[tdwg-tag] Any TCS users with experiences to report?

Roderic Page r.page at bio.gla.ac.uk
Sat Nov 3 06:58:19 CET 2012

Playing devil's advocate I think there are several issues here:

1. The example you gave of an OGC query illustrates what for me is a major limitation of existing approaches (such as DiGiR and TAPIR), they focus on standardising queries not identifiers. Hence we can query databases in a consistent (if cumbersome) way, but have no easy way to refer to the things (taxa, specimens, etc.) we retrieve. Having stable, reusable, resolvable identifiers would be a step forward.

2. Taxonomic concepts aren't much use unless connected to data. Arguably the most widely used taxonomic database in biodiversity is the NCBI taxonomy database, which has stable identifiers, an API, and taxa that are connected to data (sequences and publications). The GBIF backbone classification is also connected to data (specimens and observations) although its taxon identifiers (like its occurrence ids) aren't terribly stable.

3. I think the standards-first approach tends to put the cart before the horse. I'm not sure it's the lack of standards that is the problem, it's the lack of usable information in taxonomic databases. Apart from NCBI and GBIF, what science can I do with taxonomic databases? What questions do they allow me to ask?



Sent from my iPhone

On 3 Nov 2012, at 03:41, <Tony.Rees at csiro.au> wrote:

> Hi Jessie, also others who have responded thus far,
> You said:
>> I think it would be great if the major databases that describe taxa (not
>> just list names) described their data as concepts and allowed people to
>> link to their databases when identifying specimens and when sequencing
>> etc, this would be the start of a really useful biodiversity network.
> Agreed! And also the databases that "just list names" are dealing with concepts as we know, comprising a valid name plus all listed synonyms in these cases...
> My feeling is the reason that there is not yet any standardization in this area - every data resource does its own thing using its own home-grown schema in the main (that is, presuming a web service is even offered) and the "standards group" (TDWG) has not pushed a model of any sort of standard client which expects to be able to access distributed taxonomic information in a standard way, so there is no incentive for the sources to provide this. Sort of like a fax machine with no-one on the other end wishing to communicate with it. By contrast (for example) the OGC has defined standards for geospatial web services which, once adhered to, allow one wants one's own data to be accessed by standards-compliant remote client apps in a standard way, so if I publish a layer (map) from my geoserver here (http://www.cmar.csiro.au/geoserver/ ) as layer name = bioreg:CAAB37020002 then any remote client can access it via standard syntax which will retrieve it in a specified format, for example
> http://www.cmar.csiro.au/geoserver/wms?service=WMS&version=1.1.0&request=GetMap&layers=bioreg:CAAB37020002&styles=&bbox=109.0,-44.5,156.5,-8.5&width=512&height=388&srs=EPSG:4326&format=image/gif
> So maybe for either TCS, DwC and so on a missing part of the task is to define the syntax for such calls (plus relevant expected responses) for taxonomic data and then create some example both publishing and retrieving (client) software to exercise this - provided there is an interest in doing so of course!
> More soon,

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