May 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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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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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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Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
by Richard Pyle 31 May '13

31 May '13

Thanks Ramona; Actually, the basic elements of our data mode precede DwC by quite a bit. What weve tried to do, however, is mold the data model to be more compatible with DwC, to make the task of mapping for data export & exchange that much easier. Of course, DwC is not (and is not intend to be) a data model in any sense of the word; however, its impossible to avoid representing core elements of a bona-fide data model within DwC. This is especially true when it comes to each of the ID terms (and doubly-especially true when the ID terms correlate to class terms). The existence of an ID term implies that some class of object exists to which an ID value is applied. The ID value itself is never useful data/metadata it is just a way to reference a data record that (presumably) contains properties that can be expressed as data/metadata for the object represented by the ID value. This was all well-understood when the original DwC was being drafted; but as it evolved into its current iteration (with the addition of all the ID terms), it has been drawn ever more (in some ways subtly, and in some ways not-so-subtly) in the direction of a data model. Of course, what we all (desperately!) need is a robust ontology that fits our world. The task is not easy in part because our data domain is not so easily modeled, in part because different sections of our broader community have different priorities, and in part because there is always a delicate balance between developing a model or ontology that is practical and useful for the data providers and consumers, with one that is robust and detailed and flexible, to allow asking questions of the data that were never even considered at the time the model/ontology were conceived. The parallel experience in database modeling is normalization (as Paul Kirk likes to say: Normalize until it hurts; then de-normalize until it works). The original DwC was completely flat. The current DwC moved into the direction of more complex structures by clustering terms into classes and sprinkling with ID terms. It even tip-toed into RDF-space with dwc:ResourceRelationship. I think thats definitely an improvement, but it still must strike a delicate balance between the needs by some to represent a robust data model, and the needs by others to have a simple/practical mechanism to exchange biodiversity data in a standard form. It will never be all things to all people; but at least it is enough things to enough people that it represents an important flag pole around which our community has (more or less) successfully rallied. Hmmmm. Now Ive forgotten what my point was. I guess I was just in a ramblin mood. Well.sorry about the bandwidth! Aloha, Rich From: Ramona Walls [mailto:rlwalls2008@gmail.com] Sent: Thursday, May 30, 2013 6:05 PM To: Richard Pyle Cc: Jason Holmberg; TDWG Content Mailing List; John Deck; Robert Whitton Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Jason, Thanks for sharing how you have been using the Darwin Core terms. I am intrigued by the data structure you have developed. It is quite interesting how both you and Rich have adapted the DwC to fit your specific needs. While I am often troubled by the vagueness of DwC, I guess in some ways it is that vagueness allows it to be used in many different applications. Of course, I don't think vagueness is necessary for wide application, or a good thing for data exchange, but it does seem to be working for a lot of different purposes. Ramona On Thu, May 30, 2013 at 3:07 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Hi Jason, Many thanks for this input. If I understand you correctly, then you are using Encounter as equivalent to what we have been using Occurrence for. That is, by our definition, an Occurrence is the instance representing an intersection between an Event (i.e., where, when, who, etc.) and what we have been calling an Individual (i.e., what); and the properties we attach to the Occurrence are the how bits (including things like size, etc.). In my mind, the essence of an Individual is the collective physical material of the individual. If I see a fish on a reef, its Occurrence on that reef and at that time exists (and is worth documenting) regardless of whether I took an image of it (what we would call Evidence), or whether I took a tissue sample from it, or whether I collected and killed the whole damn thing. To me, the essence of the individual or its occurrence at an event is unaffected by what I end up doing to it. By extension, following a hierarchical model of individual, a sub-sample (materialSample) extracted from it is just another instance of Individual. This is why I generally think of materialSample (if it were represented as a class which it is currently not propsed for DWC) as a subclass of a broader concept (e.g., material, but what I have naively been referring to as Individual). That part of our model has proven to be very stable and effective for representing the information as we want it. Where it gets complicated is instances of taxonomically heterogeneous objects treated as a single individual which (in my mind) includes such things as soil samples. In that contect, I see (and agree) with John and others that really its a