[tdwg-content] InstitutionCode - InstitutionID

Peter Desmet peter.desmet at umontreal.ca
Tue Jul 3 15:09:59 CEST 2012


Hi Aaike,

I took me a while too to figure out how to populate institutionCode and
institutionID. For Canadensys we now do the following:

institutionCode = "Université de Montréal Biodiversity Centre". As most of
our universities/museums/institutions don't have an official code, we went
for the full name, which is easier to understand worldwide. We use the same
practice for righsHolder and ownerInstitutionCode. It's also the same value
as the institution the dataset is registered with at GBIF:
http://gbrds.gbif.org/browse/agent?uuid=ff7bd5db-b724-4932-b496-10ea298851f9
.
In combination with the datasetName (= title of the dataset on IPT) and
datasetID (= url of the dataset on IPT), it allows us to generate a
suggested citation: [datasetname] from [institutionCode]. [datasetID]
(accessed on yyyy-mm-dd)

institutionID = I think MVZ is an exception in that it has a GUID at
biocol.org. All of our institutions don't (but their collections do, used
in collectionID). The alternative could be the UUID issued by GBIF
("ff7bd5db-b724-4932-b496-10ea298851f9", from
http://gbrds.gbif.org/browse/agent?uuid=ff7bd5db-b724-4932-b496-10ea298851f9)
or the data publisher page at GBIF:
http://data.gbif.org/datasets/provider/375. GBIF is working on better
citations and maybe DOIs for these entities, so we're currently not
populating the term.

Peter

On Tue, Jul 3, 2012 at 8:36 AM, Chuck Miller <Chuck.Miller at mobot.org> wrote:

> Paul,
> Thanks.
>
> Chuck
>
>
>
> On Jul 2, 2012, at 11:01 PM, "Paul J. Morris" <mole at morris.net> wrote:
>
> > Chuck,
> >
> > Look again at the AppleCore guidance on codes and numbers
> https://code.google.com/p/applecore/wiki/CodesAndNumbers I strongly
> suspect that your sense of the institution is the entity identified by the
> herbarium acronym, for which collectionCode and collectionID apply under
> the AppleCore guidance, rather than the larger entity (e.g. university,
> museum) of which the named herbarium is a part.
> >
> > -Paul
> >
> > On Tue, 3 Jul 2012 03:35:54 +0000
> > Chuck Miller <Chuck.Miller at mobot.org> wrote:
> >
> >> Actually, my question to John W was about originalInstitutionID (if
> >> that were the way to do it) not originalCollectionID and whether
> >> there were a way to distinguish two institutionIDs for the same
> >> specimen. But I gather, so far, the answer is that there is not.
> >>
> >> Chuck
> >>
> >>
> >>
> >> On Jul 2, 2012, at 9:25 PM, "Bob Morris" <morris.bob at gmail.com> wrote:
> >>
> >>> So, if a proposal were made to add a term, say
> >>> "originalCollectionID", whose value is the collectionID of the
> >>> collection from which the duplicate set was distributed, what
> >>> questions---especially what scientific questions---would that ID
> >>> answer besides "what is the collection from which the duplicate set
> >>> was distributed?"
> >>>
> >>> Just asking....
> >>>
> >>> Bob Morris
> >>>
> >>> p.s. I guess I could think of some questions in the domain of the
> >>> history of science, but I suspect DwC has lots of shortcomings for
> >>> that domain anyway....
> >>>
> >>>
> >>>
> >>> On Mon, Jul 2, 2012 at 9:45 PM, Paul J. Morris <mole at morris.net>
> >>> wrote:
> >>>> On Mon, 2 Jul 2012 23:05:38 +0000
> >>>> Chuck Miller <Chuck.Miller at mobot.org> wrote:
> >>>>> In the botanical world of duplicate specimens and gifting of
> >>>>> specimens to a specialist in exchange for a determination, a plant
> >>>>> specimen can have multiple institutions actually annotated on it
> >>>>> and therefore multiple institutionIDs potentially associated with
> >>>>> it. Does DwC have a way to distinguish multiple institutionIDs
> >>>>> for a specimen - e.g. original collecting institution and current
> >>>>> repository institution?
> >>>>
> >>>> Many bits are there, some bits aren't.  The occuranceID is a GUID
> >>>> for the duplicate set (except untill we get the duplicate sets
> >>>> sorted out, everyone is going to be serving distinct occuranceIDs
> >>>> for each sheet in the set.  There isn't a property to hold GUIDs
> >>>> for specimens, so we are left with the hopefully unique DarwinCore
> >>>> doublet of collectionID/collectionCode and catalogNumber (under
> >>>> the AppleCore guidance, we can ignore
> >>>> institutionCode/institutionID for the most part in botany, as
> >>>> herbarium acronyms are placed in collectionCode and GUIDs for
> >>>> herbaria are placed in collectionID).  Available for trying to
> >>>> cluster duplicates are recordedBy for the collector name and
> >>>> recordNumber for the collector's number.    Once we do have sets
> >>>> of duplicates linked with occurranceID, we don't, as you point
> >>>> out, have any way to determine which collectionID was the
> >>>> collection from which the duplicate set was distributed.
> >>>>
> >>>> -Paul
> >>>>
> >>>>>
> >>>>> Chuck
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Jul 2, 2012, at 4:44 PM, "John Wieczorek" <tuco at berkeley.edu>
> >>>>> wrote:
> >>>>>
> >>>>>> Hi Aaike,
> >>>>>>
> >>>>>> The institutionID is definitely meant to be a GUID, and as such
> >>>>>> would not likely be of much use within an institutional database,
> >>>>>> where the institutionID would likely be the same for every
> >>>>>> record. Instead, it is meant to identify an institution in a
> >>>>>> persistent, hopefully resolvable way, where resolution would be
> >>>>>> able to give more information about the identified institution.
> >>>>>>
> >>>>>> Identifiers for institutions do exist. An example is
> >>>>>> urn:lsid:biocol.org:col:34777, the institutionID in the
> >>>>>> Biodiversity Collections Index for the University of California
> >>>>>> Berkeley Museum of Vertebrate Zoology (MVZ), within which there
> >>>>>> are several collections, each with its distinct collectionID,
> >>>>>> such as urn:lsid:biocol.org:col:34818 for the Herpetology
> >>>>>> Collection at the MVZ.
> >>>>>>
> >>>>>> The IDs are useful to provide the possibility of a link to other
> >>>>>> information that may not be shared in original record. They are
> >>>>>> also useful to distinguish the institutions and collections from
> >>>>>> each other. For example, MVZ is the acronym used for the
> >>>>>> Institution as a whole where the collections are housed, and it
> >>>>>> is also used independently by each of the collections when
> >>>>>> specimens are cited in literature. In other words, the
