The International Arabidopsis Informatics Consortium (IAIC) has existed since 2010 to facilitate the maintenance, development and evolution of informatics tools that primarily support Arabidopsis researchers.
They have recently published a White paper on the future of Arabidopsis bioinformatics resources.
As we all know the first published plant genome was that of Arabidopsis thaliana in 2000 and since that time Arabidopsis has been used extensively around the globe as the primary plant experimental organism.
At the present time the use of Arabidopsis as a model organism has plateaued in most Western countries but is still on the rise in China and, as reported in the 2018 Multinational Arabidopsis Steering Committee (MASC) Annual Report, there remain more Arabidopsis-focused papers published than those than focus on any other single plant, although rice is catching up fast!!
Therefore with such a large number of researchers requiring effective bioinformatic tools to help their experimental planning and analysis it is essential that these tools are maintained and expanded.
The current situation sees TAIR and Araport existing as two complimentary resources. Active since 1999, TAIR is the older resource and now emphasizes high quality functional annotation. Araport was established in 2014 following a community recommendation from the last IAIC White paper and now focuses on the computational aggregation of diverse resources. TAIR is funded through an innovative subscription model that has maintained the resource over the past 5 years, Araport was funded by NSF and but unfortunately since publication of the White Paper it has emerged that NSF’s currently will not renew this funding.
Both these resources are clearly US-based as a holdover from the early uptake of Arabidopsis research in that country. As mentioned above TAIR received subscriptions from across the world so it remains to be seen how Araport might be funded as there is a clear community need for this resource.
In order to plan for the next phase of bioinformatics support for Arabidopsis and wider plant science researchers, the IAIC met in St Louis in May 2018 and the White Paper resulted from that meeting. One common theme that emerged from the meeting was the importance of metadata standards to facilitate comparable reuse of any deposited data. In addition it became clear that a robust upfront plan for gene ID assignment was critical for the future facile comparison of data from different experiments, across ecotypes and even between species.
Overall the workshop
discussions resulted the formulation of the following recommendations:
Integration of data and tools: Identifying a need for a system for standardiSing and integrating data that is sustainable and not overly dependent on a few individuals. This can be achieved by development of a PlantHub or Arabidopsis Super-Portal as well as overseeing a managed expansion of fully integrated analysis tools.
Data formats and standards: This is extremely challenging but there should be community agreement on ontologies, standards and formats, their usage, and enforcement across all types of data. This would allow linkage with independently developed annotation and datasets and thus would require an authority to maintain a gold standard.
Tool development: With more data generation comes the requirement for new ways of browsing genomes that can be integrated with other overlapping ‘omic databases and then compared across genomes and networks. This type of higher level software development will need collaboration with the larger IT community, especially if the end goal is a set of simple GUIs (graphical user interfaces) that encompass more complex underlying information.
As ever the primary challenge lies in obtaining the funding and manpower to meet these recommendations. This should be a global effort given the international uptake of the resources that has been initially developed using US-based funding sources. The TAIR-type funding model is sufficient to maintain their excellent service but development of new tools requires a significant new commitment.
Over the short term the recommendations have resulted in the set up of an Arabidopsis Community Hub hosted by TAIR. This contains a list of software tools that will be of broad interest to plant scientists. They are happy to include additional appropriate links to other well-used tools. This site links to the GARNet Resources page that also contains a similar set of resources, arranged over a broader set of headings.
Please visit the TAIR Arabidopsis Community site and watch this space for updates on how the Arabidopsis bioinformatics community will evolve over the coming years.
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