Interactive guide to the Tom.bio ID Framework

Image display of Mitopus morio from a visualisation(If you are just looking for a link to download the framework, here it is: https://github.com/burkmarr/tombiovis/releases.)

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The Tom.bio ID Visualisation Framework is a set of tools for creating and publishing interactive web-based Identification Resources, including multi-access keys. These ID resources are driven by spreadsheets containing taxonomic knowledge (knowledge-bases). If you can use Excel - or any other spreadsheet - and you have taxonomic knowledge of a group of animals or plants, you can create ID resources like this. You don't have to have access to a website to deploy your resources- you can run them locally on your computer. But you can also deploy them to websites too. The framework contains all the tools and information you need to do this.

The example visualisation shown below is being driven by the example biscuits knowledge-base provided with the framework. The framework comes with four different visualisations - switch between them using the drop-down list at the top of the visualisation. The 'Two-column key' and 'Single-column key' visualisations are multi-access keys. The other two visualisations are not keys, but they are identification tools. All four visualisations are driven from exactly the same knowledge-base (here the biscuits knowledge-base).

 

The spreadsheet below drives the visualisations shown above. If you can build a similar spreadsheet representing a taxonomic group that interest you, then you are 99% of the way to creating new ID visualisations for that group - including multi-access keys.



We've provided comprehensive documentation which can all be dowloaded from the framework repository. If you download the framework (the first video below shows you how) you will find all the PDFs in the 'documentation' folder. The documentation currently includes the following:

  • Quickstart Guide (all you need to get started)
  • Getting started (more detailed than the Quickstart Guide)
  • Building a knowledge-base (essential guide for knowledge-base developers)
  • Deploying your visualisations (how to make your visualisation available to other people)
  • Character scoring (only for those who want more detail on the framework's mechanism for scoring with multi-access keys)
  • Notes for coders (only for programmers who want to extend or modify the framework)

But before you do any reading, you might like to look the videos on this page which take you through the whole process of installing the framework on your computer and getting up and running as well as the first steps to developing your own knowledge-based visualisations.

You may find all you need here to set you on your way, but for those who prefer to learn in the company of others with direct tuition, we can run day-long workshops - contact Rich Burkmar if this interests you.


The link to the release page of the Tom.bio framework GitHub page mentioned in the video is: https://github.com/burkmarr/tombiovis/releases

Once you've downloaded and installed the framework, you might want to spend some time looking at the sample 'biscuits' knowledge-base that comes with it. But very soon you'll want to start creating a knowledge-base of your own. The next video shows you how to create a new knowledge-base, using the biscuits knowledge-base as a template, and use it within the framework on your own computer.

(You may notice some slight differences between the framework illustrated in the following videos and that which you downloaded, because the videos were all made with the first release of the framework. For example the 'Reload' button has been replaced by an option on the top drop-down list.)


The first thing you'll want to do when creating your own knowledge-base is to add some taxa and some morphological characters. When doing this for the first time, we recommend that you add just a few of your taxa and a few morphological characters to get a feel for how to do it.

When you really get going, you will want to read the full guide to Building a knowledge-base.

In the videos which follow you are shown the basic principles using a very small number of taxa and characters.

This video takes you through the fist steps of adding taxa and characters to a new knowledge-base for use with the framework.


This video provides more information on adding characters to a knowledge-base and, in particular, it deals with characters of numeric type.


This video describes how ordinal characters work and how to add them to the knowledge-base. In addition, it describes character grouping.


You've seen the basics of how to add characters and taxa to your knowledge base. You will likely want to add text and images to provide help to people that use it. The next video shows you how to do that.


They say that a picture paints a thousand words and ID knowledge-bases are normally very much enhanced by adding images - which can be photographs or other artwork - to depict the organisms being represented. When adding pictures to your visualisations, bear in mind how you intend to deploy you knowledge-base: if it is only intended for use on your own (or perhaps other people's) computer, then you can get away with large photographs since they will be 'served' to your browser from your own computer. But if you intend to deploy your visualisations on the internet, remember that the photos will have to be served to users over the internet from a web server and large photographs take longer to download than smaller ones.

If you want to talk to us about the ID framework, please contact Rich Burkmar.