“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]





PubMed’s Higher Sensitivity than OVID MEDLINE… & other Published Clichés.

21 08 2011

ResearchBlogging.orgIs it just me, or are biomedical papers about searching for a systematic review often of low quality or just too damn obvious? I’m seldom excited about papers dealing with optimal search strategies or peculiarities of PubMed, even though it is my specialty.
It is my impression, that many of the lower quality and/or less relevant papers are written by clinicians/researchers instead of information specialists (or at least no medical librarian as the first author).

I can’t help thinking that many of those authors just happen to see an odd feature in PubMed or encounter an unexpected  phenomenon in the process of searching for a systematic review.
They think: “Hey, that’s interesting” or “that’s odd. Lets write a paper about it.” An easy way to boost our scientific output!
What they don’t realize is that the published findings are often common knowledge to the experienced MEDLINE searchers.

Lets give two recent examples of what I think are redundant papers.

The first example is a letter under the heading “Clinical Observation” in Annals of Internal Medicine, entitled:

“Limitations of the MEDLINE Database in Constructing Meta-analyses”.[1]

As the authors rightly state “a thorough literature search is of utmost importance in constructing a meta-analysis. Since the PubMed interface from the National Library of Medicine is a cornerstone of many meta-analysis,  the authors (two MD’s) focused on the freely available PubMed” (with MEDLINE as its largest part).

The objective was:

“To assess the accuracy of MEDLINE’s “human” and “clinical trial” search limits, which are used by authors to focus literature searches on relevant articles.” (emphasis mine)

O.k…. Stop! I know enough. This paper should have be titled: “Limitation of Limits in MEDLINE”.

Limits are NOT DONE, when searching for a systematic review. For the simple reason that most limits (except language and dates) are MESH-terms.
It takes a while before the indexers have assigned a MESH to the papers and not all papers are correctly (or consistently) indexed. Thus, by using limits you will automatically miss recent, not yet, or not correctly indexed papers. Whereas it is your goal (or it should be) to find as many relevant papers as possible for your systematic review. And wouldn’t it be sad if you missed that one important RCT that was published just the other day?

On the other hand, one doesn’t want to drown in irrelevant papers. How can one reduce “noise” while minimizing the risk of loosing relevant papers?

  1. Use both MESH and textwords to “limit” you search, i.e. also search “trial” as textword, i.e. in title and abstract: trial[tiab]
  2. Use more synonyms and truncation (random*[tiab] OR  placebo[tiab])
  3. Don’t actively limit but use double negation. Thus to get rid of animal studies, don’t limit to humans (this is the same as combining with MeSH [mh]) but safely exclude animals as follows: NOT animals[mh] NOT humans[mh] (= exclude papers indexed with “animals” except when these papers are also indexed with “humans”).
  4. Use existing Methodological Filters (ready-made search strategies) designed to help focusing on study types. These filters are based on one or more of the above-mentioned principles (see earlier posts here and here).
    Simple Methodological Filters can be found at the PubMed Clinical Queries. For instance the narrow filter for Therapy not only searches for the Publication Type “Randomized controlled trial” (a limit), but also for randomized, controlled ànd  trial  as textwords.
    Usually broader (more sensitive) filters are used for systematic reviews. The Cochrane handbook proposes to use the following filter maximizing precision and sensitivity to identify randomized trials in PubMed (see http://www.cochrane-handbook.org/):
    (randomized controlled trial [pt] OR controlled clinical trial [pt] OR randomized [tiab] OR placebo [tiab] OR clinical trials as topic [mesh: noexp] OR randomly [tiab] OR trial [ti]) NOT (animals [mh] NOT humans [mh]).
    When few hits are obtained, one can either use a broader filter or no filter at all.

In other words, it is a beginner’s mistake to use limits when searching for a systematic review.
Besides that the authors publish what should be common knowledge (even our medical students learn it) they make many other (little) mistakes, their precise search is difficult to reproduce and far from complete. This is already addressed by Dutch colleagues in a comment [2].

The second paper is:

PubMed had a higher sensitivity than Ovid-MEDLINE in the search for systematic reviews [3], by Katchamart et al.

Again this paper focuses on the usefulness of PubMed to identify RCT’s for a systematic review, but it concentrates on the differences between PubMed and OVID in this respect. The paper starts with  explaining that PubMed:

provides access to bibliographic information in addition to MEDLINE, such as in-process citations (..), some OLDMEDLINE citations (….) citations that precede the date that a journal was selected for MEDLINE indexing, and some additional life science journals that submit full texts to PubMed Central and receive a qualitative review by NLM.

Given these “facts”, am I exaggerating when I am saying that the authors are pushing at an open door when their main conclusion is that PubMed retrieved more citations overall than Ovid-MEDLINE? The one (!) relevant article missed in OVID was a 2005 study published in a Japanese journal that MEDLINE started indexing in 2007. It was therefore in PubMed, but not in OVID MEDLINE.

An important aspect to keep in mind when searching OVID/MEDLINE ( I have earlier discussed here and here). But worth a paper?

Recently, after finishing an exhaustive search in OVID/MEDLINE, we noticed that we missed a RCT in PubMed, that was not yet available in OVID/MEDLINE.  I just added one sentence to the search methods:

Additionally, PubMed was searched for randomized controlled trials ahead of print, not yet included in OVID MEDLINE. 

Of course, I could have devoted a separate article to this finding. But it is so self-evident, that I don’t think it would be worth it.

The authors have expressed their findings in sensitivity (85% for Ovid-MEDLINE vs. 90% for PubMed, 5% is that ONE paper missing), precision and  number to read (comparable for OVID-MEDLINE and PubMed).

If I might venture another opinion: it looks like editors of medical and epidemiology journals quickly fall for “diagnostic parameters” on a topic that they don’t understand very well: library science.

The sensitivity/precision data found have little general value, because:

  • it concerns a single search on a single topic
  • there are few relevant papers (17- 18)
  • useful features of OVID MEDLINE that are not available in PubMed are not used. I.e. Adjacency searching could enhance the retrieval of relevant papers in OVID MEDLINE (adjacency=words searched within a specified maximal distance of each other)
  • the searches are not comparable, nor are the search field commands.

The latter is very important, if one doesn’t wish to compare apples and oranges.

Lets take a look at the first part of the search (which is in itself well structured and covers many synonyms).
First part of the search - Click to enlarge
This part of the search deals with the P: patients with rheumatoid arthritis (RA). The authors first search for relevant MeSH (set 1-5) and then for a few textwords. The MeSH are fine. The authors have chosen to use Arthritis, rheumatoid and a few narrower terms (MeSH-tree shown at the right). The authors have taken care to use the MeSH:noexp command in PubMed to prevent the automatic explosion of narrower terms in PubMed (although this is superfluous for MesH terms having no narrow terms, like Caplan syndrome etc.).

But the fields chosen for the free text search (sets 6-9) are not comparable at all.

In OVID the mp. field is used, whereas all fields or even no fields are used in PubMed.

I am not even fond of the uncontrolled use of .mp (I rather search in title and abstract, remember we already have the proper MESH-terms), but all fields is even broader than .mp.

In general a .mp. search looks in the Title, Original Title, Abstract, Subject Heading, Name of Substance, and Registry Word fields. All fields would be .af in OVID not .mp.

Searching for rheumatism in OVID using the .mp field yields 7879 hits against 31390 hits when one searches in the .af field.

Thus 4 times as much. Extra fields searched are for instance the journal and the address field. One finds all articles in the journal Arthritis & Rheumatism for instance [line 6], or papers co-authored by someone of the dept. of rheumatoid surgery [line 9]

Worse, in PubMed the “all fields” command doesn’t prevent the automatic mapping.

In PubMed, Rheumatism[All Fields] is translated as follows:

“rheumatic diseases”[MeSH Terms] OR (“rheumatic”[All Fields] AND “diseases”[All Fields]) OR “rheumatic diseases”[All Fields] OR “rheumatism”[All Fields]

Oops, Rheumatism[All Fields] is searched as the (exploded!) MeSH rheumatic diseases. Thus rheumatic diseases (not included in the MeSH-search) plus all its narrower terms! This makes the entire first part of the PubMed search obsolete (where the authors searched for non-exploded specific terms). It explains the large difference in hits with rheumatism between PubMed and OVID/MEDLINE: 11910 vs 6945.

Not only do the authors use this .mp and [all fields] command instead of the preferred [tiab] field, they also apply this broader field to the existing (optimized) Cochrane filter, that uses [tiab]. Finally they use limits!

Well anyway, I hope that I made my point that useful comparison between strategies can only be made if optimal strategies and comparable  strategies are used. Sensitivity doesn’t mean anything here.

Coming back to my original point. I do think that some conclusions of these papers are “good to know”. As a matter of fact it should be basic knowledge for those planning an exhaustive search for a systematic review. We do not need bad studies to show this.

Perhaps an expert paper (or a series) on this topic, understandable for clinicians, would be of more value.

Or the recognition that such search papers should be designed and written by librarians with ample experience in searching for systematic reviews.

