January 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/

3 2

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

2 2

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 >

10 17

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

2 5

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>.

6 9

Re: [tdwg-content] Darwin Core Standard - proposed change in governance
by Simon.Cox＠csiro.au 26 Jan '15

26 Jan '15

A property to indicate membership in an ontology appears to be missing from the standard semweb stack. Some folks use rdfs:isDefinedBy to point from resources to an ontology, but rdfs:isDefinedBy is also used for other things. AFAIK there is no inverse-ish property whose domain includes owl:Ontology that can be used to assemble a set of classes and properties to be deemed to be part of the ontology. I sometimes use dct:hasPart but that doesn't seem quite strong or specific enough. Maybe just rdfs:member . Simon -----Original Message----- Date: Thu, 22 Jan 2015 16:35:36 +0100 From: ?amonn ? Tuama [GBIF] <eotuama(a)gbif.org> Subject: Re: [tdwg-content] Darwin Core Standard - proposed change in governance To: "'Steve Baskauf'" <steve.baskauf(a)vanderbilt.edu>, "'Tim Robertson'" <trobertson(a)gbif.org> Cc: 'TDWG Content Mailing List' <tdwg-content(a)lists.tdwg.org>, '"Markus D?ring (GBIF)"' <mdoering(a)gbif.org> Message-ID: <00d101d03659$119e2330$34da6990$@org> Content-Type: text/plain; charset="iso-8859-1" Dublin Core tackles the issue of ?borrowing? from other vocabularies through the construct of Dublin Core Application Profiles [1] ? something separate from the specification of DC itself. ?amonn [1] http://dublincore.org/documents/2009/05/18/profile-guidelines/ From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Steve Baskauf Sent: 22 January 2015 15:41 To: Tim Robertson Cc: TDWG Content Mailing List; "Markus D?ring (GBIF)" Subject: Re: [tdwg-content] Darwin Core Standard - proposed change in governance I'm not sure whether anyone ever established that there was a consensus on this, but it has been suggested repeatedly that the basic Darwin Core vocabulary should have minimal restrictions and semantics imposed upon it. This allows other layers to be built upon it (XML schemas, RDF-based ontologies, etc.) that are intended to serve more specialized purposes. >From the standpoint of the normative RDF document, that means that it should include very little in the way semantics that would create entailments for semantic clients. That doesn't mean that there is no value in having that RDF, because the resources defined by that document can be nodes that can be linked and restricted by other ontologies. This has been done or is being done by Darwin-SW and BCO, for example. Having the RDF document contain few machine-interpretable properties is a separate issue from whether it is a good idea for that document to be normative. Bob makes a good point that if it is the normative document yet does not contain the information required for defining how the terms should be used, it may be inadequate. We already have that situation with the Dublin Core terms. Since they are defined as RDF by DCMI, we don't include them in our normative RDF document. So if potential users were to try to use Darwin Core by looking solely at the normative document (which they should be able to do, at least in theory), they would not know that Darwin Core includes Dublin Core terms. This is a point that should be considered in discussions on a TDWG-wide policy on vocabulary documentation. It's an even bigger issue in Audubon Core, since a much higher proportion of its terms are "borrowed" from other vocabularies than DwC. Steve Tim Robertson wrote: Hi all, I don?t think there has ever been any intention for DwC to impose that kind of restriction, regardless of the format chosen for the authoritative version (e.g. be it wiki text, RDF, HTML or PDF). I?d expect a schema to define that restriction (xsd, class definition etc). Is that how others see it? I believe this is what John meant when he wrote the spec [1]: "There is meant to be a clear separation between the terms defined in this standard and the applications that make use of them. For example, though the data types and constraints are not provided in the term definitions, recommendations are made about how to restrict the values where appropriate." Cheers, Tim [1] http://rs.tdwg.org/dwc/index.htm

1 0

Darwin Core Standard - proposed change in governance
by John Wieczorek 22 Jan '15

