VASCAN functionalities

This post is also available in French.

Our Database of a vascular plants of Canada (VASCAN) is a bit over a year old now (launched on October 22, 2010) and the response has been great so far! The site is averaging 1,850 visits / 20,500 page views a month from over a 100 countries, and is used as a source for vernacular names in Wikipedia and as a tool in the horticultural sector. We thought this would be a good time to summarize some of the things you can do with VASCAN:

What is VASCAN?

You can read all about VASCAN in the about page. If you want a more visual explanation, here’s a presentation about VASCAN (also embedded at the end of this post).

Name search

You can search for any scientific or vernacular name by using the name search. The full search allows you to search on parts of names (starting from the beginning, e.g. Carex ag) and the dropdown box will offer suggestions and provide shortcuts to name pages.

vascan-functionality-dropdown

Name pages

A name page interprets the scientific or vernacular name provided in the URL (e.g. http://data.canadensys.net/vascan/name/acer saccharum) and shows relevant information if the name has been found. The system will automatically forward unique synonym and vernacular names to the accepted taxon name, displaying more relevant information (e.g. Acer saccharum subsp. saccharum or Sugar maple), but this functionality can be turned off by appending “?redirect=no” to the link. If a name is linked to multiple taxa, a disambiguation page will be shown (e.g. white maple or Solanum nigrum).

You can use name pages to create dynamic links in your spreadsheet, database or website. Just concatenate “http://data.canadensys.net/vascan/name/” with the name. Please exclude the author and provide the infrageneric or infraspecific rank (“sect.” or “subsp.”) in the name if applicable. It is not necessary to capitalize names correctly or encode space characters as “%20″. An example of a formula you can use in Excel to create links to VASCAN is:

= HYPERLINK("http://data.canadensys.net/vascan/name/" & A2, A2)

vascan-functionality-namelinks

Checklist builder

Interested to know which trees are native in Newfoundland, which genera are introduced in all of the prairies or which Salix species occur in British Columbia, but not in the rest of Canada? You can find it out with the checklist builder, which allows you to combine a set of selection criteria (taxonomic group, habit, distribution, status or a combination of these) and display criteria (ranks to include, sort preference) to create your own customized checklist.

vascan-functionality-checklist-builder

Once your happy with the result you can download the checklist as a simple tab delimited text file or as a standardized Darwin Core archive following the GBIF Global Names Architecture Profile. The latter one also includes the vernacular names and synonyms.

The data are there to be used, which is why we licensed them under the Creative Commons Attribution-ShareAlike 3.0 Unported License, allowing you to build upon our work (read more about it here). You can also download the full database as a Darwin Core archive.

Feedback

If you discover an issue with the data or interface, or you want to send a suggestion, you can do so by clicking the feedback button on the right of every page. So far, the response has been amazing: users have submitted over 700 suggestions for correction, improving the overall quality of the database. All issues are recorded in our public Google Code issue tracker, and we take each one into consideration. You can read more about it here and here.

Summary

And that pretty much sums it up. If you want an overview of the data and functionality, we gave a VASCAN demonstration at the Consortium of Northeastern Herbaria meeting in Philadelphia, June 2011, which is embedded below. Let us know what you think!

  • Anonymous

    Nice work, Peter and Christian. Name reconciliation and the checklist builder tool are superbly crafted. What’s the proportion of crafted checklist downloads relative to downloads of the whole DwC-A? Has a bulk name search ever been requested (i.e. a textarea and/or a POST)? I’m also curious about the bibliographic metadata in your core taxon.txt rather than in an extension such as http://rs.gbif.org/extension/gbif/1.0/references.xml. Surely an extension would make for a smaller download. Did users request this more denormalized representation?

  • http://www.linkedin.com/in/peterdesmet Peter Desmet

    Thanks David!

    I don’t have statistics for the full DwC-A download for two reasons: 1) we recently changed where that file is hosted (now on IPT) and 2) Google Analytics doesn’t track downloads of files by default. I recently discovered this and I suggested a fix for IPT: http://code.google.com/p/gbif-providertoolkit/issues/detail?id=812

    For the crafted checklist downloads (for which I can count the number of generated files on the server, but I should probably implement my fix here as well), the flat text files are far more popular (80%) than the DwC-A (20%). I think this answers in part if users prefer a denormalized representation, but it’s probably also due to the fact that Darwin Core is not very known outside the biodiversity informatics community and that often a flat file with names and distribution is all you need.

    A bulk name has not been requested yet, but it’s something I’ve been thinking about. I’d like to create a synonymizer, where you can upload your list of names, and VASCAN annotates them with status, accepted name, family, etc. We just don’t have the time to do it. We knows, now that VASCAN is open source (including the whole MySQL database), someone else can develop this. :-)

    I’ve looked at the bibliographic extension, but it only allows to add more references to one taxon (star schema with taxon as core), not the other way around, I believe. And even if it did, we also have references in our distribution and vernacular name extensions. The size of the file would not be affected that much I think, as repeated data can be zipped very efficiently. And yes, I believe most users prefer denormalized data, which is why we also include a denormalized view of the classification (with the fields class, order, family, etc.). In fact, the new IPT doesn’t even use default values in the meta.xml anymore (see issue http://code.google.com/p/gbif-providertoolkit/issues/detail?id=730), to make the data more readily useable by data consumers.

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