Prompted by the appearance on the BHL blog of an article about BioStor I've thinking about how to improve what is basically a fairly clunky tool.One major weakness is searching the collection of nearly 40,000 articles extracted from BHL. Note the word "extracted." BioStor isn't a tool like PubMed or Google Scholar where the goal is to find articles on a topic.
Inspired by the forthcoming Hack4Knowledge I've put together a service that enables you to assert that you are the author of a paper using the Mendeley API.If you are impatient, give it a try at: http://iphylo.org/~rpage/hack4knowledge/iwrotethat/To use it you need a Mendeley account. When you go to I wrote that you will be asked to connect to your Mendeley account.
I would like to know what you think of a grant proposal I plan to submit to the UK Natural Environment Research Council at the end of the month.
Last December I released a web site called Australian Faunal Directory on CouchDB, which was part of my ongoing exploration of how to build a simple yet useful database of taxonomic names. In particular, I want to link names directly to the primary taxonomic literature.
My institute is going through various reviews of staff performance and, frankly, I'm feeling somewhat vulnerable given my somewhat unorthodox (at least amongst my colleagues) approach to doing science.
Each year the grandly titled International Institute for Species Exploration (IISE) publishes list of the top 10 species described in the previous year.
My article describing BioStor — "Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library" — has finally seen the light of day in BMC Bioinformatics (doi:10.1186/1471-2105-12-187, the DOI is not working at the moment, give it a little while to go live, meantime you can access the article here).Getting this article published was more work than I expected.
One of the many biggest challenges I've faced with the BioStor project, apart from dealing with messy metadata, has been handling page images. At present I get these from the Biodiversity Heritage Library. They are big (typically 1 Mb in size), and have the caramel colour of old paper.
How to cite: Page, R. (2011). Dark taxa: GenBank in a post-taxonomic world.
Interest in archiving data and data publication is growing, as evidenced by projects such as Dryad, and earlier tools such as TreeBASE. But I can't help wondering whether this is a little misguided. I think the issues are granularity and reuse.Taking the second issue first, how much re-use do data sets get? I suspect the answer is "not much". I think there are two clear use cases, repeatability of a study, and benchmarks.
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.