March 2015 - tdwg-content - lists.tdwg.org

Recap - Darwin Core Standard - proposed changes in governance
by John Wieczorek 23 Apr '15

23 Apr '15

Dear all, There has been consistent agreement (though I would hesitate to say consensus prematurely) about some aspects of the proposal to redefine which documents comprise the Darwin Core standard. The discussion has been fruitful and appreciated. Yet, I believe we are at an impasse in terms of implementing the proposed changes because a) I have not followed the correct process so far, and b) the interim TDWG Standards Process that are supposed to govern the process is not amenable to the changes that were proposed. I'll try to explain briefly. The proposal was to redefine which documents comprise the Darwin Core standard, not to make additions or changes to the Darwin Core terms, The latter would fall under Darwin Core's "internal" namespace policy[1]. Instead, this proposal is a change to the structure as well as documentary content of the standard as a whole, which falls under the interim TDWG Standards Documentation Specification[2], as Steve Baskauf pointed out[3]. To fulfill those requirements is an onerous task (my heartfelt pity for those who have had to go through it) - too onerous, I believe, for what we are trying to accomplish here, which is to change an existing standard (indeed, make it easier to manage) rather than create a new one. We are not allowed to do that according to the interim TDWG Standards Documentation Specification, which states, "Once a standard has been ratified it cannot be changed in any substantive way; it must be superseded by a standard with a different name." All question of versioning aside, we would have to follow the process of creating a new standard. Unless there is a way to get an Executive override of the interim process standard in order to allow us to make the proposed changes and liberate Darwin Core to evolve more effectively, I think we have to wait for the overhaul of the Standards Documentation Specification. The Task Group Charter to do that work has been submitted, but the results are not slated to be fully realized until 1 Jan 2016. This is unfortunate, as it leaves a huge body of work to refactor Darwin Core and its management [4] unrealizable in an official capacity. Ideas welcome. Cheers, John [1] Darwin Core Namespace Policy. http://rs.tdwg.org/dwc/terms/namespace/index.htm [2] TDWG Standards Documentation Specification. http://www.tdwg.org/standards/147/ [3] tdwg-content email from Steve Baskauf. http://lists.tdwg.org/pipermail/tdwg-content/2015-January/003429.html [4] Github branch of Darwin Core repository for streamlined management.

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Darwin Core Proposal - environment terms
by John Wieczorek 23 Apr '15

23 Apr '15

Dear all, This message pertains to a proposal[1] set forth in September 2013 concerning the environment terms biome, environmentalFeature, and environmentalMaterial. I'm renewing the proposal because so much time has passed and the original proposal was not carried through to completion. There were no objections to the addition of those terms during the initial public commentary. Discussion revolved around how the recommendations for how to populate them. The recommendations for all three terms will suggest using a controlled vocabulary such as ENVO. The examples will be based on the set of subclasses of the corresponding ENVO terms for biome[2], environmentalFeature[3], and environmentalMaterial[4]. As with all Darwin Core terms, the constraints on content are not part of the definition - they are only illustrative recommendations. The importance of these terms was recognized anew at a Darwin Core and MIxS Hackathon in Florence in Sep 2014[5]. One important outcome of that workshop was the the realization that there is currently no possibility of a Darwin Core PreservedSpecimen or MaterialSample record to meet the minimum requirements of a Mimarks Specimen record[6], as there is currently no way to share required environment terms. This creates a huge and easy to solve barrier to integration of data across the collection, sample, and sequence realms. This proposal is not substantively different from the one discussed in 2013. It differs from the final amended previous proposal in two ways, 1) only the three terms biome, environmentalFeature, and environmentalMaterial are proposed here (the proposal to change to the term 'habitat' has been dropped), and 2) the term definitions have been updated to agree with those in ENVO. The terms will be in the Darwin Core namespace (following the TDWG community consensus in the previous discussion as well the consensus to coin the MaterialSample class in the Darwin Core namespace rather than use obi:specimen, with the equivalency being made on the ontology side in BCO[7]). The complete definitions of the three proposed terms is given below the following references. This reopens the 30-day public commentary period for the addition of new terms as described in the Darwin Core Namespace Policy[8]. [1] Original tdwg-content proposal for environment terms. http://lists.tdwg.org/pipermail/tdwg-content/2013-September/003066.html [2] ENVO biome. http://purl.obolibrary.org/obo/ENVO_00000428 [3] ENVO environmentalFeature. http://purl.obolibrary.org/obo/ENVO_00002297 [4] ENVO environmentalMaterial. http://purl.obolibrary.org/obo/ENVO_00010483 [5] DwC MIxS Meeting Notes. https://docs.google.com/document/d/1Zexgsiol6WC83vDzMTCF3uUB7DcFmKL15DFEPbw… [6] Table of the core items of Mimarks checklists. http://www.nature.com/nbt/journal/v29/n5/fig_tab/nbt.1823_T1.html [7] Biological Collections Ontology. https://github.com/tucotuco/bco [8] Darwin Core Namespace Policy. http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges Term Name: biome Identifier: http://rs.tdwg.org/dwc/terms/biome Namespace: http://rs.tdwg.org/dwc/terms/ Label: Biome Definition: An environmental system to which resident ecological communities have evolved adaptations. Comment: Recommended best practice is to use a controlled vocabulary such as defined by the biome class of the Environment Ontology (ENVO). Examples: "flooded grassland biome", "http://purl.obolibrary.org/obo/ENVO_01000195". Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2015-03-26 Has Domain: Has Range: Refines: Version: biome-2015-03-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD Term Name: environmentalFeature Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature Namespace: http://rs.tdwg.org/dwc/terms/ Label: Environmental Feature Definition: A material entity which determines an environmental system. Comment: Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO). Examples: "meadow", "http://purl.obolibrary.org/obo/ENVO_00000108". Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2015-03-26 Has Domain: Has Range: Refines: Version: environmentalFeature-2015-03-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD Term Name: environmentalMaterial Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial Namespace: http://rs.tdwg.org/dwc/terms/ Label: Environmental Material Definition: A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. Comment: Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO). Examples: "scum", "http://purl.obolibrary.org/obo/ENVO_00003930". Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2015-03-26 Has Domain: Has Range: Refines: Version: environmentalMaterial-2015-03-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD

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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 24 Mar '15

24 Mar '15

IAO:example of usage is widely used with object properties. I don't know how often it is used with data properties, but I don't know is any reason it could not be. I will file an issue about the truncated definition of iao:example of usage. 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, Mar 24, 2015 at 4:00 AM, <tdwg-content-request(a)lists.tdwg.org> wrote: > Send tdwg-content mailing list submissions to > tdwg-content(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-content > or, via email, send a message with subject or body 'help' to > tdwg-content-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-content-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-content digest..." > > > Today's Topics: > > 1. Re: Darwin Core Proposal - term content recommendations to > comments (?amonn) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 23 Mar 2015 16:48:54 +0100 > From: ?amonn ? Tuama [GBIF] <eotuama(a)gbif.org> > Subject: Re: [tdwg-content] Darwin Core Proposal - term content > recommendations to comments > To: 'Markus D?ring' <mdoering(a)gbif.org>, "'John Wieczorek'" > <tuco(a)berkeley.edu> > Cc: 'TDWG Content Mailing List' <tdwg-content(a)lists.tdwg.org> > Message-ID: <014601d06580$ddaf3210$990d9630$@org> > Content-Type: text/plain; charset="iso-8859-1" > > I can see how minting an additional term "dwcattributes:example" has a > certain consistency given the namespace is already in use but, as a close > alternative, and following best practice of not reinventing terms (and thus > making it easier for 3rd parties trying to process the RDF directly), I > think ?skos:example? is also worth considering. I am not familiar with > "iao:example of usage" but checking the definition [1]: > > ?A phrase describing how a class name should be used. May also include > other > kinds of examples that facilitate immediate understanding of a class > semantics, such as widely known prototypical subclasses or instances of the > class. Although essential for high level terms, examples for low level > terms > (e.g., Affymetrix HU133 array) are not? (definition looks truncated) > > > > ? it refers to classes rather than properties. The majority of DwC terms > are > properties. So, can "iao:example of usage" be applied to them? > > > > ?amonn > > > > [1] <http://purl.obolibrary.org/obo/IAO_0000112> > http://purl.obolibrary.org/obo/IAO_0000112 > > > > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Markus D?ring > Sent: 20 March 2015 14:35 > To: John Wieczorek > Cc: TDWG Content Mailing List > Subject: Re: [tdwg-content] Darwin Core Proposal - term content > recommendations to comments > > > > Thanks John, > > > > mostly repeating what I said earlier I would prefer to coin the new example > term in the existing dwcattributes namespace. > > It feels more consistent, is very straight forward and as you say we can > always declare same as relations elsewhere if that is really useful to > anyone. > > I cannot see any immediate advantage of reusing either the skos or the iao > term over minting a new one in the single dwcattributes namespace that > helps > documenting our dwc terms. > > > > Markus > > > > > > On 20 Mar 2015, at 14:14, John Wieczorek <tuco(a)berkeley.edu> wrote: > > > > > > Dear all, > > > > I would like to summarize my understanding of the state of the proposal to > put term content recommendations in comments consistently, rather than in > the definitions where they can sometimes be found. There has been universal > support for this idea. > > > > A second part of the proposal was to take this opportunity to separate the > examples from the comments using a distinct property to do so in the rdf > definitions of the terms. There has also been universal support for this > idea. > > > > Discussion revolved around how to accomplish the second part of the > proposal. I originally proposed a new attribute "dwcattributes:example", > which would be included once for every distinct example of term usage - > with > potentially many per Darwin Core term. There was universal support for the > idea of enabling this capability, though there was mixed opinion about > using > an existing term instead of minting a new one in the dwcattributes > namespace. Specifically, "skos:example" and "iao:example of usage" were > discussed. Potential problems with "skos:example" were pointed out. Similar > concerns about "iao:example of usage" were addressed, leaving this option > still open for consideration. > > > > It is not entirely clear technically (to me, anyway) how the annotation > property "iao:example of usage" would be imported into the normative rdf > document. I'm unaware of an OWL to RDF import mechanism. That doesn't mean > much, because I am not an expert. If there is not, I suppose we would have > to define an rdf file ourselves for the iao term and import that into > dwcattributes or into the normative Darwin Core rdf file(s) directly. I > don't think this would be a rigorous solution, but it would demonstrate our > intent fairly well, especially if there were comments to that effect in the > rdf files. Some guidance here might help us make a final decision on this > topic. > > > > If there is no clear and rigorous solution to the rdf import problem from > IAO, then it may just be easier to coin "dwcattributes:example" as > originally proposed, at least for now, and worry about it's equivalence to > "iao:example of usage" on the ontology side (BCO). > > > > I would really like to get the broader issue resolved soon, as we do > already > have consensus on making the contents of the definitions and comments > consistent. If we can't resolve how to separate the examples (even though > we > agree that it is a good idea), I will propose that we forget that added > part > of the proposal and just deal with the consistency issue first. > > > > Comments encouraged, as always. > > > > Cheers, > > > > John > > > > On Thu, Feb 5, 2015 at 10:01 AM, Ramona Walls <rlwalls2008(a)gmail.com> > wrote: > > As far as I know, iao:example of usage also allows both literals and URLs > as > the range. However, I fail to see a serious problem with that, and to me, > the benefits of re-using existing properties far outway the benefits I > could > see from having a separate set of properties for literals. Also, I don't > know anyone who reasons over annotations properties, although I am sure > there are those who do. > > In response to Paul Morris's comment, simply using iao:example of usage > does > not import all of IAO, and therefore does not include any of the "baggage" > of using IAO. > > 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 Thu, Feb 5, 2015 at 10:48 AM, Richard Pyle <deepreef(a)bishopmuseum.org> > wrote: > > Like others, I like the idea in principle, but I?m not well-versed in the > implications of alternate approaches to implementation to weigh in on that. > Whatever technical solution is adopted, I would like to hope that it > supports the representation of more than a single example; as sometimes it > is useful to show alternate forms of acceptable content. > > > > Aloha, > > Rich > > > > > > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of John Wieczorek > Sent: Thursday, February 05, 2015 7:22 AM > To: Paul J. Morris > Cc: TDWG Content Mailing List; Ramona Walls > Subject: Re: [tdwg-content] Darwin Core Proposal - term content > recommendations to comments > > > > Does anyone have similar concerns about iao:example? > > > > On Thu, Feb 5, 2015 at 2:09 PM, Paul J. Morris <mole(a)morris.net> wrote: > > On Thu, 5 Feb 2015 11:17:58 -0500 > Bob Morris <morris.bob(a)gmail.com> wrote: > > But skos:note and its subproperties (including skos:example) can take > > literals or references [1]. To me, that weighs more than the > > baggage of minting two new terms. > > Also, SKOS, unless care is taken to import the Owl-DL version, brings > you into Owl-Full, with undesirable consequences for those who wish to > do reasoning. In early versions of dwcFP, we did include SKOS terms, > but removed them because of the consequences for reasoning. > > SKOS has some nice terms, reuse is a nice idea, but it comes with > significant knowledge engineering consequences. > > -Paul > -- > Paul J. Morris > Biodiversity Informatics Manager > Harvard University Herbaria/Museum of Comparative Zo?logy > mole(a)morris.net AA3SD PGP public key available > > _______________________________________________ > 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 > > > >

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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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