NOTE:
* = truncation=search for different word endings; [tiab] = title and abstract; [ti]=title; mh=mesh; pt=publication type

Photo credit

The image is taken from the Dragonfly-blog; here the Flickr-image Brain Vocab Sketch by labguest was adapted by adding the Pubmed logo.

References

  1. Winchester DE, & Bavry AA (2010). Limitations of the MEDLINE database in constructing meta-analyses. Annals of internal medicine, 153 (5), 347-8 PMID: 20820050
  2. Leclercq E, Kramer B, & Schats W (2011). Limitations of the MEDLINE database in constructing meta-analyses. Annals of internal medicine, 154 (5) PMID: 21357916
  3. Katchamart W, Faulkner A, Feldman B, Tomlinson G, & Bombardier C (2011). PubMed had a higher sensitivity than Ovid-MEDLINE in the search for systematic reviews. Journal of clinical epidemiology, 64 (7), 805-7 PMID: 20926257
  4. Search OVID EMBASE and Get MEDLINE for Free…. without knowing it (laikaspoetnik.wordpress.com 2010/10/19/)
  5. 10 + 1 PubMed Tips for Residents (and their Instructors) (laikaspoetnik.wordpress.com 2009/06/30)
  6. Adding Methodological filters to myncbi (laikaspoetnik.wordpress.com 2009/11/26/)
  7. Search filters 1. An Introduction (laikaspoetnik.wordpress.com 2009/01/22/)




3rd Call for Submissions for “Medical Information Matters”: Tools for Searching the Biomedical Literature

8 05 2011

It takes some doing to breathe life into Medical Information Matters” (blog carnival about medical  information).
A month ago I wrote a 2nd call for submissions post for this blog carnival. Unfortunately the next host, Martin Fenner, didn’t have time to finish a blog post and has come up with a new (interesting) variation on the theme “A Wish list for better medical information”.

Martin asks you to philosophize, blog and/or comment about “Tools for Searching the Biomedical Literature.

You can base your contribution on a recent (editable) survey of 28 different PubMed derivative tools by Zhiyong Lu (NCBI) [1].

Thus, write your thoughts on the various PubMed derivative tools mentioned here or write about your own favorite 3rd party PubMed tool (included or not).

For details, see Martin’s blog post announcing this upcoming edition. The Blog Carnival FAQs are here.

And if you don’t have time to write about this topic, you may still find the survey useful, as well as the views of others on this topic. So check out Martin’s blog Gobbledygook once in a while to see if the blog edition has been posted.

Note [1]: If you have already submitted a post to the carnival, or would like to write about another theme, we will take care that your post (if relevant)  will be included in this or the next edition. You can always submit here.

Note [2]: Would you like to host “Medical Information Matters” at your blog? Please comment here or write to: laika dot spoetnik at gmail dot com. We need hosts for June, July, August and September (submission deadline first Saturday of every month, posting on the next Tuesday)

  1. Lu Z. PubMed and beyond: a survey of web tools for searching biomedical literature. Database. 2011 Jan;2011. doi: http://dx.doi.org/10.1093/database/baq036




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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Problems with Disappearing Set Numbers in PubMed’s Clinical Queries

18 10 2010

In some upcoming posts I will address various problems related to the changing interfaces of bibliographic databases.

We, librarians and end users, are overwhelmed by a flood of so-called upgrades, which often fail to bring the improvements that were promised….. or which go hand-in-hand with temporary glitches.

Christina of Christina’s Lis Rant even made rundown of the new interfaces of last summer. Although she didn’t include OVID MEDLINE/EMBASE, the Cochrane Library and Reference manager in her list, the total number of changed interfaces reached 22 !

As a matter of fact, the Cochrane Library was suffering some outages yesterday, to repair some bugs. So I will postpone my coverage of the Cochrane bugs a little.

And OVID send out a notice last week: This week Ovid will be deploying a software release of the OvidSPplatform that will add new functionality and address improvements to some existing functionality.”

In this post I will confine myself to the PubMed Clinical Queries. According to Christina PubMed changes “were a bit ago”, but PubMed continuously tweaks  its interface, often without paying much attention to its effects.

Back in July, I already covered that the redesign of the PubMed Clinical Queries was no improvement for people who wanted to do more than a quick and dirty search.

It was no longer possible to enter a set number in the Clinical Queries search bar. Thus it wasn’t possible to set up a search in PubMed first and to then enter the final set number in the Clinical Queries. This bug was repaired promptly.

From then on, the set number could be entered again in the clinical queries.

However, one bug was replaced by another: next, search numbers were disappearing from the search history.

I will use the example I used before: I want to know if spironolactone reduces hirsutism in women with PCOS, and if it works better than cyproterone acetate.

Since little is published about this topic,  I only search for  hirsutism and spironolactone. These terms  map correctly with  MeSH terms. In the MeSH database I also see (under “see also”) that spironolactone belongs to the aldosterone antagonists, so I broaden spironolactone (#2) with “Aldosterone antagonists”[pharmacological Action] using “OR” (set #7). My last set (#8) consists of #1 (hirsutism) AND #7 (#2 OR #6)

Next I go to the Clinical Queries in the Advanced Search and enter #8. (now possible again).

I change the Therapy Filter from “broad”  to “narrow”, because the broad filter gives too much noise.

In the clinical queries you see only the first five results.

Apparently even the clinical queries are now designed to just take a quick look at the most recent results, but of course, that is NOT what we are trying to achieve when we search for (the best) evidence.

To see all results for the narrow therapy filter I have to go back to the Clinical Queries again and click on see all (27) [5]

A bit of a long way about. But it gets longer…


The 27 hits, that result from combining the Narrow therapy filter with my search #8 appears. This is set #9.
Note it is a lower number than set #11 (search + systematic review filter).

Meanwhile set #9 has disappeared from my history.

This is a nuisance if I want to use this set further or if I want to give an overview of my search, i.e. for a presentation.

There are several tricks by which this flaw can be overcome. But they are all cumbersome.

1. Just add set number (#11 in this case, which is the last search (#8) + 3 more) to the search history (you have to remember the search set number though).

This is the set number remembered by the system. As you see in the history, you “miss” certain sets. #3 to #5 are for instance are searches you performed in the MeSH-database, which show up in the History of the MeSH database, but not in PubMed’s history.

The Clinical query set number is still there, but it doesn’t show either. Apparently the 3 clinical query-subsets yield a separate set number, whether the search is truly performed or not. In this case  #11 for (#8) AND systematic[sb], #9 for (#8) AND (Therapy/Narrow[filter]). And #10 for (#8) AND the medical genetics filter.

In this way you have all results in your history. It isn’t immediately clear, however, what these sets represent.

2. Use the commands rather than going to the clinical queries.

Thus type in the search bar: #8 AND systematic[sb]

And then: #8 AND (Therapy/Narrow[filter])

It is easiest to keep all filters in Word/Notepad and copy/paste each time you need the filter

3. Add clinical queries as filters to your personal NCBI account so that the filters show up each time you do a search in PubMed. This post describes how to do it.

Anyway these remain just tricks to try to make something right that is wrong.

Furthermore it makes it more difficult to explain the usefulness of the clinical queries to doctors and medical students. Explaining option 3 takes too long in a short course, option 1 seems illogical and 2 is hard to remember.

Thus we want to keep the set numbers in the history, at least.

A while ago Dieuwke Brand notified the NLM of this problem.

Only recently she received an answer saying that:

we are aware of the continuing problem.  The problem remains on our programmers’ list of items to investigate.  Unfortunately, because this problem appears to be limited to very few users, it has been listed as a low priority.

Only after a second Dutch medical librarian confirmed the problem to the NLM, saying it not only affects one or two librarians, but all the students we teach (~1000-2000 students/university/yearly), they realized that it was a more widespread problem than Dieuwke Brand’s personal problem. Now the problem has a higher priority.

Where is the time that a problem was taken for what it was? As another librarian sighed: Apparently something is only a problem if many people complain about it.

Now I know this (I regarded Dieuwke as a delegate of all Dutch Clinical Librarians), I realize that I have to “complain” myself, each time I and/or my colleagues encounter a problem.

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Medical Information Matters 2.8 is up!

15 10 2010

The new edition of Medical Information Matters (formerly Medlibs round) is up at Danielhooker.com.

The main theme is “Programs in libraries or medical education”.
Besides two posts from this blog (A Filter for Finding Animal Studies in PubMed” and more on the topic: An Educator by Chance) the following topics are included: a new MeSH (inclusion under mild librarian pressure), PubMed in your pocket, embedding Google Gadgets in normal webpages and experiences with introducing social bookmarking to medical students.
If you find this description to cryptic (and I bet you do), then I invite you to read the entire post here. I found it a very pleasant read.

Since we are already midway October, I would like to invite you to start submitting here (blog carnival submission form).

Our next host is Dean Giustini of the The Search Principle blog. The deadline is in about 3 weeks ( November 6th).

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Ten Years of PubMed Central: a Good Thing that’s Only Going to Get Better.