separate axis of classification from what I have called Individual. I dont expect that to make a lot of sense (I barely understand it myself). Aloha, Rich From: Jason Holmberg [mailto:holmbergius@gmail.com] Sent: Thursday, May 30, 2013 11:28 AM To: Richard Pyle Cc: Ramona Walls; TDWG Content Mailing List; John Deck; Robert Whitton Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Hi everyone. List lurker here. DWC has been a great inspiration in my work, so I hope I can contribute some small amount of insight on the "individual" and "material sample" threads. I have no grand thoughts on the subject, but I can tell you how the DWC has inspired my own information architecture for open source mark-recapture software: http://www.ecoceanusa.org/shepherd/doku.php?id=manual:2.0.x:1_overview I felt the very clear need for a distinct Individual Class and to separate that from the concept of a sample taken from nature. When reviewing DWC, I interpreted Occurrence.individualCount to be somewhat contradictory to Occurrence.individualID, so I created a one-individual-at-a-point-in-time class called Encounter that reuses quite a bit of DWC.Occurrence. Occurrence I then broadened to include the potential for multiple marked individuals. I neither present this as "right" nor "good" (though they have worked very well for us). I just present it as a practical example from mark-recapture in which we have tried to adhere to DWC in order to expose data to GBIF, iOBIS, etc. The concepts of "material sample" and "individual" are very important to us, and this is how we have defined them. Cheers, Jason Holmberg ECOCEAN Whale Shark Photo-identification Library http://www.whaleshark.org Please consider adopting a shark to support our mission: http://www.whaleshark.org/adoptashark.jsp On Wed, May 29, 2013 at 4:13 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Hi Ramona, Yes, I agree, and thanks. Ive always felt that there has been a trend towards trying to push too much ontology (or other semantic meaning) onto DWC terms and classes, when DWC was fundamentally intended to represent an mechanism for data exchange; not a mechanism to describe the ontological landscape of biodiversity data. The only reason I brought this up now (and, I think, why we discussed it in 2010), is that the term individualID in DWC sort of hinted that something like Individual was the forgotten class for DWC. I sincerely hope that BCO and DSW gain more traction (and, ideally, harmony between them) than earlier attempts at developing ontologies in this space have met and clearly that is the right path forward. My main concern for this thread (and the reason I engaged in it), was to: 1) Find out the status of the discussions that began in 2010; and 2) Clarify where the current materialSample proposal overlaps, or does not overlap, with that earlier effort. Steve has very adequately answered the first question, and you, John, and others have answered the second, and Im happy with both sets of answers. Im sorry for the voluminous exchange, but I felt the discussion was both important, and very helpful (certainly to me). Aloha, Rich From: Ramona Walls [mailto:rlwalls2008@gmail.com] Sent: Wednesday, May 29, 2013 1:03 PM To: Richard Pyle Cc: John Deck; Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Hi Rich, Sorry I didn't mention this sooner, but your emails were also helpful to me in describing an important and generalizable use case. I don't know whether or not the TDWG community is ready to deal with the level of abstraction we are talking about, but my assessment is that whether or not they are ready, the Darwin Core is not constructed to deal with it. That is why (among other reasons) we started work on the BCO, and perhaps one reason why Steve and others developed DSW. Our goal with the material sample proposal was not to overhaul DwC, but to work within the DwC framework to make it more compatible with other standards such as MIxS. That is why we tried to keep our proposal fairly narrowly focused. Ramona On Wed, May 29, 2013 at 3:21 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Thanks, Ramona this is an *extremely* helpful email! It helps clear things up a lot in my mind. Just to be clear, what I am looking for is the notion of a defined physical object (what I think you mean by material entity), and I explicitly mean the material entity itself. Yes, there is information (properties) that relate to that material entity, but to me that is a separate issue. What I would like to see clearly defined is the class representing the material (physical) entity which seems to me to be a superclass of what materialSample is intended to represent. Perhaps our (TDWG/DWC) community is not yet ready to deal with this level of abstraction (unfortunately, I absolutely have to, because Occurrence is simply way too overloaded a class for me to use independently of what I have been calling individual and what I have been calling Evidence). In that case, I guess the best thing to do is accept materialSample as a basisOfRecord for Occurrence and move on. But this is more or less the same thing that happened the last time we engaged in this conversation (2 years or so ago), and I was hoping this conversation about materialSample could leverage progress on the larger issue. As Ive said before, the last thing I want to do is confuse or otherwise slow down the process of incorporating the term materialSample into DWC. Its just that I saw enough overlap with that other issue, that I was hoping we could find a reasonable pathway forward on both. Thanks again for the very helpful comments. Aloha, Rich From: