Monday, 7 April 2014

Digitised Botanical Resources

These are my notes from a presentation by Bronwyn and Anna from the Centre for Australian National Biodiversity Research (CANBR) to the Scientific Group of the Friends of ANBG.

I will actually start at the end of the presentation, because it was the catalyst for the presentation.  This was when a leader of the Friends group found Anna delving into some biographical material trying to understand relationships in the Giles family after a member of which Eremophila christopheri was named.  As explained in this ANBG webpage there were a father and son named Christopher Giles and an unrelated friend Ernest Giles (who scored E. gilesii).  He thought - IMHO correctly - that this area of research would be a topic of more general interest.

The talk was in three sections.

The need for standards and reference material.

A key point is that rules are needed for stability.  (Given the current state of naming for orchids one might say this is a "guideline" rather than a "rule".)  The rules are covered by the International Code for nomenclature of algae, fungi and plants usually referred to as The Code, or a reference such as The Melbourne Code to indicate it is the version published after a Conference in Melbourne in 2012.  It is revised about every 6 years.

The first reference point for a species is the type specimen.  This is defined by the original person describing the species as a 'typical' example, and all taxonomic stuff from then on uses this as the reference point.  They are stored in Herbaria and are essentially irreplaceable.  Thus it is a bit of a disaster when a boat with cargo containing type specimens, being loaned to another herbarium' sinks.

The description of a species (the protologue) used to be required to be in Latin, but it was becoming difficult to find translators so from 2012 onwards a protologue could be in Latin or English.  From the time of Linnaeus publishing "Species Plantarum" (1 May 1753) to the Melbourne Conference in 2012 these had to be in hardcopy in a few Journals.  Now they can be on line (subject to some controls).

Because many of the collectors of early Australian plants were European (in which I include Poms) many of the type specimens are in Europe.  This applies in spades to African and Latin American species.

Global Plants Initiative GPI

This grew out of the African (2003) and Latin American (2007) Plant initiatives attempting to overcome the costs of travelling to look at type specimens (the holders of which are reluctant to lend them  - see reference to shipwrecks above).  In 2009 it was decided to go from global (the charge being led by the Smithsonian and Kew).  Now >300 institutions in >70 countries (few Arabic or Asian countries are involved).

The system is hosted by JSTOR and now apparently referred to as Global Plants. It seems that individuals have some level of free access to this as well as the Big Science of Museums, Academia Libraries and Herbaria,  I will have a snuffle at this later.

The images can be up to 400Mb in size which allows lots of zooming.  This enables researchers to resolve some issues without actually seeing the specimen itself.  For example if they want to comment on seed pods but they are not evident in the image of type specimen then it won't help them to look at the specimen itself.  Clearly looking at images minmises the transport risk to the specimen or cost to the researcher.

Some spiffy scanners have been developed to capture the images.  Having soft copies of the types is good insurance: there are many backups.

Biodiversity Heritage Library (BHL)

This is much wider than plants. It is primarily a set of scanned in images o f books that are out of copyright (ie up to 1923).  15 libraries/herbaria are contributors to this (but not CANBR).  The Museum of Voctoria (supported by ALA is the main player in Australia.

It includes 41.5m pages , covering 118,000 items and has had about 4m visitors.  IN the US and UK the task of scanning stuff is outsourced but  in Victoria they use volunteers who are apparent ly very enthusiastic about the work.

The material covered is very useful for Australian Plant Names Index work  and the Australian Plant Census.  In the past this relied on inter-library loans which were complex to specify and slow - 6-8 weeks.  It was also very dependent on the supplying librarian being empathetic - realising what the searcher needed rather than exactly which pages were specified.  Now they get the whole book to their desk in a few minutes.

This also includes a Flickr stream and social media stuff (which seems to be thought of by some people  as a good thing).


As giving insights into how the people in CANBR, and similar organisations, work this was an excellent presentation.  It was also good to see how a bunch of organisations are cooperating to access the benefits of current technology.
  • Will it help me ID plants in the field?  Probably not.
  • Will it help me understand why the names of plants identified by others have changed?  Quite possibly!


Ian Fraser said...

That last outcome can only be a good thing Martin! It will give you spare spleen to vent more profitably elsewhere... Nice report thanks, from which I learnt a few things. I'd have enjoyed that talk.

Flabmeister said...

Thanks Ian!

It was a good talk.

The problem with spleen venting is not so much needing a bit of spare, but finding a target where it will do some good!