[Taxacom] the hurdle for all biodiv informatics initiatives

David Patterson dpatterson at eol.org
Mon Feb 22 07:32:13 CST 2010

To add to the answers to Tony's questions.

I mentioned off-list that the EOL LifeDesks are being built in tight collaboration with ScratchPads. The intent is to emerge with a diverse yet interoperable array of tools in many flavorts to suit many users.  I'll answer the questions from the perspective of LifeDesks (Dave Shorthouse the architect may have more to say) and GNA on the understanding that anything an LD can do, a SP will be able to do too. 

So, to Tony's questions.

- How do Scratchpads approach the "enter once, use many times" paradigm - i.e., if information is entered or updated in one Scratchpad, can this be propagated automatically to others? (E.g. cf. the WoRMS approach - a sponge expert modifies the World Porifera Database, other DB's which utilise the same shared master taxon list e.g. ERMS, RAMS are instantly updated)

LifeDesks  can release a standards-compliant feed for use by other environments.  This feed currently delivers LifeDesk content into EOL.  Classifications can also be released.  In due course (within the next few months) the classifications will be released into GNA so that they are available to anyone who wishes to use GNA services.  That is, we are making headway. In my view, it is critical that the design of the system is fully dynamic so that we don't allow dated copies of information to predominate over current information.

- Is it possible to do a single query across multiple Scratchpads, for a taxon or taxon name of interest

LifeDesks is now introducing a Solr search function that searches across all LDs

- Are there scalability issues, i.e. will a Scratchpad break if you try to load e.g. 1 million taxon names, or 10 million into it (as per current uBio content, etc.)

Scale remains a problem, but as there are occasional needs to deal with systems that access all names, it will be addressed.

- Is it possible to obtain a database or tabular dump of up-to-the minute taxonomic information, preferably from all Scratchpads, for local processing or upload to other systems?


We (EOL, Data Conservancy, GNA) are building a taxonomy editing environment as part of the GNA space.  It is called GNITE.  It is designed to do the tasks Tony would like.  I will provide a description of this project in due course. GNITE is being built off the LD taxonomic editor, and any features within GNITE will be available to both LifeDesks and ScratchPads.  We are hoping to release a beta GNITE by July.


David J Patterson
Senior Taxonomist, EOL
CoPI Life Sciences, Data Conservancy

Biodiversity Informatics
Marine Biological Laboratory
Woods Hole, Massachusetts 02543, USA.

(+) (1) 508 289 7260
dpatterson at mbl.edu

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