26 05 2010

PubMed Central (PMC) is a free digital archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health (NIH), developed and managed by NIH’s National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM) (see PMC overview).
PMC is a central repository for biomedical peer reviewed literature in the same way as NCBI’s GenBank is the public archive of DNA sequences. The idea behind it “that giving all users free access to the material in PubMed Central is the best way to ensure the durability and utility of the electronical archive as technology changes over time and to integrate the literature with other information resources at NLM”.
Many journals are already involved, although most of them adhere to restrictions (i.e. availability after 1 year). For list see http://www.ncbi.nlm.nih.gov/pmc/journals/

PMC, the brain child of Harold Varmus, once the Director of the National Institutes of Health, celebrated its 10 year anniversary earlier this year.

For this occasion Dr. Lipman, Director of the NCBI, gave an overview of past and future plans for the NIH’s archive of biomedical research articles. See videotape of the Columbia University Libraries below:

Vodpod videos no longer available.

more about “Ten Years of PubMed Central | Scholar…“, posted with vodpod

The main points raised by David Lipman (appr. time given if you want to learn more about it; the text below is not a transcription, but a summary in my own words):

PAST/PRESENT

  • >7:00. BiomedCental (taken over by Spinger) and PLoS ONE show that Open Access can be a sustaining way in Publishing Science.
  • 13:23 Publisher keeps the copyright. He may stop depositing but the content already deposited remains in PMC.
  • 13:50 PMC is also an obligatory repository for author manuscripts under various funding agencies mandates, like the NIH and the UK welcome trust.
  • 14:31 One of the ideas from the beginning was to crosslink the literature with the underlying molecular and other databases. For instance NCBI is capable of mining out the information in the archived text and connecting it to the compound and the protein structure database.
  • 16:50 There is a back issue digitization for the journals that are participating, enabling to find research that you wouldn’t have easily found otherwise.
  • PMC has become international (not restricted to USA)
  • The PMC archive becomes more useful if it becomes more comprehensive
  • Before PMC you could do a Google Scholar search and find a paper in PubMed, that appeared funded by NIH, but then you had to pay $30 for it in order to get it. That’s hard to explain to the taxpayers (Lipman had a hard time explaining it to his dad who was looking for medical information online). This was the impetus for making the results of NIH-sponsored results freely available.

PRESENT/FUTURE

  • 23:00 Discovery initiative: is the use of tracking tools to find out which changes to the website work for users and which don’t. Thus modifications should lead to alterations in users behavior (statistics is easy with millions of users). Discovery initiative led to development and improvement of sensors, like sensors for disease names, drug names, genes and citations. What is being measured is if people click through (if it isn’t interesting, they usually don’t) and how quickly they find results. Motto: train the machine, not the users.
  • 30:37 We changed the looks of PMC. Planning to make a better presentation on the i-phone and on broad monitors.
  • 31:40. There are almost 2 million articles in PubMed Central, 585 journals fully participate in PMC
  • 32.30 It takes very long to publish a paper, even in Open Access papers. Therefore a lot of people are not publishing little discoveries, which are not important enough to put a lot of time in. Publishing should be almost as easy as writing a blog, but with peer review. This requires a new type of journal, with peer review, but with instant feedback from readers and reviewers and rapid response to comments. The Google Knol authoring system offers a fast and simple authoring system where authors (with a Google profile) can collaborate and compose the article on the server. Uploading of documents and figures is easy, the article updates are simple and fast, there is a simple workflow for moderators. After the paper is accepted you press a button, the paper is immediately available and the next day PMC automatically gets the XML content. There is also a simple Reference Manager included to paste citations.
  • Principle: How you can start a journal with this system (see Figure). Till now: 60 articles in PLOS Currents Influenza. There are also plans for other journals: the CDC is announcing a Systematic Reviews journal, for instance.

QUESTIONS (>39:30):

  • Process by which “KNOL-journal” is considered for inclusion in NLM?
    • Decide: is it in scope?, implicit policy (health peer review being done), who are the people involved, look at a dozen articles.
  • As the content in PMC increases, will it become possible to search in the full text, just like in Google Scholar?
    • Actually the full text is searchable in PMC as apposed to PubMed, but we are not that happy with the full text retrieval. Even with a really good approach, searching full text works just a little bit better than searching PubMed.
      We are incorporating more of the information of PMC into PubMed, and are working on a separate image database with all the figures from books and articles in PMC (with other search possibilities). Subsets of book(chapter)s (like practice guidelines) will get PubMed abstracts and become searchable in PubMed as well.
  • Are there ways to track a full list of our institutions OA articles in PMC (not picking up everything in PubMed)
    • Likely NIH will be contacting offices responsible for research to let them know what articles are out of compliance,  get their assistance in making sure that those get in.
    • Authors can easily update the electornic My Bibliography (in My NCBI in PubMed).
    • Author ID project, involves computational disambiguation. Where you are asked if you are the author of a paper if you didn’t include it. It may also be possible to have automatic reporting to the institutions.
  • What did it took politically to get the appropriation bill passed (PMC initiative)?
    • Congress always pushed more open access, because it was already spending money on the research. Most of the initiative came more from librarians (i.e. small libraries not having sufficient access) and government, than from the NIH.
  • Is there way to narrow down to NIH, free full text papers from PMC?
    • In PubMed, you can filter free full text articles in general via the limits.
  • Are all the articles deposited in PMC submitted the final manuscript?
    • Generally, yes.

HT: @bentoth on Twitter





Adding Methodological Filters to MyNCBI

26 11 2009

Idea: Arnold Leenders
Text: “Laika”

Methodological Search Filters can help to narrow down a search by enriching for studies with a certain study design or methodology. PubMed has build-in methodological filters, the so called Clinical Queries for domains (like therapy and diagnosis) and for evidence based papers (like theSystematic Review subset” in Pubmed). These searches are often useful to quickly find evidence on a topic or to perform a CAT (Critical Appraised Topic). More exhaustive searches require broader  filters not incorporated in PubMed. (See Search Filters. 1. An Introduction.).

The Redesign of PubMed has made it more difficult to apply Clinical Queries after a search has been optimized. You can still go directly to the clinical queries (on the front page) and fill in some terms, but we rather advise to build the strategy first, check the terms and combine your search with filters afterwards.

Suppose you would like to find out whether spironolactone effectively reduces hirsutism in a female with PCOS (see 10+ 1 Pubmed Tips for Residents and their Instructors, Tip 9). You first check that the main concepts hirsutism and spironactone are o.k. (i.e. they map automatically with the correct MeSH). Applying the clinical queries at this stage would require you to scroll down the page each time you use them.

Instead you can use filters in My NCBI for that purpose. My NCBI is your (free) personal space for saving searches, results, PubMed preferences, for creating automatic email alerts and for creating Search Filters.
The My NCBI-option is at the upper right of the PubMed page. You first have to create a free account.

To activate or create filters, go to [1] My NCBI and click on [2] Search Filters.

Since our purpose is to make filters for PubMed, choose [3] PubMed from the list of NCBI-databases.

Under Frequently Requested Filters you find the most popular Limit options. You can choose any of the optional filters for future use. This works faster than searching for the appropriate limit each time. You can for instance use the filter for humans to exclude animals studies.

The Filters we are going to use are under “Browse Filters”, Subcategory Properties….

….. under Clinical Queries (Domains, i.e. therapy) and Subsets (Systematic Review Filters)

You can choose any filter you like. I choose the Systematic Review Filter (under Subsets) and the Therapy/Narrow Filter under  Clinical Queries.

In addition you can add custom filters. For instance you might want to add a sensitive Cochrane RCT filter, if you perform broad searches. Click Custom Filters, give the filter a name and copy/paste the search string you want to use as filter.

Control via “Run Filter” if the Filter works (the number of hits are shown) and SAVE the filter.

Next you have to activate the filters you want to use. Note there is a limit of five 15 filters (including custom filters) that can be selected and listed in My Filters. [edited: July 5th, hattip Tanya Feddern-Bekcan]

Under  My Filters you now see the Filters you have chosen or created.

From now on I can use these filters to limit my search. So lets go to my original search in “Advanced Search”. Unfiltered, search #3 (hirsutism  AND spironolactone) has 197 hits.

When you click on the number of hits you arrive at the results page.
At the right are the filters with the number of results of your search combined with these filters (between brackets).

When you click at the Systematic Reviews link you see the 11 results, most of them very relevant. Filters (except the Custom Filters) can be appended to the search (and thus saved) by clicking the yellow + button.

Each time you do a search (and you’re logged in into My NCBI)  the filtered results are automatically shown at the right.

Clinical Queries zijn vaak handig als je evidence zoekt of een CAT (Critical Appraised Topic) maakt. In de nieuwe versie van PubMed zijn de Clinical Queries echter moeilijker te vinden. Daarom is het handig om bepaalde ‘Clinical Queries’ op te nemen in ‘My NCBI’. Deze queries bevinden zich onder Browse Filters (mogelijkheid onder Search Filters)

Het is ook mogelijk speciale zoekfilters te creëeren, zoals b.v. het Cochrane highly sensitive filter voor RCT’s. Dit kan onder Custom Filters.

