You know those days when you spend hours investigating various software packages – download, unpack, compile, tweak, test, discard – and at the end of the day, none of them worked as you hoped and you’ve achieved essentially nothing? Today was one of those days.
My quest for a usable Linux bibliographic solution continues. Here’s what I want:
- Automated searches of PubMed with a set of topics at set intervals
- Storage of results either in MySQL or a standard ASCII format
- Search facility
- Citation of selected references preferably into an OpenOffice document
- Optional: multi-user, shared and personal databases
I’d had my hopes pinned on RefDB, but it has become very broken, at least on my system. I had it working a year or two ago but the latest version won’t even compile. It requires the latest libdbi (0.8.1) – Debian unstable is 0.7.2 and all my attempts to grab the latter version and compile against it have failed. It looks to me like a project suffering from over-engineering, always being tweaked to the point of unusability. A shame, because it has good import/export facility – it would be easy to run a weekly search via cron and Perl code using Bio::Biblio, import the pubmed xml direct to MySQL and export as RIS or whatever.
I tried Refbase which looks quite nice but lacks import filters. So now I’m thinking of a solution that gets PubMed xml in an automated search, runs it through Bibutils for conversion and just stores as flat files. Pybliographer would feature in there somewhere as might Bibus.