Ramona Walls [mailto:rlwalls2008@gmail.com] Sent: Wednesday, May 29, 2013 9:14 AM To: Richard Pyle Cc: John Deck; Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Rich, I now understand more fully what you are asking for ( a clear definition goes a long way!). A material sample, as we discussed it at the Kansas and Oxford workshops, does indeed need to be physically removed from its environment. This is also the case with the OBI term material sample, which, as a subclass of OBI:specimen is the output of some collecting process. It is true that concept of material sample could be defined to include sampling in an observational sense, but that is not how it is defined at this point. Based on this, material sample is NOT the term you are looking for or defined as : "The category of information pertaining to the physical basis of a sampling, subsampling, or observational event. In biological collections, the [SuperclassTerm] is typically a defined group of organisms, a single whole organism, or a part of a whole organism that is collected or otherwise documented in nature, and either preserved, destructively processed, or documented through some form of Evidence (such as images or reported visual observations)." What you have defined is a category of information (whatever that may be) that pertains to some material entity. Not the material entity itself, but information about that entity. The "SuperclassTerm" you refer to in the definition sounds an awful lot like a material entity from the Basic Formal Ontology, which is used for defining material sample in OBI and the Bio-collections Ontology. Ramona On Wed, May 29, 2013 at 11:51 AM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Many thanks, John. This is extremely helpful! First of all, in the context of a distinct term for basisOfRecord, I see absolutely no problem with adding the term MaterialSample. I fully support your proposal (although if this is simply a basisOfRecord term to be used alongside Occurrence, PreservedSpecimen, LivingSpecimen, FossilSpecimen, HumanObservation, MachineObservation; does it need a defined ID term? Do all the others have defined ID terms?). However, Im excited by this conversation because I think we are very close to solving a bigger problem (which was the focus of the 2010 discussion on this list around IndividualOrganism). This bigger problem involves the need for a defined concept (Im hesitating to say class), and an associated ID, in dwc that refers to the physical/material basis of an Occurrence. We dont yet have a term for this concept in dwc (IndividualID hinted at the need for one, but that term was not well-defined, and the term itself seems to cause confusion). As Steve Baskauf and I have both been advocating for the establishment of new class in dwc for exactly this purpose, I just want to make sure that were on the same page about what each concept is. The more I understand about what you need for materalSample, the more convinced I am that both of our needs can be met with the same concept. I am perfectly happy to adopt the term MaterialSample, but I guess it all boils down to this: In order for something to be a MaterialSample, must it necessarily be removed from nature? If the answer is No, then I think we can merge the two concepts into one. If the answer is Yes, then I think materialSample is best characterized as a subclass of what Steve and I have been pushing for (setting aside, for the moment, the additional complexity of taxonomically homogeneous vs. heterogeneous). In the latter case, I would define the superclass (whatever term is used for it), along the lines of: "The category of information pertaining to the physical basis of a sampling, subsampling, or observational event. In biological collections, the [SuperclassTerm] is typically a defined group of organisms, a single whole organism, or a part of a whole organism that is collected or otherwise documented in nature, and either preserved, destructively processed, or documented through some form of Evidence (such as images or reported visual observations)." Aloha, Rich From: jdeck88(a)gmail.com [mailto:jdeck88@gmail.com] On Behalf Of John Deck Sent: Wednesday, May 29, 2013 4:01 AM To: Richard Pyle Cc: Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton; Ramona Walls Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples 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 In the text of the issue submitted for MaterialSample ( <https://code.google.com/p/darwincore/issues/detail?id=167> https://code.google.com/p/darwincore/issues/detail?id=167) we noted cases where the current basisOfRecord terms pertaining to the Occurrence class (Occurrence, PreservedSpecimen, LivingSpecimen, FossilSpecimen, HumanObservation, MachineObservation) do not adequately cover certain cases, including: environmental sample (for metagenomic analysis), transcriptomes (measuring genes but not taxa), and destructive samples (e.g. tissues destructively sampled in order to generate genomic DNA). The term we borrowed from OBI (http://purl.obolibrary.org/obo/OBI_0000747) is broad enough to be utilized across various cases that fulfill our criteria while still maintaining a consistent, clear and human understandable meaning. For our purposes, we can think of Material Sample as any type of matter that we can use in order derive further evidence needed for identifications, and taxa, whether it is taxonomically homogenous, heterogenous, a single individual, sets of individuals, or populations. 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 this material entity is an individual (sensu individualID in DwC) is an independent axis of classification. As was already pointed out, 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. We maintain our position on the proposal for MaterialSample as a value for the basisOfRecord, with an associated materialSampleID to identify instances of them. Per Steves initial comments, we have already withdrawn the proposal for a MaterialSample class distinct from that in the Darwin Core type vocabulary, which should make it easier to evaluate the implications of what were discussing. ******************** NOTES, MaterialSample from OBI: OBI has fairly broad definitions of samples & specimens that are meant to be utilized across many different scientific activities. Material Sample is defined as a material entity that has the material sample role, while a material sample role is defined as a specimen role borne by a material entity that is the output of a material sampling process, and a material sampling process is a specimen gathering process with the objective to obtain a specimen that is representative of the input material entity. On Mon, May 27, 2013 at 11:59 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Hi Markus, Great question! Particularly because this is exactly the sort of use case we designed our model around. > if you take a tissue sample of the same tree every year, would the identifier > in individualID be the same for all of them or be different? WIth the current > dwc:individualID definition it would be the same for all samples. If I > understand you correct each sample would have its own "individual" > identifier in your proposal? It can't see how you can collapse these two things > into one definition. No, that is not how we would handle it. In our model, there would be one IndividualID to represent the tree, spanning the time period beginning (more or less) when the seed was germinated, until the time at which the entire physical structure of the tree was disintegrated. It is an individual tree. There would be multiple Occurrence instances, for each time that someone observed or sampled or otherwise wished to document some condition of that tree. All of these Occurrence instances would refer to the same individualID value (i.e., the "tree"). In the example above, this means there would be a different Occurrence instance for each year that a sample is taken -- because in each case, an assertion that the full tree existed at a certain time and place can be made (I understand that trees tend not to move around very much, so the Location for each event associated with each Occurrence would, in this case, remain the same; but the other Event properties -- such as eventID, samplingProtocol, samplingEffort, eventDate, eventTime, startDayOfYear, endDayOfYear, year, month, day, verbatimEventDate, habitat, fieldNumber, fieldNotes, eventRemarks -- would be documented accordingly for each sampling Occurrence instance). Suppose that the tree is visited every month, but only sampled once per year. In that case, there would be an Occurrence record for every monthly visit. In other words, an Occurrence instance exists regardless of whether a physical sample was made or not. Any in-situ images made of the tree would likewise be associated with the specific Occurrence instance, and each image would represent a separate instance of "Evidence". Now, let's focus on the annual samplings. Every time a new sample is taken from the tree, at least one new instance of Individual (with a unique individualID value) is created to represent the sample. This sample (individual instance) may be a "gathering" (set of multiple individual specimens gathered at the same time), or it may be a single specimen, or it may be simply a tissue sample intended for destructive analysis. In any case, it's a new individual instance derived from the "parent" individual instance representing the whole tree. In our implementation, "Individual" can be hierarchical, such that a whole-organism tree can be sub-sampled with many "child" instances of "gatherings" (say, one gathering each year), and each gathering may have multiple child "specimen" individuals (e.g. individual botanical sheets created from the multiple items of a single gathering), and each specimen may have further "child" subsamples extracted for DNA analysis (or whatever), and the hierarchy can continue on down to whatever derivatives that people feel a need to keep track of (e.g., aliquot). The point is, all Individual instances are well-defined physical objects (or well-defined sets of physical objects), and they can be arranged in a n-tiered hierarchy. Moreover, each Individual that can be characterized as a "sample" (what we refer to as a "CollectionObject") may also have a property value for "CollectionOccurrenceID" -- which refers to the specific Occurrence instance at which the sample was obtained. So, for example, if the tree is visited on May 27, 2013 and a specimen (sample) is taken, then: 1) An Event instance is generated to represent the event where the tree was visited; 2) An Occurrence instance is generated, which refers to the new EventID, and the existing IndividualID for the whole tree, and includes whatever other Occurrence properties are relevant for the tree at the time of this Occurrence 3) An Individual instance is generated for the specimen, which has a property value for parentIndividualID that refers to the individualID for the whole tree, and a property value for collectionOccurrenceID that refers the Occurrence instance where the specimen was collected. So, to summarize the answer to your question: - There are multiple Occurrence instances that refer