Controleer wel via ‘Run Filter” of het filter werkt en sla het daarna op.

Daarna moet je het filter nog activeren door het hokje aan te vinken. Dus je zou alle filters van de ‘Clinical study category’ kunnen opnemen en deze afhankelijk van het domein van de vraag kunnen activeren.

Zo heb je altijd alle filters bij de hand. De resultaten worden automatisch getoond (aan de rechterkant).

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The New PubMed: Trick or Treat?

31 10 2009

31-10-2009 8-53-21 the new pubmed entry

The New PubMed: Trick or Treat?

After a long days work, when looking at the screen,

there it was: PubMed’s new interface, so it seemed,

But one blink – and it had gone

To come back the following dawn.

The change itself was long announced,

we could play with the new “Advanced”.

Still I postponed and procrastinated,

Pointless: the new PubMed couldn’t wait

any longer, but this Redesign isn’t it for me….

Sure, the front page looks web-2-ish, minimalistic & clean,

which is perfect for the Google-Generation,

the hurry-don’t think-just-slash-i-got-one-publication-

PhD’s, for whom all alterations have been made. 2989360212_882aff28d8 trick or treat

Some people think you just have to wait

& see and get used to it.

but I’m already fed up with it.

I know you all think it is just a Librarian-rant.

Librarians they can stick with the new “Advanced”,

“Advanced” however, is just Limits & Index…

But boy did they make this page look complex!

Sure, the basic researchers seem to be quite pleased.

Busy physicians too, they think it is more easy.

They tell me librarian not to wine:

Go MEDLINE OVID! we stay with this design.”

This is no new idea, didn’t you know:

I long seek refuge in OVID MEDLINE, although1810987271_9044fb5ca0 candy

only for exhaustive searches, that much is true.

So why -having this alternative- am I still feeling blue?

Well, I’m not complaining for myself, but for you.

I don’t speak as a searcher, but as a teacher too.

It is so frustrating that I have to explain to you

that each step you take is now multiplied by two.

NLM says all functionalities are still there.

The problem is you have to find where

I don’t mind the present front page,

but the so called “Advanced” gives no advantage,

at least not for doctors searching evidence.

I teach them “Googling doesn’t make sense“.

Just choose the most important concepts,

work from the History and search words separately.

Begin to find the MesH-terms, and although it is complex

add textwords too, to find papers not yet indexed.

Combine synonyms with “OR” and concepts with “AND”,

Go to the Clinical Queries and use the appropriate command”..

But now it takes so many steps. It is a BIG FAIL

sometimes. You start at the front page, look at the Details,

mapping is wrong, go to Advanced, scroll, scroll, scroll..

to Mesh, “send to Pubmed”, where am I? out of control,

again on the Start page? Go to Advanced again.

Away with Limit and other boxes! – I don’t need them!

The Index yields a MeSH that doesn’t exist?!

Darn, via automatic mapping the multi-term-word is split

in 3 separate words, complete out of context,

as I see In the Details -so I have to re-enter them,

And where have the Clinical Queries gone?

Right, have to scroll the entire “Advanced” page… Yawn…

While it is true that I’m a “bit” exagerating,

my point is that the new PubMed creation

could have been so much better:

not only the functionality, the route also matters.

The redesign is a missed opportunity,

to build an entire new PubMed you see.

The interface is still quite orthodox.2946761628_2eb3e8b009 bittersweet

I want clickable and movable boxes

with MESH in clouds thru which you can “walk”

and Clinical Queries that you can drag and drop

with a mapping tool-you can adjust,***

and savings of your settings, that is  a must.

“But the new PubMed”, you ask me

“what is it: a-trick-or-a-treat?”….

“It looks like a nicely wrapped candy,

but tasting a bit bittersweet?!”

Notes

* These links come from Eagle Dawg-blog: Pubmed: All in the attitude

** doesn’t apply to quick and dirty searches on the front page

*** i.e. allow to split or not

Photo Credits:

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PubMed® Redesign is here… to try.

1 10 2009

30-9-2009 23-35-13 pubmed try the redisgned PubmedWe have been waiting months for it, it has been announced several times, we have seen previews, webinars, small changes were introduced over time, till suddenly, today (30-09-09) there was a bright button on the front page of PubMed inviting you to “Try the redesigned PubMed”.

You can click on the button or go directly to http://preview.ncbi.nlm.nih.gov/pubmed.

As a matter of fact @pfanderson already informed fellow tweeting librarians about the PubMed preview link the day before (see Tweet) and within minutes the entire Twitter Librarian community was buzzing about it (see the start of the discussion, taken from Eagledawg post on this subject). People thought that the link was not meant to be public, because it was picked up from a webinar, and no official announcement had been made. But today the new PubMed (first time I see the ®?) is live -although still optional-, accompanied by an official announcement of the redesign at NLM Technichal Bulletin (later followed by a post on Linkout in the PubMed Redesign).

Patricia has depicted the changes in a Powerpoint Slide (see post at Emerging Technologies Librarian: What I most want to be able to find in the new Pubmed.

My take on this:

  • While the front page looks “Functional, clear, ‘modern’” as  someone on Patricia’s blogpost said, I agree with David Rothman, that there are “TONS of wasted screen real estate on that front page”. Why is the search bar hidden at the top?
  • The buttons themselves are relatively easy to find and understand. Although some options like “PubMed Quickstart” are not always straightforward (mistaken for “easy search option” instead of HELP). But that is probably just a matter of getting used to the new design.
  • But what happens if you search: The Details-tab is no longer there and the History is gone. Yes, Limits, Preview/Index, History and Details tabs’ features have been consolidated in Advanced search (see techbull).
  • This means in practice that the front page only lends itself for performing one-search-at-the–time, without being able to check the Details-tab (only indirectly by going to Advanced Search). It needs little imagination to foresee what will happen. Users will type in (“Google”) terms, the combinations of which are inspired by the “Auto suggest” function. There is no way to check the mapping of the words, there is no way to combine MeSH and textwords (unless you know them by head). Basically this search page only lends itself to “quick and dirty searches”, the “One string only”-Google searches. The new PubMed Interface is all about “Serependity”. Some people may like that. I don’t (mostly…).
  • Once done it is easier to save the search or take and RSS-feed (but given the quality of the search…) .
  • No functionalities have gone, all there has been done is replacing the functions. But this can (and in my view) has implications for the functionality of PubMed itself,
  • Thus advanced searchers have to use the “Advanced Search”. But in contrast to the front page this one is full of limits, indexes and bars that should be wisely (and often not) applied. For people searching for evidence this site is not handy at all. In fact, I find it a real nuisance to use.
    I agree with Creaky: some 3rd party tools seem more adequate for beginners/simple searches. But for advanced searches I will move to OVID MEDLINE, for good. Alas I still have to teach my clients and students PubMed. It will be quite a task to see how that can be best done.

So I conclude:

“It is possible that I am about to preach to the choir, but I am going to come right out and say it anyway. I hate PubMed. I hate it with a burning passion. For a site that is as vital to scientific progress as PubMed is, their search engine is shamefully bad. It’s embarrassingly, frustratingly, painfully bad.”

Looks familiar? Anna Kushnir said that almost one and a half year ago... And Anna did get her way. Her ranting elicited a response of Dr. Lipman of the NCBI who reassured her “that a number of changes are underway that will make PubMed work better for her and many other users”. Pubmed is now “easy to use” for people like her. Will there come a PubMed that suits me too?


You may also want to read:

  • Kraftylibrarian: The PubMed redesign is here
  • Pubmed changes at the front door (2009/04/01/)
  • Advanced Neuritis in Pubmed (2009/03/08/)
  • Pubmed: past present and future – part iii: the future (2008/06/27/)
  • Pubmed: past present and future – part-ii/ the present (2008/06/15/)
  • Pubmed: past present and future – part-i/ the past(2008/06/11/)
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    MEDLIB’s ROUND 1.6

    27 09 2009

    shht-librarian-costume1Welcome to the sixth edition of MedLib’s Round, a blog carnival of “excellent blog posts in the field of medical librarianship”.

    First I have to apologize for the postponement in publication. There were so few submissions (5, including one on this blog), that I needed more time to find some material myself. Time that I didn’t have at that moment.

    After a flying start with many volunteering hosts and submissions the enthusiasm for the Medlib’s Round seems to have faded somewhat. There are far less submissions. Luckily there is a core of  enthusiastic people regularly submitting to the Medlib’s Round and I’m very grateful for that. However, there are many more bloggers out there, who also write very useful MedLib stuff. Why aren’t they contributing? Are they not aware of the round, do they lack time, don’t they like blog carnivals? Should the rounds be better promoted or differently organized? I know that postponement does the round no good, but it is a bit the chicken-and-egg problem. Anyway, I would like to hear your thoughts on this.

    But lets start…..

