For PubMed haters, new solutions emerging

It is possible that I am about to preach to the choir, but I am going to come right out and say it anyway. I hate PubMed. I hate it with a burning passion. For a site that is as vital to scientific progress as PubMed is, their search engine is shamefully bad. It’s embarrassingly, frustratingly, painfully bad.

So begins Harvard scientist Anna Kushnir's recent screed against PubMed, the US National Library of Medicine's medical publications web search engine. ("Can I even call it an engine?" asks Ms Kushnir in the post on her blog Lab Life. "It’s more like a tricycle.")

Ms Kushnir is not alone in her disdain for the ubiquitous website. "I hate you Pubmed. I hate you with a passion so great it defies existence," another blogger laments. "I HATE PUBMED AND MEDLINE!!! becos it's so frigging hard to find anything useful," yet another has said, apparently too incensed to even use spell-check.

What's with all the PubMed hate?

Well, some of the complaints include -- but are by no means limited to -- the following:

• failing to return an obvious result
• returning too many results
• getting mixed up between authors' first and last names
• getting even more mixed up when there are multiple authors by the same name
• the difficulty of keeping up to date on a certain topic using its search function
• its opaque search methodology
• its occasionally incomplete article titles
• the number of journals it indexes
• and just being confusing in general.
  

To name just a few.

"Science cannot proceed at a decent clip if researchers cannot find the most basic necessary information," writes Ms Kushnir, and really, who could argue?

Many researchers have decided to give up on PubMed altogether and have begun looking for alternatives. There's Google Scholar, Scirus, Microsoft Live Search Academic and eTBlast. Others have been working on different ways to use and display the data available through PubMed, such as GoPubMed, SLIM and PubCrawler.

But, as it turns out, PubMed has anticipated much of the competition and already introduced a solution in 2005 to help users who want to stay updated on a particular topic. It's now possible, as this 2005 National Library of Medicine Technical Bulletin explains, to get alerts when a new item appears that matches your search terms, using Really Simple Syndication, or RSS. For instance, you can check out my RSS feed for articles about "monkeys in space" here. (I know that's maybe not the most useful search imaginable, but you never know what NASA is working on. I actually do use one very useful PubMed RSS feed using HubMed that picks up all new studies that refer to officially registered clinical trial data.)

Anna Kushnir's strongly worded complaint about PubMed even elicited a reply from Dr David J Lipman of the National Center for Biotechnology Information, which helps operate PubMed. His message was posted in full in the comments section below Ms Kushnir's rant:

Although the current engine works well for some users and some queries, I understand Anna’s frustration and we are in the midst of a number of changes that will make PubMed work better for her and many other users. One type of query she is doing – essentially a form a targeted search/citation matching – will be handled much better within the next couple of weeks. We’re putting in a CitationSensor approach that will run the default search (but one which is itself somewhat improved) but have a separate set of heuristics for picking up Anna’s type of query.

Especially for someone writing a thesis or paper, they are often simply trying to find a particular paper, perhaps using author names, or terms from a title, or even just cutting & pasting a reference from another online paper. So this will be a big improvement for them.

We will be adding a number of other “sensors” which will run in parallel with the default search. From monitoring results of enhancements we’ve added to some of our other Entrez databases, it’s clear that users will be taking advantage of this.

A number of these complaints are fair and we’ll be doing our best to address them. With the large number of users we have, it will be clear what areas we’ll improving and what areas will need more work. And wish her good luck on her defense!

Good news for friends of PubMed and PubMed haters alike! The times they are a-changin' for biomedical research database searches.

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