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.

The new look Biodiversity Heritage Library has just launched. It's a complete refresh of the old site, based on the Biodiversity Heritage Library–Australia site. If you want an overview of what's new, BHL have published a guide to the new look site. Congrats to involved in the relaunch. One of the new features draws on the work I've been doing on BioStor.

Quick note on an experimental version of BioStor that is (mostly) hosted in the cloud. BioStor currently runs on a Mac Mini and uses MySQL as the database. For a number of reasons (it's running on a Mac Mini and my knowledge of optimising MySQL is limited) BioStor is struggling a bit. It's also gathered a lot of cruff as I've worked on ways to map article citations to the rather messy metadata in BHL.

If we are ever going to link biodiversity data together we need to have some way of ensuring persistent links between digital records. This isn't going to happen unless people take persistent identifiers seriously. I've been trying to link specimen codes in publications to GBIF, with some success, so imagine my horror when it started to fall apart.

Just noticed that BioStor now has just over 70,000 articles extracted from the Biodiversity Heritage Library. This number is a little "soft" as there are some duplicates in the database that I need to clean out, but it's a nice sounding number. Each article has full text available, and in most cases reasonably complete metadata.

This post arose from an ongoing email conversation with Tony Rees about extracting and annotating taxonomic names. In BioStor I use the GBIF classification to display the taxonomic names found in the OCR text in the form of a tree. The idea is to give the reader a sense of "what the paper is about". I also use the classification to help link to GBIF occurrence records.

Brief update on yesterday's post about finding specimens in BioStor. BioStor has some 66,000 articles from BHL, from which I've extracted 143,000 cases of a specimen code being cited in the text. Of these 143,000 occurrences, 81,000 have been matched to an occurrence in GBIF.

Following on from exploring links between GBIF and GenBank here I'm going to look at links between GBIF and the primary literature, in this case articles scanned by the Biodiversity Heritage Library (BHL). The OCR text in BHL can be mined for a variety of entities. BHL itself has used uBio's tools to identity taxonomic names in the OCR text, and in my BioStor project I've extracted article-level metadata and geographic co-ordinates.

Recently I've been thinking about the best ways to make article-level metadata from BioStor more widely available. For example, for someone visiting the BHL site there is no easy way to find articles, which are the basic unit for much of the scientific literature. How hard would it be to add articles to BHL?

Tomorrow is the Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond meeting. It should be an interesting gathering, albeit overshadowed by the sudden death of Frank Bisby.