    Social Media

    A previous host and regular contributor to the round, Nikki Dettmar (@eagledagw) of the Eagle Dawg Blog makes a good point in  “Social Media & Emergency Preparedness: Can Your Family Text?”: “Does your family know to text when there is an emergency? Traditional phone lines may be down and traditional methods of communication may not be working.” Learn about an upcoming drill conducted by a national safety foundation and the Federal Emergency Management Agency (FEMA) over the next few months to use texting and social media channels for emergency communication. And don’t forget to instruct your mother. By the way, the use of Twitter is included in the advise.

    Another regular contributor to the Medlib’s round is Ves Dimov (@DrVes). Dr. Dimov is an Allergy and Immunology Fellow at Creighton University and the author of the Clinical Cases and Images – Blog. Blogging for several years and with more than 7000 RSS readers we can trust him for some good advice on blogging In What makes a blogger go on in a field where so many others stop, fail and disappear?” Dr Ves shortly gives 4 reasons and several tips from his own experience.

    Google Health

    Alisha

    Speaking about blogging, it is only a half year ago that Alisha Miles (@alisha764) started with her blog Alisha 764 saying: “I am no longer a mushroom, I am now a tree.” Which refers to @sandnsurf‘s post: Is Twitter the essential blogging nutrient and his comment on my blog: “the most important thing is that you are actually a tree in this ecosystem, you are out there experimenting, thinking and trying to drive the revolution further…Most of my colleagues are still mushrooms….
    Alisha, who is a contributor to this round from the start, has definitely developed into a full blossoming tree, a top librarian blogger and tweeter,  She is featured, for instance, in Novoseek’s top 10 medical librarian list (as all current librarian submitters with a public blog).
    Her submitted post is a classical post already. It is quite long (hear, hear who is saying) but offers good information. In “Google Health® Information: Surprising Facts” she describes the pros and cons of Google Health®, concluding:

    “It is a good product; however, it should be used with caution. Remember Google Health® is not bound by HIPPA, resources should always be double or triple checked, the Google® Health Drug Interaction program is missing some key interactions, and the Google Health® Topics are missing the reference section, reviewer information, and date stamp.

    Again, I applaud Google® for its efforts and for including links to MedlinePlus® as a trusted resource. As with any information source, even MedlinePlus®, all information should be checked against at least 1 other source.”

    With regard to MedlinePlus and Google, Rachel Walden wrote a post: “Where is MedlinePlus in Google Drug Search Results?” where she notices that Google searches for drug information no longer seem to return results from MedlinePlus and FDA pages.

    PubMed, MeSH and the like

    Rachel

    Rachel Walden (@rachel_w on Twitter) is the woman behind the successful blog Women’s Health News and writer for Our bodies ourselves. She not only knows a lot about women’s health and medical information, but she is always ready to reach a helping hand or join a discussion on Twitter, which is actually a quality of all MEDLIB round contributors.  In “Improving the Findability of Evidence & Literature on DoulasRachel describes  the lack of a specific MeSH for “Doula” in PubMed. A doula is an assistant who provides various forms of non-medical and non-midwifery support (physical and emotional) in the childbirth process. MeSH (or Medical Subject Headings) are controlled terms in MEDLINE, or as explained by Rachel:

    MeSH are “right” terms to use to conduct a literature search in PubMed, it can really help to start with the MeSH term database, because you know those are the official subject terms being assigned to the articles. MeSH is a hierarchy, and it can help you focus a search, or expand it when needed, by moving up and down the list of subject words. It’s a nice tool to have, when it works.

    As highlighted by Rachel, this gap in the MeSH makes searching less efficient and less precise: for instance, nursing and midwivery are too broad terms. But instead of whining, Rachel decided to do something about it. Via this form she send the National Library of Medicine a request to add the “doula” concept to the MeSH terms. I would recommend others to do the same when terms they search for are not (appropriately) covered by the MESH.

    Librarian Mark Rabnett agrees hartfully with Rachel as he has encountered exactly the problems and yes, “there is no question that this is a satisfactorily distinct and widely accepted term, and its entry into the MeSH pantheon is long overdue.”
    On his blog Gossypobima Mark had earlier posted the “Top 5 results to improve PubMedfrom the brainstorming suggestions during the Canadian Health Libraries Association conference. These include “Adding adjacency and real string searching” (YES!) and “Improval of the MeSH database”. His group found “The MeSH database stiff and laboured , and the visual display of the thesaurus and subheadings not intuitive, the ‘Add To’ feature for inserting MeSH terms to a search box kludgy, and the searching for MeSH headings difficult and unpredictable. [..] So he concludes with: “We need a MeSH mashup.”

    Wouldn’t that be wonderful indeed? Rather than the current “enhancements”, why not introduce some web 2.0 tools in PubMed? As Patricia Anderson tweeted a long time ago:

    “It would be so cool to do a # search, then display word cloud of top major MESH terms in results.”

    Yes I would like a visual MeSH, but even better, one that would show up in the sidebar and that you would be able to “walk up and down (and sideways) and with “drag and drop to your search possibilities”. That would be cool. My imagination runs away with me when I think of it.

    Grey Literature

    cappadocia1_bigger shamshaNot having a public blog @shamsha has contributed to this round by writing a guest post on this blog. This interesting post is about grey literature: what is grey literature, why do you need it and why not have guidelines for searching grey literature? She gives many tips and a wealth of references, including links to her own delicious page and a wonderful resource from the Canadian Agency for Drugs and Technologies in Health.

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

    This concludes the official part of this MEDLIB’s September round.

    The next round is hosted by Alisha Miles on her blog Alisha 764.
    Officially the deadline is next Saturday
    . (But it may be postponed a little. If so I will post the new deadline here)
    Anyway, Alisha is looking forward to your posts. So send them in as soon as possible HERE at the Blog Carnival form.
    (registration required; see the medlibs-archive for more information.
    )

    And some good news about the round: We already have hosts for November and December, namely Walter Jessen of Highlight Health and Valentin Vivier of at the Novoseek Blog.

    Would you like to host the Medlibs round in 2010? It is never to early! Please dm me at twitter, comment on this post or write an email to laika.spoetnik@gmail.com.

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

    Bonus

    Here are some other posts I also found worth while to read.
    (I didn’t include too recent ones, so they can be included in the next round)

    Dr Mike Cadogan (@Sandnsurf) writes  frequently about medical information on his blog Life in the fast Lane (his blog has moved to http://lifeinthefastlane.com, so check out old links that you may have). One of the co-authors of the blog,  Chris Nickson (precordialthump) gives emergency physicians advise how to deal withinformation-overload”. Needless to say the tips are useful to all people dealing with medical information-overload.

    Dr Shock also writes a lot about medical information and web 2.0 tools. Here a video he posted about iPhone and iPod Touch as a Medical Tool.

    Another good source for info about i-phones, palms can be found on http://palmdoc.net/. Medical librarians frequently writing about this subject include the Krafty Librarian and David Rothman.

    I don’t have a palm or sophisticated phone, nor does our library supports its use, so I choose some other posts from these excellent bloggers.

    From the KraftyLibrarian Michelle: Rapid Research about Rapid Research Notes , a new resource developed by the National Center for Biotechnology Information (NCBI) to quickly disseminate the research results to the public in an open access archive. Michelle wonders why only PLOS-articles are included and not other quality information from for instance EBSCO and Cochrane.

    From palmdoc : Evernote as your peripheral brain (Evernote is a note taking application)

    Rapid Research Notes is also covered by Alison of Dragonfly, a previous host of the round. She also mentions the fact that Medlineplus is now on Twitter.

    David Rothman ‘s paternity leave seems over since he posts several interesting posts per week on his blog Davidrothman.net. Typically he shortly refers to a new tool or a post he encountered, like:

    Dean Giustini of the The Search Principle blog published part one of a Top Fifty Twitter Users List in Medicine and has written a post on Using Twitter to manage information.

    Patricia Anderson of Emerging Technologies Librarian is been very active lately with posts on social media, like “Conversation and Context in Social Media (Cautionary Tales)“, with four scenarios, including the Clinical Reader fiasco. And as always she has a lot of tips on web 2.0 tools. There is for instance a post on Listening Tools to track what your community is saying about you or to you and about Social Media Metrics

    Another techy librarian working at the National University of Singapore is Aaron Tay. Aaron Tay (@aarontay) is not working in the field of medicine, but his web 2.0 tips are useful for anyone, and his blog Musings about Librarianship is certainly a must for libraries that want to use web  2.0 tools to the benefit of their users. Personally, I found the tips onViewing research alerts – full text within Google reader very useful.

    Phil Bradley highlights Google Fast Flip and Bing’s Visual Search.

    Alan from The health Informaticist discusses in “NHS Evidence boo vs guidelinesfinder hurrah” that a simple search for backpain in NHS Evidence yielded 1320 hits (!) of which only a handful are useful guidelines, whereas the good old Guidelines Finder (now a ’specialist collection’), yields 47 mostly useful and relevant hits. He ends this discussion with a  request to NICE: please keep the specialist collections. And I agree.

