Category: Information

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Blogging the state of our plants

Our friend Nora Castañeda attended the State of the World’s Plants Symposium a couple of weeks back and was kind enough to send us some of her impressions. We’ll publish them in instalments over the next few days. Thanks, Nora.

Last week, Kew organized and hosted the very first State of the World’s Plants Symposium. The event was preceded by the publication of the State of the World’s Plants report, which this blog and other press outlets have mentioned already. The report is complemented by an interactive website that in a very user-friendly interface enables visitors to explore further details and useful data sources (some of the data sources are only available online).

The State of the World’s Plants report and symposium come at a perfect time. As Prof. Kathy Willis said in the introduction of the event, we currently have state of the world reports for a plethora of topics (including fathers), but not for plants. Until now. The report serves as a baseline of our current knowledge of plant diversity, the global threats that plants are currently and will face in the future, and the policies affecting plants. The idea is that for the next five years, we’ll see an annually updated global assessment of the state of our plants, where we’ll be able to gauge progress on the main topics addressed by the report.

As for the symposium, if I had to describe it in few words, I would say it was a series of interesting and captivating talks, combined with the participation of a very enthusiastic audience (we even became a trend on twitter with the hashtag #SOTWP. But I’d like to use the space of this and subsequent posts to share my own impressions of the symposium, together with some interesting links for the curious.

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Nibbles: Botanical gardens, Glass flowers, Remarkable trees, Rhubarb history, Expensive pumpkin, Back to the future, Quinoa glut, Citrus greening biocontrol

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Nibbles: GRIN-Global, Old gardens, Grain buildings, Roman eating, Armenian wine, Coffee GI, PAPGREN, Tamar Haspel double

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Food and plant resources roundup

A couple of meta-resources today. First, a handy database of botanical illustrations, with thanks to Mark Nesbitt of Kew for the tip:

Plantillustrations.org is a non-commercial website and will not trouble you with irritating advertisements or ask you for donations. It provides a searchable index so that you can easily find plant illustrations by using accepted or synonymous botanical names. The database is copyrighted but most illustrations can be used freely under the Creative Commons License. Please visit the website of the original contributors for further details. You can find them on the left side of the HD illustration page. If you want to use photographs please ask Max Antheunisse or contact Jan Koeman.

Second, a list of food museums from the Oxford Symposium on Food & Cookery:

Symposiasts and followers of our Facebook page responded enthusiastically when I asked about their favourite food museums. There is, in fact, a searchable online listing of some 1400 such museums compiled by Shirley Cherkasky and friends at http://foodhistorynews.com/directory.html.

But for the fun of it, here is a rather more selective listing of the ones that our symposiasts and Facebook followers came up with. Feel free to suggest others through your comments! My personal favourites are The Endangered Cake Museum and The Burnt Food Museum.

Yeah, I know. There goes your afternoon.

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Following Brassica into Genebank Database Hell

Scientists at The Genome Analysis Centre (TGAC) have released the first web repository for Brassica (mustard plants) trait data to tackle reproducibility, user controlled data sharing and analysis worldwide. Scoring the versatile crop’s beneficial traits will assist Brassica breeders in improving their crop yields, increased nutritional benefits and reduce our carbon footprint through biofuel production.

Very worthy, of course. But also, alas, an opportunity missed. How so? Come with me to Genebank Database Hell.

Let’s start with a random germplasm line from the Brassica portal: DEU146_BRA_02028. That’s a weird but somewhat familiar name. People in the know will recognize DEU146 as the code for the German national genebank, IPK. But the organization is given in the portal as CGN, the Dutch national genebank. What’s going on? Stay with me, don’t panic. The portal does provide the following metadata for the material in question:

Provenance: Brassica.xls file downloaded from http://documents.plant.wur.nl/cgn/pgr/brasedb/, March 3rd 2010
Comments: Line name concatenated from resource collection code and genetic resource collection “accession” number; associated data availabel from European Brassica Database of Genetic Resource Collections
Entered by: graham.king@bbsrc.ac.uk
Entry date: 2010-03-03

One’s first instinct of course is to look for the BRA_02028 bit of the name among the DEU146 material in Genesys, but that would be too easy. You have to strip out the assorted underscores, and indeed the leading zero, and that gets you to the right accession, which happens to be from Ethiopia. Breathe.

You could also Google the European Brassica Database of Genetic Resource Collections, as per the metadata, which is hosted by CGN, hence the reference to that organization in the portal. If you search for BRA 2028 you get to the same thing as in Genesys, and eventually to the original record at IPK.

So, to recap: a British guy entered into the Brassica portal some data hosted (as part of a European project) by the Dutch genebank, pertaining to an accession in the German genebank collected in Ethiopia and originally conserved in the old West German national genebank. The actual URL quoted in the metadata returns a 404 error.

Look, I’ve said it before, and no doubt I’ll say it again. It’s great that gene-jockeys like the ones at TGAC build their own databases with all kinds of fancy genotypic and phenotypic data for breeders and other researchers to use. It’s really great, I mean it. It’s what’s going to get the stuff in genebanks used, and we all want that. But please, please, make sure that those breeders and researchers don’t have to go through what I’ve just described to actually get their hands on the seeds. Because I’m pretty sure they won’t. Go through it, I mean. They have better things to do.