February 2015 - tdwg-content

Re: [tdwg-content] If you need something for referring to a population, then it is probably best to do it as a related class
by Nico Franz 05 Jun '25

05 Jun '25

Hello all: I have a few inserted comments, hopefully with some clarifying effect: On 5/4/2011 10:54 AM, Peter DeVries wrote: > Hi Steve, > > I may have overloaded the term specimen to make the explanation easier > to follow. > > A specimen could be an individual or it could be part of an individual. > > To some extent you need to think about how these models will be used. > > If you subscribe to the model that a species is whatever a taxonomists > says it is then it is difficult to make statements like. > > X% of the world's species will be extinct by 2050. > > If you mean a species as defined by the concept documented at this URI > which is supported by these specimens, images, and DNA then you are on > firmer ground. > > Species in the natural world do a pretty good job recognizing those > individuals that are appropriate mates. In other words members of > their own species. > > Are we modeling species or variations in human conceptualizations of > species? > >> Assuming that there was only one individual organism identified >> there is really one one species (or hybrid). > Aaaaaaaaaaaaaah! Please Nico C., don't take this one up! > > > I stick with this. Assuming you don't have a hybrid individual. That > individual is one species. The fact that human may disagree on what > species it is a human issue. > > Again, Are we modeling species or variations in human > conceptualizations of species? NMF: I believe there is a history of biodiversity database engineering that actually led some people, initially in Australia (Greg Whitbread?) and Europe (Berendsohn's group) to place more emphasis on modeling human conceptualizations of taxa. I understand this happened in the late 80s / early 90s. The motivation was, apparently, that no long-term consensus seemed available to model a single and sufficiently widely accepted taxonomy of, say, Central European vascular plant species or mosses. I believe that projects such as the Euro + Med PlantBase (http://www.emplantbase.org/home.html) are examples of the persistence (success?) of this 20+ year old practice. I think this is the kind of background that Steve is referring to. > > Which of these is of primary importance to decision makers and > non-taxonomist biologists? > Part of the problem with various publications relating to ontologies > and taxonomy is that their species models entail a specific > phylogenetic hypothesis. > > In the real world taxa are not as clean as some would like to make > them out to be. > > Each individual is a unique combination of thousands of separate gene > lineages which often do not follow clean monophyletic paths. > > I would argue that most of those who work with species related data > see them as useful typological constructs which in general follow the > biological species model. NMF: The solution of how to properly model things such as species in RDF, OWL (etc.) should ideally accommodate all "species concepts" (BCS, ESC, PSC, GSC, there's dozens), i.e. it should be neutral towards this issue. The examples below are too simple, ignoring for example cases such as pro parte synonymy, or a concept ("species") that appears unique and monophyletic to one author but (vastly) polyphyletic to another. To do an accurate mapping in that latter case (which is not super-common but it's real), I think one would have to come down on saying we're modeling human conceptualizations. They are not just that, so really it's not a strict dichotomy, meaning that by modeling conceptualizations we do not have to say "the species only exist on our heads", or "well, then anything goes". I agree (sheepishly) that it does come down to what the input data look like, and what the expectations are towards just accommodating the user community versus pushing them in a particular direction. Some of this also on p. 47 of this PDF: https://journals.ku.edu/index.php/jbi/article/view/3927/3852 > > /Aedes triseriatus/ owl:sameAs /Ochlerotatus triseriatus/ > > Others seem to see them as phylogenetic end nodes which entail a > specific phylogenetic history. > > /Aedes triseriatus/ distinctFrom /Ochlerotatus triseriatus/ > / > / > If you are primarily interested in understanding issues of ecology, > disease, diversity and conservation the former model is more > appropriate than the later. > > Respectfully, > > - Pete Regards, Nico Nico M. Franz, Ph.D. Assistant Professor Director, UPRM Invertebrate Collection Department of Biology University of Puerto Rico Call Box 9000 Mayagüez, PR 00681-9000 Phone: (787) 832-4040, ext. 3005 Fax: (787) 834-3673 E-mail: nico.franz(a)upr.edu Laboratory website: http://academic.uprm.edu/~franz/ UPRM-INVCOL: http://uprm-invcol-project.tumblr.com/

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Notes on the Biological Collections Ontology
by Quentin Groom 27 Mar '15

27 Mar '15

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? 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. 3. Vernacular name should be associated with a language and a geographic area where it is used? 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. 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. 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. 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. 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. 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. 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? 11. Controlled vocabularies: Many terms suggest using a controlled vocabulary, but most don’t have one. Is this an area we should work on? 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. 13. What is the difference between fieldNumber and recordNumber? 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. 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? 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(a)br.fgov.be Skype name: qgroom Website: www.botanicgarden.be

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Darwin Core terms sex and lifeStage with mixed content
by John Wieczorek 26 Mar '15

