[tdwg-content] Notes on the Biological Collections Ontology

[John Wieczorek]

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>
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, 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
> Skype name: qgroom
> Website:    www.botanicgarden.be
>
> _______________________________________________
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>

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
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