Retrieve and manage PubMed records

2006-05-09
2013-05-28
  • Nobody/Anonymous

    Hello!
    Can I retrieve *filtered records* from pubmed and manage them? The authors here where I work wants to selec their works and delete the rest from the database records obtained from pubmed becouse records contains omonymous.
    Thankx a lot.

     
    • Matthias Steffens

      Hi,

      I'm not sure what you mean by "filtered records". Do you mean a special search results set on the PubMed page or where does what kind of filtering take place?

      Currently, refbase (CVS version) imports whatever PubMed records (in MEDLINE or PubMed XML format) you paste into the import form. You can, of course, cut out any unwanted records before importing or import only selected records by specifying the record's position within the pasted data in the import form. But I guess this is not what you meant?

      We have plans to provide a little bookmarklet which would allow users to import all records currently displayed on a PubMed web page. So if you are able to gather only those records which you'd like to import, this may also work (in the future). We also plan to provide an "Import by PMID" feauture which may also work for you to import particular records only.

      If this is not what you're asking for, please explain in more detail what you'd like to accomplish.

      Thanks, Matthias

       
    • Nobody/Anonymous

      Hello,
      thank you very much for your help. You have been so fast in reply.
      Sorry for my english.....
      I work in an University and the doctors here are authors of some PubMed publications.

      Let me try to explain with an example:

      I have 3 names of authors: Smith J., Cooper R., Black M. ....
      I need to run a search on PubMed by author name using the list above.
      The result will contain some records for "Smith J." but doctor Jason Smith never write some of them. This because Jason Smith and John Smith (an unknown) are different persons but the work is signed "Smith J."
      **In this case Only the author can recognize his works**.
      So, I import all the records in Web Reference Db and then every author working at the University would access to the Db to delete foreigners works.

      My questions are:
      Can I put the authors list somewhere in this database to retrieve all the records from PubMed?

      Or should I have to search manually on PubMed and after import somehow the records in Web Reference Db?

      Can authors access by account to Web Reference Db and delete the unknown works?
      Thank you a lot.

       
      • Matthias Steffens

        Hi,

        thanks for the detailed explanation, I do understand your problem now.

        > Can I put the authors list somewhere in this database to retrieve all
        > the records from PubMed?

        Currently, refbase does not offer automatic querying of PubMed. We have plans to support querying of remote servers (such as PubMed) in the future, but it may take some time until this gets actually implemented.

        > Or should I have to search manually on PubMed and after import somehow
        > the records in Web Reference Db?

        Yes. Currently you'll have to perform your searches manually in PubMed, export found records in MEDLINE or PubMed XML format and finally import these records into refbase.

        > Can authors access by account to Web Reference Db and delete the
        > unknown works?

        This depends on which user did perform the import. In refbase, the imported records are "owned" by the user who initially added the records to the database. This means that regular users (your authors) can only delete those records which were added by themselves, i.e. they can only delete records which they "own" (and which nobody else owns). The database administrator is allowed to delete any record, though.

        I can see two ways to achieve what you're after:

        1. You could temporally allow your authors to login as admin and let them delete any unwanted records. When they're done, change the admin password so that they cannot login as admin anymore.

        2. Instruct your authors to put a unique keyword (such as "#delete#") into the keywords field of all records that shall be deleted. Then login as admin and remove all the flagged records. This can be done as a batch operation from within 'sql_search.php':

        DELETE from refs WHERE keywords RLIKE "#delete#"

        Hope this helps, Matthias

         
    • Nobody/Anonymous

      Hi,
      that's all I need to know. Now I have to start a plan for the management as you suggest.

      I'll never stop to thank you.
      You're great.

      Francesco.

       

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