26 Mar '15

Dear all, There is a body of topics surrounding Darwin Core terms for which it is tempting to overload the content in an effort to provide richer data than the standard would seem to support. We have a pair of older open issues on this general topic in the Darwin Core issue tracker. https://github.com/tdwg/dwc/issues/35 https://github.com/tdwg/dwc/issues/36 You can see in the discussions on those issues that there is some consensus that the content of Darwin Core terms should remain consistent with the definitions and not mix concepts. I've had recent questions in particular about the fields 'sex' and 'individualCount'. Here is an example. How should one populate Darwin Core terms for a record of 2 males and 5 females in a single lot? I propose that part of this is easy - the individualCount should be 7. The definition of the sex term (without looking for clues in the Comments) might be seen as a little ambiguous, "The sex of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary." Strictly speaking, there is no single sex that matches the biological individuals in this example lot Occurrence record, and so the sex fields should be left blank. There are a number of terms in Darwin Core whose definitions suggest that a list (formatted with ' | ' as a separator) be used to match multiple values. Though it might seem that sex could be one of these terms, it isn't currently. Again this argues for a single value for sex from a controlled vocabulary. The biggest problem is with the Comment on the sex term, which gives an example with different semantics from what the definition says - namely "8 males, 4 females". I pose that this is an error and must be corrected. Yet, all hope of retaining information in the Occurrence record is not lost. To capture the richness of the information in the multi-sex lot example, I would recommend the use of dynamicProperties. How should one populate Darwin Core terms for a record of 2 males and 5 females in a single lot? I would do this: sex = null individualCount = 7 dynamicProperties= { "count of males":2, "count of females":5 } Hope that makes sense. Since this topic has arisen from multiple independent sources, I would like to formally propose changes to the sex and lifeStage terms to remove the spurious examples. Today begins a minimum 30-day public commentary period to close on 5 March 2015 if no dissenting opinions are made in this public forum. Here is how the new terms would appear if the changes are accepted: Identifier: http://rs.tdwg.org/dwc/terms/sex Namespace: http://rs.tdwg.org/dwc/terms/ Label: Sex Definition: The sex of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary. Comment: Examples: "female", "hermaphrodite", "male". For discussion see http://terms.tdwg.org/wiki/dwc:sex Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2008-11-19 Date Modified: 2015-02-05 Has Domain: Has Range: Version: sex-2015-02-05 Replaces: Sex-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/Occurrence ABCD 2.06: DataSets/DataSet/Units/Unit/Sex Identifier: http://rs.tdwg.org/dwc/terms/lifeStage Namespace: http://rs.tdwg.org/dwc/terms/ Label: Life Stage Definition: The age class or life stage of the biological individual(s) at the time the Occurrence was recorded. Recommended best practice is to use a controlled vocabulary. Comment: Examples: "egg", "eft", "juvenile", "adult". For discussion see http://terms.tdwg.org/wiki/dwc:lifeStage Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2008-11-19 Date Modified: 2015-02-05 Has Domain: Has Range: Version: lifeStage-2015-02-05 Replaces: LifeStage-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/Occurrence ABCD 2.06: DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalSexualStage or DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalLiveStages/MycologicalLiveStage (Note DwC spec uses ”MycologicalLifeStage” or DataSets/DataSet/Units/Unit/ZoologicalUnit/PhasesOrStages/PhaseOrStage Cheers, John

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Re: [tdwg-content] Darwin Core Proposal - term content recommendations to comments
by Ramona Walls 23 Mar '15

