June 2013 - tdwg-content - lists.tdwg.org

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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iDigBio Train-the-Trainers Georeferencing Workshop Oct 8 - 12, 2012
by Deb Paul 09 Aug '13

09 Aug '13

** Hi Everyone, The Georeferencing Working Group at iDigBio is pleased to announce our first "Train-the-Trainers" Georeferencing Workshop for Thematic Collections Networks (TCNs) and others in engaged in the digitization of biological collections in the United States. See: https://www.idigbio.org/content/idigbios-first-train-trainers-georeferencin… for details. Three slots are still available in this workshop that is designed to focus on training participants to teach others to georeference. If you are interested, please send an application describing the reason(s) for your interest in the workshop, the current and future projects that will benefit from your attendance, and any previous experience you have with georeferencing to iDigBio's Program Assistant, Cathy Bester, cbester(a)flmnh.ufl.edu What: Train-the-Trainers -- Georeferencing Workshop Where: University of Florida, Gainesville, FL Who: Interested members of current TCNs and others in the biodiversity natural history collections community. When: October 8-12, 2012 Contact: Deborah Paul dpaul(a)fsu.edu for further information. Best, Deb and the iDigBio Georeferencing Working Group Deborah Paul User Services, iDigBio Institute for Digital Information, iDigInfo Florida State University Tallahassee, Florida 32308 850-644-6366

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A radical proposal for Darwin Core
by joel sachs 03 Jul '13

03 Jul '13

Hi Everyone, Darwin Core remains poorly documented, occasionally inconsistent, and frequently misunderstood. (Does anyone disagree with that characterization?) I believe this is one of the reasons we're seeing a proliferation of overlapping and sometimes incompatible ontologies building on Darwin Core terms. One of the suggestions that came up on the TDWG-RDF mailing list is to have a clean-up-a-thon/document-a-thon for TDWG namespaces and terms. I suggest that, until such a clean up of Darwin Core occurs, TDWG accept no additions to the Darwin Core standard. There are several examples in support of my claim that we're building on a shaky foundation - an obvious one is that, as Steve is currently pointing out, there is no consensus on what constitutes a Darwin Core occurrence. (Can anyone name an instance of the class "http://rs.tdwg.org/dwc/terms/Occurrence"?) The clean-up-a-thon proposal was enthusiastically endorsed within the RDF group, but no one volunteered to organize it. I propose that we self-organize, and find a way to carve out two days at the coming meeting to hash out as much as we can, with a follow-on workshop if necessary. But first, I'd be interested to know - am I the only one who feels this way? Sincerely, Joel. p.s. I've said this before, but it bears repeating - Darwin Core is almost an excellent standard, and almost ideally suited to be the foundation for a semantic web for biodiversity informatics. I have great respect for those who were involved in its creation and continued curation - for their hard work, and clear thinking, and patience for people like me struggling to understand. But all that work, thought, and patience will be for naught, if the gyre is allowed to widen much further.

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Revised Material Sample Proposal
by John Deck 28 Jun '13

28 Jun '13

NOTE: Following discussion on the TDWG content list, discussions with OBI developers, and discussions with MIxS developers, we have modified the original Material Sample Term Proposal in the following document. The original document sent to the Darwin Core community for Material Sample proposed the OBI term Material Sample ( http://purl.obolibrary.org/obo/OBI_0000747) which we are now modifying to instead reference OBI Specimen (http://purl.obolibrary.org/obo/OBI_0100051) The reason for this change is that it came to light that the intention of OBI Material Sample “should be representative of the whole from which it is sampled”. Since this definition places an unnecessary constraint on its use we have opted to use OBI Specimen instead, which is more closely aligned with our original intent. In addition to this change, we have also modified the proposal based on the feedback from this list. -John Deck, Rob Guralnick, Ramona Walls **** New Term Request: Material Sample This is a proposal for two new terms in Darwin Core, relating to the addition of the concept, “Material Sample”, described by the identifier http://purl.obolibrary.org/obo/OBI_0100051. The two terms are: 1) A new BasisOfRecord term MaterialSample with label “Material Sample” that references http://purl.obolibrary.org/obo/OBI_0100051 2) A new Darwin Core property term, MaterialSampleID. Submitters: John Deck, Rob Guralnick and Ramona Walls Justification The current values in the DwC Type Vocabulary ( http://rs.tdwg.org/dwc/dwctype/) do well in representing some types of biocollections and observations. However, the more general notion of a sample is not well represented, because the existing terms are too specific. For example, the DwC terms “Preserved Specimen”, “Fossil Specimen”, and “Living Specimen” are appropriate for use in the museum community but assume particular properties pertaining to museum collections, which “material samples” may or may not have. Examples of “material samples” we are considering (beyond the examples above) are surveys that involve soil and water sampling, bulk sampling of specimens from, e.g., trawls, microbiological sampling, metagenomics, etc. These sampling approaches often rely on field sub-sampling processes and laboratory techniques (e.g., DNA extraction and sequencing) which transform the physical material and produce distinct information content and thus represent a type of information that is distinct from what DwC has typically dealt with. The proposal for adding “Material Sample” as a DwC class is to maintain consistency with the way Darwin Core terms are managed and organized. This term comes from the Ontology for Biomedical Investigations (OBI) class OBI:specimen. We use the class concept definition directly from OBI but provide the more familiar label “Material Sample” for use within the biodiversity community and annotate how that definition applies in the domain of biological collections. A “material sample” can pertain to general matter in which organisms may exist, in whole, in part, or in conjunction with many other organisms. The “material sample” may exist for a brief period, such as a tissue that is converted to extracted DNA. It may also represent a collection of multiple taxa, such as a soil or water sample that is used with the intention of describing the diversity of organisms, whether the actual organisms are later recovered from such a sample, or whether that sample is processed in order to generate a set of derivatives from organisms (e.g.16S sequences from a metagenomics run). A “material sample” may also yield connections to other indicators of biodiversity aside from taxa, such as a transcriptome, indicating which DNA is actively being expressed at a particular point in time. For the purposes of biological collections, we can think of “material sample” as any type of matter that we can use in order derive further evidence needed for identification of taxa, whether it is taxonomically homogenous, heterogenous, a single individual, sets of individuals, or populations. However, the definition of the term does not exclude its use in broader contexts outside the scope of biological collections. How is the term “Material Sample” different from “Individual”? The intent of individualID is fairly clear: since an Occurrence represents an organism at a place and time, the individualID term allows us to assign an instance identifier for a particular organism that can be present in at multiple events. MaterialSampleID, on the other hand, is intended to allow users to say that the basis of an occurence is a material entity (i.e. matter) that has been sampled according to some particular method. Whether or not this material entity is an individual (sensu individualID in DwC) represents an independent axis of classification. There is no restriction on specifying that an occurence is associated with more than one type, so any occurrence can have both an individualID and a materialSampleID. Adding this term will help align DwC to two other significant projects: the Ontology for Biomedical Investigations (OBI), from which we will be adapting this term, and the MIxS family of checklists. The MIxS vocabulary is proposing to adopt MaterialSampleID by clarifying the existing term source_mat_id to read: “A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/MaterialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection provide additional context and suggested syntax for this identifier for data submitted to INSDC databases.” The MIxS source_mat_id term clarification proposal is pending based on the outcome of this proposal. Connecting a DwC Record to a MIxS record would have the advantage of aligning DwC terminology (geospatial, taxonomic) with sequencing terminology (investigation, environment, nucleic acid sequence source, sequencing) and with OBI (investigation, roles, processes), using “Material Sample” as the pivot point between the standards. Definition: >From OBI ((http://purl.obolibrary.org/obo/OBI_0100051) “A material entity that has the specimen role.” A specimen role (http://purl.obolibrary.org/obo/OBI_0000112) in OBI is defined as “a role borne by a material entity that is gained during a specimen creation process and that can be realized by use of the specimen in an investigation”. The operative word is “can”. That is, the specimen is not required to be realized by use in an investigation. However, it is worth nothing that deposition into a museum or biobank can fulfill the criteria of “use in an investigation”, if necessary (for discussion, see http://sourceforge.net/p/obi/obi-terms/677/) We have chosen to use the label “Material Sample” instead of using the OBI label “Specimen” for this definition. This allows us to distinguish this term from other types containing the word “Specimen” currently in use in the Darwin Core vocabulary, which have their own meaning, distinct from the concept we are proposing. In the natural history community, biological specimens have a colloquial meaning, typically referring to a voucher held by a biorepository for research. We intend a more inclusive definition, and thus, when we refer to “DwC Material Sample” here, we are actually referring to the class of entities defined by “OBI Specimen”. In order to clarify how this definition may be considered in a biological collections context, we wish to include a http://www.w3.org/2000/01/rdf -schema#comment annotation within the DwC vocabulary which would read: “In biological collections, the material sample is typically collected, and either preserved, transformed by some process, or destructively processed” Further clarification on the use of this term, including this document, would be provided in the supplementary documentation and the Darwin Core wiki. Comment: N/A Refines: N/A Has Domain: N/A Has Range: N/A Replaces: N/A Summary: Term Name: MaterialSample Identifier: http://rs.tdwg.org/dwc/dwctype/MaterialSample<http://rs.tdwg.org/dwc/terms/MaterialSample> Namespace: http:/rs.tdwg.org/dwctype/ <http://rs.tdwg.org/dwc/terms> Label: Material Sample Definition: A resource describing the physical results of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed. Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: <http://purl.obolibrary.org/obo/OBI_0000747> http://purl.obolibrary.org/obo/OBI_0100051<http://purl.obolibrary.org/obo/OBI_0000747> Status: proposed Date Issued: 2013-03-28 Date Modified: 2013-05-25 Has Domain: Has Range: Refines: Version: MaterialSample-2013-06-24 Replaces: IsReplaceBy: Class: ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Term Name: materialSampleID Identifier: http://rs.tdwg.org/dwc/terms/MaterialSampleID<http://rs.tdwg.org/dwc/terms/MaterialSample> Namespace: http://rs.tdwg.org/dwc/terms/<http://rs.tdwg.org/dwc/terms/MaterialSample> Label: Material Sample ID Definition: An identifier for the MaterialSample (as opposed to a particular digital record of the material sample). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the materialSampleID globally unique. Comment: For discussion see http://code.google.com/p/darwincore/wiki/MaterialSample (this page will not exist until the term is ratified). Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/identifier Status: proposed Date Issued: 2013-03-28 Date Modified: 2013-05-25 Has Domain: Has Range: Version: materialSampleID-2013-05-25 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Occurrence ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

