side bar of the Basic PubMed page. And there is a link to the MeSH-database (see NLM Technical Bulletin November 2008).
Although these are real improvements, the links to the Queries and to the MeSH database are inconspicuous, at the end of the page below all kind of limits. My major objections to the Advanced Search is that people are more inclined to narrow their search by using as many limits as possible (because these are so prominently present) and that the MeSH cannot be easily looked up and/or are wrongly translated. Previously I gave some examples, where lung cancer[mesh] was searched, whereas the MeSH is lung neoplasms, or where recurrent pregnancy loss[MeSH] returns no result, because the term is habitual abortion (see previous post).

I avoid Advanced Search as long as I can, but the problem is, the library-users don’t. They like to experiment, especially when they consider themselves as advanced searchers.

Last month a Neurologist asked me if I could check his search for a Diagnostic Systematic Review. A search for a Systematic Review should be comprehensive and thus contain both MeSH-terms (Controlled terms of MEDLINE) and free text words (tw).

He was a resident in Neurology for 5 years and knew how to search PubMed.

Below is the first part of his search.

((((((((motor neuropathy[MeSH Terms] OR motor neuron[tw] OR motor neuropathy[tw]) OR multifocal motor neuropathy[tw]) OR demyelinating neuropathy[tw]) OR multifocal demyelinating motor neuropathy[tw]) OR neuropathy[tw]) OR neuropathies[tw]) AND (((((((((((((((((((((((((…..

Grosso modo it looked all right and well structured. The awful number of brackets is often seen when people combine directly in PubMed (although I was already glad there were no brackets around every single word and he didn’t copy the entire translation from the Details-Tab). And some terms were superfluous: you don’t have to search for multiword terms with neuropathy (i.e. motor neuropathy) because these are already found by searching neuropathy.

So we made the search simpler, like this:

(motor neuropathy[MeSH Terms] OR motor neuron[tw] OR neuropathy[tw]) OR neuropathies[tw]) AND (………

Just to be sure I asked him: “Do you mind if we check the MeSH? Motor Neuropathy looks just fine, but you never know.”

To my surprise, typing motor neuropathy in the MeSH search bar yielded 4 suggestions, none of which was motor neuropathy.

pubmed-motor-neuropathy-mesh-1

The most suitable term appeared Neuritis. When bringing this MeSH-term to PubMed we got exactly the same number of hits as with Motor Neuropathy. Mere coincidence? No, the hits weren’t any different (#1 NOT #4 giving zero results).

pubmed-motor-neuropathy-search-1

Looking Up the Query Translation under the Details Tab confirmed my suspicion: motor neuropathy[mesh] was translated as “neuritis”[MeSH]. This is disturbing. Not only doesn’t there exist any MeSH specific for motor neuropathy, people are put on the wrong track since it looks like motor  neuropathy[mesh] is recognized as such.

pubmed-motor-neuropathy-search-1b-details

Then it came to my mind that I had seen a similar odd “translation” when using PubMed Advanced Search (see above). And I asked him: “Did you by any chance use the Advanced Search”, which he did.

To check this I searched in Advanced Search for the MeSH: motor neuropathy. And, yes indeed, the motor neuropathy[MeSH] was searched so it seemed. (in reality we now know: Neuritis was searched). The difference with searching the MeSH database is that here I know that I search for neuritis (I choose to), whereas the Advanced search misleads me by suggesting I’m searching for motor neuropathy.

pubmed-motor-neuropathy-2

pubmed-motor-neuropathy-2a

Why do I bother? Why don’t I just use motor neuropathy[mesh]. First because I don’t get what I want: I get neuritis[mesh] not neuropathy! Second, and most important, because it is not the most appropriate MeSH-term.

To find more appropriate MeSH I use a trick. I look for MeSH-terms assigned to articles, having motor neuropathy in their title, assuming that motor neuropathy is an important aspect of those papers.

Although you can look up MeSH assigned to each individual citation in PubMed in the citation display format, it takes a lot of time to go through the papers one at a time. Therefore I rather use GoPubMed or even better PubReminer for this purpose, because these give you a frequency list of the MeSH assigned.

