[tdwg-content] Notes on the Biological Collections Ontology
Quentin Groom
quentin.groom at br.fgov.be
Fri Mar 27 15:27:46 CET 2015
Hi John,
thanks for taking the time to answer my varied questions.
I'll have to have a think about your questions and see if I can progress
them.
Regards
Quentin
John Wieczorek wrote:
> Hi Quentin,
>
> This is very old, but still relevant. Sorry for the delay. Responses
> inline.
>
> On Wed, Dec 10, 2014 at 5:04 AM, Quentin Groom
> <quentin.groom at br.fgov.be <mailto:quentin.groom at br.fgov.be>> wrote:
>
>
> Dear All,
>
> To acquaint myself with the Biological Collections Ontology I went
> through
> it and made some notes. John Wieczorek suggested I share these
> notes so
> that they can be responded to openly. They are as follows, I look
> forward
> to your comments.
>
> 1. Why are the dates clustered together in one branch, but day, month,
> year separate?
>
>
> In what context are they clustered together? Is it simply a matter of
> alphabetical listing? In Darwin Core they are organized within the
> Event class except when they are dates for a distinct activity, such
> as georeferencedDate
> (http://rs.tdwg.org/dwc/terms/index.htm#locationindex).
>
>
> 2. eventDate: regarding date ranges. Sometimes an event continues
> for a
> period such as a field trip, but often a date range is required
> because
> although the event took place in a certain time frame, the exact event
> date is not known. There should perhaps be a way of distinguishing
> between
> these two situations.
>
>
> The definition of eventDate
> (http://rs.tdwg.org/dwc/terms/index.htm#eventDate) recommends the use
> of ISO 8601:2004(E), which is quite expressive and covers the cases
> you brought forth here. Have a look at the examples in the comment
> section of the term at the URL above.
>
>
> 3. Vernacular name should be associated with a language and a
> geographic
> area where it is used?
>
>
> Agreed, and it does act thus in the context of a Vernacular Names
> extension
> (http://tools.gbif.org/dwca-validator/extension.do?id=http://rs.gbif.org/terms/1.0/VernacularName),
> which allows multiple vernacular names to be associated with a related
> Taxon.
>
>
> 4. verbatimSRS, footprintSRS and geodeticDatum are similar but not the
> same. They seem to overlap. The SRS has a clear definition epsg-
> registry.org <http://registry.org>, but geodeticDatum is a more
> general term. The definitions
> and usages could be stronger.
>
>
> Do you have recommendations for improvement?
>
>
> 5. There is a need for local grid reference systems. Many
> countries have
> their own ways of writing grid references and verbatimLongitude and
> verbatimLatitude are not suitable for these. For example, the UK
> has grid
> references such as NZ28F, which mean something very specific in the
> country. It is a similar situation in Belgium and I imagine other
> countries.
>
>
> For these cases, the terms verbatimCoordinates is recommended,
> accompanied by a verbatimCoordinateSystem.
>
> 6. georeferenceVerificationStatus &
> identificationVerificationStatus: It
> is not clear how these should be used. The names are similar, but the
> described usage is very different. I find it hard to imagine how they
> would be used in practice.
>
>
> Both terms are meant to give a statement about the nature of the
> effort to verify that the subject (georeference or determination) are
> correct. Using the georeferenceVerificationStatus as an example,
> suppose a user of the data calls into question the coordinates or
> uncertainty for a location and informs the responsible party at the
> data source. Suppose that person spends an hour looking through all
> the details associated with the collecting event and determines that,
> in fact, the georeference is as good as it can be given remaining
> documentation. Having spent all of that energy, and given
> institutional memory at the scale of museum time, it is worth noting
> that the georeference has been confirmed to be as good as it can be by
> the curator at the time. The georeferenceVerificationStatus would be
> set to "verified by curator", the georeferencedBy should be updated to
> include the curator's name, the georeferencedDate should be updated,
> and georeferenceRemarks should be added to capture the information
> that would avoid the same question arising in the future - all to save
> doing the same thing over and over.
>
>
> 7. There are occasions within biogeographic databases where you
> want to
> indicate that an observation or collection is not trusted. I can’t
> see a
> place where a record can be verified as a whole. For example, if it is
> suspected that the label has been muddled up or the collector is
> suspected
> of fraud. With an observation there is no specimen to verify, but the
> record should be verifiable.
>
>
> That is true. Confidence is not covered in Darwin Core other than in
> specific contexts. One could go further and say who says what is
> wrong, when, and why. There are other contexts where annotations of
> great richness can be provided for (attached to) specific aspects of
> data. See, for reference, Filtered Push
> (http://wiki.filteredpush.org/wiki/).
