[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 

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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>     tdwg-content at lists.tdwg.org <mailto:tdwg-content at lists.tdwg.org>
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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

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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