22 Jan '15

Dear all, Peter Desmet, Markus Döring, and I have been working on the transition of Darwin Core maintenance from the Google Code Site to Github. We've taken the opportunity to streamline the process of making updates to the standard when they are ratified, such as scripts to produce the human-readable content and auxiliary files from the RDF document of current terms. As a result of this work, we see further opportunities to simplify the maintenance of the standard. They center on the following proposal. We would like to propose that the *RDF document of current terms* be made to represent the *normative standard for Darwin Core* rather than *Complete History normative document* we use now. We would also like to make that new normative document the only document in the standard. Under this proposal: 1) the normative standard for Darwin Core would consist of a single document at http://rs.tdwg.org/terms/dwc_normative.rdf (not currently active). 2) information currently held in http://rs.tdwg.org/dwc/rdf/dwctermshistory.rdf (the current normative document) and the corresponding Complete History web page ( http://rs.tdwg.org/dwc/terms/history/index.htm) would be retained only in a history document http://rs.tdwg.org/terms/history.html (not currently active). 3) all documents other than the proposed normative document would not be part of the standard. The proposed changes require community consensus under the existing rules of governance of the Darwin Core. This means that the proposal must be under public review for at least 30 days after an apparent consensus on the proposal and any amendments to it is reached, where consensus consists of no publicly-shared opposition. The implications of this proposal are many. One of the most important is that the rules governing changes to the standard ( http://rs.tdwg.org/dwc/terms/namespace/index.htm) would no longer be a part of the standard. Instead, we would promote the adoption of these rules across TDWG standards rather than just within Darwin Core. It may be that TDWG is not ready to accommodate this at the moment. If so, the Namespace Policy could remain within the Darwin Core standard until the broader governance process for TDWG can cover it, at which point we would propose to remove the Namespace Policy from the Darwin Core. Other comments about the proposed changes: Having one RDF document for the terms in the dwc namespace will avoid confusion. Only those with status 'recommended' would be in the normative document. Having the term history (all versions, including deprecated, superseded, and recommended ones) in a web page only is what Dublin Core does. It means no one would be able to reason over old versions of the Darwin Core. Would anyone do that? Having no document other than the normative one as part of the standard would free the whole rest of the body of Darwin Core documentation from the requirements of public review and Executive Committee approval. This would make that documentation much more open to broader contributions and easier to adapt to evolving demands. We do not propose to lose any of the documentation we have. Please share your comments! Cheers, John

11 18

Re: [tdwg-content] Darwin Core Standard - proposed change in governance
by John Wieczorek 21 Jan '15