>
> 8. member, lithostratigraphicTerms, bed etc etc. I don’t know anything
> about geology, but these terms seem to overlap and could perhaps be
> thought of as synonymous. It would be valuable to find records
> where these
> terms are required to see how they are used in practice.
>
>
> These terms arose from the Paleontology community long before (1 Jun
> 2005) Darwin Core became a ratified standard at the Workshop on
> Paleontology Collection Digitization in Springfield, Illinois - a
> workshop to define a Darwin Core Paleontology Extension
> (http://wiki.tdwg.org/twiki/bin/view/DarwinCore/PaleontologyElement),
> which became subsumed in ratified Darwin Core (see
> http://rs.tdwg.org/dwc/terms/history/versions/index.htm#paleo).
>
> 9. county & stateProvince: These are parochial terms. There are many
> nested subdivisions of countries and there is probably a better way to
> describe them. Perhaps there is already a hierarchical ontology to
> describe geographic areas.
>
>
> Yes, these are legacy terms arising from the first implementation of
> Darwin Core in the Species Analyst network (see
> http://en.wikipedia.org/wiki/Biodiversity_informatics#History_of_the_discipline_of_Biodiversity_Informatics).
> In the ontology world, there is GAZ
> (http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=GAZ). In a
> (technologically) flattened world we need slots to put things in, and
> geography is particularly recalcitrant in this respect, even when
> "restricted" to administrative boundaries (see appendix to this message).
>
> 10. Abundance estimates: There are several ways to describe
> estimates of
> abundance, such as DOMAIN, DAFOR, percent coverage, is there a way to
> accommodate these?
>
>
> There is as of 19 Mar 2015 with the advent of the sampling event terms
> (see
> http://rs.tdwg.org/dwc/terms/history/decisions/#Decision-2015-03-19_18).
>
>
> 11. Controlled vocabularies: Many terms suggest using a controlled
> vocabulary, but most don’t have one. Is this an area we should
> work on?
>
>
> This is an area best fit for specific domains, I think. Those who need
> them should work on them, definitely.
>
>
> 12. Consider the importance of citation and providence the
> “according to”
> information seems rather weak. There should perhaps be a space for an
> identifier (ORCID). Also, biographic information such as date of
> birth,
> date of death, institutional association. These are useful for
> providence,
> but also for validation of records.
>
>
> Whereas I agree with the importance of sources, in Darwin Core terms
> are added when a demonstrated need to share information arises among
> at least two "independent" parties (i.e., not just for the purposes of
> a single project). To date no such need has been demonstrated.
>
>
> 13. What is the difference between fieldNumber and recordNumber?
>
>
> These terms are used interchangeably in some contexts, but in Darwin
> Core they are distinct concepts. A recordNumber applies to an
> Occurrence of an organism at a place and time (such as a single bird
> specimen), while the field number applies to an Event that might
> correspond to a set of many organisms of distinct taxa from something
> like a trawl in the ocean. Both concepts are in common use.
>
> 14. establishmentMeans: the description seems to conflate three
> concepts,
> the length a taxon has been established at a location (e.g.
> native); the
> way it got to the location (e.g. introduced) and the dispersive
> ability of
> the taxon (e.g. invasive). To my mind the latter is not required
> as it is
> an opinion about the taxon as a whole not the observation. The
> first two
> should be separated to make them useful. People need to distinguish
> between the native status of a species at a location and how it got to
> that location. Invasive species biologists are particularly
> interested in
> the vectors of introduction.
>
>
> Agreed. This term has been discussed on this list
> (http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001650.html),
> and has received criticism on multiple occasions elsewhere, but an
> overhaul has not before been proposed or championed.
>
> 15. The health of an animal or plant can be noted on an
> observation and is
> useful for analysis. Is there some way of stating that the
> organism was
> dead when the specimen or observation was made?
>
>
> The term "behavior" seems like a stretch for this case, so I will
> suggest, "No, there is not." :-)
>
> Hope you (and others) find some of this useful.
>
> Cheers,
>
> John
>
> (Don't forget the appendix below if you are a geography enthusiast.)
>
>
>
> 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 br.fgov.be <mailto:quentin.groom at br.fgov.be>
> Skype name: qgroom
> Website: www.botanicgarden.be <http://www.botanicgarden.be>
>
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>
>
> Appendix:
>
> A few current administrative level names, going at times up to six
> levels deep.
