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.

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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..

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Bug My NCBI repaired

8 10 2008

I’m pleased to announce that the bug in PubMed’s My NCBI, that I pointed out a week ago, has been repaired.

For two weeks, since the update of My NCBI, searches comprised of setnumbers were incorrectly saved in My NCBI, thus literally as #1 AND #2, or in the example I gave as: #3 + RCT filter instead of: hirsutism and spironolactone (+ RCT-filter), which was the actual search behind it. (see Figures below)

This was the response I just received from someone of the U.S.National Library of Medicine:

“You can now save searches with search statement (aka History) numbers. Unfortunately, any that you recently created that didn’t work are not going to work, so please delete those.

As part of the fix, we made some changes to how links for saved search names work in My NCBI. On the screen where you used to see “View Results,” use the search name to link to run the search in PubMed. The “Edit” link now takes you to where you can change the specs of the search. These changes are not yet finished. When we have things running normally we will provide more detailed information in our newsletter.

Thank you for your patience.”

I’ve checked it and it really works. Thank god it does. It is really an essential feature, especially for the unexperienced searcher: the (correct number of) brackets are automatically in the right positions.

I’m also pleased with the way the saved searched are presented. It is far more logic that the search is executed when clicking at the underlined name (which looks like a link) and that you can edit where it says “edit”.

I’m looking forward to the other enhancements.

search was erroneously saved as (#3) AND ....

Search is now saved as: (((hirsutism) AND (spironolactone) AND ....

The old (wrong) and updated search in My NCBI (in the new layout)





About “1 AND 2 = 3” in My NCBI

1 10 2008

The PubMed My NCBI feature has been updated. The navigation is entirely different and -in my view- less intuitive and more complex. The increased complexity may relate to the new features, some seeming rather unnecessary (filters), others looking promising: my bibliography, persistent cookies, no limit to the number of saved searches or collections per account (hurray!).

You can find details about the My NCBI changes in the NLM-bulletin and in MyNCBI-help.

For now, I just want to address one point, that hopefully is a “temporary error”.

I noticed it last Friday, thought that it was just a technical error of the kind that frequently occurs these days in PubMed, but will be restored without any notice.

But the mistake (?) is still there. It is about HOW PubMed searches are saved

Before, if you combined two sets, say: “#1 AND #2”, set #3 would be created: #1 AND #2.
If you would save #3 in My NCBI, you would save the entire search behind #1 AND #2, but now only the string “#1 AND #2” is saved. You can easily imagine that set numbers #1 AND #2 are only meaningful if #1 AND #2 are still present and the same as in the original search.
A Dutch colleague just shouted out he got an error message when trying to execute a saved search. Set X was not recognized….

Example.

Suppose you want to find an answer to the following question: Is spironolactone useful (compared to cyproterone acetate for instance) to reduce hirsutism in women with PCOS?

You search for:

  • hirsutism (#1) and spironolactone (#2) (checking that these are mapped to the appropriate MeSH using Details)
  • combine the two sets with AND.
  • Subsequently combine #3 with a narrow filter for the Therapy Domain (filter for RCT’s) in the Clinical Queries.
  • Set #4 (=#3 AND filter) gives 23 results.
  • You save set #4 in My NCBI.
  • But what happens:
    It is saved as #3 AND filter, not as: hirsutism AND spironolactone AND filter.
    Reexecuting the search if the original History is gone yields 0 results (or an erroneous result).

Personally I can circumvent most problems, because I optimize my searches in Word (also nice as safeguard when the PubMed servers are overheated), but for most users this is an unnecessary extra step.

I hope this bug (?, I hope it is a bug) is quickly restored by NLM.

Please inform them by writing to the PubMed helpdesk (at the bottom of the PubMed front page). I will do the same.





Cochrane Library: saved searches (2) … and recent changes

5 05 2008

The previously reported problem with accessing saved searches on the Cochrane Library has been fixed (as off April 23th). Users should now be able to run all of their saved searches.

Hopefully the often encountered problems with the saved searche feature are now resolved once and for all. Indeed continued access to these searches is critical to Trial Search Coordinators and other users frequently running (or editing) saved searches.

Also, with the Issue 2, 2008 load, there were changes in the status indicators (“Update”, “Commented”, “Withdrawn”) used on the Cochrane Library. E.g. The ‘Update’ flag no longer exists and instead has been replaced with the more accurate flags ‘New search’ ‘Conclusions changed’ and ‘Major change’.
The specifics of these changes are posted on the Issue change notice at this PDF.

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Het eerder gemelde probleem met het aanpassen en uitvoeren van “opgeslagen searches” in de Cochrane Library is verholpen (vanaf 23 april). Alle opgeslagen zoekacties kunnen nu weer uitgevoerd en aangepast worden.

Hopelijk zijn nu de “saved search”-problemen de wereld uit, want het afgelopen deden zich frequent problemen voor. Dit is bijzonder vervelend, vooral voor de Trial Search Coordinators en andere gebruikers die frequent searches updaten/uitvoeren.

Ook vermeldenswaardig: bij de 2e upload dit jaar (de Cochrane Library wordt 4x per jaar “ververst”) zijn de status indicators van de Cochrane Reviews (“Update”, “Commented”, “Withdrawn”) gewijzigd. Zie verder deze PDF.





No editing of Saved Searches in the Cochrane Library the next 24 hours!

22 04 2008

The last few weeks there have been errors in running saved searches in the Cochrane Library.

Since engineers will introduce some changes to the Cochrane Library, users are discouraged to edit or save existing searching over the next 24 hours.

Hopefully the problems will be resolved by then.

Notice at the home page of the Cochrane Library: