Thursday, April 5, 2012

THIS is how you do a scratchpads site.

Behold the organized glory of Mosquito Taxonomic Inventory (MTI).

Scratchpads, if you aren't familiar with the platform, is a biodiversity networking tool created by ViBRANT, an EU funded project. The intent is to provide open-access, creative commons licensed software for a global community of taxonomists, natural historians, and other comparative biologists to draw together their knowledge in web-based format. As MTI shows, scratchpads can be an excellent tool, on level with the software behind AntWEB. This is clear with the preliminary information already hosted there.

I am quite impressed. But the reason I am impressed is sad. Until today I thought scratchpads was a flawed platform, a messy pooled slew of overwhelming, hard to navigate options that lead to either a sloppy mess or a webpage never updated. I admit, the majority of my exposure to this software has been through Fungus Gnats Online (FGO). Eventually my frustration with the search engine, poor organization and lack of control lead me to create Keroplatiwiki, I now have more control, but it is not nearly as slick as scratchpads can be if used properly.

Here is what makes MTI such a great example:

  • The front page is clean and clear: There are no unnecessary animations, no eye candy. In other words, it's not killing my eyes to look at the format. The header is a simple icon and the name of the network, all in those same cool, unobtrusive colors. Equally important is the content. The page explains not only what Mosquito Taxonomic Inventory is, but also exactly how to navigate the site's resources. Two small, clear photographs highlight the right side of the text, and that is all that is necessary. There is no extra clutter; the news tab and other messages are on a separate page.

  • Simple taxonomic navigation on the left bar: The left side has two expandable taxonomic hierarchies, and aside from a two sentence contact statement and a visitor map, that's it. One is for extant species, the other for fossils. The front page explains how to use these with relative ease. Above these is a search box, which is really not even necessary, a couple seconds faster retrieval of pages far down the hierarchy, if that.

  • Useful links (only!) on the right hand side: One of the things that absolutely drives me nuts about FGO are the huge number of categories listed in the sidebar. This is where my sense of organization and will to improve starts to go numb. Where do I even start? What's the difference between 'annotated bibliography' and 'biblio'? What is the 'character project'? What is 'page'? When are each of these necessary? How should I use them individually? Even clicking on the categories doesn't make that especially clear. And there's no indication on the home page, only a short blurb and 'recent' updates.
    MTI, on the other hand, has perfectly clear categories, all explained on the home page. There is a short hierarchy leading to individual morphology pages (e.g. head, thorax, and abdomen), links to individual parts of the Anatomical Glossary, the single, alphabetic by author bibliography, and four links to some general resources on classification and a list of valid names. No 'biblio', no 'page' and no clutter.

  • The individual pages are wiki-style: I know the claims of the scratchpads hub page. "Your data [images of different online databases, including Google] builds your site [!]" In theory this is a good idea. Why wouldn't you want to quickly gather as much information from as varied sources as possible and just insert it all, and voila! You have your complete network, ready to 'use'. In practice, it looks just about like what you would expect a hacked together site to look like, that is, a messy pile of useless crap. This is another one of those things that drives me nuts about FGO. The species pages are mostly populated by empty boxes, making them pretty much a copy of Encyclopedia of Life's relevant (or irrelevant, maybe) species pages. You can get the same information in the same format through Google, so why even have a network? The glory of MTI's chosen page format is that it filters down all the relevant information into a clear, written summary. If GBIF had a relevant piece of media, you could easily insert it later, but the initial choice of simplicity means that future clean up projects will not be necessary. More work initially, but more useful in the long run.

  • The Anatomical Glossary: I wanted to talk about this individually because it is absolute genius. The overview page explains the navigation of the glossary, but it is in about the clearest format I could want. Nine categories link to an alphabetic listing (by first letter) of all anatomical terms relevant to an individual life stage or structure type. Just as the rest of the site, the structure pages are wiki-style, with links to adjacent and similar anatomy, and a list of synonyms at the bottom. If every family of insects had one of these, we would be light years in distance ahead of the taxonomic problems we are now facing. This. Makes. Me. Giddy.

