03-12-2009 07:35 PM
In an effort to include PMIDs and PMCIDs in my EndNote X1 library, as well as clean up errors in the library, include abstracts, etc., I exported my library and, via Perl scripts and NCBI's eUtilities, downloaded all the references (~1,500) in Medline format. I imported the Medline records into a new library, and then exported this new library to XML format, where, via Perl scripts, I italicized various things, like bacterial and gene names. So far, so good.
In the XML file, there are two fields, rec-number and foreign-keys, e.g..:
<key app='EN' db-id='9dkgkfdkkfioflbbm5hhxd9m0krs0khtjtp0'>1019</key>
I was anticipating being able to set these fields such that, when the properly italicized data is imported into the final new database, the record numbers would match those of the original library, allowing the new-and-improved library to continue to be used on legacy papers, grant applications, etc.
Alas, the program seems to ignore these fields entirely on import; the records in the final database are numbered by their position alphabetically. I have tried manipulating the XML data such that the order of the records themselves in the XML file matches the record numbers of the original database, but this too was unsuccessful. If these fields are not useful on import, why are they there?
Is there a way to do what I am attempting to do -- preset the record numbers in some form of a text file so that on import the record numbers remain faithful to the original library? I have an index relating the original record numbers to the PMID numbers included in the <accession-num> field.
Thank you for any suggestions...
Solved! Go to Solution.
03-12-2009 08:12 PM
Unless the company can do this for you, I am pretty sure you can't. The program is written to assign those numbers.
I would instead import them into either the Label or the Accession field which you can use instead of the record number. You could even append it with a different unique character, to distinguish it from the record number, and then you would replace the # of the unformated reference with the new character, or try with no character (you can also use page numbers as identifiers). This is changed in preferences, temporary citations. I would try this on a small part of the library.
You should also note that after unformating and reformating a paper, if Endnote can't find the Author, Year #RecNo match in the open library, it will show you the matching Author, Year records, and it is usually pretty easy to pick the correct record to insert (especially if you authored the document). It doesn't take long to go thru the document. Often if my students add new references to a copy of the lab library and they get different numbers after we transfer them into the main lab library, it is relatively painless to run thru and reassign them to the numbers in our permanant lab library, which I prefer to depending on the travelling library.
03-13-2009 11:40 AM
It is true that EndNote will ignore the record numbers. But what I have done in the past to resolve this is to:
1) Sort the references by record number
2) Create places holder references to fill any gaps in record numbers
3) Import into a new library
4) Delete the place holders
08-13-2009 03:35 AM
I've got a rather tricky question to this topic...
Given that I have two libraries I'm working with- my own and one "shared one" into which several of my colleagues and I drag & drop our references to make them available to all of us.
It is clear that all of our libraries save the references under a different record number. This unfortunately sometimes leads to problems in the respective word documents as EndNote time and again seems to access the record number from another library than the one open.
I checked the "Libraries used" tab from the Format Bibliography Option but nonetheless EndNote seems to use another one.
How can I assure (at least as much as possible) that when I am making modifications to references in our "shared library" also my colleagues documents are changed accordingly? Does it suffice to use the "Format Bibliography Option" or do I have to take account of something else I haven't thought of so far?
Thanks in advance for your help!