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A less radical proposal for Darwin Core
by joel sachs 27 Jun '13

27 Jun '13

This is an open letter to Steve Baskauf. <context> For those who don't know, Steve came to TDWG a few years ago for answers on how to share data about plants, and and data about images of plants. He was, at the time, supplying three aggregators with data, and had to format his data differently for each one. Each of the aggregators had, in theory, embraced the semantic web, as had TDWG. So he started, in 2009, to ask some innocuous questions on the TDWG-content list regarding how to use TDWG standards. These questions led to such a cacophony of answers that he realized that TDWG needed help, and he agreed, in 2011, to co-convene the TDWG RDF-Task group, under the sponsorship of the TDWG TAG. He shares the vision, espoused by many, that it would be better to build a "semantic layer" on top of Darwin Core, than to have to rebuild a "semantic Darwin Core" from scratch. The reason for this is that everyone has different semantic web needs, and, if forced to start from scratch, will build different semantic Darwin Cores. Then BCO and Darwin-SW and DWC-FP and Pyle/Whiton will have no way of understanding each other, while if they shared a basic underlying vocabulary [1], there would at least be a chance for data interoperability. </context> <email to Steve> Steve, I proposed a moratorium on additions to Darwin Core until some fundamental things are cleaned up. I'm only aware of two additions pending: the addition of MaterialSample and MaterialSampleID to the "dwctype:" namespace; and the Darwin Core RDF guide, still receiving feedback from the task group. I do think that the MaterialSample proposal would be better framed atop a clearer semantics of existing terms and usage patterns, but who knows. I trust the proposers of the new terms to make good choices. My current proposal (below) follows Guralnick's advice to narrow scope. It is partly motivated by the fact that you made a perfectly reasonable plea for clarification regarding the meaning of "occurrence", and no one is responding. (Yes, you only made the plea three days ago, but you've made many versions of it in the past.) In my opinion, it is unreasonable to expect the RDF Task Group to produce a guide for expressing Darwin Core in RDF unless some effort is made to clarify the semantics of a few Darwin Core terms. So my current, less radical, proposal is this: <proposal> That the RDF Task Group not release the draft guide for public comment until we (i.e. TDWG) improve the documentation around dwc:Occurrence and dwctype:Occurrence. By "improve", I mean: i. Configure the rs.tdwg.org server to set an xml mime type for http://rs.tdwg.org/dwc/rdf/human-dwctype.xsl and http://rs.tdwg.org/dwc/rdf/human.xsl . (Currently the mime type is set to "text/plain", which results in users being unable to view either the raw RDF or the human-readable RDF in a standard browser.) ii. In a single document, served by tdwg.org, list the valid usages/interpretations of dwc:Occurrence and dwctype:Occurrence. (I believe there are six.) Currently, to be aware of the various semantics of "Occurrence", a person needs to read half a dozen or so different documents. That's not necessarily bad, but there should at least be a "Guide to Standard 450", that links to and briefly explains the contents and purposes of each document. </proposal> Is that too much to ask of ourselves? Now, you might say, "Fine, we should do that, but I'm not delaying release of the guide, which has already taken way too long to produce." And if you say that, I'll support you. But if we go ahead and release the guide without fixing some basic underlying things, I don't think it will have the impact that it should, for several reasons. Here's one of them: <Example of how we're limiting ourselves> The draft guide is excellent. For many examples of what people want to do, the guide essentially creates a matrix with the dimensions "technical approaches" and "conceptual approaches", and proceeds to fill in every cell of this matrix with a valid usage pattern. It is meticulous. Yet there is a significant omission. There is no example of representing a Darwin Core occurrence in RDF! In the guide's defence, there is no way to do this without making significant assumptions about just what a Darwin Core occurrence is. </Example of how we're limiting ourselves> Anyway, those are my thoughts, and some of my arguments. I will defer to your judgement on the best way to proceed. Best, Joel. </email to Steve> 1. Notice I said "vocabulary" and not "ontology". The less ontology there is in the shared Core, the easier it will be for people to build on it to suit their needs. But a lack of ontology does not imply a lack of semantics. For proof, look at a dictionary - it has the complete semantics of the language. Similarly, Darwin Core - a "bag of terms", i.e. a glossary - is a perfect candidate to be a shared base layer for the semantic web … once it clarifies a few basic things.

