[IPT] Darwin Core Star Schema

[Quentin Groom]

Having now experimented a little.

I've had most success with a completely flat file

The validator works OK except for the following 3 errors, which are
presumably due to the recent changes to Darwin Core.

   - Unknown term

   http://rs.tdwg.org/dwc/terms/organismQuantity

    mapped to column 9
   - Unknown term

   http://purl.org/dc/terms/license

    mapped to column 16
   - Unknown term

   http://rs.tdwg.org/dwc/terms/organismQuantityType

    mapped to column 8


The IPT also seems to accept a flat file and I can get all the fields
mapped. However, I'm not clear why it shows zero records in this summary. A
problem???
[image: Inline images 1]

Using, Event as the core file and occurrence as an extension the validator
works OK, but it does create an error "The extension data file contains
references to core IDs that do not exist:", but I think this is something
to do with where it assumes the core IDs are in the file (i.e. not in the
1st column).

I think I've also got it working in the IPT, though I'm not yet seeing the
benefit of the star format over the flat format. Are the benefits of the
Star Schema format only related to the size of the DWC-A, or are there
another benefits. If it does just relate to the size then I think it would
be best to recommend the flat file format for all but the big users.
Regards
Quentin





Dr. Quentin Groom
(Botany and Information Technology)

Botanic Garden Meise
Domein van Bouchout
B-1860 Meise
Belgium

ORCID: 0000-0002-0596-5376

Landline; +32 (0) 226 009 20 ext. 364
FAX:      +32 (0) 226 009 45

E-mail:     quentin.groom at plantentuinmeise.be
Skype name: qgroom
Website:    www.botanicgarden.be


On 11 November 2015 at 14:15, Tim Robertson <trobertson at gbif.org> wrote:

> Thanks Quentin
>
> So if I understand correctly, the event file can be used as a Core, just
> as Taxon and Occurrence can be Core files.
>
>
> Yes, that’s correct
>
> Though as there can only be one Core ID I will still need to keep my taxon
> information in the Occurrence file.
> Although I don't think this is a problem, it can get a little confusing in
> the documentation due to the crossover of terms between taxon and
> occurrence files.
>
>
> I’m afraid that is the kind of limitation I was eluding to about star
> schemas… You have to denormalise things into a format which flattens what
> you might otherwise model as 2 tables.
>
> Currently a "Taxon” can’t be used as an extension, so you would need to
> use Occurrence.  Adding Taxon as an option would be technically possible,
> but that would be completely decoupled from the occurrences.  It would
> however allow you to have:
>
> Core: Rows of Sampling event documenting e.g. a square on the ground
> sample on a specific period
>   Extension taxon: List of species observed within the sampling event
>   Extension occurrence: Documented evidence of specimens collected or
> observed
>
> At the moment though, you would have to express species lists as
> occurrences, which might make some sense because they are effectively
> observations.
>
> I'm happy to be a Guinea pig. I'll experiment with the validator if you
> think this should work and let you know how I get on.
>
>
> Thanks for this,
>
> All the best,
> Tim
>
>
> Regards
> Quentin
>
>
>
> Dr. Quentin Groom
> (Botany and Information Technology)
>
> Botanic Garden Meise
> Domein van Bouchout
> B-1860 Meise
> Belgium
>
> ORCID: 0000-0002-0596-5376
>
> Landline; +32 (0) 226 009 20 ext. 364
> FAX:      +32 (0) 226 009 45
>
> E-mail:     quentin.groom at plantentuinmeise.be
> Skype name: qgroom
> Website:    www.botanicgarden.be
>
>
> On 11 November 2015 at 11:58, Hannu Saarenmaa <hannu.saarenmaa at helsinki.fi
> > wrote:
>
>> Quentin & Co
>>
>> It depends what you mean by "survey".   I would put each visit to a
>> sampling location (such as a plot) in the event core, and put all the taxa
>> that are observed in a non-core table.   The properties of the entire
>> survey (project) would go to the EML metadata.
>>
>> Hannu
>>
>>
>> On 2015-11-11 10:20, Quentin Groom wrote:
>>
>> I'm rather confused how the Darwin Core Star Schema is meant to work for
>> survey data.
>>
>> Darwin Core can have one of two Core files, taxon or occurrence. The most
>> appropriate for a survey would seem to be occurrence. So I imagine that in
>> the star schema you could also have a related event file detailing the date
>> and location of each survey and a non-core taxon file detailing the taxa
>> that are observed.
>>
>> However, this does not seem to be possible. The DWC-A validator (
>> http://tools.gbif.org/dwca-validator/), assumes only on core id in the
>> core file so you can't link an occurrence both to a taxon and to an event.
>> This is also true in the Darwin Core Archive Assistant (
>> http://tools.gbif.org/dwca-assistant/). The solution seems to be to put
>> all the information from the taxon core file into the occurrence file, but
>> keep the separate event file linked with the core occurrence id.
>>
>> Is this correct? It seems rather counter intuitive.
>>
>> Regards
>> Quentin
>>
>>
>> Dr. Quentin Groom
>> (Botany and Information Technology)
>>
>> Botanic Garden Meise
>> Domein van Bouchout
>> B-1860 Meise
>> Belgium
>>
>> ORCID: 0000-0002-0596-5376
>>
>> Landline; +32 (0) 226 009 20 ext. 364
>> FAX:      +32 (0) 226 009 45
>>
>> E-mail:     quentin.groom at plantentuinmeise.be
>> Skype name: qgroom
>> Website:    www.botanicgarden.be
>>
>>
>> _______________________________________________
>> IPT mailing listIPT at lists.gbif.orghttp://lists.gbif.org/mailman/listinfo/ipt
>>
>>
>> --
>>
>> Hannu Saarenmaa, Research Directorhannu.saarenmaa at uef.fi
>> Mobile +358-50-4479668
>>
>> University of Eastern Finland
>> Digitarium, SIB Labs, Joensuu Science Park
>> Länsikatu 15 (P.O. Box 111)
>> FI-80101 Joensuu
>> www.digitarium.fi/en - Service Centre for High-Performance Digitisationwww.eubon.eu - EU BON - GEO BON - Data Integration and Interoperability
>>
>>
>
>
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