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 http://biostor.org/microcitation.php. 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.

Nomenclators + digitised literature = fail

Continuing with RSS feeds, I've now added wrappers around IPNI that will return for each plant family a list of names added to the IPNI database in the last 30 days. You can see the list at here.

One thing which is a constant source of frustration for me is the disconnect between nomenclators (lists of published names for species) and scientific publishing. The unit of digitisation for a publisher is the scientific article, but nomenclators often cite not the article in which a name was published, but the page on which the name appears.

For example, consider IPNI record 77096979-1 (or, if you prefer LSIDs urn:lsid:ipni.org:names:77096979-1). It is for the begonia Begonia ozotothrix, and the citation is:

Edinburgh J. Bot. 66(1): 105 (-110; figs. 1, 4-5, map). 2009 [Mar 2009]

Very detailed, and great if I have access to a physical library that has the Edinburgh Journal of Botany -- I just find volume 66 on the shelf and turn to page 105. But, I want this on my computer now ("library" - who they?). How do I find this reference on the web? The answer, is not easily. Tools such as OpenURL, which could be used, assume that I know at least the starting page of the article, but IPNI doesn't tell me that. Nor do I have an article title, which might help, but a Google search on "Begonia ozotothrix" finds the article:

TWO NEW SPECIES OF BEGONIA ( BEGONIACEAE) FROM CENTRAL SULAWESI, INDONESIA
D C Thomas, W H Ardi and M Hughes
Edinburgh Journal of Botany 66, 103 (2009)
doi:10.1017/S0960428609005320

Note the DOI! This article exists on the web, so why can't IPNI give me the DOI? They've gone to a lot of trouble to describe the citation in great detail, but adding the DOI brings the record into the 21st century and the web (the DOI is even printed on the article!).

I think nomenclators need to make a concerted effort to integrate with the digital scientific literature, otherwise they will remain digital backwaters that make the implicit assumption that their users have access to libraries such as that at the Royal Botanic Gardens, Edinburgh (pictured).

For recently published articles there's absolutely no reason not to store the DOI. Finding these retrospectively is a pain, but I need these for my RSS feed (and other projects) so one thing I added a while ago to bioGUID's OpenURL resolver is the ability to search for an article given an arbitrary page. For example,

http://bioguid.info/openurl/?genre=article&title=Edinburgh J. Bot.&volume=66&pages=105

will search various sources (such as CrossRef) to find an article that includes page 105. Now, I just have to have a parser that can make sense of IPNI bibliographic citations...