Proposal for further development online knowledge base on Sciaroidea [Fungus Gnats Online]

Current state
For 16 month that FGO have been existing it got 44 users, and, we are happy to say, as of today, has the largest number of viewings among all Scratchpads. Scratchpads are based on a very flexible and extendable Content Management System, Drupal.
Technology. FGO users can easily publish almost any kind of information. There are numerous content types and it is possible to create custom content types (for example species description). Images can be fully annotated. Specimen and location records are Darwin Core 1.2 compatible, which means they can exchange data with other databases. Many other features are coming up.
All content types can be conveniently displayed on one page using Panels, for example: Mycetophilidae
TinyTax ClassificaionContent.
Bibliography: 2658 bibliographic records. Not complete, some records duplicated, many need editing, but it is growing and improving.
Taxonomy: 7308 names. The very heart of a Scratchpad site is biological Taxonomy. In general, taxonomy in Drupal, which Scratchpads are based on, is a list of tags, or keywords, which helps to order nodes (pages, blog entries, images, bibliographic records etc.) Biological taxonomy of Scratchpads is similar to classification, it is a hierarchical list of valid names. Every node can be tagged with these names, and that is how different pieces of information are linked. For example, when user clicks on a term in a list, say "Diadocidia " or "Diadocidia halopensis " s/he will be taken to a page, where all information on the taxon is displayed. A special block (TinyTax module) at right side menu area represents Sciaroidea taxa as a tree. Clicking on names user can navigate the tree, click on a blue cross next to the name takes user to a Panel view for the particular taxon. At the moment it is possible to have only one classification, so in case of conflicts over taxonomical position or status of a particular species the community has to arrive to a consensus. The taxonomy is not complete and needs checking. Excel file is available for download.
Library. Due to generosity of Eirik Rindal and Paul Beuk we have online access to more than 500 pdfs of taxonomic papers. If you have e-reprints absent in the library and would like to share it please contact Vladimir Blagoderov or Paul Beuk.

What can we do?
First of all we envisage FGO as a reference site, a workbench of a taxonomist, a place where you start your taxonomic project from, mini-EoL. Secondly, it may be an information source for anybody interested in fungus gnats, going a little further than Wikipedia. You can check examples of other scratchpads - how other communities achieve their goals.

We thought of following priorities:
1. Annotated bibliography.
For each taxon we could have a list of references with a list of keywords showing what particular information on the taxon is in this paper. It may be displayed on a panel Bibliography and look something like that:

Mycomya marginata

Sciophila marginata Meigen, 1818:249 original description
Mycomya marginata Keilin, 1919: Pl. III, fig. 7-10 description of larva
Mycomya limbata Landrock, 1913: 25 synonym
Mycomya marginata Vaisanen, 1984: 230 redescription, key to species

A little bit more difficult to do the same for distribution. Let me know how would you like to have distribution (verbal description, check boxes for countries or TDWG codes, Google maps or other)
2. Species pages.
The idea is to have diagnoses/descriptions for all species eventually, to eliminate most laborious library search and easy species comparison, see for example Diadocidia papua and Panel view for the species
3. Images.
Images can be easily published, annotated, commented, and assembled to galleries. All images, if properly tagged can be displayed on panel pages.
4. Keys. There is no easy way to do keys in Scratchpads. We could use:

  • Static pages with traditional dichotomous keys
  • Static pages with pictorial keys and lots of links
  • Mindmaps
  • Viewer for DELTA files embedded on pages

VB would prefer more universal solution, like DELTA files, although there is no software for Mac available. BR inclines towards traditional dichotomous keys, like this , for example. Please let us know what you think.
5. Specimen records and distribution.
As it was mentioned, it would be great to have a biblio reference for each distribution record, but it may not be feasible. Specimen and location records can be easily created/imported and displayed with Google maps. We do not have it set up yet, but you can get an idea from Milichiidae site

Some problems
Legal aspects and first of all copyright is a very sensitive issue and worth of a separate discussion. In February there EDIT conducted a very productive meeting on Intellectual Property Rights in the Kew Gardens, on WP6 sites also report of the workshop and presentations can be found