23 Mar '15

This is a good idea. In theory the recommendation could go into a separate annotation (e.g., we use "example of usage" in BCO), but I don't think that is necessary for DwC at this juncture. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Research Associate, Bio5 Institute, University of Arizona Laboratory Research Associate, New York Botanical Garden On Tue, Jan 20, 2015 at 4:00 AM, <tdwg-content-request(a)lists.tdwg.org> wrote: > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-content digest..." > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 19 Jan 2015 14:58:06 +0100 > From: John Wieczorek <tuco(a)berkeley.edu> > Subject: [tdwg-content] Darwin Core Proposal - term content > recommendations to comments > To: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> > Message-ID: > <CAHwKGGc7sK3Dg8KTN_NYe4S+OYk= > YE+-dRxjKPS-dNnGhAvjMw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > During the process of reviewing the recent set of changes to the Darwin > Core standard in early November 2014, it was proposed to make the > definitions and comments for terms more consistent in their treatment of > content recommendations. The specific proposal is logged in the Darwin Core > issue tracker as https://github.com/tdwg/dwc/issues/26. > > The gist of the proposal is that recommendations on how to populate a term > are often in the definition whereas we would like them to be consistently > in the comments section. The list of affected terms is given below for > reference. > > This message is to elicit responses from any who might have a reason to > recommend against these changes, which are not semantic in nature. We will > leave this proposal open for commentary until 19 February 2015 unless > further discussion arises resulting in amendments. > > Cheers, > > John > > > The following terms have recommendations in the definitions, which we would > like to move to comments: > > datasetID > occurrenceID > sex > lifeStage > reproductiveCondition > behavior > establishmentMeans > occurrenceStatus > organismID > organismScope > materialSampleID > eventID > eventDate > eventTime > locationID > higherGeographyID > continent > waterBody > islandGroup > island > country > countryCode > municipality > locality > minimumDistanceAboveSurfaceInMeters > maximumDistanceAboveSurfaceInMeters > locationAccordingTo > decimalLatitude > decimalLongitude > geodeticDatum > coordinateUncertaintyInMeters > pointRadiusSpatialFit > verbatimCoordinates > verbatimLatitude > verbatimLongitude > verbatimCoordinateSystem > verbatimSRS > footprintWKT > footprintSRS > footprintSpatialFit > georeferencedDate > georeferenceVerificationStatus > geologicalContextID > identificationID > dateIdentified > identificationVerificationStatus > taxonID > scientificName > subgenus > taxonRank > nomenclaturalCode > taxonomicStatus > measurementID > measurementType > measurementUnit > measurementDeterminedDate > relationshipOfResource > relationshipEstablishedDate > > while the following terms already have the recommendations in the comments: > > institutionID > collectionID > basisOfRecord > dynamicProperties > recordedBy > preparations > disposition > associatedMedia > associatedReferences > associatedSequences > associatedTaxa > otherCatalogNumbers > associatedOccurrences > associatedOrganisms > previousIdentifications > higherGeography > georeferencedBy > georeferenceSources > typeStatus > identifiedBy > identificationReferences > higherClassification > measurementDeterminedBy >

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Darwin Core Proposal - sampling event terms
by John Wieczorek 20 Mar '15

20 Mar '15

Dear all, I am following up with the proposal for sampling event terms that have been discussed earlier in this forum in a few threads [1,2,3]. Below is the final proposal for five new terms as it stands ready to be presented to the Executive Committee for ratification after taking into account the commentaries to date. As this summary consists of no semantic changes over what has been discussed already, the proposal should be ready for presentation on 23 Jan 2015, barring any expressed objections to the current proposal. Term Name: parentEventID Identifier: http://rs.tdwg.org/dwc/terms/parentEventID Namespace: http://rs.tdwg.org/dwc/terms Label: Parent Event ID Definition: An identifier for the broader Event that groups this and potentially other Events. Comment: May be a globally unique identifier or an identifier specific to the data set. Example: “A1” as parentEventID to identify the main Whittaker Plot in nested samples, each with its own eventID (e.g., “A1:1”, “A1:2”). For discussion see http://terms.tdwg.org/wiki/dwc:parentEventID. Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2014-11-07 Date Modified: 2014-12-23 Has Domain: Has Range: Version: parentEventID-2014-12-23 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD Issue reference: https://github.com/tdwg/dwc/issues/9 Term Name: sampleSizeValue Identifier: http://rs.tdwg.org/dwc/terms/sampleSizeValue Namespace: http://rs.tdwg.org/dwc/terms Label: Sample Size Value Definition: A numeric value for a measurement of the size (time duration, length, area, or volume) of a sample in a sampling event. Comment: A sampleSizeValue must have a corresponding sampleSizeUnit. Example: “5" for sampleSizeValue with "metre” for sampleSizeUnit. For discussion see http://terms.tdwg.org/wiki/dwc:sampleSizeUnit. Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2014-11-07 Date Modified: 2014-12-23 Has Domain: Has Range: Version: sampleSizeValue-2014-12-23 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD Issue reference: https://github.com/tdwg/dwc/issues/10 Term Name: sampleSizeUnit Identifier: http://rs.tdwg.org/dwc/terms/sampleSizeUnit Namespace: http://rs.tdwg.org/dwc/terms Label: Sample Size Unit Definition: The unit of measurement of the size (time duration, length, area, or volume) of a sample in a sampling event. Comment: A sampleSizeUnit must have a corresponding sampleSizeValue, e.g., “5" for sampleSizeValue with "metre” for sampleSizeUnit. Examples: “minute”, “hour”, “day, “metre”, “square metre”, “cubic metre”. Recommended best practice is to use a controlled vocabulary such as the Ontology of Units of Measure http://www.wurvoc.org/vocabularies/om-1.8/ of SI units, derived units, or other non-SI units accepted for use within the SI (e.g., minute, hour, day, litre). For discussion see http://terms.tdwg.org/wiki/dwc:sampleSizeUnit. Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2014-11-07 Date Modified: 2014-12-23 Has Domain: Has Range: Version: sampleSizeUnit-2014-12-23 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD Issue reference: https://github.com/tdwg/dwc/issues/11 Term Name: organismQuantity Identifier: http://rs.tdwg.org/dwc/terms/organismQuantity Namespace: http://rs.tdwg.org/dwc/terms Label: Organism Quantity Definition: A number or enumeration value for the quantity of organisms. Comment: An organismQuantity must have a corresponding organismQuantityType, e.g., “27” for organismQuantity with “individuals” for organismQuantityType; “12.5” for organismQuantity with “%biomass” for organismQuantityType; “r” for organismQuantity with “BraunBlanquetScale” for organismQuantityType. For discussion see http://terms.tdwg.org/wiki/dwc:organismQuantity. Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2014-11-07 Date Modified: 2014-12-23 Has Domain: Has Range: Version: organismQuantity-2014-12-23 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Occurrence ABCD 2.0.6: not in ABCD Issue reference: https://github.com/tdwg/dwc/issues/12 Term Name: organismQuantityType Identifier: http://rs.tdwg.org/dwc/terms/organismQuantityType Namespace: http://rs.tdwg.org/dwc/terms Label: Organism Quantity Type Definition: The type of quantification system used for the quantity of organisms. Comment: An organismQuantityType must have a corresponding organismQuantity, e.g., “27” for organismQuantity with “individuals” for organismQuantityType; “12.5” for organismQuantity with “%biomass” for organismQuantityType; “r” for organismQuantity with “BraunBlanquetScale” for organismQuantityType. For discussion see http://terms.tdwg.org/wiki/dwc:organismQuantityType. Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2014-11-07 Date Modified: 2014-12-23 Has Domain: Has Range: Version: organismQuantityType-2014-12-23 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Occurrence ABCD 2.0.6: not in ABCD Issue reference: https://github.com/tdwg/dwc/issues/13 [1] http://lists.tdwg.org/pipermail/tdwg-content/2014-November/003380.html [2] http://lists.tdwg.org/pipermail/tdwg-content/2014-December/003394.html [3] http://lists.tdwg.org/pipermail/tdwg-content/2014-December/003410.html

