You can manage your references with the refdbc command line client. A subset of this functionality is also available through the web interface of refdb. The examples in this chapter will use only the command-line client. We will demonstrate the interactive use of refdbc, but feel free to use the non-interactive batch mode instead if you prefer. We'll also use a conservative, least error-prone approach whenever there are several ways to achieve the same goal. E.g. we'll use intermediate files instead of piping so we can verify what we got at every stage. Once you're sure about what you're doing, you can still speed up things.
Adding references boils down to running addref with proper input files. The input files have to be valid RIS files. They may contain one or more RIS datasets.
You can set some fields to default values with the -g defaultfile option of the addref. This will add the tags given in the defaultfile to the end of every dataset before they are added to the database. This means that these values override any values given in the datasets. This option may be convenient e.g. to set the reprint status of all datasets that you add in one fell swoop instead of editing them individually.
Note: Please be aware that the ID tag is (mostly) ignored when you add references with the addref command. refdb assigns an automatically generated ID to every new reference, so you can't enforce any existing IDs. You can however use the -k option of the addref command to write the existing ID into the U5 field.
If you want to overwrite an existing reference with a given ID, use the updateref command instead.
Let's assume we just downloaded a bunch of references from PubMed (the largest database for biomedical publications). We saved them in the "Medline" format, ending up with several small files containing one or more references each. How do we get them into the database?
First we convert all references in the files (we prudently named them pm001.txt, pm002.txt and so on) to the RIS format and write the result into an intermediate file, using the nmed2ris input filter:
~# nmed2ris -o foo.ris pm* |
We could now open foo.ris in our favourite text editor and make a few changes. We could enter additional keywords, provide personal notes (e.g. why we currently find the article worth the paper its printed on, something that may not be apparent a few months later), or specify the reprint status and availability.
Then we switch to (or start) the refdbc command line client and type the following command at the prompt to add the references to the database bar (use the full path to foo.ris if necessary):
refdbc: addref -d bar foo.ris |