Roger Hyam

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. Continue reading »

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 reading »

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: Continue reading »

William Curtis (1746-1799)

This is a sideline to my working on the Edinburgh Rhododendron monographs.

The monographs often quote references to illustrations (icons) of species. This is useful as we know that these are illustrations that have been determined by the author of the account and are therefore “correctly” determined. What a shame we only have an abbreviated text string that can really only be understood by a human. An example might be “Rhododendron & Camellia Yearbook 25: f.58 (1970)”. Because these are in the botanical monographic style it is near impossible even to turn them into an OpenURL that a resolver could make sense of – so we have a bit of a challenge.

For the just-under-four-hundred species accounts I have extracted from the first two monographs I have 445 icon strings. Of these 144 contain ‘Bot. Mag.’ – for Curtis’ Botanical Magazine and so they look like a good set to try and parse and link up. The Biodiversity Heritage Libary have digitized that proportion of Bot. Mag. prior to 1920 that is out of copyright thanks to Missouri Botanic Gardens. I just need to join it all up. In fact I could download the relevant images and embed them in my data because they are out of copyright.

So a happy afternoon was spent learning about the BHL API and writing XSLT and regular expressions to parse the strings I had. The result was a match up of just 59 illustrations. About the same number I could have done manually in an afternoon! The rest of my Bot. Mag. references are post 1920 and so locked up in copyright.

But a happy by-product of the process was the fact that I downloaded and parsed all the metadata for Bot. Mag. in BHL and extracted the item IDs (books) and page IDs for what I believe are all the illustrations – a total of 8,215. So if you are faced with the same issue as me you don’t have to go to the bother of doing it. Here is a CSV file of the full list.

All Curtis Illustrations In BHL (CSV)

I have included the URLs to the resources in BHL although these are just trivial concatenations of the page IDs or item IDs and an http prefix. Continue reading »

The first two parts of the monograph to be looked at were published in Notes from the Royal Botanic Garden Edinburgh – the house journal of the gardens until 1990.

• Cullen, J. (1980) Revision of Rhododendron. I. subgenus Rhododendron sections Rhododendron and Pogonanthum. Notes from the Royal Botanic Garden Edinburgh. 39:1-207.
  
• Chamberlain, D.F. (1982) A revision of Rhododendron. II. Subgenus Hymenanthes. Notes from the Royal Botanic Garden Edinburgh. 39:209-486.

Between them these publications cover 544 species – more or less half the genus.

The entire run of the Notes has now be digitized to page images for BHL-Europe and so I have access to good quality pictures of the text. We have an in-house OCR service that I can drop these images into to create text or other outputs. I started by dropping all 200+ images from the first publication into the OCR and creating 200+ text files but this didn’t make sense because many of the species accounts ran across multiple pages. What I needed was the contiguous text for the whole publication. I could have concatenated the text files but I figured the OCR software would do a better job if it was working through one big document as it would learn from previous pages – OK maybe this is fantasy but it is worth a try. By using Preview (the Mac’s default PDF and image viewer) I created a single PDF containing all the images and put that through the OCR processor. The result was not only a single text file but also a PDF of the whole publication including OCR’d text. Job done! Can I stop now?

This process showed how easy it is to create digital versions of publications. The  PDFs produced are not very friendly being almost 100mb in size for each of the two publications but they can be read on line and indexed so do fulfill the basic requirements of making ‘legacy’ publications available. Because of their size I do not attach the PDFs here.

Two points jump to mind:

1. The accuracy of the OCR is masked because the text is hidden behind the page images. Although the document is searchable we can’t be sure that, if a search term is not found, it is because it isn’t there or because the OCR failed for that word in that location. This digitization process is likely to engender a false sense of security.
2. The PDF’s of the publications do not enable re-mixing or querying of the data beyond simple text searching. Question like “What species occur in Yunnan, China?” can only be answered by working through the text manually – something that might be quicker with the printed version.

Making text available to read on line is useful in that it facilitates distribution and discovery of that text but that is all it does.

The next step is to try and turn what is basically a descriptive narrative into more useful information that can be used to answer the simple questions people are likely to ask of about biodiversity. At the least it has to be massaged into a set of web pages, one for each species, for use in EOL. There are two aspects to this process:

• Syntax – this is really the easy bit although time consuming. The text of the monograph has a particular syntax – ordering of characters into words and sentences. We need to mark up the document with another syntax that will allow a machine to extract chunks of information. This isn’t too difficult to do at a course level because the monographs are highly structured but it becomes harder the more finely granular the syntax becomes. It inevitably involves a lot of manual work and I’ll cover it in another post.
• Semantics – this involves tougher decisions but isn’t that time consuming. We need to decide what chunks of information in the document we want to extract and what chunks we can practically extract and reach some kind of compromise. Different chunks of text can be seen in the document. Some of these chunks have no biological meaning at all e.g. a page or a paragraph. Others have useful biological meaning e.g. a distribution string like “NE Burma, China (Yunnan, Sichuan, W Guizhou)” in the context of a species description. The decisions made about what to extract will effect the syntax used and how long it will take to impose that syntax on the raw text of the document. Making these decisions will be the subject of another blog post.