Computing For Taxonomies and Biology

Scientific insights can be enabled by providing an interactive visual taxonomy management system. To achieve this it is important to structure, manage, and enable understanding of complex scientific information to enable scientists to collaborate using a systems approach. The main subject will be editing and display of taxonomies/phylogenetic knowledge, this could make possible new insights.

Creation, editing, and customisation of biology taxonomies
The primary aim for this research is to establish a method to represent complex taxonomies in a way that is interactive, accessible and understandable by a wide range of people. Seeing information in a new context can mean discovery of new truths. This will be enabled by use and further development of a Semantic Web infrastructure, and building on end-user programming research to enable the necessary interactivity. An objective is to enable communication between disciplines to allow a systems approach. A further objective is to enable biologists to use and customize automated translations from biological data that is often held in flat file structures that are difficult to parse. These can be connected into Semantic Web structures, to enable biologists to use freely available open standard technologies for search and structuring of information. This could save large amounts of time, so freeing researchers to concentrate on the scientific problem they want to examine. Better visualisation of information can aid scientists to improve their models. Semantic Web and Web 2.0 techniques will enable provision of visualisation and interactivity resources that allow scientists to create and edit visualisations. This allows emergence of knowledge for the benefit of scientists and public understanding. This will make it easier for science researchers to collaborate and explain their research to others, enabling new insights and progress. Visualisation will also provide a way of conveying this interdisciplinary science to the public.

The main strands to this research are –

Provision of a system for managing, editing, and viewing explicit taxonomies.
Enabling scientists to create and customise software for their research problems more easily.
Use of the taxonomy system for complex scientific problems.
Provision of a web based taxonomy system to be available to the public, and explanation and promotion of this system to enable public understanding of science.

Semantic Web representation can be used even when the scientific information structure has not been finalised and when this structure is subject to frequent change. Dynamic systems enable new information and connections to come to light, these can then be incorporated in the system rather than having to redefine the system around new knowledge. Semantic Web techniques enable standardisation of visualisation, parsing and searching. Thus, new insights can be obtained from information already known and from connectivity that has been visualised.

There has been an explosion of taxonomic/phylogenetic information in biosciences. Interacting with this information is problematic and could be aided by visualisation. This research will assist with collaboration for interdisciplinary solving of complex scientific problems where a systematic approach is required. There is an opportunity for assisting scientists cross boundaries to enable systems biology approaches and for public engagement, with the aid of visualisation. This is necessary to enable systems biologists to interact with earth systems scientists to undertake environmental systems analysis. Then it is also necessary to concentrate on enabling solutions to problems that cannot be solved by scientists without the need for programming, thus making it possible for scientists to create their own software to solve these problems. The interactivity that this can provide is important as the end-user programming techniques will improve facilities for uploading and managing information for amateurs as well as professionals. This interactivity is also important because of the quantity of information that needs to be made widely available and managed. To achieve this an online systematic representation of scientific information that gives a holistic view of related knowledge should be provided. This will reuse information and ideas provided by other researchers. So it is necessary to investigate systems that organise and visualise information. This is discussed in my Ezine article ‘Web Taxonomy Creation’.

Semantic Web technology allows us to encourage and improve non-programmer involvement in visualisation of the problem domain. Beneficiaries are scientists who are enabled to collaborate in a systematic way with others on large problems, and who will have better tools for conveying their findings to other scientists and the public.
The benefits are –

Assistance with collaboration by interdisciplinary scientists.
Enabling scientists to model their problems without having to spend large amounts of time learning compute science in order to search and parse information.
Increased collaborative interdisciplinary involvement in taxonomy development to enable faster updating of information, creation and use of tools, and better communication to other scientists and the public.
Availability of taxonomy information and interactive visualisation using browser based software, so enabling development of models for new scientific insights and public understanding.
Opening up opportunities to those currently outside formal education, and promotion of science, this can make science less remote from the public.

This project will bridge the gap between computer literate non-programmer scientists and software creation, so making new applications possible such as collaborative taxonomy development amongst researchers and other people formerly not linked.