December 2014 - 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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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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Re: [tdwg-content] 'quantity'
by Simon.Cox＠csiro.au 16 Dec '14

16 Dec '14

My intention in raising this concern is not to suggest that you don't need the concept of measurable-property-type-whose-value-is-an-item-from-an-enumerated(-possibly-ordered)-set, but rather just to caution that people from other domains might be surprised to see such a thing referred to as a 'quantity'. My concern is the loss of interoperability. If the latter is a goal, then you might consider tweaking the terminology. Of course if there is a unique mapping from values in the enumerated(-and-ordered)-set to scaled numbers, then 'quantity' is fine. But if the set of 'quantityTypes' that have enumerated values is distinct from the set that have scaled numeric values, then why not recognise this in the name? Simon ------------------------------ Message: 4 Date: Tue, 16 Dec 2014 09:02:19 +0100 From: ?amonn ? Tuama [GBIF] <eotuama(a)gbif.org> Subject: Re: [tdwg-content] Fwd: [dwc] quantity (#12) To: 'Markus D?ring' <m.doering(a)mac.com>, "'Paul J. Morris'" <mole(a)morris.net> Cc: 'TDWG Content Mailing List' <tdwg-content(a)lists.tdwg.org> Message-ID: <000101d01906$9d8f3250$d8ad96f0$@org> Content-Type: text/plain; charset="utf-8" Simon's distinction of scaled number vs discrete set could probably be captured using DWC MeasurementOrFact properties. However, as discussed previously, we felt that because measurements of abundance/density/coverage were of fundamental importance in field studies, and in the spirit of DwC's pragmatic approach, they merited their own high level term(s), rather than "burying" them under MeasurementOrFact - hence the proposal of "quantity" and "quantityType" where the term "quantity" seems the most inclusive label for what we are trying to express. Following John's recommendation, we have removed the references to examples in the definitions and expanded the examples in the comment section so it is clear how they are to be used. quantity #Definition A number or enumeration value for the entity being quantified in quantityType. #Comment The terms quantity and quantityType are required to be used as a pair. The value of quantity is a number or enumeration, e.g., ?27? for a quantityType ?individuals?, ?12.5? for a quantityType ?%biomass?, or ?r? for a quantityType ?BraunBlanquetScale?. quantityType #Definition The entity to which the number or enumeration reported in quantity refers. #Comment The terms quantity and quantityType are required to be used as a pair. The value of quantityType (i.e., the entity being measured) is expected to be drawn from a small controlled vocabulary with terms such as ?Individuals?, ?%Biomass?, ?%Biovolume?, ?%Species?, ?%Coverage?, ?BraunBlanquetScale?, ?DominScale?. Examples when combined with quantity values: + on DominScale; 5 on BraunBlanquetScale; 45 for %Biomass. ?amonn -----Original Message----- From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Markus D?ring Sent: 15 December 2014 15:48 To: Paul J. Morris Cc: TDWG Content Mailing List Subject: Re: [tdwg-content] Fwd: [dwc] quantity (#12) "r" is a value for very few individuals in the Braun Blanquet cover abundance scale which is used a lot in vegetation studies. It is like various others a non continous scale with discrete values. I do not think we should restrict quantity to contious numeric scales. Markus > Am 15.12.2014 um 15:36 schrieb Paul J. Morris <mole(a)morris.net>: > > Markus can probably answer this question: > > What would be the expected value of QuantityType for a Quantity of "r"? > > A comment Bob Morris occasionally makes is: "1 is greater than 2 for > sufficently large values of 1". If some particular quantity type has > a standard set of codes that represent numbers, then it might be > appropriate to use those standard codes as values of quantity. > > -Paul > > On Mon, 15 Dec 2014 12:48:06 +0100 > John Wieczorek <tuco(a)berkeley.edu> wrote: > >> 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>. > > > -- > 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 ------------------------------ _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content End of tdwg-content Digest, Vol 67, Issue 8 *******************************************