> >>>>>> institutionCode (MVZ) is not distinct from the collectionCodes
> >>>>>> (MVZ), and the collectionCodes within the institution are not
> >>>>>> unique (all MVZ). The IDs are meant to overcome this and other
> >>>>>> problems of reference and uniqueness.
> >>>>>>
> >>>>>> I hope that helps,
> >>>>>>
> >>>>>> John
> >>>>>>
> >>>>>> On Mon, Jul 2, 2012 at 7:03 AM, Aaike De Wever
> >>>>>> <aaike.dewever at naturalsciences.be> wrote:
> >>>>>>>
> >>>>>>> Dear all,
> >>>>>>>
> >>>>>>> While composing a template and recommendations for the Darwin
> >>>>>>> Core fields to supply for the BioFresh project
> >>>>>>> <http://www.freshwaterbiodiversity.eu/>, similar to what Peter
> >>>>>>> Desmet did for herbaria in Apple Core
> >>>>>>> <http://code.google.com/p/applecore/>, I came across a number of
> >>>>>>> terms which I haven't yet completely understood and hope to get
> >>>>>>> some feedback on from this community.
> >>>>>>>
> >>>>>>> Two of these terms are:
> >>>>>>>
> >>>>>>> InstitutionCode - InstitutionID
> >>>>>>> http://rs.tdwg.org/dwc/terms/institutionCode -
> >>>>>>> http://rs.tdwg.org/dwc/terms/institutionID
> >>>>>>>
> >>>>>>> The name (or acronym) in use by the institution having custody
> >>>>>>> of the object(s) or information referred to in the record. / An
> >>>>>>> identifier for the institution having custody of the object(s)
> >>>>>>> or information referred to in the record.
> >>>>>>>
> >>>>>>> I guess that the latter term is supposed to be a DOI/GUID for
> >>>>>>> the institute, but am wondering if there is such a thing or
> >>>>>>> whether this field is rather for internal database purposes?
> >>>>>>>
> >>>>>>> Any advise would be appreciated!
> >>>>>>>
> >>>>>>> With best regards,
> >>>>>>> --
> >>>>>>> Aaike De Wever
> >>>>>>> BioFresh Science Officer
> >>>>>>> Freshwater Laboratory, Royal Belgian Institute of Natural
> >>>>>>> Sciences Vautierstraat 29, 1000 Brussels
> >>>>>>> Belgium
> >>>>>>> tel.: +32(0)2 627 43 90
> >>>>>>> mobile.: +32(0)486 28 05 93
> >>>>>>> email: <aaike.dewever at naturalsciences.be>
> >>>>>>> skype: aaikew
> >>>>>>> AIM: aaike at mac.com
> >>>>>>> LinkedIn: <http://be.linkedin.com/in/aaikedewever>
> >>>>>>> BioFresh: <http://www.freshwaterbiodiversity.eu/> and
> >>>>>>> <http://data.freshwaterbiodiversity.eu/>
> >>>>>>> Belgian Biodiversity Platform: <http://www.biodiversity.be>
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> tdwg-content mailing list
> >>>>>>> tdwg-content at lists.tdwg.org
> >>>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >>>>>> _______________________________________________
> >>>>>> tdwg-content mailing list
> >>>>>> tdwg-content at lists.tdwg.org
> >>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >>>>> _______________________________________________
> >>>>> tdwg-content mailing list
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> >>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >>>>
> >>>>
> >>>> --
> >>>> Paul J. Morris
> >>>> Biodiversity Informatics Manager
> >>>> Harvard University Herbaria/Museum of Comparative Zoölogy
> >>>> mole at morris.net  AA3SD  PGP public key available
> >>>> _______________________________________________
> >>>> tdwg-content mailing list
> >>>> tdwg-content at lists.tdwg.org
> >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >>>
> >>>
> >>>
> >>> --
> >>> Robert A. Morris
> >>>
> >>> Emeritus Professor  of Computer Science
> >>> UMASS-Boston
> >>> 100 Morrissey Blvd
> >>> Boston, MA 02125-3390
> >>>
> >>> IT Staff
> >>> Filtered Push Project
> >>> Harvard University Herbaria
> >>> Harvard University
> >>>
> >>> email: morris.bob at gmail.com
> >>> web: http://efg.cs.umb.edu/
> >>> web: http://etaxonomy.org/mw/FilteredPush
> >>> http://www.cs.umb.edu/~ram
> >>> ===
> >>> The content of this communication is made entirely on my
> >>> own behalf and in no way should be deemed to express
> >>> official positions of The University of Massachusetts at Boston or
> >>> Harvard University.
> >>> _______________________________________________
> >>> tdwg-content mailing list
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> >>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >
> >
> > --
> > Paul J. Morris
> > Biodiversity Informatics Manager
> > Harvard University Herbaria/Museum of Comparative Zoölogy
> > mole at morris.net  AA3SD  PGP public key available
> _______________________________________________
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>



-- 
Peter Desmet
Biodiversity Informatics Manager
Canadensys - www.canadensys.net

Université de Montréal Biodiversity Centre
4101 rue Sherbrooke est
Montreal, QC, H1X2B2
Canada

Phone: 514-343-6111 #82354
Fax: 514-343-2288
Email: peter.desmet at umontreal.ca / peter.desmet.cubc at gmail.com
Skype: anderhalv
Public profile: http://www.linkedin.com/in/peterdesmet
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