On a recent trip to the Natural History Museum, London, the subject of DNA barcoding came up, and I got the clear impression that people at the NHM thought classical DNA barcoding was pretty much irrelevant, given recent developments in sequencing technology. For example, why sequence just COI when you can use shotgun sequencing to get the whole mitogenome? I was a little taken aback, although this is a view that's getting some traction, e.g.
The following is a guest post by Bob Mesibov. The i4Life project has very kindly liberated Catalogue of Life (CoL) data from its database, and you can now download the latest CoL as a set of plain text, tab-separated tables here.
The GBIF Ebbe Nielsen Challenge is open! From the official announcement First prize is €20,000, full details on prizes and entry requirements are on the Challenge web site.
Quick notes on an experimental feature I've added to BioNames. It attempts to identify possible taxonomic synonyms by extracting pairs of names with the same species name that appear together on the same page of text. The text could be full text for an open access article, OCR text from BHL, or the title and abstract for an article.
I'm going to the TDWG Identifier Workshop this weekend, so I thought I'd jot down a few notes. The biodiversity informatics community has been at this for a while, and we still haven't got identifiers sorted out. From my perspective as both a data aggregator (e.g., BioNames) and a data provider (e.g., BioStor) there are four things I think we need to tackle in order to make significant progress.
The recent jump from ~11000 to ~17000 articles in JournalMap is mostly due to JournalMap ingesting content from my BioStor database.
Following on from the discussion of the African chameleon data, I've started to explore Angelique Hjarding's data in more detail. The data is available from figshare (doi:10.6084/m9.figshare.1141858), so I've grabbed a copy and put it in github. Several things are immediately apparent. There is a lot of ungeoreferenced data. With a little work this could be geotagged and hence placed on a map.
Just back from GB21, the GBIF Governing Board meeting (the first such meeting I've attended). It was in New Delhi, and this was also my first time in india, which is an amazing place.
My BioNames project has been going for over a year now, but I hadn't gotten around to providing bulk access to the data I've been collecting and cleaning. I've gone some way towards fixing this. You can now grab a snapshot of the BioNames database as a Darwin Core Archive here.
Note to self for upcoming discussion with JournalMap. As of Monday August 25th, BioStor has 106,617 articles comprising 1,484,050 BHL pages. From the full text for these articles, I have extracted 45,452 distinct localities (i.e., geotagged with latitude and longitude). 15,860 BHL pages in BioStor pages have at least one geotag, these pages belong to 5,675 BioStor articles. In summary, BioStor has 5,675 full-text articles that are geotagged.