[API-users] What happens to previous data after dataset/crawl?

Herbario SANT sant.herbarium at gmail.com
Mon Aug 29 12:58:37 CEST 2016

El lunes, 29 de agosto de 2016, Tim Robertson <trobertson at gbif.org>

> (...) I’m afraid it is a little messy, but I will try and explain.
> The original thinking by the DwC authors was that *dwc:occurrenceID*
> would be used to identify an occurrence in nature, while *dc:identifier*
> would be a digital record identifier.
> (...)
> If a provider adds occurrenceID and leaves those 3 fields the same, we
> will recognise this and update the records.  If they were to remove one of
> those triplets, we would insert new records and the old ones would be
> deleted at some point.  It is a manual process to allow us to engage with
> publishers before running deletions.

Thanks Tim. I understood your explanation about occurrenceID / identifier

Can you elaborate a bit more on what happens if a provider using triplets
decides to add occurrenceID?
You said GBIF reindex (1st reindex) will recognize them and update the
What if LATER ON (after 1st reindex) a record is changed so occurrenceID
KEEPS STABLE but the triplet value is deleted or modified? Shouldn't next
GBIF reindex (2nd and later) keep using the already extant occurrenceID?
So, the record should be updated, not inserted.

>From your comment I understood it would be inserted but I guess you meant
that happens if both changes (occurrenceID added + triplet changed) are
done at the same time (same GBIF reindex).
Would this two steps strategy make a difference to avoid us asking you to
delete records?

And yes, I think it makes sense to use some kind of UUIDs for occurrenceID
I understand these only need to be unique only in the dataset context, but
its better to make them globally unique for linking purposes, right?

Thanks for your help, and indeed for the new incoming GBIF filtering options


> I notice that the dataset you linked to was published in 2007, before
> dwc:occurrenceID existed.  It is therefore using the *dwc:insitutuionCode*
> , *dwc:collectionCode* and *dwc:catalogNumber *identifier strategy.
> Please note, that Darwin Core recommends concatenating the 3 fields to
> create a *dwc:occurrenceID*.  Please be aware that this approach means
> that should someone chose to e.g. change the collection code, the
> occurrence record ID will also change thus removing all linkability.  If
> this is expected, then forging unique ids for records using e.g. UUIDs or
> similar would be a more robust longer term solution and in general we
> recommend targeting this.
> We do recommend people strive to provide occurrenceID, even on older
> data.  This simplifies things going forward.
> I hope this helps, but please feel free to ask me any questions around
> this.
> This is off topic, but while you are reading please know that we expect
> stateOrProvince to be a filter on GBIF next week along with locality,
> protocol, license, organismID, publishingOrgKey (API only), crawlID (API
> only).  I know you have interest in this functionality.
> Best wishes,
> Tim
> From: API-users <api-users-bounces at lists.gbif.org
> <javascript:_e(%7B%7D,'cvml','api-users-bounces at lists.gbif.org');>> on
> behalf of Herbario SANT <sant.herbarium at gmail.com
> <javascript:_e(%7B%7D,'cvml','sant.herbarium at gmail.com');>>
> Date: Sunday 28 August 2016 at 16:00
> To: "api-users at lists.gbif.org
> <javascript:_e(%7B%7D,'cvml','api-users at lists.gbif.org');>" <
> api-users at lists.gbif.org
> <javascript:_e(%7B%7D,'cvml','api-users at lists.gbif.org');>>
> Subject: Re: [API-users] What happens to previous data after
> dataset/crawl?
> Hi
> I take the opportunity to ask about the difference between two GBIF terms:
> What is the difference of "occurrenceID" compared to "identifier"?  Both
> have the same value in this dataset:
> http://www.gbif.org/occurrence/1291766512/verbatim
> http://api.gbif.org/v1/occurrence/1291766512
> I see "occurrenceID" well explained here:
> http://gbif.blogspot.com.es/2014/04/ipt-v21.html
> http://rs.tdwg.org/dwc/terms/#occurrenceID
> But I can't find the explanation for "identifier", which I think some
> institutions have been incorrectly understanding as "occurrenceID".
> For example:
> http://www.gbif.org/occurrence/142907792/verbatim
> http://api.gbif.org/v1/occurrence/142907792
> There is an "identifier" in that occurrence, but no "occurrenceID".
> 1) What is exactly the meaning of that "identifier"?  Why is it not
> explained in dwc terms page?
> 2) What happens if the data provider keeps all data UNCHANGED, but adds
> the "occurrenceID" which was missing?
>     Would next GBIF reindex keep the same number of records and add their
> occurrenceIDs? (perhaps looking at the triplet in that "identifier"?)
>     Would later on be safe to change any fields in the dataset (even
> "identifier", "catalognumber", ...) if that data provider keeps those
> occurrenceIDs stable?
> Thanks
> On 27 August 2016 at 08:01, Roderic Page <Roderic.Page at glasgow.ac.uk
> <javascript:_e(%7B%7D,'cvml','Roderic.Page at glasgow.ac.uk');>> wrote:
>> Just wanted to check the consequences of the following dataset operation.
>> Say I have a dataset with 10 occurrences with occurrence ids 1-10. In my
>> local database I now assign those 10 occurrences new identifiers a-j. If I
>> create a new DwCA file for my data and crawl the new archive, my
>> expectation is:
>> 1. Old data with ids 1-10 is deleted from GBIF index
>> 2. New data with ids a-j is indexed
>> So, end result is dataset has 10 occurrences. I'm asking because I know
>> in the past the some datasets have changed identifiers and this has
>> resulted in records with old and new identifiers coexisting in GBIF index,
>> resulting in duplicated data.
>> Obviously it would be nice to have stable, unchanging identifiers for
>> occurrences, but the for data set I'm working with the creators have
>> changed their minds between versions of the data :(
>> Regards,
>> Rod
>> Get Outlook for iOS <https://aka.ms/o0ukef>
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> --
> David García San León
> Herbario SANT
> Facultade de Farmacia - Laboratorio de Botánica
> Universidade de Santiago de Compostela
> 15782 - Galicia (Spain)
> http://www.usc.es/herbario

David García San León
(dixitalización / control de fondos)
Herbario SANT
Facultade de Farmacia - Laboratorio de Botánica
Universidade de Santiago de Compostela
15782 - Galicia (Spain)
Tel. +34 881815022
Fax +34 981594912
Skype: herbarium_sant
Twitter: @SANT_Herbarium
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