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RFC 2119: Re: Public comment on the Darwin Core RDF Guide
by Paul J. Morris 14 Dec '14

14 Dec '14

Bob Morris noted that it may be appropriate for the DarwinCore RDF Guide to follow RFC 2119 (something for which at least the TDWG GUID applicability statement provides precedent). The key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be interpreted as described in RFC 2119. Internet Engineering Task Force (IETF). RFC 2119. Key words for use in RFCs to Indicate Requirement Levels. http://www.ietf.org/rfc/rfc2119.txt This RFC notes: "These words are often capitalized" and "Imperatives of the type defined in this memo must be used with care and sparingly. In particular, they MUST only be used where it is actually required for interoperation or to limit behavior which has potential for causing harm". There are 69 occurrences of "should" in the guide, many of these instances appear to have the intent of colloqual english and probably other words should be substituted in those cases. I've taken a stab here at a set of cases where it feels like it might be appropriate to use the RFC 2119 imperatives. A question is whether it is the role of the guide to use MUST/MUST NOT/REQURED anywhere (except where that is forced by inheritance from elsewhere)? A potential place for asserting MUST/MUST NOT is the distinction between dwc and dwciri namespaces. I've put more discussion under the headings 2.4.1.2 and 2.5 below. -Paul ---- 1.3.2.1 Persistent Identifiers s/the provider should take care to ensure/the provider SHOULD take care to ensure/ s/it must be converted to an IRI/it MUST be converted to an IRI/ ---- 1.3.2.2 HTTP IRIs as self-resolving GUIDs s/through RDF should plan to implement GUIDs/through RDF MUST plan to implement GUIDs/ For consistency with "Must" in the GUID applicability statement. ---- 1.4.1 Well-known vocabularies s/the provider should assign the term an IRI,/the provider SHOULD assign the term an IRI,/ ---- 1.4.3 Use of Darwin Core terms in RDF s/each value should be referenced/each value MUST be referenced/ By the nature of object references. ---- 1.4.4 Limitations of this guide s/Darwin Core property terms should be used as RDF predicates and specifies that Darwin Core class terms should be used in rdf:type/Darwin Core property terms SHOULD be used as RDF predicates and specifies that Darwin Core class terms SHOULD be used in rdf:type/ ---- 1.5.5 Implications for expressing Darwin Core string values as RDF s/in which RDF should be structured/in which RDF SHOULD be structured/ ---- Example 1: s/Predicates must be identified by IRIs/Predicates MUST be identified by IRIs/ ---- 2.2 Subject resources s/it must be referenced by an IRI/it MUST be referenced by an IRI/ ---- 2.2.2 Associating a string identifier with a subject resource s/dcterms:identifier should be used to/dcterms:identifier SHOULD be used to/ s/it is acceptable to present it as a string literal value for dcterms:identifier/it MAY be presented as a string literal value for dcterms:identifier/ ---- 2.3.1.1 rdf:type statement s/The class should be identified by an IRI reference/The class MUST be identified by an IRI reference/ ---- 2.3.1.3 Explicit vs. inferred type declarations s/data providers should exercise caution in using any such term in a non-standard way/data providers SHOULD NOT use any such term in a non-standard way/ s/the provider should type the resource/the provider MAY type the resource/ ?? Or ?? s/the provider should type the resource/the provider SHOULD type the resource/ ---- 2.3.1.4 Other predicates used to indicate type s/in an RDF description should be considered optional, while including rdf:type should be considered highly recommended/in an RDF description is OPTIONAL, while rdf:type SHOULD be included/ s/A dwciri: analogue (Section 2.5) of dwc:basisOfRecord should not be used/A dwciri: analogue (Section 2.5) of dwc:basisOfRecord MUST NOT be used/ ---- 2.3.1.5 Classes to be used for type declarations of resources described using Darwin Core s/that should also be used/that SHOULD also be used/ ---- Example 9: s/a provider should include an xml:lang/a provider SHOULD include an xml:lang/ ---- Example 10: I'm not sure about this one: /language tags should be interpreted by clients s/may initially choose to expose literals