Thursday, March 03, 2011

Microcitations: linking nomenclators to BHL

One of the challenges of linking databases of taxonomic names to the primary literature is the minimal citation style used by nomenclators (see my earlier post Nomenclators + digitised literature = fail).

For example, consider Nomenclator Zoologicus. Volumes 1-10 of this list of generic names in zoology were digitised in 2004 and put online by uBio (for more details of this project see Taxonomic informatics tools for the electronic Nomenclator Zoologicus, pmid:16501061). In Nomenclator Zoologicus the citation for the genus Abana is:

Ann. Mag. nat. Hist., (8) 2, 72.

The challenge is to link this short citation to the digital version of the corresponding article. I've been sitting on a copy of the digitised Nomenclator Zoologicus kindly provided by Dave Remsen, and I've finally started to look at the problem of mining it for links to databases such as BHL.

You can see the first attempt at This form takes a genus name and the short citation and attempts to locate the corresponding page in BHL. It then checks whether the name is present on that page. Locating a page in a journal can be a challenge given the often rather ropey metadata in BHL, but BioStor uses a combination of fuzzy string matching and crude kludges to find the best match. But a further complication is that OCR errors may mean the taxonomic name we are looking for might not be detected on the page.

For example, if we search for the citation for the genus Aethriscus, Ann. Mag. nat. Hist., (7) 10, 329. we find two candidate pages in the journal Ann. Mag. nat. Hist, but neither contains the string "Aethriscus". However, if we use approximate string matching we find the OCR text for one page has the string "thriscus". This differs by only two characters from "Aethriscus", and so is a possible match (shown in orange).


Looking at the scanned page we can see the likely source of the problem:

In the original publication the name Aethriscus was written as Æthriscus. The ligature Æ has been corrupted by the OCR engine, and in Nomenclator Zoologicus the name is written without the ligature, hence the failure to exactly match the name with the text. These are some of the challenges faced when trying to close the circle and link names to literature.

The microcitation parser is still pretty crude, but usable. You can get results in either HTML or JSON, so the task of mapping microcitations to BHL pages can be automated. At present the name matching assumes you are looking at a single word (e.g., a genus), I need to extend it to handle binomials.