nodalpoint.org - Bibliographies - Comments

1.1

Neil — Sat, 16 Aug 2003 02:28:09 +0000

What I mean is that I have to know which PDF corresponds to which PubMed ref and enter that information manually. I like the PubMed download feature in v1.1. I'm someone who spends a lot of time writing scripts where sequences go in one end and cool analyses come out the other with minimum intervention - that's what I want for handling my refs.

Librarian

Anonymous — Thu, 14 Aug 2003 07:57:00 +0000

Hi. I am the author of Librarian. I'm not sure what you mean by manual operation. Please note, that as of version 1.1, you can use automated download of annotations from PubMed database. With this tool recording an article takes up to one minute.

martin

failures in networks and file formats

Neil — Wed, 13 Aug 2003 13:20:12 +0000

I've never found anything that does what I want (i.e. make sense of several hundred PDFs in a directory with arbitrary names ;-) ). Problem is, high-throughput data people like us tend to save files first, assume there's a solution later. There are 2 basic, obvious problems: (1) PDF format, which is neither marked up nor parseable, (2) no direct link between a PubMed ref and its corresponding PDF. I think the only solution is to name those PDFs as others have suggested.
There are a couple of tools I like. One is RefDB. It comes with scripts that convert Medline to RIS, then you can import RIS to MySQL. There is also Librarian, though this requires a lot of manual operation, reference by reference. But in both cases, I like the idea of a shared repository. Also there is PDFSearch, which essentially converts PDF to plain text and allows searching. I keep thinking I should be able to pattern match fields from my RefDB database to text from the PDFs and add an AV: field to the RIS record if it all matches, but haven't got around to it.
Literature management is an area I wish I had more organised, but at the end of the day I spend more time doing data analysis than reading/writing papers. It's an area ripe for faffing about, procrastination and displacement activity.

Latex

chris — Wed, 13 Aug 2003 01:24:49 +0000

I switched over to bibtex so I can reference latex documents. I don't have to use Bibtex input, but it makes things simpler, since I only have to have bibs in one format. I would have thought that Medline and Bibtex would be the two most commonly used formats, though...

Input format

alf — Tue, 12 Aug 2003 14:37:55 +0000

Is there a reason why you prefer BibTeX rather than MEDLINE input to Pybliographer? I'd like to make it easy to export the right format and keys from HubMed, so it would be interesting to know what people use.

Naming schema

chris — Tue, 12 Aug 2003 08:07:58 +0000

I use [Author][Journal][date].pdf for all my files. It would still be nice to have integrated access/link curation, though...

Don't keep them loose on the couch

alf — Tue, 12 Aug 2003 07:32:34 +0000

Name the PDFs as AuthorYear (as with each bibliography entry) and keep them all in a special folder? That's what I do. In fact, here's the rest of what I do (it would be handy if someone could write a Linux equivalent).

Bibliographies

chris — Tue, 12 Aug 2003 03:38:00 +0000

This from a conversation with Neil. There are several bibliographic solutions out there for the discerning scientist. For my money, Bibtex through Pybliographer is hard to beat.