without datatype attributes, they should/MAY initially choose to expose literals without datatype attributes, they SHOULD/ ---- 2.4.1.2 Terms intended for use with literal objects I'll put a stake in the ground for discussion here: Is the guide sufficiently normative to assert MUST (other than where that property is inherited from elsewhere)? If so, then the distinction between dwc and dwciri is the place to make that assertion: s/that terms in the dwc: namespace should be restricted to use with literal objects/that terms in the dwc: namespace MUST be restricted to use with literal objects/ ---- 2.4.2.1.1 Objects identified by LSIDs This one needs to be checked for consistency with the LSID Applicability Statements: s/version of the LSID should be used instead/version of the LSID SHOULD be used instead/ ---- Example 17: s/particular terms should be used with literal objects, or with IRI reference objects/particular terms SHOULD be used with literal objects, or SHOULD be used with IRI reference objects/ ---- 2.4.3.2 Literal values for non-literal resources in Darwin Core s/existing Darwin Core term in the dwc: namespace should have the same structure/existing Darwin Core term in the dwc: namespace SHOULD have the same structure/ ---- 2.5 Terms in the dwciri: namespace This is the companion case to 2.4.1.2 - is the distinction between dwciri and dwc to be asserted as SHOULD or MUST - using them incorrectly does have the "potential for causing harm" in the language of RFC 2119, but does the guide rise to the level of specifying an "absolute requirement of the specification". s/IRI reference objects and should NOT be used with literal/ IRI reference objects and MUST NOT be used with literal/ ---- 2.5.1 Definition of dwciri: terms s/resource described by a dwciri: property should be the subject of a triple for each value on the list/resource described by a dwciri: property SHOULD be the subject of a triple for each value on the list/ A counter example here comes from the Harvard List of Botanists, where http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/305dcac3-a748-4f47-8a18-… references the collector team "J. D. Hooker & A. Gray", that is, http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/cc3b7080-5fbb-4ea5-9655-… and http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/3f8c70aa-1862-4784-8a53-… ---- 2.5.3 Expectation of clients encountering RDF containing dwc: and dwciri: terms Instances of "should" here again cut to the heart of how strong the guidance is concerning dwc and dwciri. ---- Table 3 s/they should be used rather than using the Darwin Core ID/they SHOULD be used rather than using the Darwin Core ID/ ---- Example 22: s/The following points about the Example 22 should be noted:/Note the following points about Example 22:/ s/related non-literal resources should use/related non-literal resources SHOULD use/ /LSIDs are the objects of triples, they should be As with 2.4.2.1.1, this guidance needs to be checked against the GUID and LSID applicability statements. I think I'm reading the GUID applicability statement as s/should/MUST/ here. ---- 2.7.1 What purpose do convenience terms serve? s/In general, it should not be necessary for a data provider/In general, a data provider does not need/ ---- 2.7.3 Ownership of a collection item s/of the collection item should be indicated/of the collection item SHOULD be indicated/ ---- 2.7.4 Description of a taxonomic entity s/It is considered to be out of the scope of this document to specify how taxon concepts should be rendered as RDF/It is out of the scope of this document to specify how to render taxon concepts as RDF/ s/terms for taxonomic entities should be properties of dwc:Identification/terms for taxonomic entities MAY be properties of dwc:Identification/ s/The task of describing taxonomic entities using RDF must be an effort outside of Darwin Core/The task of describing taxonomic entities using RDF is out of scope of this document/ ---- 2.8.3 Expressing Darwin Core association terms as RDF with URI references s/it should be used to declare the type/rdf:type SHOULD be used to declare the type/ ---- Tables 3.4 to 3.7. s/should/SHOULD/ -------- -- Paul J. Morris Biodiversity Informatics Manager Harvard University Herbaria/Museum of Comparative Zoölogy mole(a)morris.net AA3SD PGP public key available