21 Jan '15

Dear all, There seems to be some consensus forming that simplification is good, and that the history should be part of the normative document. Without committing to a stance on RDF versus anything else as a normative document, we (Markus, actually) have made scripts to produce the human readable version from the RDF so that the two will be easy to synchronize. In fact, the script generates several documents to keep everything in sync. Right now that human-readable version is similar to the present standard Quick Reference Guide (http://rs.tdwg.org/dwc/terms/index.htm) with very little explanation aside from the terms, and only a few of the properties for the terms. If we have a normative document, then it must contain all of the properties of the terms, as in the present Complete History document ( http://rs.tdwg.org/dwc/terms/history/index.htm) There is more in those term definitions than most people need. So, if we go with a human-readable document (HTML?), it should contain as little explanatory text that could change over time as possible. I also suggest that we should have an even more prominent human-readable page that has only what most people need (a la the Quick Reference Guide). Every derived document (Quick Reference, RDF document, XML schemas, terms list, term pages on the GBIF Media Wiki) should have a reference to the normative document, and they should absolutely be kept in sync with the normative document. Is this a sound alternative proposal? Do I get the sense that for now the standard should retain the Namespace Policy, until TDWG can set up a broader policy? Cheers, John On Wed, Jan 21, 2015 at 4:59 PM, Bertram Ludaescher <ludaesch(a)gmail.com> wrote: > +1 for "human readable" > > (last time I checked, humans were still doing most of the thinking on > planet Earth :) > > Oh and "parsers" were one of the first things computer scientists invented > to make human-readable things also machine-readable. I think they still > make those ;-) > > Over the years, we might have gone overboard with "one size fits all" > (XML, RDF, <insert your favorite language here> ... ) > > My 2 cents.. > > Bertram > > > On Wed, Jan 21, 2015 at 9:49 AM, Éamonn Ó Tuama [GBIF] <eotuama(a)gbif.org> > wrote: > >> Seems like RDF expression in combination with a privileged XSLT to human >> readable doc might do. I still like the idea of the RDF doc as the >> normative one. At least it is concise. The W3C specification pages are a >> rather messy mix of different sections some headed by "This section is >> non-normative.", and see, e.g., the page for the DCAT vocab [1] "As well as >> sections marked as non-normative, all authoring guidelines, diagrams, >> examples, and notes in this specification are non-normative. Everything >> else in this specification is normative." >> >> While RDF might excel as a graph definition langauge, I think there is >> still value is using it without domain and range statements (if these don't >> exist) to simply define labels, definitions and comments (examples) in a >> machine readable way. >> >> >> >> [1] http://www.w3.org/TR/vocab-dcat/ >> >> -----Original Message----- >> From: tdwg-content-bounces(a)lists.tdwg.org [mailto: >> tdwg-content-bounces(a)lists.tdwg.org] On Behalf Of Bob Morris >> Sent: 21 January 2015 15:13 >> To: John Wieczorek >> Cc: TDWG Content Mailing List >> Subject: Re: [tdwg-content] Darwin Core Standard - proposed change in >> governance >> >> John et al. Thanks for all the work you've put into this >> >> I favored this at first, but thought a lot since it was proposed and now >> oppose item 1). >> >> Short argument: RDF is meant for machines to read, not humans to read. >> If an RDF document is normative, mainly RDF experts will be able to argue >> about it and about conformance to it. >> >> More(?) important, RDF is a graph definition language, not a >> specification definition language. Not even RDF has an RDF file as its >> normative definition. In fact, it seems both W3C and IETF regard most >> (all?) of their normative artifacts for specification (respectively >> "Recommendation" and "Request For Comment") as nothing other than human >> readable documents. >> >> This is not to say there should not be one or more normative RDFS >> serializations of a human readable specification. It may even be that >> there should be a privileged RDFS document, together with a privileged >> transformation (e.g. in xslt) and a privileged platform for synthesizing a >> human readable form of DwC. But it's that web document that should be >> normative (and human readable.) This is what Audubon Core does, except >> that the base "generation data" comprises, annoyingly, but robustly, calls >> to the MediaWiki template language. >> (The annoyance of designing MediaWiki templates may ease in the future >> due to [1]) >> >> Certainly there are exceptions to the principle of "make only human >> readable as the base normative artifact". The XML schemaSchema [2] is an in >> example. But DwC doesn't seem to fit that model. DwC is not a DwC object. >> >> My position is a little influenced by [3], a lot of with which I >> disagree. But it reminds me of something my Daddy taught me: >> "multi-purpose tools are often poor at all their purposes, except in >> simple cases." But really, my reluctance here is that I see no reason we >> should imagine that DwC data is always a graph and that is why we should >> model it with a graph description language. Worse, my experience is that >> the most common potholes in the RDF world arise when using it without >> understanding the underlying graph theory. >> >> Bob Morris >> >> [1] http://www.mediawiki.org/wiki/Lua_scripting >> [2] http://www.w3.org/TR/xmlschema11-1/#normative-schemaSchema >> [3] http://manu.sporny.org/2014/json-ld-origins-2/ >> >> On Tue, Jan 20, 2015 at 10:18 AM, John Wieczorek <tuco(a)berkeley.edu> >> wrote: >> > Dear all, >> > >> > Peter Desmet, Markus Döring, and I have been working on the transition >> > of Darwin Core maintenance from the Google Code Site to Github. We've >> > taken the opportunity to streamline the process of making updates to >> > the standard when they are ratified, such as scripts to produce the >> > human-readable content and auxiliary files from the RDF document of >> > current terms. As a result of this work, we see further opportunities >> > to simplify the maintenance of the standard. They center on the >> following proposal. >> > >> > We would like to propose that the RDF document of current terms be >> > made to represent the normative standard for Darwin Core rather than >> > Complete History normative document we use now. We would also like to >> > make that new normative document the only document in the standard. >> > >> > Under this proposal: >> > >> > 1) the normative standard for Darwin Core would consist of a single >> > document at http://rs.tdwg.org/terms/dwc_normative.rdf (not currently >> active). >> > >> > >> > 2) information currently held in >> > http://rs.tdwg.org/dwc/rdf/dwctermshistory.rdf (the current normative >> > document) and the corresponding Complete History web page >> > (http://rs.tdwg.org/dwc/terms/history/index.htm) would be retained >> > only in a history document http://rs.tdwg.org/terms/history.html (not >> > currently active). >> > >> > >> > 3) all documents other than the proposed normative document would not >> > be part of the standard. >> > >> > >> > The proposed changes require community consensus under the existing >> > rules of governance of the Darwin Core. This means that the proposal >> > must be under public review for at least 30 days after an apparent >> > consensus on the proposal and any amendments to it is reached, where >> > consensus consists of no publicly-shared opposition. >> > >> > >> > The implications of this proposal are many. One of the most important >> > is that the rules governing changes to the standard >> > (http://rs.tdwg.org/dwc/terms/namespace/index.htm) would no longer be >> > a part of the standard. Instead, we would promote the adoption of >> > these rules across TDWG standards rather than just within Darwin Core. >> > It may be that TDWG is not ready to accommodate this at the moment. If >> > so, the Namespace Policy could remain within the Darwin Core standard >> > until the broader governance process for TDWG can cover it, at which >> > point we would propose to remove the Namespace Policy from the Darwin >> Core. >> > >> > >> > Other comments about the proposed changes: >> > >> > >> > Having one RDF document for the terms in the dwc namespace will avoid >> > confusion. Only those with status 'recommended' would be in the >> > normative document. >> > >> > >> > Having the term history (all versions, including deprecated, >> > superseded, and recommended ones) in a web page only is what Dublin >> > Core does. It means no one would be able to reason over old versions >> > of the Darwin Core. Would anyone do that? >> > >> > >> > Having no document other than the normative one as part of the >> > standard would free the whole rest of the body of Darwin Core >> > documentation from the requirements of public review and Executive >> > Committee approval. This would make that documentation much more open >> > to broader contributions and easier to adapt to evolving demands. >> > >> > >> > We do not propose to lose any of the documentation we have. >> > >> > >> > Please share your comments! >> > >> > >> > Cheers, >> > >> > >> > John >> > >> > >> > _______________________________________________ >> > tdwg-content mailing list >> > tdwg-content(a)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 >> >> >> Filtered Push Project >> Harvard University Herbaria >> Harvard University >> >> email: morris.bob(a)gmail.com >> web: http://efg.cs.umb.edu/ >> web: http://wiki.filteredpush.org >> http://wiki.datakurator.net >> http://taxonconceptexplorer.org/ >> http://www.cs.umb.edu/~ram >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> > >

1 0

Darwin Core Proposal - term content recommendations to comments
by John Wieczorek 19 Jan '15

19 Jan '15

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

3 3