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New Darwin Core terms proposed relating to material samples
by John Wieczorek 24 Jun '13

24 Jun '13

Dear all, TDWG could see a lot of activity in 2013 in anticipation of the meeting in Florence in October. Much of the activity is related to enabling integration across multiple parts of our domain. We have the Audubon Core under review for biodiversity-related media and an impending RDF Guide to supplement the already extant Text and XML Guides for Darwin Core. This message is to bring your attention to another integrative initiative, to introduce terms into Darwin Core that will form a nexus between Occurrences and the interesting things that happen with physical materials that result from them, such as, but not limited to, genetic sequencing. A series of meetings for a little over the past year have inspired our colleagues in the Genomics Standards Consortium (GSC) to propose to their constituency to align their terms with Darwin Core, including adopting some of the Darwin Core terms in place of their own that have the same meaning. Out of these discussions has come the realization that neither community has terms to accommodate the concept of an identifiable (objectively, not taxonomically), trackable material sample. This message constitutes such a proposal. This proposal would have no impact on those publishing purely taxonomic data. It would also have no impact on those publishing occurrence data unless they want to increase their capacity to distinguish material samples from organisms more rigorously than is now possible using only the dwc:preparations term. The initial request for new terms can be found in the Darwin Core Issue tracker as http://code.google.com/p/darwincore/issues/detail?id=167. Below I have elaborated nad formalized the request into the three distinct terms under consideration, initiating the 30 day minimum public review process to seek consensus on their inclusion in the Darwin Core standard. Your job, should you choose to accept it, is to discuss the merits or any perceived problems in the inclusion of these three terms in Darwin Core. Below I will give the proposed properties of three terms as they would appear in the Darwin Core Quick Reference Guide, though these properties would be included in the RDF of the normative form of the documentation. A new MaterialSample class: This is for the purpose of organizing properties, just as the existing classes (Occurrence, Event, Location, GeologicalContext, Identification, Taxon, etc.) do, without having any terms declare this class as their domain. Term Name: MaterialSample Identifier: http://rs.tdwg.org/dwc/terms/MaterialSample Namespace: http:/rs.tdwg.org/dwc/terms Label: Material Sample Definition: The category of information pertaining to the physical results of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed, with the intention of being representative of a greater whole. Comment: For discussion see http://code.google.com/p/darwincore/wiki/MaterialSample (this page will not exist until the term is ratified). Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: proposed Date Issued: 2013-03-28 Date Modified: 2013-04-08 Has Domain: Has Range: Version: MaterialSample-2013-03-28 Replaces: IsReplaceBy: Class: ABCD 2.0.6: not in ABCD (someone please confirm or deny this) A Darwin Core Type Vocabulary value for basisOfRecord is needed to represent this new class of information. Luckily, a term already exists in the Ontology for Biomedical Investigations ( http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org…) We and the GSC both propose to reuse this class within Darwin Core as below, making it the cross-ver point between the two domains. Term Name: MaterialSample Identifier: http://rs.tdwg.org/dwc/terms/MaterialSample Namespace: http://purl.obolibrary.org/obo/OBI_0000747 Label: material sample Definition: A material entity that has the material sample role Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines:http://purl.obolibrary.org/obo/OBI_0100051 Status: recommended Date Issued: 2013-03-28 Date Modified: 2013-03-28 Has Domain: Has Range: Version: MaterialSample-2013-03-28 Replaces: IsReplaceBy: Class: ABCD 2.0.6: not in ABCD In keeping with all other classes in Darwin Core, the Material Sample class would have a corresponding identifier property. The Genomics Standards Consortium (GSC) is in the process of proposing this term. If it is accepted, we propose to use it, and its properties would be as below, otherwise, the properties would be the same, but have the Darwin Core namespace and identifier URI. Term Name: materialSampleID Identifier: http://gensc.org/ns/mixs/materialSampleID Namespace: http://gensc.org/ns/mixs Label: Material Sample ID Definition: An identifier for the MaterialSample (as opposed to a particular digital record of the material sample). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the materialSampleID globally unique. Comment: For discussion see http://code.google.com/p/darwincore/wiki/MaterialSample (this page will not exist until the term is ratified). Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/identifier Status: proposed Date Issued: 2013-03-28 Date Modified: 2013-04-08 Has Domain: Has Range: Version: materialSampleID-2013-03-28 Replaces: IsReplaceBy: Class: http://purl.obolibrary.org/obo/OBI_0000747 ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