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errata in RDF guide
by Steve Baskauf 13 Dec '14

13 Dec '14

I was examining the definition of dwc:organismScope (http://rs.tdwg.org/dwc/terms/organismScope ) and noticed that its comment specifically says "To describe the kind of Organism using a URI object in RDF, use rdf:type ... instead." The Darwin Core RDF Guide includes dwc:organismScope in the category of terms having analogues in the dwciri: namespace (i.e. having an IRI-reference object). I believe that it should be removed from that list and placed in Table 3.8 [1] with an explanation that rdf:type should be used instead in accordance with the term comment. Steve Baskauf [1] https://code.google.com/p/tdwg-rdf/wiki/DwcRdfGuideProposalRevised#3.8_Darw… -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu http://vanderbilt.edu/trees

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terms for sample data in DwC
by Éamonn Ó Tuama [GBIF] 12 Dec '14

12 Dec '14

In compliance with the directions for requesting changes to the Darwin Core (DwC) vocabulary, we hereby submit to the TDWG Content list a proposal for five new terms to express information on sample-based data. Sample-based data is a type of data available from thousands of environmental, ecological, and natural resource investigations. These can be one-off studies or monitoring programmes. Such data are usually quantitative, calibrated, and follow certain protocols so that changes and trends of populations can be detected. This is in contrast to opportunistic observation and collection data which today form a significant proportion of openly accessible biodiversity data. Sample-based data are often not shared because the underlying protocols have been hard to encode in a standardised way. For further background information and examples, please consult the sample data primer document [1]. We cannot emphasise enough that our intention here is not to establish how data should be captured or modelled but rather demonstrate one way data can be exposed to maximize discoverability and reuse. In particular, GBIF, in association with EU BON [2] project partners, is exploring how the IPT and Darwin Core Archives can enable the flow of sample based data in support of GEO BON Essential Biodiversity Variables (EBVs) [3]. While DwC already provides many terms that are relevant for describing sample-based data, based on several inputs (GBIF organised workshop on sample data, May 2013 ; previous discussions on the TDWG mailing list; discussions on the EU BON mailing list), we have identified a need for five new terms. These are: sampleSize <https://github.com/tdwg/dwc/issues/10> https://github.com/tdwg/dwc/issues/10 #Justification Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e., sampling events). For an introduction to the sampling proposal please see <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer. #Definition A numeric value for the time duration, length, area or volume involved in the sampling event. #Comment The terms sampleSize and sampleSizeUnit are required to be used as a pair. The value of sampleSize is a number. Example: 5 for the value part of 5m. #Term group Event sampleSizeUnit <https://github.com/tdwg/dwc/issues/11> https://github.com/tdwg/dwc/issues/11 #Justification Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e., sampling events). For an introduction to the sampling proposal please see <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer. #Definition The unit of measurement used in the sampling event. #Comment The terms sampleSize and sampleSizeUnit are required to be used as a pair, e.g., 5 metre. Example values of sampleSizeUnit include 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/> 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). Example: metre for the unit part of 5m. #Term group Event quantity <https://github.com/tdwg/dwc/issues/12> https://github.com/tdwg/dwc/issues/12 #Justification Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e. sampling events). For an introduction to the sampling proposal please see <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer. #Definition The quantity, per sampling event, given as a number or enumeration value for the quantityType. #Comment The terms quantity and quantityType are required to be used as a pair. The value of quantity is a number or enumeration. Examples: 12.5, r #Term group Occurrence quantityType <https://github.com/tdwg/dwc/issues/13> https://github.com/tdwg/dwc/issues/13 #Justification Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e., sampling events). For an introduction to the sampling proposal please see <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer. #Definition The entity to which the number or enumeration reported in quantity refers. #Comment The terms quantity and quantityType are required to be used as a pair, e.g., 14 individuals. The value of quantityType (i.e., the entity being measured) is expected to be drawn from a small controlled vocabulary. Examples: Individuals, % Biomass, % Biovolume, % species, % coverage, BraunBlanquetScale, DominScale. #Term group Occurrence parentEventID <https://github.com/tdwg/dwc/issues/9> https://github.com/tdwg/dwc/issues/9 #Justification Allows arbitrary linking of sub sampling events, e.g., for nested sampling plots. This was demanded by several people during the discussion of the TDWG sample based data session. For an introduction to the sampling proposal please see <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer. #Definition An event identifier for the super event which is composed of one or more sub-sampling events. #Comment The value must refer to an existing eventID. If the identifier is local it must exist within the given dataset. Example: A1 identifying the main Whittaker Plot in nested samples, each with their own eventID (e.g., A1:1, A1:2). #Term group Event None of the existing DwC terms is sufficient for any of the proposed terms although two are somewhat related: sampleEffort ("The amount of effort expended during an Event") and individualCount ("The number of individuals represented present at the time of the Occurrence"). Neither are adequate sampleEffort just provides a free text statement so is hard to parse in comparison to sampleSize and sampleSizeUnit and individualCount refers exclusively to individuals and not percentages or entities like biomass, biovolume, etc. [1] <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer [2] <http://eubon.eu/> http://eubon.eu [3] <http://www.earthobservations.org/documents/cop/bi_geobon/ebvs/201301_ebv_pa per_pereira_et_al.pdf> http://www.earthobservations.org/documents/cop/bi_geobon/ebvs/201301_ebv_pap er_pereira_et_al.pdf ____________________________________________________ Éamonn Ó Tuama, Markus Döring, GBIF Secretariat