>
> Administrative area, Administrative county, Administrative Region,
> Aimag, Amt, Aprinki, Apskritis, Area, Arrondissement, Arrondissements,
> Arrondissment, Atoll, Autonomou, Autonomous city, Autonomous Commune,
> Autonomous Community, Autonomous Island, autonomous province,
> Autonomous Region, Autonomous Republic, Autonomous sector, Avtonomiuri
> respublika, Avtonomnaya oblast, Avtonomnyy okrug, Aymag, Baladiyah,
> Bibhag, Borough, Bundeslander, Canton, Capital city, Capital district,
> Capital Metropolitan City, Capital region, Capital Territory, Capitale
> d'état - zone spéciale, Castello, Census Area, Census Division,
> Centrally Administered Area, Cercle, Chantun, Chuan-shih, Circle,
> City, City and Borough, City and County, City Municipality,
> City/Municipality, Ciudades autónomas, Comarca, Comisaría,
> Commissiary, Commonwealth, Commune, Commune Autonome, Comuna,
> Comunidad Aut¢noma, Comunidad autónomas, Concelho, Constituen y,
> Constituency, Corregimiento, Corregimiento de, Country, County,
> Daerah Khusus ibuk, Daerah Istimewa, daerah-daerah, Departament,
> Departamento, Département, Départements, Departments, Dependencias
> Federales, Dependency, Development Region, Diamerismata, Distirct,
> District, District Municipality, Distrikkaya, Distrikt, Distrito,
> Distrito Capital, Distrito Federal, Distrito Municipal, Distrito
> Nacio, Division, Do, Dzongkhag, Economic Prefecture, Eilandgebieden,
> Emirate, Entity, Estado, Faritany Mizakatena, Faritra, Federal
> Dependency, Federal District, Federal Territory, Fivondronana,
> Fovaros, Fu, Fylke, Gorod, Gorsovet, Governorate, grad, Gwangyeoksi,
> Hlavni mesto, Hoofdstedelijke gewest, Hsien, Independent City,
> Independent Town, Intendancy, Intendencia, Intendency, Island, Island
> council, Island group, Island Region, Judet, Kabupaten, Kaghak,
> K'alak'i, Kampeng nakhon, Kanton, Kaupstadir, Kayaing, Ken, Khêt,
> Khetphiset, Khoueng, Kingdom, Kommuner, Kotamadya, Kraj, Kraje, Kray,
> Kreisfreie Städte, Krong, Laen, Land, Länd, Lander, Landsvæðun, Local
> Authority, Maakond, Magisterial district, Marz, Megye, Mehoz,
> Metropolis, Metropolitan City, Miesto savivaldybė, Mintaqah, Mkoa,
> Moughataas, Muhafazah, Municipality, Municipio, Municipio Especial,
> Municipiu, Muong, National capital - special zone, National Capital
> Area, National Dist, National Territory, Neutral City, Neutral Zone,
> Nomos, Oblast, Oblasy, Opcine, Opština, Ostan, Parish, Parròquia,
> Part, Partido, Police Station, Prefecture, préfecture, préfecture
> economique, Prefegitura, propinsi, Province, Provincia, Província,
> Provincie, Provinsie, Pyine, Qark, Région capitale, Raion, Raione,
> Rajoni, Rajono savivaldybė, Rayon, Reef, Regency, Região,
> Regierungsbezirk, Region, Région, Región Autónoma, Regional council,
> Regional District, Regional Municipality, Regione, Republic,
> Respublika, Ressort, Rural Distirct, Sahar, Savivaldybė, Sector,
> Sector autónomo, See, Senatorial District, Sha`biyah, Sheng, Shih, Si,
> sous-préfecture, Sous-régions, Special City, Special district, Special
> Municipal, Special municipality, Special region, Special region or
> zone, Srok, State, Statistical Region, Statisticna regij, Subdistrict,
> Sub-district, Sub-prefecture, Sub-region, Sýsla, Syssel, Taluk,
> Tarafa, Territoire, Territorial authority, Territorial Unit,
> Territorio Nacional, Territory, Teukbyeolsi, Thana, Thanh Pho, Tinh,
> To, Todof, Town council, Traditional county, Union territo, Union
> territor, Unitary authority, United Counties, unknown, Upazila, Urban
> district, Urban prefectur, velayat, Vikas kshetra, Village, Ville
> Neutre, Voblasts', Voivodship, water bodies, Wilaya, Wilayah
> persekutuan, Wilayat, Wojewodztwa, Yin, Zila, Zizhiqu, Zupanija, županija
>
> No virus found in this message.
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--
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 br.fgov.be
Skype name: qgroom
Website: www.botanicgarden.be
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