    On EBM and Clinical Support Librarians@UCHC this month an overview of current news, advisories and practical information about Pandemic Flu (H1N1) .

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    his imagination had run away
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    10 + 1 PubMed Tips for Residents (and their Instructors)

    30 06 2009

    The next Grand Round, the weekly rotating carnival featuring the best medical blog posts, will be hosted by Edwin Leap, a practicing emergency physician. Because the  Grand Rounds are on June 30 -one day before July 1st, which is the traditional start of that thrilling and harrowing journey called ‘residency,’- Edwin decided to make the following theme: ‘What would you like to say to future physicians?’

    I’m sure doctors will give plenty advice on the skills that are most important (i.e., see here). But what advice can I give them? I’m not a doctor. I could give them some examples of “how not to behave”, but I’m sure that will be covered well by fellow patients, and probably also by blogging nurses (i.e. see the perfect Intern Survival Guide by Mother Jones RN).

    So I will stay with my expertise: searching. And to make it workable, I will restrict myself to PubMed, the platform that offers free  access to 18 million citations from MEDLINE and other life science journals. 18 million, that is a tremendous amount of literature! And that is one of the main problems: the sheer amount makes it very difficult to “pick the needle from the haystack”.

    Of course, literature searching is not a primary skill for doctors. It is far more important that a doctor is knowledgeable, handy, and a good communicator (!). But at one time or another, he/she has to look things up or wants to check whether current practice is the best way. Or at the very least, doctors have to stay on top of the best and  latest information. And that’s when they need to search for medical information.

    Below are some tips for beginning as well as more advanced PubMed searchers. Obviously, these are only tips, this post is no tutorial and I give but a few elaborate examples. However, I plan to show entire searches in future posts. Perhaps you can help me by sending in examples or asking questions/propose cases.

    Here are the 10 PubMed tips:

    Tip 1 : Look before you leap.
    Before even thinking of going to the PubMed site, consider whether this is the most obvious source to begin with. First decide whether you have a back- or a foreground question.
    A background question asks for general knowledge and/or “facts” (questions often starting with who, what, when, why, which). “How can one  diagnose appendicitis?” “Which treatments are available for advanced prostate cancer?”  These questions can be best answered by textbooks, handbooks and certain databases. UpToDate is usually perfect for these kind of questions. A question like “Which dose of drug X should I prescribe to a woman of 65 kg with disease Y.” looks very specific, but can generally be looked up in a Pharmacopeia (“general knowledge”). Some subjects are covered by in-house protocols or specialist guidelines.

    When you have a foreground question it is often better (especially for those “new” to the subject) to search evidence in aggregate or pre-filtered resources, like National Guideline Clearinghouse, the TRIP-database and/or the Cochrane Library. This will save you time, because it lowers the number needed to read: individual studies have been sought, selected, appraised and summarized for you.

    Besides PubMed there are also so called 3rd party Pubmed/MEDLINE tools, which can be handy for certain questions or approaches. I’m in the middle of writing about these tools, so keep in touch. Meanwhile you may want to read an excellent overview of many of these tools and more on the blog of Mike Cadogan: Medical search for physicians. Earlier I also wrote about the handy use of PubReminer and GoPubMed to analyze text words and MeSH-terms.

    Although very useful and intuitive, most of these 3rd party PubMed tools don’t have the power of PubMed and are not suitable for elaborate searches.

    Tip 2: A review article from PubMed.
    PubMed can be useful for quickly finding good reviews.
    Below is one such example. A few months ago, Bertalan Mesko (intern then) asked advice on twitter, because his professor had difficulties finding the cause of recurrent acute pancreatitis in a young adult. Considering this was a background question- I just did a quick and dirty search as follows:

    • Go to PubMed: www.pubmed.gov
    • Type acute pancreatitis in the search bar (pancreatitis may be ‘safer’, but will yield more results).
    • Click the Limits Tab and tick off the following options:
      • Facultative: Links to free full text (if you have no subscriptions/access to the medical library)
      • Facultative: Added to PubMed in the last 5 years (or read the first few hits)
      • Subsets: Core Clinical Journals
      • Type of article: Review
      • Tag-Terms: Title.
    • Click: Go

    28-6-2009 12-12-32 PubMed acute pancreatitis  sonder language restr

    So you search for acute pancreatitis in the title of review articles in core (English) clinical Journals. There are just 28 results in the last 5 years, including reviews in the Lancet and NEJM.

    28-6-2009 12-38-45 results acute pancreatitis kort 4 vd 28 its

    The Lancet review gives me a good suggestion:

    In most patients, acute pancreatitis is caused by gallstone obstruction or alcohol, and no genetic testing is needed. However, unexplained recurrent acute pancreatitis might be associated with known genetic mutations in the cationic trypsinogen gene protease serine 1 (PRSS1), SPINK1, or CFTR. Mutations in the PRSS1 gene are seen in most patients with hereditary pancreatitis. In the most frequent mutations, the function of trypsinogen is increased, causing premature enzyme activation and autolysis of acinar cells.

    Note that I didn’t limit on age and I didn’t add recurrent to the search, as I’m looking for a review that may discuss many forms of this disease in all age categories. Recurrent or young adult may not be mentioned in the abstract (nor in the MeSH), so I may miss important overviews if I add these terms to my search.

    If you get to many hits,  you may always narrow the search later.

    A similar approach has been used by drW to search for review articles on heparin induced thrombocytopenia (part 1 and 2).

    UpToDate is a good source as well, ..and clinical experience. Ves Dimov responded on Twitter that he had described a similar hereditary pancreatitis case on his blog.

    Note that at the end of the summer Limits will be under the Advanced Search.#

    Tip 3: PubMed is just one NCBI-database.
    As you may infer from the official web address of PubMed: http://www.ncbi.nlm.nih.gov/, PubMed is (just) one of the (freely available) databases of NCBI (National Center for Biotechnology Information) . If you click on the NCBI-logo (in PubMed) you reach the Entrez cross-database search page. Most databases are particularly suited for genetics, genomics and proteomics. Several of the residents I know are also involved in research  and may make ample use of GEO (gene expression database) and/or other databases.

    If you type for instance acute pancreatitis in the search bar, you see the hits per database, including the PubMed and MeSH database. In this case OMIM seems the most interesting of the genetic databases. OMIM is the “Online Mendelian Inheritance in Man” database. It contains full-text, referenced overviews with information on all known Mendelian disorders and over 12,000 genes and is intended for intended for use primarily by physicians and researchers.

    29-6-2009 2-58-03 NCBI acute pancreatitis

    There are 33 hits in OMIM which we could limit further (using the Limit Tab) to for instance the chromosome. Hits 3-5 describes the genes mentioned in the Lancet review and gives references to relevant studies. There is even an overview of labs performing certain tests (see for instance here)

    29-6-2009 23-53-39 OMIM 12

    In stead of going to Entrez, you can also directly search OMIM from the PubMed database (see Figure)

    30-6-2009 11-18-27 3x oMIM

    Tip 4: Looking up Citations
    One of the recent alterations to PubMed is that you can just type the title in PubMed’s search bar to find a specific article. You can also type in other specifications or an entire reference. But it doesn’t always work. When you type Lancet acute pancreatitis you get too many papers (if you would look for a primary study) but if you copy the following reference from Google: Frossard JL, et al. Acute pancreatitis Lancet 2008; 371(9607) you will get zero results. This is because different Journals have different reference-styles (order, initials, punctuation) and people often make mistakes while citing.

    Another possibility, much loved by librarians because of its versatility, is the Single Citation Matcher in the blue side bar. # You can fill in any field you like and some fields like “author name” have an auto-fill function.

    In this case I searched for the “Author name” Frossard JL (tick “only first author“) and the First page: 143.

    I get exactly 1 paper: the correct one.

    30-6-2009 1-06-47 SCM

    Tip 5: Saving your search and making alerts: RSS and MyNCBI
    It is important for a doctor to keep up with the new developments in your field. There are ample possibilities in PubMed. One is RSS. A previous post descibes how it can be created in PubMed.

    Another possibility is MyNCBI. Old fashioned? Not at all. In PubMed, I find it more useful and easier than RSS. You can find MyNCBI at the upper right or in the blue side bar#.

    You have to create a free account. Once you do that, you can save searches (single searches or set numbers, but NOT the entire Search History). You can immediately save a search after performing it [1] or you can left-click the set number in the History, in this case #14, and a pop-up with options appears [2]

    30-6-2009 2-02-47 save search

    Searches can be saved, and executed/adapted at later timepoints or can be used to create an alert. Alerts can be mailed at any frequency you like. If searches overlap it is good to combine them, so you don’t read the same items twice (or more).

    Other possibilities are: “Save Collections” (individual articles), make filters (see Tip 1) and share them.
    The Save function also works in some other NCBI-databases

    A nice gadget: under preferences, you can activate a highlight function: When logged in, the terms you search for are highlighted in the desired colors. That’s why acute pancreatitis and review are highlighted yellow in the PubMed search shown above.

    For more information see the FAQ

    30-6-2009 2-45-29 myncbi2

    Tip 6: Stop Googling PubMed: why you find too much or too little

    O.k. this is something you may not want to give up, because you’re from the Internet generation and you’re used to intuitive interfaces and searching by trial and error. You’re used to just take a glance at the first few hits out of thousands of records ranked by “relevance” , that exactly match the terms you entered.

    This is not what you should aim for in PubMed: finding a paper because the authors use exactly the same words as you search for – and looking at the first few hits (there is no ranking in PubMed, hits are shown chronologically) do not necessarily mean it is the most relevant to you.  It only matters if the study answers your question (for your particular patient), and if it is of good quality.

    Thus, don’t aim for wording similarities, aim to find the papers that provide you (and your particular patient) with the best answer.

    How do you do that?

    It depends on your question, but generally speaking it is not the best thing to type a whole sentence or the entire PICO in the search bar.

    Usually it is best to search per term and start with the most important term first and leave out the terms that do not really matter.

    So how would you search for the following question?

    Does  spironolactone (anti-androgenic) effectively reduce hirsutism in a female with PCOS? Is it safe and is it comparable to Cyproterone acetate?

    Some people type: PCOS hirsutism spironolactone treatment cyproterone acetate and add gender and age as well. This yields a few results which are on the topic, but yet you may miss the most relevant ones.

    A better way is to search for the two most important concepts: hirsutism AND spironolactone and to look for systematic reviews and RCT’s because these provide the best evidence (see TIP 9). If necessary PCOS can be added afterwards.

    Treatment is usually a superfluous term. It is (usually) better to look for RCT’s or -second best “cohort studies” (because these are the best study designs assessing effectiveness of interventions). Also take care not to apply unnecessary limits.

    Always ask yourself: is this word crucial? And does adding this word/limit reduce the chance that I find a relevant paper?

    Tip 7: Use Details to see how PubMed interpreted (mapped) your search

    Whether you use tip 6 or not, at the very least, check the translation of your search by clicking the Details Tab. Yes, your search is interpreted or ‘mapped’, didn’t you know? That is usually a good thing, because PubMed’s keywords (MeSH) are automatically found, if you use terms that PubMed considers as synonyms for certain MeSH. This can enhance your search, but sometimes the translation is either wrong or you didn’t use the correct word (according to PubMed).

    So if you check the search PCOS hirsutism spironolactone you will see that hirsutism and spironolactone are correctly mapped to a MeSH, whereas PCOS is not. Seeing this you must be alarmed, because it is very likely that there is a MeSH for such a common disease. The correct MeSH is polycystic ovary syndrome. But in this case you might as well leave PCOS from the search.

    30-6-2009 4-05-06 details pcosSometimes your term is wrongly translated. If you search for (early) mobilization (of patients), PubMed will translate this as: “metabolism”[MeSH Terms] (as well as “metabolism”[subheading], that is a qualification of a MeSH term). You can imagine that this may easily result in many irrelevant papers. Rather you should use MesH terms like early ambulation and/or the opposite: immobilization. (How, I will tell you in advanced Tips, to be published later)

    By taking ONE second to check Details you become aware of wrong translations and can do something about it. Exclude the term or modify the search. Or you can see that the translation is ok and leave it like that.

    Tip 8: MeSH or textwords?

    There are people who merely use MeSH and people who swear by textwords. I use them both.

    MeSH are keywords, added by indexers to the record. It would be a pity if you would miss relevant MeSH-terms, because this will inevitably lead to missing relevant articles.

    MeSH are incredibly useful for finding a group of diseases. Suppose I would like to search for the usefulness of exercise to lessen fatigue in cancer patients (no matter which cancer). If I just type cancer in the search bar, this term is not only translated into the MeSH neoplasms, but it is also automatically exploded, which means that all narrower terms (terms lower in hierarchy) are also searched for. Thus papers are found whether they are indexed with neoplasms, lymphoma or breast neoplasms.

    On the other hand, if you use only MeSH you will miss new non-indexed papers or ‘wrongly’ indexed papers, while some terms may not even have an appropriate MeSH.

    Therefore I usually use both MeSH and free textwords.

    In the above example it is sufficient to search for hirsutism AND spironolactone. By checking “Details” you know you’re searching for the right MeSH as well.

    If the MeSH is very different from the textwords you may search for both , thus: in case of early mobilization you may search:

    early ambulation[mh] OR immobilization[mh] OR early mobili* (* means that you truncate the term and find early mobilised/mobilized, moblisation(s) etc. =Note that when you use an asterisk there is no longer any mapping with the MeSH!!).

    Tip 9: Searching for Evidence: Clinical Queries or other search filters

    When u search for the best evidence, Clinical Queries may be very handy. These are prefab search filters that aim to find the best evidence.

    It is best to first search aggregate evidence by using the systematic review filter, which is really much broader because it also searches for reviews of clinical trials, evidence-based medicine and guidelines.

    You just can type some terms in the Search box, but I prefer to make a basic search in PubMed’s main page first (to check the terms) and to fill in the set number, i.e. #9, later. (see Figure)

    30-6-2009 13-33-33 Clinical Queries

    30-6-2009 13-41-52 SR spironolactoneYou only get 10 very relevant hits, including one synthesis of evidence in Clinical Evidence, several Cochrane Reviews and other systematic reviews. Since these are all very recent papers you may decide to stop here.
    If you like, you can check for individual trials as well by searching by Clinical Study Category (choose the default: therapy narrow and enter search #9 again). This gives 24 hits.

    One word of caution: Not all filters are that good. The Systematic Review Filter and the Narrow Therapy filter are quite good for a quick search though. Tip: you can adapt the filters yourselves.

    Tip 10: Search Logic (and Boolean operators)

    What do you think you search for if you type: hand OR arm AND foot?

    You probably mean to search for (hand or arm) AND foot, but Pubmed follows another logic, depending on the order of the words. In this case it puts (invisible) brackets round arm and foot, not hand or arm. Result: you find far more (irrelevant) articles, because you retrieve every(!) article using the word “hand” and a few extra with (arm and foot).

    29-6-2009 1-44-31 hand foot pubmedYou can keep it under control by placing the brackets yourselves.
    With complex searches I rather combine synonyms with OR and  concepts with AND using the history. It looks like this:

    30-6-2009 14-17-36 foot arm history(when you don’t add operators PubMed uses the AND-operator, thus #8 #9 means #8 AND #9).
    You can add another term to the search as well, or apply a clinical query or limit. The final search you can save in MyNCBI. It shows the search with the appropriate brackets when you execute it.

    Besides OR (synonyms) and AND (narrowing) you have the boolean operator NOT.

    Please, generally do not use NOT to get rid of articles that are irrelevant, but rather try to select positively. Why? Because by using NOT you might exclude relevant articles.

    Suppose you want to find articles about nosebleeds in children by using NOT adults. Then you also exclude articles about adults AND children.

    NOT can be very handy however to subtract searches from each other. Suppose you have screened 100 articles (#1) and you get a brilliant idea using another word, which gives set #5. You can go through 120 articles, but you can also subtract the two searches from each other: #5 NOT #1 : and you only have to check 20 instead of 12o records.

    Extra Tip (10+1): Use your library and librarian

    As an extra tip, this final and probably most useful tip.
    Follow library courses if you didn’t do so already during our internship, ask your librarian to help setting up a search for an automatic alert and to deduplicate results from different databases (i.e. MEDLINE and EMBASE) and ask the help of your librarian if you want to perform exhaustive or difficult searches or if you just want some advice. It is no shame to go to your librarian. We’re there for you.

    Let me end with a statement of a fellow librarian (Suzanne Bakker, freely adapted):

    “Doctors learn what a Hb-test is, but that doesn’t mean that they have to do the lab test themselves, each time a patient needs a test?! The same applies to searching. It is good that doctors learn the basic stuff, and understand some pitfalls, but they need not become information specialist”

    You don’t need to become an information specialist to become a very good doctor…

    ———————————————–

    #Some functionalities may move from the current page (tabs and blue side bar) to the advanced search this summer

    Note: Thanks to Edwin Leap who had the patience to await my post, while it was going out of hand and getting much bigger than intended…





    New OvidSP-release, Version 2 – Part I

    21 08 2008

    Thursday August 14th, the new OVID-release went live.

    It seems that the release comes in two phases, the first focusing on workflow improvement and the second on new features (My Projects, a workspace area for saving and managing files, and Ovid Universal SearchTM, a cross-platform search) (see OVID-SP latest news ; OVID-SP-screenshots and blogpost of Michelle Kraft; follow this link to register for a webex course).

    The following changes have now been implemented: (Note that I avoid the word ‘enhancements’, because I’ developed an allergy against the recent abuse of this term, although in this particular case “enhancement” may be justified)

    * A new Multi-Field Search tab.
    Makes me think of advanced search beta in PubMed, or searching in the Cochrane Library, just as it reminds Michelle Kraft of EBSCO-searching. Like Michelle says, this tab basically allows you to easily search for multiple things within multiple fields all at one time. Perhaps useful for the beginner, but not of much use to the advanced searcher, who knows the field codes by head.