There is a lot of good quality information at MTI. One general flaw I can see is that, as of now, it is much more of a personal project than a network. But, please go check it out and compliment Ralph Harbach on his fine work. And if you are planning on making your own or are already hosting a scratchpads network, please shoot for this level of excellence!


Vladimir Blagoderov said...

Dear Zachary,

while I largely agree that FGO is a mess and take some responsibility for that, let me ask you just one thing. What have you done to change the situation? You have not posted anything, not even try to comment on anything there. I understand that Scratchpads are not trivial to use, and unstructured wiki are much easier. I am frustrated with it at times myself, but then remember potential benefits of atomising data. However, the most important thing about FGO is that it build community of fungus gnats workers, which did not exist before.

Differences in structure between FGO and MTI reflect not only differences in minds of particular personalities, but also state of taxonomy of these two groups. So, if you have any constructive suggestions - you are always welcome. We will be migrating to Scratchpad2 platform very soon and this is the great opportunity to implement your ideas.



ZL "Kai" Burington said...


I have not done anything to change the situation because I have no control to change the situation. Yes, I could have made comments, but it is not even clear where to make such comments on that site, or even if such comments were welcome. As an alternative I have used this blog as a platform for my frustration. I do not mean to offend; I am grateful for the work you have put in getting that community going.

In addition to the things I said in my post, I have a few more comments:

1. I understand that Sciaroidea includes Cecidomyiidae. Is that group going to be included in the hierarchy at some point? It seems there is a conflicting theme between using Sciaroidea and fungus gnats, when the two do not quite completely correspond.

2. Would it be possible to have some training on using the site? I feel my frustrations would be much improved with some assistance on using the various components.

3. If I were to add content, what level of control would I have over its format? Would it be possible to add content in a wiki style? Much of what I have been putting on the Keroplatiwiki is personal research, and given that FGO is going to be linked directly to EoL pages in the future, I wonder if my content would be unacceptable.

After checking this ( presentation on Scratchpad 2, I am quite excited about the prospect. It includes many of the changes I noted in my post.

Thanks for your time and your comment. I hope we can work together in the future.

~Zachary L. "Kai" Burington

stho002 said...

very simple message: if what you want to do is keep a taxonomic hierarchy updated, with links to literature and images, then Wikispecies is the simplest and best option ... cheers

Vince Smith said...

Dear Kai,

Thanks very much for taking the time to do such a detailed review of the Mosquito Taxonomic Inventory (MTI) Scratchpad. I know that the site author has put a lot of time into this, so your comments are much appreciated, both by him and the Scratchpad team.

We set out with the Scratchpads to make a flexible system that anyone could pick up. MTI demonstrates what can be done, but for many authors the original version of the Scratchpads was just a bit too flexible or too hard to use. As a result, many of the sites work for the particular communities that contribute to them, but are inaccessible to everyone else. As part of redeveloping the Scratchpads we have put a lot of effort into addressing this issue and a number of other problems, some of which you touch on here. Many of these improvements relates to navigation, layout and presentation, so that we retain the flexibility needed by the communities using the sites, while guiding them toward creating more consistent and structured sites that are easy to navigate. You can read about many of the improvements in an article I published back in November 2011 ( At the moment we are working on migrating the 350 current sites to the new version. This process is largely automated and once it is complete, there should be a marked improvement in how people access and use the sites.

Regarding training, we do offer a number of courses (8 this year, see and you can download the training materials and request a training site if you can’t make it to any of these. You can also play with the Scratchpad 2 Sandbox ( if you would like to see what Scratchpad 2 offers. As of April 2012, all new sites have been built using the Scratchpad 2 software, and we are hoping to complete the migration for the majority of the 350 other sites by the middle of 2012. Finally the site will be getting a major facelift in the next couple of months so it should be easier to find out what the project is all about, and access help resources.

Thanks again,

Vince Smith (Scratchpads)
NHM, London

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