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Consensus on what constitutes an Occurrence? (was Re: New Darwin Core terms proposed relating to material samples)
by Steve Baskauf 24 Jun '13

24 Jun '13

I have quoted below part of an email which has been sitting in my inbox for a month. It been stuck there because there was a statement in it that (in my mind) needed clarification. In John Deck's email, he says "...since an Occurrence represents an organism at a place and time...". What I am wondering is whether there is actually a consensus that an Organism represents an organism at a place and time. Caveat: I use "individual organism" here in a general way that probably includes more than individual organisms. But that is a different issue, so let's not rehash that in this thread. The history of the discussion of the meaning of Occurrence is extensive. You can find my attempt to summarize it at: http://code.google.com/p/darwin-sw/wiki/ClassOccurrence so I won't repeat that here. In a nutshell, it seems to me that people have used dwc:Occurrence in three general ways: - to indicate that we know from aggregate records that a taxon occurs or ever occurred, in a particular geographic area (the "checklist" meaning of Occurrence) - as a broad term that includes both preserved specimens and observations (the "superclass" meaning of Occurrence) - as a join between Events and individual organisms [database description]/as a node connecting Event instances to instances of individual organisms [RDF description]/as a tuple of (individual organism,Event) with properties to connect it to the individual organism and Event [computer science description] (the "node" meaning of Occurrence). It has been noted that the "checklist" meaning of Occurrence is related to Occurrence as a primary unit of data gathering ("superclass" and "node" meanings; see history reference for details) but the "checklist" meaning is probably the least likely to be considered a consensus view, so I'm going to ignore it for the moment. The "node" meaning of occurrence corresponds to what is described by John Deck (quoting Markus Döring) in his email below. It is also the view taken by Darwin-SW and is reflected in Rich Pyle's emails (related since Darwin-SW was influenced by Rich Pyle's emails!). However, although it isn't explicitly stated as such, the Darwin Core standard as it currently stands really reflects the "superclass" meaning. I was involved in a conversation with John Wieczorek a few months ago which was on the topic of "fixing" dwc:Occurrence (i.e. getting rid of the ambiguity surrounding it). In that conversation, I confirmed with John W. that as things stand currently, Darwin Core effectively considers dwc:Occurrence to be a superclass of PreservedSpecimen and Observation. So to me it does not seem that there actually is a consensus about what dwc:Occurrence means. Is an Occurrence the *thing* that documents the presence of an organism at a place and time ("superclass" meaning), or is the Occurrence an *abstract resource* connecting organisms to place/time with the thing itself as documentation for the abstract resource ("node" meaning)? In order to "fix" Occurrence by clarifying its meaning, it seems to me that there are two courses of action: 1. Declare clearly that Occurrence is a superclass of PreservedSpecimen and Observation and create a new term for the more abstract "organism at a place and time". 2. Declare clearly that Occurrence is an organism at a place and time and that it is NOT a superclass of PreservedSpecimen and Observation. The second course of action would be the easiest from the standpoint of making a change to the standard. However, it might be the worst from an implementation standpoint because of the thousands (millions?) of specimen records that are typed as Occurrence. If we can clarify these two uses of Occurrence, then the terms currently listed in DwC under the dwc:Occurrence class could be separated among the two "kinds" of Occurrence. Terms related to the recording of the presence of an organism at a time and place (dwc:recordedBy, dwc:behavior, etc.) would be separated from terms related to the specimens themselves (dwc:preparations, dwc:disposition, etc.). This may not seem like a big deal for flat specimen records, but it would be very helpful from the standpoint of advancing the use of DwC in RDF to clarify the types of resources that these terms can serve as properties of. I would be interested in hearing some discussion about concrete steps that could be taken to "fix" Occurrence. The "best" solution would probably be to create a robust consensus ontology that includes Occurrence. However, that is not likely to happen on the timescale of a year or less. Given that this issue has dragged on for at least two years already, in the interest of moving forward it would be good to take some kind of decisive action in the near term. Steve -------- Original Message -------- Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Date: Wed, 29 May 2013 16:00:35 +0200 From: John Deck <jdeck(a)berkeley.edu> To: Richard Pyle <deepreef(a)bishopmuseum.org> CC: Markus Döring <m.doering(a)mac.com>, Steve Baskauf <steve.baskauf(a)vanderbilt.edu>, TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org>, Robert Whitton <whittonr(a)gmail.com>, "Ramona Walls" <rlwalls2008(a)gmail.com> References: Since the original proposal was from a group of folks, we decided to put our heads together to construct a general response to the various issues and ideas expressed on this thread. John Deck for Rob Guralnick, Ramona Walls, and John Wieczorek ... How is MaterialSample different from Individual? The intent of individualID is fairly clear: since an Occurrence represents an organism at a place and time (per Markus’ email), the individualID term allows us to assign an instance identifier for a particular organism that can be present in multiple events. MaterialSampleID, on the other hand, is intended to allow users to say that the basis of an occurence is a material entity (i.e. matter) that has been sampled according to some particular method. Whether or not ... -- 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

