[Taxacom] Software for building taxonomic catalogues, species lists, etc.

[Donat Agosti]

Dave

In collaboration with the Hymenopteran Name Server (HNS)(and hopefully soon
Zoobank) at Plazi (http://plazi.org) we have a workflow to extract catalogue
related information that begins with OCR documents, convert them into
temporary Html docs and convert and enhance them with GoldenGATE into XML
documents that include the links to external sources, for example via LSID
to the HNS, of GenBank numbers to NCBI, or in fact anything where we can
find API's to gather enough information to produce such a link. This works
as well for entities that are not in the respective database, such as names.
In the case of new names, we have an upload procedure to enter new names and
the related metadata into HNS. Once the upload is successful the respective
LSID is returned and added into the text. The finished marked-up document is
then stored in a dedicated database from where various flavors of the
treatments are available.

GG as makr-up editor is pretty flexible and the mark-up is semiautomatic.
The more specific the customization, the more formal a publication, the
faster and more automatic the mark-up. Essentially, all the elements needed
for a particular catalogue could be marked up this way, eg all the elements
need to demonstrate that a new name is available.

Right now, there are over 12,000 descriptions of over 500 different
publications online accessible at Plazi. All ant publications are instantly
marked up, the names added to HNS and the treatments are available at Plazi,
as well as all the fish taxonomy publication in Zootaxa to 2007 and all the
ant publications to today. It is a system that works.

Donat
 

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of David Remsen
Sent: Monday, November 02, 2009 3:05 PM
To: TAXACOM
Subject: [Taxacom] Software for building taxonomic catalogues, species
lists,etc.

Taxacomers,

I'm preparing a presentation for a GBIF meeting in Asia that will be  
attended by participants with a wide range of technical knowledge.   I  
would like to be able to provide them with a list of software tools  
that individuals can use to create and manage taxonomic catalogues,   
regional floras or faunas,  or basic taxonomically-organised species  
lists.    The emphasis is on tools actually in use, not in  
development.  It would be useful to know if any tools are tied to a  
particular workflow (such as Aphia being a component of WoRMS or the  
ITIS Taxonomic Workbench supporting the development of ITIS).

Does such a list or directory already exist that someone might point  
me to?  If not,  can you provide me with information on tools you  
might use for such purposes.   Web or desktop, I am open to any.   If  
you have suggestions,  a basic title and URL is probably enough to get  
me started.

Many thanks,

David Remsen
GBIF Secretariat




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