    * New and Improved User Workflow Tools

    1. Collapsible Search Aid box
    2. Results Manager is collapsible and available above and below the main search box
    3. Ability to move the Search History above the main search box, sort searches in ascending or descending order, and identify each search by search type
    4. Customize common limits on the main search page
    5. Ability to create, edit, and add multiple annotations to a citation
    6. Browse Books and Browse Journals links are now on the Select a Database page
    7. Browser support for adjusting font size
    8. When logged into their personal accounts, users will see their name and institution.

    To begin with the last point, I was unpleasantly surprised that I had to fill in a whole list of details (name, address, institution) when I assessed one of my saved searches. With the emphasis on one. I’ve literally a few dozens of accounts, at least one for each patron. Should I fill in the patron’s name or mine?…each time? Dee (on twitter) said she just filled in 0 in most boxes. You can also press the back button.
    OVID apparently requires this personally identifiable information for My Projects so you can create a community to collaborate with others later on.

    But what an improvements! 🙂 This is really what I had hoped for (see this post on the new OVID SP; and a previous one about Ovid causing RSI). ‘All’ boxes collapsible, and movable… Although I first didn’t succeed in moving the Search History, but via the OVID-SP-screenshots I found out that it was just a little grey square you had to press (with a pop-up if you move your mouse over it, see figure above). No more endless scrolling, no more pain in my wrists after a whole day searching. Almost, almost ideal… If..If …the Search Tip wasn’t so prominent. 😦 As I said before, the Tip (that never gave me any useful information) fills 1/3 of the search screen. Because of this, the unnecessary addition of the field “Search Type” and the broad columns, the search history itself comprises less than 1/4th of the screen. Thus it is difficult to keep a good overview over large searches (see for instance the screenshot and the video below )

    Compare the “usual view”

    with the search in “print” format

    And see the original search in this ultrashort video:

    I’m not the only one that dislikes the Tipbox. According to a recently finished survey on the original OvidSP-version redesign earlier this year the number one thing people wanted to change was to remove or hide the Ovid Tips (see PDF of Danielle Worster’s and Debbie Pledge’s poster here). Overall one of the main concerns was the usage of screen space by the new design including features- including the Tips on the right hand side and the new placement of Results Manager.

    But, as Danielle points out at her (shared) blog The healthinformaticist, the response was quite heterogenous, what was “annoying” to one person was “fine” to another! And vice versa!

    With Danielle I wonder how the recent changes will be perceived. Will the people who complained about the new interface be pleased with the new arrangements? And what about the people that just thought it was fine? And those who’s main frustration was the adaptation to the new interface? One librarian sighed at the MEDLIB-list: “what is the credibitiy of the library in promoting the 3rd Ovid advanced search version in less than a year over the relatively consistent PubMed interface?” It is interesting how perceptions can differ. Personally I find it much harder to explain why functionalities (like ATM!) change radically while the interface looks the same (and are therefore not noticed).

    Isn’t it most important that adaptations represent (1) improvements, (2) preferably easy to understand? Of course there is a limit to the number of substantial changes and their frequency. We know that the second update of OvidSP version 2 lies ahead and I sure wish that it will be soon followed by a third one that brings us an optional TIP-box. I don’t hope that the suggestion raised at Danielle’s blog, that “the Tip-box was created for advertising (commercials?) to recover the cost of all these (unnecessary) changes” is true.
    More basic changes concerning Reference Manager as discussed by Krafty are also welcomed, at least by me.

    ——————–

    Afgelopen week, op donderdag 14 augustus, “ging de nieuwe OVID release in de lucht”.
    De release gaat in 2 stappen. Deze eerste stap dient om het zoekproces te versoepelen, bij de 2e komen er nieuwe functionaliteiten bij (My Projects en Ovid Universal SearchTM) (zie OVID-SP nieuws ; OVID-SP-screenshots, blogpost van Michelle Kraft; en volg evt. deze link om u op te geven voor een webex instructie).

    Dit zijn in grote lijnen de veranderingen:

    * Multi-Field Search tab.
    Een manier om tegelijk op verschillende termen in verschillende velden te zoeken. Misschien handig voor de beginner, maar voor een gevorderde die de commando’s kent werkt advanced search veel sneller.

    * Nieuwe Tools

    1. Inklapbare Search Aid (nooit gebruikt)
    2. Results Manager inklapbaar; zowel boven als onder het zoekvak aanwezig.
    3. Zoekgeschiedenis verplaatsbaar, sorteren in op- of aflopende volgorde. Elk zoektype aangeduid.
    4. Algemene limieten op de hoofdpagina zijn aangepast .
    5. Mogelijkheid tot het maken van notitities bij een record.
    6. Browse Books and Browse Journals links zijn nu aanwezig op de “Select a Database” pagina.
    7. Grootte van het lettertype kan aangepast
    8. Na inloggen (op persoonlijk account) verschijnt naam en instituut.

    Om met dat laatste te beginnen, ik werd nogal onaangenaam verrast dat ik een hele waslijst met gegevens moest invullen (naam, adres instituut, titel, beroep etc) toen ik één van mijn opgeslagen searches wilde openen. Met de nadruk op één. Ik heb namelijk tientallen accounts, tenminste 1 voor elke klant. Moet ik mijn of zijn/haar naam invullen? Elke keer opnieuw? Dee (op twitter) zei dat ze gewoon 0 in alle vakjes invulde. Je kunt ook ‘n pagina terug gaan in je browser.
    OVID heeft kennelijk deze persoonlijke gegevens nodig voor ‘My Projects’ zodat je later een eigen samenwerkingsgroep kunt creeeren.

    Maar wat een verbetering zeg, deze versie, geweldig! 🙂 Hier had ik aan het begin van het jaar niet op durven hopen (zie bijv. dit bericht over OVID en RSI). Bijna alle vakjes inklapbaar, of verplaatsbaar… Hoewel het wel even duurde voordat ik door had hoe je de Zoekgeschiedenis nu kon verplaatsen (niet dat ik dat wilde, maar om ff te checku)… maar de OVID-SP-screenshots brachten uitkomst: je moest gewoon op een klein grijs blokje rechtsboven klikken (zie Figuur hierboven). De toelichting verschijnt als je er met de muis overgaat, maar dat moet je maar net weten.
    Geen eindeloos gescroll meer, geen pijn meer in mijn polsen na een-hele-dag-Ovid-zoeken. Haast ideaal, ware het niet … dat de zoektip nog steeds zo prominent in beeld staat. Zoals ik al eerder heb gezegd neemt de (voor mij nutteloze) TIP 1/3 van het zoekscherm in horizontale richting in beslag. Daarnaast is in de zoekgeschiedenis ook nog een extra kolom toegevoegd (zoektype) en zijn veel kolommen onnodig breed. Resultaat: zoekactie wordt gecomprimeerd tot 1/4e van het scherm. Het is dan moeilijk om overzicht te behouden, het leest naar en je moet alsnog scrollen (zie fig en video hierboven).

    Gelukkig sta ik niet alleen. Uit een recent onderzoek naar de tevredenheid van ervaren informatiespecialisten over de OvidSP-makeover begin dit jaar, bleek dat het verwijderen of verbergen van de OvidSP Tip met stip op nummer 1 van het wensenlijstje stond (zie hier voor poster van Danielle Worster en Debbie Pledge). In het algemeen was de ruimte-inname door het nieuwe design een veelgehoorde klacht.

    Maar zoals Danielle op haar (gedeelde) blog The healthinformaticist vermeld, was de respons nogal uiteenlopend. Wat de een vervelend vond, vond de andere wel best!

    Ik ben, met Danielle, benieuwd hoe men tegen de huidige veranderingen aankijkt. Zullen de mensen die klaagden over de nieuwe interface nu wel tevreden zijn? En de mensen die het allemaal juist prima vonden? Of diegenen wier grootste frustatie het steeds weer wennen aan de nieuwe interface was? Een informatiespecialist verzuchtte hoe je als bibliotheek nog geloofwaardig kunt zijn als je in minder dan een jaar 3x een nieuwe Ovid advanced search moet promoten terwijl PubMed redelijk hetzelfde blijft” Grappig hoe verschillend mensen tegen iets aan kunnen kijken. Zelf vind ik het veel moeilijker uit te leggen waarom een ogenschijnlijk identiek Pubmed achter de schermen toch de zoekactie anders uitvoert (ATM).

    Is het niet het belangrijkste dat de veranderingen die doorgevoerd worden ook verbeteringen zijn en niet te moeilijk op te pakken? Natuurlijk is er een grens aan hoe veel en hoe vaak je een interface verandert. We weten dat er een 2e update van OvidSP version 2 in het verschiet ligt en ik mag hopen dat de 3e ons een optionele OvidSP-TIP brengt. Meer fundamentele veranderingen bijv. voor wat betreft Reference Manager (zoals gesuggereerd door Krafty zijn ook zeer welkom, zeker wat mij betreft.