Another Search Bug? Now in the Cochrane Library!

16 10 2008

It seems that I’m becoming an expert in search problems and bugs.
Partly because I search a lot, but also because my colleagues and I often share our search problems.

This time, while giving a class, Hanny and Heleen noticed that (a) combining two terms in the Cochrane Library Search Bar with ‘and’ gives less hits than when you (b) search for those terms individually and combine them in the History with ‘and’ (see Figures). This is odd, because it should not make any difference whether you look these words up individually (which takes more time) or combine them directly. The field in which both these terms should occur is in the title, abstract and/or keyword field.
(c) Searching via advanced search has the same effect as searching the terms separately in the search bar (#7, #9)

The 3 search modes (click to enlarge)

Two examples are given below: (1) obesity and sibutramine (sets #1-#9) and (2) sibutramine and body weight (#10-#14).
Both obesity and body weight are MeSH (key words from MEDLINE).

Search History showing results two examples (click on Figure to enlarge)

It is unclear why certain records can’t be found when combining them in the search bar. The order doesn’t matter, for instance. It might have something to do with certain keywords not being found when the keyword command is not directly next to term sought (set #12 in Search History, and figure below).

Anyway this is highly undesirable. Especially for the beginner, who just wants to find a cochrane systematic review by doing a quick search. Hopefully this ‘bug’ will be fixed soon, because important papers might be missed (see below).

Missed papers (have one of the terms exclusively in the keyword (MeSH)section

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Another bug in My NCBI?

15 10 2008

This bug is now fixed (15-11-2008) !!!

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It is confusing, but each week I have another post on the appearance, disappearance or reappearance of a bug in PubMed’s My NCBI:

For me this is an essential feature of My Collections.Often, when I develop a sensitive search, I collect all relevant studies, especially the ones that were not in my search (i.e. found by checking references or ‘related articles’). Then I optimize the search and hope all the relevant records will be found. This can be checked by combining (a) search(es) with the collection(s). If the search is good all relevant records will be found.

Of course this will only work when you CAN combine the collection from My NCBI with one or more searches in the History.

A cumbersome solution, that only works for one collection at the time, is that you send the collections (executed in PubMed) to the Clipboard and combine this set (#0) with the searches, but I prefer a simpler solution. In fact it has always been possible in the past….

Well we will write again to the help desk.
Hopefully I will report the bug repair next week and there will be no follow up.

—————————-

Voor de tweede keer een bug in My NCBI. Dit keer gaat het om “My Collections”. Als je een “collection” activeert, worden de desbetreffende records (in het voorbeeld 39 items) wel uitgevoerd in PubMed, maar komen ze niet in de History terecht.

Dat vind ik erg vervelend, omdat ik My Collections vooral gebruik om uitgebreide zoekacties op te zetten.

Ik sla alle relevante artikelen op in My Collections en voer ze op een later tijdstip uit. Dan combineer ik ze met een of meer searches. Ik kan zo checken of ik met zo’n search alle relevante artikelen (bijv. gekregen van klant of via related articles) vind. Is dat niet het geval, dan is het een manier om ontbrekende termen te vinden.

Deze procedure werkt nu dus niet meer, omdat een set uit My Collections niet in de History terechtkomt.

Ik heb wel een voorlopige kunstgreep bedacht, t.w. deze items in Pubmed naar het Clipboard sturen, zodat ze alsnog als set #0 in de History komen te staan. Dat werkt natuurlijk maar met 1 set tegelijk en is tamelijk omslachtig.

Voorheen werkte dit trouwens wel altijd, dus het zal wel weer liggen aan de overhaaste ‘reparaties’ en aanpassingen.

Nou, dat wordt weer een mailtje richting helpdesk.

Hopelijk wordt het snel verholpen en hoort u even niet meer van mij..





Finding assigned MeSH terms and more: PubReMiner

24 09 2008

Generally when searching PubMed I use both MeSH and textwords. If you already have some nice articles, either by performing a quick and dirty search or looking at the Related Articles or your colleague gave you one or two, then you can find the MeSH assigned to these papers by looking in citation format (see Fig). However going through a set of articles looking at all indexed terms takes quite some time and one doesn’t easily get an overview of the overall frequency of MeSH in a set of records.