to the same Individual instance representing the whole tree (and, hence can be collapsed to the same IndividualID value). - Any Individual can have derivatives that are themselves unique Individual instances. - Individuals are arranged hierarchically, and certain properties can be inherited up or down the hierarchy, depending on the properties and their associated logical constraints. At some point, I will assemble a set of other specific use cases, and how we manage them through our use of the "Individual" instance (although I will probably not use the word "Individual", as this seems to cause too much confusion in these discussions). Aloha, Rich -- John Deck (541) 321-0689 <tel:%28541%29%20321-0689> _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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NESCent summer course: "Ontologies for Evolutionary Biology"
by Matt Yoder 31 May '13

31 May '13

Apologies in advance- this is a little off topic but I think it should be of interest to many here. For a second year we are teaching a "Ontologies for Evolutionary Biology" sponsored by NESCent on July 29th in Durham, NC. Details are here: http://bit.ly/ZAQ6Dt . Please forward this to any interested parties. Last year we had a broad spectrum of "students", from advanced undergrads to Professors nearing retirement. If you have questions please message me off-list. Thanks, Matt Yoder Biological Informatician Illinois Natural History Survey

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Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
by Richard Pyle 30 May '13

30 May '13

Hi Ramona, Yes, I agree, and thanks. Ive always felt that there has been a trend towards trying to push too much ontology (or other semantic meaning) onto DWC terms and classes, when DWC was fundamentally intended to represent an mechanism for data exchange; not a mechanism to describe the ontological landscape of biodiversity data. The only reason I brought this up now (and, I think, why we discussed it in 2010), is that the term individualID in DWC sort of hinted that something like Individual was the forgotten class for DWC. I sincerely hope that BCO and DSW gain more traction (and, ideally, harmony between them) than earlier attempts at developing ontologies in this space have met and clearly that is the right path forward. My main concern for this thread (and the reason I engaged in it), was to: 1) Find out the status of the discussions that began in 2010; and 2) Clarify where the current materialSample proposal overlaps, or does not overlap, with that earlier effort. Steve has very adequately answered the first question, and you, John, and others have answered the second, and Im happy with both sets of answers. Im sorry for the voluminous exchange, but I felt the discussion was both important, and very helpful (certainly to me). Aloha, Rich From: Ramona Walls [mailto:rlwalls2008@gmail.com] Sent: Wednesday, May 29, 2013 1:03 PM To: Richard Pyle Cc: John Deck; Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Hi Rich, Sorry I didn't mention this sooner, but your emails were also helpful to me in describing an important and generalizable use case. I don't know whether or not the TDWG community is ready to deal with the level of abstraction we are talking about, but my assessment is that whether or not they are ready, the Darwin Core is not constructed to deal with it. That is why (among other reasons) we started work on the BCO, and perhaps one reason why Steve and others developed DSW. Our goal with the material sample proposal was not to overhaul DwC, but to work within the DwC framework to make it more compatible with other standards such as MIxS. That is why we tried to keep our proposal fairly narrowly focused. Ramona On Wed, May 29, 2013 at 3:21 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Thanks, Ramona this is an *extremely* helpful email! It helps clear things up a lot in my mind. Just to be clear, what I am looking for is the notion of a defined physical object (what I think you mean by material entity), and I explicitly mean the material entity itself. Yes, there is information (properties) that relate to that material entity, but to me that is a separate issue. What I would like to see clearly defined is the class representing the material (physical) entity which seems to me to be a superclass of what materialSample is intended to represent. Perhaps our (TDWG/DWC) community is not yet ready to deal with this level of abstraction (unfortunately, I absolutely have to, because Occurrence is simply way too overloaded a class for me to use independently of what I have been calling individual and what I have been calling Evidence). In that case, I guess the best thing to do is accept materialSample as a basisOfRecord for Occurrence and move on. But this is more or less the same thing that happened the last time we engaged in this conversation (2 years or so ago), and I was hoping this conversation about materialSample could leverage progress on the larger issue. As Ive said before, the last thing I want to do is confuse or otherwise slow down the process of incorporating the term materialSample into DWC. Its just that I saw enough overlap with that other issue, that I was hoping we could find a reasonable pathway forward on both. Thanks again for the very helpful comments. Aloha, Rich From: Ramona Walls [mailto:rlwalls2008@gmail.com] Sent: Wednesday, May 29, 2013 9:14 AM To: Richard Pyle Cc: John Deck; Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Rich, I now understand more fully what you are asking for ( a clear definition goes a long way!). A