Comparing 2 databases (ex: ovid and pubmed)

wsetyonugroho
hi, I have question regarding comparing 2 databases.

for example, I downloaded citations from pubmed (in one foler) and also ovid (another folder).
is there any way to compare both side by side, so I can manage which one I already have ... than delete the one I dont need from one folder.

the duplicate feature allow me to choose and merge the citation, but the problem is, still appear in both folder.

--
thanks
  • dstillman
    No, not really, but I'm not totally clear on the problem. What's the issue after merging the duplicates?
  • wsetyonugroho
    suppose I download list of articles with one search keyword from pubmed into Pubmed directory. then I remove articles that I dont need.

    and
    the second one is I download list articles from Ovid into Ovid directory.

    of course I dont want to do the same process from previous database in pubmed directory.

    all I want is to automatically match, wich article that I already have in pubmed dir, and delete from ovid dir.
    the duplicate feature only do merge if it found two (or more) article in library.

    this matching features is very useful if we do literature review and comparing from many databases.
    will save lots of time
  • DWL-SDCA
    edited November 5, 2012
    "Folders" are not directories. The folder icon represents a collection within your Zotero library. When you run the duplicate detection utility and merge the items, the result is that (instead of having two different versions of the same item -- one in each collection) you will have the same version of the item in both collections.

    Are you evaluating the contents of each database (PubMed and Ovid) to assess the coverage by keyword? Are you looking at PubMed direct versus PubMed via Ovid or are you using Ovid for other databases in addition to PubMed? I've done research on the differences in literature database coverage of articles on selected topics. I used Zotero as the first step. However, there are several other tasks that must be done outside of Zotero to make the comparisons.
  • adamsmith
    (You can delete - rather than merge - individual items in the "Duplicate" folder by right-clicking them and selecting "Delete Item from Library" - make sure that only one Item is selected. Deleted items will disappear from all collections they used to be in).
  • DWL-SDCA
    edited November 5, 2012
    If you are doing a comparison of PubMed direct with the Ovid version of PubMed, did you know that the same search term can produce somewhat different results from each database? This is because each database maps a search differently. Placing the search term or phrase in quotes may have a different affect in each database. The result will also differ somewhat if you request a search with textwords or MeSH index terms. I could comment further but I have already taken this thread too far outside a discussion of Zotero.
  • wsetyonugroho
    @adamsmith
    than you for the tips. I will try it. because in last time I tried, in duplicate folder, if I click the articles , all will be highlighted.


    @DWL-SDCA
    of course I aware that merge resulted in same version in both collection.

    and yes, I have to do outside zotero many task.
    also both databases will result different result.

    in this context, is about whether zotero have ability such as dbms which can compare side by side both folder (that I created for different databases search result) and deleted or short which have duplicate and than I will remove the one that I dont need.
    this will make easier or less work, rather than I have to do the same picking out articles that I already done in first folder.
  • adamsmith
    important part is to _right_ click - left clicking will select all duplicates.
  • wsetyonugroho
    woaa ... I totally forgot about that.
    thank you
  • wsetyonugroho
    this is what I do in campus computer using endnote x4 (dont have it in my laptop)

    I search with keywords "paperless".
    2 databases use, pubmed and ovid medline.
    search with pubmed result 5, and moved to group pubmed
    search with ovid result 4, and moved to group ovid

    now, I need to remove duplicate in these two groups. just go to references -- find duplicate -- and I choose "keep"
    result : group pubmed 4 citation left, and group ovid 2 citation. TOTAL citation 6.

    NOW, in the case of Zotero
    i do the same thing, and the result each will move to pubmed and ovid collection (same thing with group in endnote)

    and, now I will remove duplicate.
    We will see basically 2 option, either merge (choose which one as master) or right click delete.

    the RESULT ?
    if we MERGE , there will be only 6 citation in My Library
    BUT
    in Pubmed collection still have 5 and in Ovid collection still have 4 collection

    if we DELETE , you know .. will remove either from collection or my library.


    THE BIG question , how to get the same result like in endnote ? rather than in zotero (my example)
  • aurimas
    edited November 23, 2012
    In EndNote:
    search with pubmed result 5, and moved to group pubmed
    search with ovid result 4, and moved to group ovid

    now, I need to remove duplicate in these two groups. just go to references -- find duplicate -- and I choose "keep"
    result : group pubmed 4 citation left, and group ovid 2 citation. TOTAL citation 6.
    This behavior is confusing to me. Why did it choose to remove 1 reference from pubmed and 2 references from ovid? Was the 1 reference removed from pubmed duplicated inside the pubmed group? Otherwise, I would expect all duplicate citations to be removed from one of the groups, but not some removed from one, while others are removed from the other group.

    Besides what adamsmith said above (about right-clicking a single reference in the duplicate "window" and selecting delete), I don't think this is possible in Zotero to be done automatically.

    But I'm not clear on where this is useful. I can imagine two situations:

    (1) I want to compare two databases to see what articles are present in one database, but not the other.

    Solution:
    1. Merge duplicates just the way Zotero does now.

    2. Use the advanced search feature with, as an example, the following parameters:
      • Collection -- is -- pubmed

      • Collection -- is not -- ovid
      This will return all items in pubmed, but not in ovid. You may want to save this search and/or tweak some settings on the advanced search panel.

    (2) I am doing a literature review (seems like what you are going for) and I don't want to read the same articles I already read in the other database.

    Solution:
    (You can of course just do the same thing as in solution to problem (1), but here's an alternative)

    1. Place both collections in another collection. E.g. "litReview"

    2. Merge duplicates just the way Zotero does now.

    3. Turn on "recursiveCollections" hidden preference

    4. Look at items in the "litReview" collection. This will display a single copy of each item from both ovid and pubmed collections.

    Is there another use case that cannot be solved with either of these methods?

    Edit: added link for advance search feature
Sign In or Register to comment.