Of the 379 hits found in GoPubMed, 219 were categorized as Motor Neuron Disease, 153 as Demyelinating Diseases and 145 as Polyneuropathies. These categories are MeSH term you can use for your search.

gopubmed-neuropathy

Similarly of the 380 references found in PubReminer, many papers were indexed with Motor Neuron Disease, Demyelinating Diseases, Polyneuropathies, peripheral nervous system diseases and motor neuron.

(Below are the number of papers, indexed with the indicated MESH in PubReminer; PubReminer shows the subheading coupled to the MeSH)

  • 65 Motor Neuron Disease/diagnosis
  • 32 Motor Neurons/physiology
  • 26 Demyelinating Diseases/diagnosis
  • 16 Peripheral nervous system diseases/diagnosis
  • 8 Polyneuropathies

Using this approach we were able to set up a more complete search in PubMed. Remember it was the neurologist’s purpose to to an exhaustive search, for a less exhaustive search we would have only used motor neuropath* and perhaps motor neuron disease[mesh].

How different is it when you use the OVID interface for searching MEDLINE.

When you type Motor Neuropathy, several MeSH are suggested, many of which are useful:

ovid-motor-neuropathy-1

When you click on Motor Neuron Disease, you see the hierarchal context and can choose which terms you would like to add. We choose not to explode Motor Neuron Disease, but only include one narrow term in our search: amyotrophic lateral sclerosis.

ovid-motor-neuropathy-2

Finally the first part of the search in MEDLINE (OVID) looked like this. It is rather broad but the second part of the search (not shown) puts it into context.

1. motor neuron disease/ or amyotrophic lateral sclerosis/
2. exp Motor Neurons/
3. Demyelinating Diseases/
4. neuromuscular diseases/ or peripheral nervous system diseases/ or neuritis/ or polyneuropathies/
5. (neuropathy or neuropathies).tw.
6. motor neuron*.tw.
7. or/1-6

OVID MEDLINE was easier to use, you get what you see (and want) and the search is easier to save and edit. Furthermore the entire MEDLINE search can be easily transformed to a search in EMBASE: just replace MESH by EMBASE keywords.

I’m not happy with the Advanced Search for reasons explained above. I don’t find the altered mapping and citation sensor a success either. I don’t like that they removed the blue side bar in some display formats. And I’m really getting depressed by NLM’s announcement (November 2008):

PubMed Advanced Search will soon no longer be a beta site. It is now the place to go to use features such as field searching and limits. In the near future the tabs for Limits, Preview/Index, History, Clipboard, and Details will be removed from the basic PubMed pages. History, Limits, Index of Fields, and a link to Details are available from the Advanced Search screen. A link for the Clipboard appears to the right of the search box on the PubMed screen when the Clipboard has content.

If I understand it correctly this means that Pubmed Advanced Search is taking over the basic search.

It looks that my original idea was right: PubMed is going for the mass, it is going for the Google-like quick searches by people that don’t know much about MEDLINE and don’t want to learn it. But you have to know some basic principles to get the most out of subject searching. It is such a pity, that PubMed tries to copy its clones, whereas it holds all the trumps. No other 3rd party tools offer the same possibilities that PubMed offers, although they are more suitable for certain purposes (see examples of GoPubMed and PubReMiner above).

At least make two interfaces, one for the beginner (the present Advanced Search) and one for librarians and other people doing subject searches.

But I don’t have the illusion that the people of PubMed/NLM will listen to me and I’m not going to contact them for a 3rd time. PubMed’s route is determined, I guess.





OVID-SP gives me RSI

20 05 2008

O.k. I don’t type well, have no ergonomic keyboard, mouse, chair or whatsoever, no software to urge a break, and I’m a little bit stressed these days, but the main reason that my shoulder, arm, elbow and wrist ache when typing (or even at rest) is introduction of OVID-SP.

OVID has changed it’s layout. It looks nice, and some tools are easier to find, but what is really bad for a heavy user and bad typist like me is the new interface.