Therefore, Rachel Walden, asked first at Twitter and then at David Rothman’ site (see here):

“What I’d like to do is to be able to enter the PMIDs of several citations and have the tool search MEDLINE via PubMed for the assigned MeSH terms, and return a single list of the terms used by any of the entered citations with a measurement of frequency. For example, if I input PMIDs 16234728, 15674923, and 17443536, the tool would return results telling me that 100% or 3 of 3 use the term “Catheters, Indwelling”, 2 of 3 use “Time Factors,” 1 of the 3 uses “Urination Disorders,” and so on. Although this example uses 3 PMIDs, I’d like to be able to input at least 10, just based on personal experience.”
(PMID is the unique PubMed-identifier, by searching for the PMID you get one specific record.)

The suggestions made by several people were summarized by David in another post (see here). The following 3rd-party PubMed/MEDLINE tools seemed most promising:

Both give useful results. The layout- is very user-friendly.

I tried my own sets of 20 PMIDs (from a systematic review search on “predictive models for in vitro fertilization”) and http://www.docmobi gave this result:


This was the result when I selected: “primary terms only“. If I selected “include secondary terms” I would find female and pregnancy as well, but at rates of 175%. First I didn’t understand, but than I realized that pregnancy occurs as “Pregnancy” and as “Pregnancy Rate”, whereas female occurs as “Female” and as “Infertility, Female”. Therefore Pregnancy and Female can occur more than once as single words in one record (thus accounting for >100%). It is odd however, that important MeSH like Pregnancy and Female (which are really check tags, MeSH that should be assigned to each article that is about pregnancy or females) are not included in the primary list.

Although useful and nicely presented I still not find this ideal:

  • Check tags are not in the list (with “primary terms only”)
  • Publication types and substance names are in neither list.
  • Subheadings are not included. For words not captured by a single MeSH, but by a combination of MeSH and subheadings this is especially important.
    For instance, there is no MeSH for EGFR-inhibitors, you have to use:
    Receptor, Epidermal Growth Factor/antagonists & inhibitors
  • Textwords are not included (not on Rachel’s wish list but on mine)
  • Personally I find the list so simple that I would have find the terms immediately myself.

Coincidentally I found another 3rd party tool which does the job much better (I think): (PubMed) PubReminer, produced by Jan Koster at our hospital (AMC, Amsterdam). I looked at it, because my colleagues and I are going to discuss it today.

This is the procedure I would recommend to find assigned MeSH and more, starting from PubMed (which is not absolutely required, because you can also search directly in PubReMiner)

  • Collect the PMID’s of the papers you want to analyze.
  • If you have selected the papers in PubMed (on the Clipboard, in My collections or in your search set) then Set the Display Tab on: UI List (Unique identifiers), and export these PMID to a textfile by choosing “to Text” from the Send to button. You get a simple list of PMID’s that you can copy/paste to PubReMiner. (not required, but handy)

  • Go to PubReminer, paste the PMID’s in the search box as one string.
  • Click: “Start PubReminer” (if you enter a search you may wish to apply limits)

  • You see the results, in the following columns: Year, Author, Journal, (Text)Word, MeSH, Substance, Country.

  • Afterwards you can decide
    – Whether the words are searched in title only, in Title and Abstract or also in MeSH and RN.
    – which columns are displayed
    – whether similar words are merged or not.
  • You can use selected terms to build up your search in PubReMiner and/or
  • You can export the terms as a text-file (!)
  • And, by the way, you can download a plugin for IE or Firefox (Fig. right)

This tool is not very intuitive, but the result is quite ideal.

You get both a list of MeSH plus their subheadings AND a list of textwords (and substance names).

There are very useful terms in here, for instance logistic models[mesh]. As textwords I should use ‘logistic regression’ or ‘multivariate analysis’. It is only a pity that terms are given individually and spread: the context is lost (‘analysis’ may for instance be too broad, it is only useful in combination with ‘multivariate’ or ‘regression’).
With respect to the MeSH only individual terms are given. ‘Pregnancy’ is mentioned 19 out of 20 times in the MeSH-list. Does this mean I’m missing one paper by searching “Pregnancy”[MesH]? No, because that paper is indexed with the narrower term “Pregnancy Rate”. (and you will find it by exploding Pregnancy).
So the context and the hierarchy are lost here as well.

But it is about as good as one can get.

I’m gonna use this tool (as an adjunct at least). Seems that it has some other potentials as well: look up genes, find the research interest of an author, determine the journal to submit your work to. Well I probably learn that in a few hours. Perhaps I will come back to it later.





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.