[Taxacom] the hurdle for all biodiv informatics initiatives

Vladimir Blagoderov vblago at gmail.com
Mon Feb 22 02:58:16 CST 2010

Dear Tony,

On Mon, Feb 22, 2010 at 07:09, Stephen Thorpe <s.thorpe at auckland.ac.nz>

> - 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)

Data exchange is the problem of all bioinformatics initiative: it is either
copy/paste, which multiplies errors across the Web or mush-up. Scratchpads
development follows accepted standards as much as possible, for example
specimen and locality records are Darwin-core 1.2.1.-compatible. So, the
data can be re-used. Perhaps you suggesting global synchronization of all
taxonomic databases? Unfortunately, we have to be realists.

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

Not at the moment, however, most of Scratchpads are taxon-oriented, and it
is possible to have multiple classifications within one Scratchpad. You also
can display information from external sources, for example the other
Scratchpads, on taxon pages and give it proper credit. I suppose that
community maintaining the Scratchpad would be interested to collect all
available information in one place.

> - 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.)

It was tested, and it does work

> - 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?

Drupal based on mySQL. In theory you can export a particular node,
selection, or entire database. How to provide this functionality is a
different question, we are working on it.

>Let me add to previous post that any so-called "error correction facility"
by way of annotation is no good unless the page that it annotates is
corrected for the error, once the annotation is confirmed. We need to get
errors weeded OUT of the taxonomic hierarchy, and not just annotated on the
side ...

Depending on permissions users can edit posts directly or add comments.
Taxonomic hierarchy can be edited visually, by drag-n-drop, Taxon Editor is
the same as in EoL LifeDesks.



Dr. Vladimir Blagoderov
Department of Entomology
The Natural History Museum
Cromwell Road, London
Tel: +44 (0) 207 942 6629 (office)
Tel: +44 (0) 207 942 6895 (SBIL)
Fax: +44 (0) 207 942 5229

vlab at nhm.ac.uk
vblago at gmail.com

Fungus Gnats Online:

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