The search history is below the search bar. The history shows the first search first and the last search last. As I said I’m a heavy user. A systematic search takes at least a few hours, and sometimes even a few days. It is a long road optimizing a search. Now in OVID every time I perform a search I have to scroll down looking for the last search, I have to think which new term I would like to add, which set(s) I want to combine or which set(s) I want to subtract. I scroll up to find the search numbers, I have to remember them: 62 not (46 or 36 or 63 or 66), scroll up again, fill in the search bar………… scroll down to look at the results….. Oh, that’s wrong, no hits….. Should have done (scroll up) 72 not (46 or 36 or 63 or 66). O.k. up again. oh I forgot, scroll down again….. No, that’s too far: I’m in the results section, scroll up, take another look, write it down so I wont’ forget, scroll up again, perform the search, scroll down, etcetera.

So it would have been far better if the search bar was under the last set in the search history (the history can be contracted if preferred, see TIP) or if the last search was shown first (like in PubMed).

In addition “the OVIDSP TIP” is in the way all the time, taking 1/3 of the active window and 1/2 of the print, making the search even look twice as long as it is. Why can’t I just click the TIP away. I have seen this a 1000 times. I know it by now. Please give me a simple pop-up.

Don’t think I hate OVID, I love it. But this is a development that is not very user friendly for the frequent user. I can’t help thinking that developers of databases like OVID, PubMed, Cochrane Library and TRIP just have the inexperienced quick searcher in mind when they try to improve the interface.

Do you experience the new interface the same way?

Scroll, scroll, scroll….. Up and down, up and down

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*****************************************************************

NL flag NL vlag

O.k. ik ben geen beste typer, ik heb geen ergonomisch keybord, muis, stoel of weet ik veel wat en geen computerprogramma dat me dwingt te pauzeren en ja ik ben de laatste tijd een beetje gestresst. Maar dat is niet de (enige) reden dat ik nu zo’n last heb van mijn schouder, arm, elleboog en pols, ook in rust. Dat komt namelijk vooral door de introductie van OVID-SP.

Sinds begin dit jaar draait OVID als OVID-SP. Het ziet er prachtig uit, frisse kleurtjes, sommige zaken zijn veel makkelijker te vinden. Maar er is niet heel goed nagedacht over de positie van de zoekregel en de zoekgeschiedenis. En dat is erg vervelend voor een intensieve gebruiker. Als ik voor een systematisch review zoek kan ik wel 1 tot enkele dagen bezig zijn.

Wat is nu het geval? De zoekgeschiedenis zit onder de zoekregel, maar de laatste zoekactie staat helemaal onderaan. Dus telkens als je een zoekactie hebt uitgevoerd, moet je weer naar beneden om te kijken hoe je verder moet. Eerst kijk je of de term iets nieuws oplevert, je gaat zoekacties combineren etcetera. Dan moet je weer naar boven scrollen om elke zoekactie uit te voeren, je vergeet het weer, moet weer naar beneden scrollen, scrollt tever door en komt in de resulaatsectie etcetera.

Als je maar een kleine zoekactie hebt heb je daar niet echt last van maar bij een opbouw van een lastige actie, waarvan de eerste 30-60 regels wel vaststaan, maar de rest niet, moet je echt nodeloos scrollen. Als je dat uren doet heb je echt een lamme arm. En stoppen durf ik ook niet echt, want het is me meermalen overkomen dat ik er dan uitgegooid werd.

Dus het zou beter geweest zijn als de zoekregel onder de laatste zoekactie van de (inklapbare) zoekgeschiedenis zou staan of als de laatste zoekactie het eerst getoond werd (zoals in PubMed).

Daar komt nog eens bij dat de “OVIDSP TIP” hinderlijk in de weg staat: het neemt bijna 1/3 van het beeld en 1/2 van de print in beslag en biedt na tig keer nou niet geweldig schokkende informatie. Waarom kun je het niet gewoon wegklikken?

Begrijp me goed, ik heb niets tegen OVID, integendeel. Het biedt zoveel meer, dat ik het graag gebruik. Maar deze verandering vind ik niet erg gebruikersvriendelijk. Ik heb echt het idee dat mensen die databases als OVID, PubMed, Cochrane Library en TRIP ontwikkelen veel meer aan de beginnende zoeker denken dan aan de ervaren rot in het vak.