Mendeley and Web Hooks

Quick, poorly thought out idea. I've argued before that Mendeley seems the obvious tool to build a "bibliography of life." It has pretty much all the features we need: nice editing tools, support for DOIs, PubMed identifiers, social networking, etc.

But there's one thing it lacks. There's not an easy way to transmit updates from Mendeley to another database. There are RSS feeds for groups, such as this one for the "Museum Type Catalogues" group, but that just lists recently added articles. What if I edit an article, say by correcting the authorship, or adding a DOI? How can I get those edits into databases downstream?

One way would be if Mendeley provided RSS feeds for each article, and these feeds would list the edits made to that article. But polling thousands of individual RSS feeds would be a hassle. Perhaps we could have a user-level RSS feed of edits made?

But another way to do this would be with web hooks, which I explored earlier in connection with updating literature within a taxonomic database. The idea is as follows:

1. I have a taxonomic database that contains literature. It also has a web hook where I can tell the database that a record has been edited elsewhere.
2. I edit my Mendeley library using the desktop client.
3. When I've finished all the edits I've made (e.g., DOIs added, etc.), the web hook is automatically called and the taxonomic database notified of the edits.
4. The taxonomic database processes the edits, and if it accepts them it updates its own records

Several things are needed to make this work. We need to be able to talk about the same record in the taxonomic database and in Mendeley, which means either the database stores the Mendeley identifier, or visa versa, or both. We also need a way to find all the recent edits made in Mendeley. Given that the Mendeley database is stored locally as a SQLite database, one simple hack would be to write a script that was called at a set time, determined which records had been changed (records in the Mendeley SQLite database are timestamped) and send those to the web hook. If we're clever, we may even be able to automate this by calling the script when Mendeley quicks (depending on how scriptable the operating system and application are).

Of course, what would be even better is if the Mendeley application had this feature built in. You supply one or more web hook URLs that Mendeley will call, say after any edits have been synchronised with your Mendeley database in the cloud. More and more I think we need to focus on how we join all these tools and databases together, and web hooks look like being the obvious candidate.

Paper on NCBI and Wikipedia published in PLoS Currents: Tree of Life

My paper describing the mapping between NCBI and Wikipedia has been published in PLoS Currents: Tree of Life. You can see the paper here. It's only just gone live, so it's yet to get a PubMed Central number (one of the nice features of PLoS Currents is that the articles get archived in PMC).

Publishing in PLoS Currents: Tree of Life was a pleasant experience. The Google Knol editing environment was easy to use, and the reviewing process quick. It's obviously a new and rather experimental journal, and there are a few things that could be improved. Automatically looking up articles by PubMed identifier is nice, but it would also be great to do this for DOIs as well. Furthermore, the PubMed identifiers aren't displayed as clickable links, which rather defeats the point of having references on the web (I've added DOI links to the articles wherever possible). But, minor grumbles aside, as a way to get an Open Access article published for free, and have it archived in PubMed Central, PLoS Currents is hard to beat. What will be interesting is whether the article receives any comments. This seems to be one area online journals haven't really cracked — providing an environment where people want to engage in discussion.

Linking the NCBI taxonomy to BBC Wildlife Finder

A few weeks ago I spent some time mapping pages from the BBC Wildlife Finder to the equivalent taxa in the NCBI taxonomy. This seemed a useful exercise because the Wildlife Finder pages have some wonderful picture, video, and audio content, as well as other nice features, such as reusing Wikipedia page titles as "slugs" in the BBC page URLs. For example, the Wikipedia page for the Yacare Caiman (Caiman yacare) has the URL http://en.wikipedia.org/wiki/Yacare_Caiman, and the BBC page has the URL http://www.bbc.co.uk/nature/life/Yacare_Caiman. Both share the slug Yacare_Caiman.

After adding these links to iphylo.org/linkout, where you can find them listed on the BBC category page, I've finally uploaded these to the NCBI, so now some 504 NCBI taxon pages have links to high quality multimedia from the BBC.

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Location:Schmiedestraße,Wetter,Germany