Category: Biodiversity Informatics

Whilst I have been working on digitizing the Rhododendron monographs I have also been providing some technical help for Stuart Lindsay who is producing a series of fact sheets for the Ferns of Thailand. This has helped crystallize my thoughts regarding monographs and how we migrate them into the digital age.

This post is a follow on from a previous one where I discuss mapping the Rhododendron monographs to EoL. It is an opinionated rant but I offer it in the hope that it will be of some use.

When monographs/floras/faunas are mentioned in the context of digitization people usually chirp up with PDF or, if they are more clued up on biodiversity informatics,  TaXMLit and INOTAXA (Hi to Anna if you are reading) or TaxonX and Plazi.org (Hi to Donat).  The point I am going to make in this blog post is not against these ways of marking up taxonomic literature but more the nature of the monographic/floristic/faunistic taxonomic product itself. I am far more familiar with the botanical side of things so apologies to zoologists in advance.

I’ve had my head down work wise for the past few weeks trying to get the Rhododendron monograph markup finished. I now have a little database with some 821 species accounts in it plus a few hundred images – mainly of herbarium specimens. The workflow has been quiet simple but very time consuming.

1. Text is obtained from the source monograph either via OCR or access to the original word processor documents.
2. The text is topped-and-tailed to remove the introduction and any appendices and indexes.
3. Text is converted to UTF-8 if it isn’t already.
4. An XML header and foot are put in place and any non-XML characters are escaped  – this actually came down to just replacing & with &
5. The text is now in a well formed XML document.
6. A series of custom regular expression based replacements are carried out to put XML tags at the start of each of the recognizable ‘fields’ in the species accounts. These have to be find tuned to the document as the styles of the monographs are subtly different. Even the monographs published in the same journal had some differences. It is not possible to identify the start and end of each document element automatically. This is for three reasons:
   1. OCR errors mean the punctuation, some letters and line breaks are inconsistent.
   2. Original documents have typos in them. A classic is a period appearing inside or outside or inside and outside a closing parenthesis.
   3. There are no consistent markers in the source documents structure for some fields. For example the final sentence of the description may  contain a description of the habitat, frequency and altitude but the order and style may vary presumably to make the text more pleasant to read. The only way to resolve this is by human intervention.
7. The text is no longer in a well formed XML document!
8. The text is manually edited whilst consulting the published hard copy to insert missing XML tags and correct really obvious OCR errors. In some places actual editing of the text is needed to get it to fit a uniform document structure as in the habitat example above.
9. The text is now back to being a well formed XML document.
10. An XSL transformation is carried out on the XML to turn it into ‘clean’ species accounts and alter the structure slightly.
11. An XSL transformation is carried out to convert the clean species accounts into SQL insert statements for a simple MySQL database. The structure of this database is very like an RDF triple store (actually a quad store as there is a column for source). A canonical, simplified taxon name (without authority or rank) is used as the equivalent of the URI to identify each ‘object’ in the database. Putting the data in a database makes it much easier to clean up and to extract some additional data. An alternative would be to have a single large XML document and write XPath queries.
    Continue ReadingSquare Peg Into A Round Hole?

This post deals with the semantics of extraction of data from the Rhododendron monographs. Another post will deal with the technicalities of the actual extraction.

The image above shows a species description entry. It was chosen as being a small and simple example for illustrative purposes. I have marked up the bits I am interested in extracting. Red indicates important fields, blue unimportant and yellow something in between – but why those bits and those priorities? Monographs contain a great deal of other stuff such as keys and descriptions of higher taxa and discussions. We could argue for hours about what should be extracted and never come to a conclusion unless we have some guiding principles on what we are trying to do. I have therefore developed five guiding principles for the project that are probably pretty general and may be applicable to other such projects:

The first two parts of the monograph to be looked at were published in Notes from the Royal Botanic Garden Edinburgh – the house journal…

The Royal Botanic Garden Edinburgh has a history of research into the genus Rhododendron stretching back over 100 years. The legacy of this work is…