material sample, as we discussed it at the Kansas and Oxford workshops, does indeed need to be physically removed from its environment. This is also the case with the OBI term material sample, which, as a subclass of OBI:specimen is the output of some collecting process. It is true that concept of material sample could be defined to include sampling in an observational sense, but that is not how it is defined at this point. Based on this, material sample is NOT the term you are looking for or defined as : "The category of information pertaining to the physical basis of a sampling, subsampling, or observational event. In biological collections, the [SuperclassTerm] is typically a defined group of organisms, a single whole organism, or a part of a whole organism that is collected or otherwise documented in nature, and either preserved, destructively processed, or documented through some form of Evidence (such as images or reported visual observations)." What you have defined is a category of information (whatever that may be) that pertains to some material entity. Not the material entity itself, but information about that entity. The "SuperclassTerm" you refer to in the definition sounds an awful lot like a material entity from the Basic Formal Ontology, which is used for defining material sample in OBI and the Bio-collections Ontology. Ramona On Wed, May 29, 2013 at 11:51 AM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Many thanks, John. This is extremely helpful! First of all, in the context of a distinct term for basisOfRecord, I see absolutely no problem with adding the term MaterialSample. I fully support your proposal (although if this is simply a basisOfRecord term to be used alongside Occurrence, PreservedSpecimen, LivingSpecimen, FossilSpecimen, HumanObservation, MachineObservation; does it need a defined ID term? Do all the others have defined ID terms?). However, Im excited by this conversation because I think we are very close to solving a bigger problem (which was the focus of the 2010 discussion on this list around IndividualOrganism). This bigger problem involves the need for a defined concept (Im hesitating to say class), and an associated ID, in dwc that refers to the physical/material basis of an Occurrence. We dont yet have a term for this concept in dwc (IndividualID hinted at the need for one, but that term was not well-defined, and the term itself seems to cause confusion). As Steve Baskauf and I have both been advocating for the establishment of new class in dwc for exactly this purpose, I just want to make sure that were on the same page about what each concept is. The more I understand about what you need for materalSample, the more convinced I am that both of our needs can be met with the same concept. I am perfectly happy to adopt the term MaterialSample, but I guess it all boils down to this: In order for something to be a MaterialSample, must it necessarily be removed from nature? If the answer is No, then I think we can merge the two concepts into one. If the answer is Yes, then I think materialSample is best characterized as a subclass of what Steve and I have been pushing for (setting aside, for the moment, the additional complexity of taxonomically homogeneous vs. heterogeneous). In the latter case, I would define the superclass (whatever term is used for it), along the lines of: "The category of information pertaining to the physical basis of a sampling, subsampling, or observational event. In biological collections, the [SuperclassTerm] is typically a defined group of organisms, a single whole organism, or a part of a whole organism that is collected or otherwise documented in nature, and either preserved, destructively processed, or documented through some form of Evidence (such as images or reported visual observations)." Aloha, Rich From: jdeck88(a)gmail.com [mailto:jdeck88@gmail.com] On Behalf Of John Deck Sent: Wednesday, May 29, 2013 4:01 AM To: Richard Pyle Cc: Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton; Ramona Walls Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples 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 In the text of the issue submitted for MaterialSample ( <https://code.google.com/p/darwincore/issues/detail?id=167> https://code.google.com/p/darwincore/issues/detail?id=167) we noted cases where the current basisOfRecord terms pertaining to the Occurrence class (Occurrence, PreservedSpecimen, LivingSpecimen, FossilSpecimen, HumanObservation, MachineObservation) do not adequately cover certain cases, including: environmental sample (for metagenomic analysis), transcriptomes (measuring genes but not taxa), and destructive samples (e.g. tissues destructively sampled in order to generate genomic DNA). The term we borrowed from OBI (http://purl.obolibrary.org/obo/OBI_0000747) is broad enough to be utilized across various cases that fulfill our criteria while still maintaining a consistent, clear and human understandable meaning. For our purposes, we can think of Material Sample as any type of matter that we can use in order derive further evidence needed for identifications, and taxa, whether it is taxonomically homogenous, heterogenous, a single individual, sets of individuals, or populations. 