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Fwd: NIH Frameworks for Community-based Standards Efforts Workshop Report Released!
by Ramona Walls 11 Dec '14

11 Dec '14

FYI ------------------------------------------------------ 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 -------- Forwarded Message -------- Subject: Frameworks for Community-based Standards Efforts Workshop Report Released! Date: Thu, 4 Dec 2014 20:54:23 +0000 From: Russell, Beth (NIH/OD) [E] <beth.russell(a)NIH.GOV> <beth.russell(a)NIH.GOV> Reply-To: Russell, Beth (NIH/OD) [E] <beth.russell(a)NIH.GOV> <beth.russell(a)NIH.GOV> To: BD2KUPDATES(a)LIST.NIH.GOV Greetings Everyone, We would like to invite all of you to review a report generated as a result of the NIH BD2K workshop "Frameworks for Community-based Standards Efforts", held last year. The workshop aimed at gaining a clearer understanding of the community-based data and metadata standards efforts, in particular, and how NIH might best relate to them. In this report the authors, who are the lead organizers and co-chairs, elaborate on the findings and indicate future directions. In conjunction with related efforts already under way at NIH, including the development of a Data Discovery Index Consortium (bioCADDIE: http://biocaddie.org) the final document will assist the NIH Office of the Associate Director (ADDS) to help move forward the NIH BD2K vision on how data, metadata and other digital research products can interact and work with each other. We invite all users, software developers and publishers to review our report. Please, post *comments by January 20, 2015*. The link to the report is: *http://www.communitybasedstandards.org <http://www.communitybasedstandards.org> * On behalf of the organizing committee and the participants, thank you for your assistance! * Michael F. Huerta* (NIH National Library of Medicine) * Leslie K. Derr* (NIH Office of Strategic Coordination Division of Program Coordination, Planning, and Strategic Initiatives) * Susanna-Assunta Sansone* (University of Oxford, Oxford e-Research Centre) * David N. Kennedy* (Department of Psychiatry, University of Massachusetts Medical Center) ------------------------------ To unsubscribe from the BD2KUPDATES list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=BD2KUPDATES&A=1

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