A number of questions related to sociology of scientific work:
Community work. This is a communal site, everybody is welcome to contribute, community is able to maintain necessary quality of publications. Surely, in a small community like ours a clash of personal ambitions can be successfully resolved
Authorship. Each post has an author and all the changes and additions can be traced. It is important that during registration users provided their real names, so their publications can be attributed.
Citation and longevity of publication. Each node has an address and can be cited. All changes can be rolled back. System automatically baks up the whole site every night, and every 6 month tapes back ups. It is possible to return the page to any particular point in time if necessary. Therefore, nodes can be cited as Author, Date, Title, HTTP Address.
Peer review can be provided through comments, for more serious publication we could think of more robust system of reviewing
Recognition for contributors is a very important issue. But with the next edition of ICZN coming up, relaxing rules for Internet publications, latter will be wider accepted by institutions and museums as valuable contributions. NHM , for example, encourages web publications as the best way of dissemination of scientific information

Technical problems.
As flexible and extendable as Drupal is, it still has a lot of limitations. A WP6 team works hard on technical aspects of Scratchpads. It will get more functionality, accommodating users' needs. If you like to learn more how Scratchpads work, a good start is help pages especially FAQs and Screencasts (coming)

Necessary actions:
1. Menu changes and simplification. Site functionality grew up a little bit too complicated for a user to be intuitive. Some functions are confusing/doubled or never used/will be used. All unnecessary items should be removed from the menu to get more usability. It was proposed that blogs, newsletters, polls, webforms, tasks are not required at the moment, but can be added later if needed. (Vlad)
2. Vocabulary for biblio annotation. (Bjoern)
3. Taxonomy published as Excel spreadsheet (Vlad)
4. Checking taxonomy. Please check taxonomy and let me know of any errors and omissions (Everybody)
5. Import guide. It might be easier to import datasets rather than to create numerous pages while online. Let me know what data would you like to publish and we will find the easiest way to do it (Vlad)
6. Excel template for species pages. Species descriptions can also be imported, an Excel template that anybody can download and fill off-line will be prepared (Vlad)
7. Sample Genus revision (Bjoern, Jan)
8. Comments and suggestion (Everybody)

A number of people expressed their interest in a workshop on Scratchpads. If we, as a community, decide what we want to do and be determined about it, such a meeting would be necessary. I had a very positive response from Dave Roberts, a leader of EDIT WP6, we could try to organize the workshop later this year or next year.

Please post your comments and suggestions on the page or on forum

Vladimir Blagoderov, Bjoern Rulik
June 2008

Mon, 2008-06-30 10:39 -- Anonymous (not verified)


Apart from the Scratchpads we are also working on a data portal and taxonomic editor in EDIT. What you propose for the annotated bibliography is what we try to show in the portal (for a very first preview see I hope that in the end we have a combination of Scratchpad and portal/editor, so that all the name data can be edited using the taxonomic editor, which will be much better equipped for this task than the Scratchpads. So, as always, try to keep your data as anatomized as possible, so that they can be imported in the taxonomic editor.
Submitted by vblago on

Dalton Amorim is on Yacatan at the moment and could not comment directly on the site, but sent me some thoughts:
"... question about the use we make of the site is interesting. I can list you some..:

1. being updated with recently published information;
2. finding earlier publications;
3. getting images of specimens we don't have in our collections.

Of these, the first two can be made with other tools, but the access to the site makes it much easier and practical. However, the third point is like having a worldwide collection --that none of us have. There is a lot of genera known from some regions that cannot be found in other regions and getting material is really a bureaucratic boring today. But if the photo is there... My photos of non-neotropical genera of mycetophilids at the NHM made a number of decisions in the last monthes much easier. At another taxonomic level, the access of photos of the types would be nice. I edited most of the 1,200 photos I took at the NHM, but there are still some to go. The everyday identification of mycetophilid material from Brazil has already shown that those photos are important enough.

...I guess that some tasks have to be attributed to given persons, because we would not use our time on producing things that maybe someone else would also be working on. I.e., I would not invest on preparing a Genus page on, e.g., Cluzobra if someone else is also working on it."

Vladimir Blagoderov

Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith