Keys and visualisation project

Jump to...

FSC punched-card multi-access keyThe research & consultation phases of Tomorrow’s Biodiversity highlighted the unfulfilled potential of computer-based multi-access keys for biological identification and considerable interest amongst biological recorders in seeing them more widely available .

FSC was involved in the development of multi-access keys in their early days - even before the advent of widespread access of computers - for example by producing a novel punch-card key to Grasses. In the early 1990s, when computers became accessible to home users, we published a computer-based multi-access key for British Carex sedges for IBM-compatible PCs and BBC microcomputers. However FSC did not maintain an interest in this area of development.

It seems certain that recent technological advances in user-interface and hardware technology, such as mobile devices, have created an environment in which multi-access keys will, at last, start to realise some of their potential.

A project supported by Tomorrow’s Biodiversity would be an opportune way for the FSC to re-open its interest in this area of identification resource delivery. Computer-based multi-access keys can be thought of as applications built on top of taxonomic knowledge-bases. This project will also explore other tools that can be built on taxonomic knowledge bases in order to help learners assimilate those knowledge bases themselves.

Tom.bio ID Visualisations

Tom.bio ID Visualisations is an evolving technical environment in which imaginative ideas about how to visualise and use taxonomic databases for identification can be realised. On one level, you can think about this as a general set of visualisation tools, including multi-access keys, that can accept any knowledge-base that is designed to a common standard. We have now published the 'Tom.bio ID Visualisations Framework' which will empower people to create their own visualisations. Follow this link for an interactive introduction to the framework.

The first knowledge-base to take advantage of the Tom.bio ID Visualisations framework is one for UK Harvestmen.

Megabunus diadema by Paul Richards Harvestman ID visualisation. This knowledge base was developed by Richard Burkmar in association with Paul Richards.

Visual features such as pattern and colour are quite hard to capture with traditional (and non-traditional) keys, but much better represented by pictures. This realisation made us concentrate some development on features that allowed us to make better use of pictures. We were fortunate in this respect that Paul Richards was able to provide a excellent and comprehensive set of photographs that we could incorporate into the knowledge base.

Multi-access keys

The multi-access keys featured below were created before the Tom.bio ID Visualisation framework was developed. These are standalone implementations - i.e. the tools and features are different from those available in the general Tom.bio ID Visualisations framework.

Earthworm.  Illustration: C Bell Earthworm multi access key. An online multi-access key to aid identification of the 27 UK earthworm species. Can also be used to explore earthworm taxonomic and ecological characteristics, via visualisation of the knowledge base in the AIDGAP key put together by Emma Sherlock. The key is built using the Data Driven Documents (D3) Javascript library to animate taxonomic entities and the jQuery UI Javascript library to provide the user-input interface.

Grasses key Grasses multi access key. A visualisation and multi-access key to provide an introduction and guide for beginners in the identification of grasses in flower. The knowledge-base construction, written information on morphological features and illustrations are the work of Sally Hyslop for The Natural History Museum's Identification Trainers for the Future project. The visualisation, key design and programming was carried out by Rich Burkmar for the Field Studies Council's Tomorrow's Biodiversity project. Images of specimens were sourced from the Natural History Museum’s British and Irish Herbarium and digitised with the help of John Hunnex.

Linyphiidae key Linyphiidae multi access key. The knowledge-base behind this key is based on a spreasheet created by Nigel Cane-Honeysett by transcribing information from the Linyphiidae tables in Michael Roberts' The Spiders of Great Britain and Ireland.

The key only uses a restricted range of characters and aims, like Roberts' original tables, to narrow down the possibilities of what is a very large group. The characters used can only be discerned on preserved specimens. Because of the large number of taxa, it is a good demonstration of the TomBio Framework Circle-pack Key visualisation.

Online maps and atlases

There is a great deal of interest in mapping biological records online both as a method for visualising the results of biological recording and as a tool to target the efforts of biological recorders to under-recorded areas. In partnership with a number of Shropshire recording groups, we are using the OpenLayers Javascript library to implement online mapping for a number of species groups.

Springtail by David Williams Shropshire Springtail Atlas. We are working with Pete Boardman and other Shropshire entomologists, biological recorders and citizen scientists to create a distribution atlas for Springtails (Collembola) for the county of Shropshire. To the best of our knowledge this is the first ever recording project in the UK that has specifically focussed on producing a county atlas for Springtails.

