[IPT] Darwin Core Star Schema
Kyle Braak
kbraak at gbif.org
Wed Nov 11 19:12:06 CET 2015
Dear Quentin,
Thank you for your feedback.
I answer your questions inline below.
Best regards,
Kyle
> On 11 Nov 2015, at 17:10, Quentin Groom <quentin.groom at plantentuinmeise.be> wrote:
>
> 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 <http://rs.tdwg.org/dwc/terms/organismQuantity> mapped to column 9
> Unknown term http://purl.org/dc/terms/license <http://purl.org/dc/terms/license> mapped to column 16
> Unknown term http://rs.tdwg.org/dwc/terms/organismQuantityType <http://rs.tdwg.org/dwc/terms/organismQuantityType> mapped to column 8
Exactly right. The validator needs to be updated to work with the latest extension versions, which use the latest Darwin Core terms.
>
> 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.png>
I strongly suspect you are looking at a ‘preview’ page of the unpublished version 1.0. After you publish version 1.0, try viewing its homepage and the number of (core) records will show as you’d expect.
>
> 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).
The ID field links records from the two sources together. In this case, each occurrence record should link to an event record via its eventID. You can refer to the IPT User Manual's section on mapping [1] for more information. If you get stuck, feel free to write to me for direct assistance.
>
> 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.
There are other benefits. The Star Schema is conceptually cleaner, easier to maintain, less prone to mistakes, etc.
Please note that you can capture additional measurements or facts using the MeasurementOrFact extension [2]. Using Occurrence as the core it’s only appropriate to capture measurements or fact relating to the species occurrences whereas using Event as the core, you can capture measurements or facts relating to the sampling event (e.g., environmental measurements like sediment temperature and redox potential (Eh)).
[1] https://github.com/gbif/ipt/wiki/IPT2ManualNotes.wiki#darwin-core-mappings <https://github.com/gbif/ipt/wiki/IPT2ManualNotes.wiki#darwin-core-mappings>
[2] http://rs.gbif.org/extension/dwc/measurements_or_facts.xml <http://rs.gbif.org/extension/dwc/measurements_or_facts.xml>
> 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 <mailto:quentin.groom at plantentuinmeise.be>
> Skype name: qgroom
> Website: www.botanicgarden.be <http://www.botanicgarden.be/>
>
>
> On 11 November 2015 at 14:15, Tim Robertson <trobertson at gbif.org <mailto: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 <mailto:quentin.groom at plantentuinmeise.be>
>> Skype name: qgroom
>> Website: www.botanicgarden.be <http://www.botanicgarden.be/>
>>
>>
>> On 11 November 2015 at 11:58, Hannu Saarenmaa <hannu.saarenmaa at helsinki.fi <mailto: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/ <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/ <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 <mailto:quentin.groom at plantentuinmeise.be>
>>> Skype name: qgroom
>>> Website: www.botanicgarden.be <http://www.botanicgarden.be/>
>>>
>>>
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>>> IPT at lists.gbif.org <mailto:IPT at lists.gbif.org>
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>>
>> --
>>
>> Hannu Saarenmaa, Research Director
>> hannu.saarenmaa at uef.fi <mailto:hannu.saarenmaa at uef.fi>
>> Mobile +358-50-4479668 <tel:%2B358-50-4479668>
>>
>> University of Eastern Finland
>> Digitarium, SIB Labs, Joensuu Science Park
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>>
>> www.digitarium.fi/en <http://www.digitarium.fi/en> - Service Centre for High-Performance Digitisation
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>>
>
>
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