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Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
by Richard Pyle 01 Jun '13

01 Jun '13

Hi Ramona, I apologize for the long emails, but this stuff is complex and unfortunately requires lots of words (to avoid - or at least minimize - misunderstanding). I will try to keep my responses to your points short. > Using the word "individual" to describe collections of organisms - > whether they are taxonomically homogenous or heterogeneous - makes no sense. > Yes, I know it is just a label, but seriously, just make a better label. Yes, I agree. But it's what we already have in DWC (http://rs.tdwg.org/dwc/terms/index.htm#individualID) I have no problem using a different term, but before we choose terms, we should first define what the concepts are. > A single organism and a collection of organisms are fundamentally different things. Actually, not really different things. Many natural history collections maintain their specimens as "lots", which may have a single individual specimen, or multiple specimens. Regardless of whether it's a single specimen or multiple specimens, the basic properties are the same (same collecting event, sme taxonomic identification, and many other identical properties). This becomes especially true for colonial organisms (like corals, where the "individual" could be interpreted as a single polyp). It's also true for other use cases we deal with that are outside the DWC/TDWG scope. > If you need a class that can cover both of them under certain circumstances, > you need to use a logical definition to define the circumstances (just like the > class material sample does by using the criterion of having a material sample role). > In order to do this, you also need to have separate classes for individual organism > and collection of organisms. We have tried to do this by distinguishing instances as "Lot" or "Whole Organism" -- which could be thought of as distinct subclasses (though again, they generally share the same properties). The same is true for tissue samples, and other "parts". > I agree whole-heartedly with the need to clearly track stakeholders needs > for different classes of things, using a logical system to decide how these > things relate to one another, examining alternative systems for creating > the classes of things, and testing them against use cases (Steve's points 1-4). > This is precisely what we are trying to do with the bio-collections ontology > (BCO). The suggestion to use the term material sample came out of just > such a process. It is important to remember that the stakeholders include > more than just the community using DwC. It seems we are all in full agreement on these points. In my case, I am especially in agreement with the last point, as much of our thinking has been independent of the TDWG/DWC thinking, but still keeping that set of use-cases in mind. Aloha, Rich

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