Acanthosoma haemorrhoidale by Maria JustamondShropshire Shieldbug Atlas. In response to a request by entomologists currently recording these insects in Shropshire we have produced this online mapping tool that presents the up-to-date distribution maps for all species. The purpose is to enable current recorders to target their efforts on the ground in order to fill in the gaps.

Dark bush cricket by David WilliamsShropshire Orthoptera and Allies Atlas. These maps were produced response to a request by entomologists currently recording these insects in Shropshire. These up-to-date distribution maps for all species enable current recorders to target their efforts on the ground in order to fill in the gaps.

Leptura_quadrifasciataShropshire Longhorns Atlas. These maps were produced response to a request by Caroline Uff - the Shropshire County Recorder for beetles. These up-to-date distribution maps for all species enable current recorders to target their efforts on the ground in order to fill in the gaps.

Trioza remota by David WilliamsShropshire Psyllid Atlas. These maps were produced response to a request by Keith Fowler - the Shropshire County Recorder for hemiptera. These up-to-date distribution maps for all species enable current recorders to target their efforts on the ground in order to fill in the gaps.

Derephysia foliacea by David WilliamsShropshire Terrestrial Heteroptera Atlas. These maps were produced response to a request by Keith Fowler - the Shropshire County Recorder for hemiptera. These up-to-date distribution maps for all species enable current recorders to target their efforts on the ground in order to fill in the gaps.

Shropshire Psocoptera Atlas. These maps were produced response to a request by Keith Fowler - the Shropshire County Recorder for Psocoptera. These up-to-date distribution maps for all species enable current recorders to target their efforts on the ground in order to fill in the gaps.

Shropshire Auchenorrhyncha Atlas. These maps were produced response to a request by Keith Fowler - the Shropshire County Recorder for Hemiptera. These up-to-date distribution maps for all species enable current recorders to target their efforts on the ground in order to fill in the gaps.

Satchellius mammalis by Rich BurkmarShropshire Earthworm Atlas.The FSC Tomorrow's Biodiversity project is working in association with the Earthworm Society of Britain (ESB) to promote earthworm recording in the UK. We have produced this online mapping tool that presents the distribution maps for the vice county of Shropshire (VC40). The main purpose is to enable current recorders to target their efforts on the ground in order to fill in the gaps.

Lumbricus castaneus by Rich BurkmarSouth Lancashire Earthworm Atlas.The FSC Tomorrow's Biodiversity project is working in association with the Earthworm Society of Britain (ESB) to promote earthworm recording in the UK. We have produced this online mapping tool that presents the distribution maps for the vice county of South Lancashire (VC59). The main purpose is to enable current recorders to target their efforts on the ground in order to fill in the gaps.

Other visualisations

An area of technology that we believe has great potential for visualising taxanomic databases is the Javascript library Data Driven Documents (D3). Read an introduction that here: Multi-access keys and D3 - what's the link? In 2015 we started to demonstrate the utility of D3 to visualise taxonomic knowledge bases and biological records. As well as using it to create multi-access keys (see previous section) we have also used D3 to create a number of other visualisations.

Taxonomy web services visualisation Taxonomy web services visualisation. A visualisation to explore taxonomies managed by both GBIF (Global Biodiversity Information Facility) and NBN (National Bioidversity Network). Search for organisms and build phylogenic trees showing their positions within the taxonomies.

Sizes of British spiders visualisation Sizes of British spiders. This is a visualisation of a small taxonomic knowledge base detailing the sizes of spiders in the British spider fauna. It demonstrates, in a small way, how morphological information on a taxonomic group can be explored in an interactive way. This visualisation also uses one of the D3 'layouts' - a circle pack - to illustrate taxonomic relationships between spiders in the British fauna.

Preston Montford Rothamsted Moths Preston Montford Rothamsted Moths. Although this visualisation is driven by a knowledge base built from biological records rather than morphological characters, it does provide another example of an interactive tool that can be a useful aid to identification. It also demonstrates some of the excellent transitioning and animation capabilities of D3.

FSC Moths FSC Moths. Another visualisation driven by a knowledge base built from biological records. This extension of the Preston Montford Rothamsted Moths visualisation adds the capability to switch knowledge bases to reflect the moths recorded at other FSC centres.