nodalpoint.org - alternative PubMed interface - Comments

Browser-free data access

Neil — Fri, 06 Dec 2002 21:23:32 -0500

This is a very nice tool, and great to see use of the "new" net technologies in action.
It strikes me that many of the biologists I know are absolutely unaware of how code like the eutils can be used to pull data from servers without the need for a browser. (Actually many biologists I know are unaware period, but anyway). Next time I have to give a "what can code do for me as a biologist" talk, this would be a great example.

A few more updates this week:

alf — Sun, 01 Dec 2002 13:34:40 -0500

A few more updates this week:

BioMail for email alerts,
Bookmarklet for easy search access,
Import filter for direct import to Endnote,
Clipboard for storing citations using cookies.

BTW Greg, you're welcome to use the RSS feeds as often as you like. I'll get the conditional GET working soon as well.

Update frequencey

Greg — Tue, 26 Nov 2002 00:43:53 -0500

Nod.

Unfortunatelly in NetNewsWire (Lite) you can not set update frequencies on a per feed basis, so I've killed that. However Drupal does allow you to set update frequencey on a per feed basis so I'll leave that as an example.

The syndicate module of RSS 1.0 can be used to deal with the update frequency issue, allowing you to specify how often any given feed is updated. The bandwith wastage has been debated in the RSS community and as a result many aggregators are supporting the syndicate module (or similar features in RSS 9.x) AFAIK.

Update: more on RSS bandwith wastage: HTTP conditional GET.

example

chris — Mon, 25 Nov 2002 21:37:29 -0500

Hi alf, nothing fancy. I was looking at the feed Greg hooked up, which was a jumble. The abstract was continuous with everything else, which made it hard to read. Formatting a la PubMed would be great:

Looks like a great effort. Nice work!

formatting

alf — Mon, 25 Nov 2002 20:53:02 -0500

Chris, can you post an example of the kind of formatting/markup you have in mind?

RSS feeds

alf — Mon, 25 Nov 2002 20:42:26 -0500

To anyone using a news aggregator to read these feeds, *please* set updates to daily, at the most (preferably manual updates). PubMed isn't updated any more often than that anyway, so it justs wastes bandwidth.

The RSS used is the most basic (valid) format possible - I'll definitely look into the extensions soon.

Lots of updates today, including graphing occurrences of search terms over time, a linkout to XplorMed, and ranking of articles related to multiple abstracts. The NCBI server is a bit shaky at the moment with results for related articles, so if the ranking doesn't work first time, wait a bit and try again.

Formatting

chris — Mon, 25 Nov 2002 19:29:43 -0500

Some formatting of citations would be nice, though. From what I can see of the source, the citations aren't marked up at all?

RSS feeds

Greg — Mon, 25 Nov 2002 18:35:01 -0500

Awesome, now I can import pubmed search results as an RSS feed directly into my news reader: NetNewsWire. This is something I've been meaning to do with the pubmed module (admittedly in rather poor shape at the moment) that runs on nodalpoint. As an example I've added a bioinformatics search to the nodalpoint news feeds.

A few points on the RSS feature:

You might want to look into support for RSS 1.0. Anyone who has followed the RSS wars will know that RSS formats are a real can of worms. However RSS 1.0 has a well written specification, includes DTDs and schema definitions for validation, modules for syndication and content encoding.

I like the web search interface and I totally agree on the cleaner faster approach to search interfaces (a la google).

Feel free to post any updates to the utility here at any time. Nice work.

alternative PubMed interface

alf — Sun, 24 Nov 2002 19:36:00 -0500

Here is an alternative front-end for PubMed, put together using Perl and the NCBI E-Utilities.