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Fwd: [dwc] quantity (#12)
by John Wieczorek 05 Mar '15

05 Mar '15

Der all, I am forwarding this comment from Simon Cox, which was submitted to the Darwin Core development site on Github. Cheers, John ---------- Forwarded message ---------- From: Simon Cox <notifications(a)github.com> Date: Mon, Dec 15, 2014 at 4:47 AM Subject: Re: [dwc] quantity (#12) To: tdwg/dwc <dwc(a)noreply.github.com> Cc: John Wieczorek <tuco(a)berkeley.edu> 'quantity' usually implies an amount, encoded as a scaled number. In most other domains it does not include a value from an enumerated set. The latter may be called 'quality'. Both quantity and quality are subclasses of 'property'. — Reply to this email directly or view it on GitHub <https://github.com/tdwg/dwc/issues/12#issuecomment-66946784>.

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Best practice for scientificNameAuthorship?
by Andréa Matsunaga 25 Feb '15

25 Feb '15

Dear experts. What is the best practice for the DwC scientificNameAuthorship when there is a specific epithet author as well as infraspecific epithet author in a scientific name? Both names concatenated by some character? Only the infraspecific epithet author? Both pieces of information would go into DwC scientificname, but I'm looking for how users would use scientificNameAuthorship and what is useful to have there. Thank you, --am

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Easting and northing
by Roderic Page 11 Feb '15

11 Feb '15

Pardon my ignorance, but has there ever been a discussion of easting and northing values in regards to Darwin Core? AFAIK the current standard doesn’t mention them. The reason I’m asking is that I’ve just come across some VerbatimLatitude and VerbatimLongitude values in a dataset that is aggregated by VertNet (and hence GBIF) where (after some head scratching) I realised that the verbatim values were actually Easting and Northing (which I didn’t know existed until yesterday). Details are here: https://github.com/ttu-vertnet/ttu-mammals/issues/11 I’m guessing this isn’t a terribly common way to record location information, but it looks like in this case the lack of support for this type of data has resulted in somebody trying to shoehorn them into VerbatimLatitude and VerbatimLongitude, resulting in values which are uninterpretable to aggregators further up the chain. Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: Roderic.Page(a)glasgow.ac.uk<mailto:Roderic.Page@glasgow.ac.uk> Tel: +44 141 330 4778 Skype: rdmpage Facebook: http://www.facebook.com/rdmpage LinkedIn: http://uk.linkedin.com/in/rdmpage Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com ORCID: http://orcid.org/0000-0002-7101-9767 Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ ResearchGate https://www.researchgate.net/profile/Roderic_Page

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