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 this material entity is an individual (sensu individualID in DwC) is an independent axis of classification. As was already pointed out, 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. We maintain our position on the proposal for MaterialSample as a value for the basisOfRecord, with an associated materialSampleID to identify instances of them. Per Steves initial comments, we have already withdrawn the proposal for a MaterialSample class distinct from that in the Darwin Core type vocabulary, which should make it easier to evaluate the implications of what were discussing. ******************** NOTES, MaterialSample from OBI: OBI has fairly broad definitions of samples & specimens that are meant to be utilized across many different scientific activities. Material Sample is defined as a material entity that has the material sample role, while a material sample role is defined as a specimen role borne by a material entity that is the output of a material sampling process, and a material sampling process is a specimen gathering process with the objective to obtain a specimen that is representative of the input material entity. On Mon, May 27, 2013 at 11:59 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Hi Markus, Great question! Particularly because this is exactly the sort of use case we designed our model around. > if you take a tissue sample of the same tree every year, would the identifier > in individualID be the same for all of them or be different? WIth the current > dwc:individualID definition it would be the same for all samples. If I > understand you correct each sample would have its own "individual" > identifier in your proposal? It can't see how you can collapse these two things > into one definition. No, that is not how we would handle it. In our model, there would be one IndividualID to represent the tree, spanning the time period beginning (more or less) when the seed was germinated, until the time at which the entire physical structure of the tree was disintegrated. It is an individual tree. There would be multiple Occurrence instances, for each time that someone observed or sampled or otherwise wished to document some condition of that tree. All of these Occurrence instances would refer to the same individualID value (i.e., the "tree"). In the example above, this means there would be a different Occurrence instance for each year that a sample is taken -- because in each case, an assertion that the full tree existed at a certain time and place can be made (I understand that trees tend not to move around very much, so the Location for each event associated with each Occurrence would, in this case, remain the same; but the other Event properties -- such as eventID, samplingProtocol, samplingEffort, eventDate, eventTime, startDayOfYear, endDayOfYear, year, month, day, verbatimEventDate, habitat, fieldNumber, fieldNotes, eventRemarks -- would be documented accordingly for each sampling Occurrence instance). Suppose that the tree is visited every month, but only sampled once per year. In that case, there would be an Occurrence record for every monthly visit. In other words, an Occurrence instance exists regardless of whether a physical sample was made or not. Any in-situ images made of the tree would likewise be associated with the specific Occurrence instance, and each image would represent a separate instance of "Evidence". Now, let's focus on the annual samplings. Every time a new sample is taken from the tree, at least one new instance of Individual (with a unique individualID value) is created to represent the sample. This sample (individual instance) may be a "gathering" (set of multiple individual specimens gathered at the same time), or it may be a single specimen, or it may be simply a tissue sample intended for destructive analysis. In any case, it's a new individual instance derived from the "parent" individual instance representing the whole tree. In our implementation, "Individual" can be hierarchical, such that a whole-organism tree can be sub-sampled with many "child" instances of "gatherings" (say, one gathering each year), and each gathering may have multiple child "specimen" individuals (e.g. individual botanical sheets created from the multiple items of a single gathering), and each specimen may have further "child" subsamples extracted for DNA analysis (or whatever), and the hierarchy can continue on down to whatever derivatives that people feel a need to keep track of (e.g., aliquot). The point is, all Individual instances are well-defined physical objects (or well-defined sets of physical objects), and they can be arranged in a n-tiered hierarchy. Moreover, each Individual that can be characterized as a "sample" (what we refer to as a "CollectionObject") may also have a property value for "CollectionOccurrenceID" -- which refers to the specific Occurrence instance at which the sample was obtained. So, for example, if the tree is visited on May 27, 2013 and a specimen (sample) is taken, then: 1) An Event instance is generated to represent the event where the tree was visited; 2) An Occurrence instance is generated, which refers to the new EventID, and the existing IndividualID for the whole tree, and includes whatever other Occurrence properties are relevant for the tree at the time of this Occurrence 3) An Individual instance is generated for the specimen, which has a property value for parentIndividualID that refers to the individualID for the whole tree, and a property value for collectionOccurrenceID that refers the Occurrence instance where the specimen was collected. So, to summarize the answer to your question: - There are multiple Occurrence instances that refer to the same Individual instance representing the whole tree (and, hence can be collapsed to the same IndividualID value). - Any Individual can have derivatives that are themselves unique Individual instances. - Individuals are arranged hierarchically, and certain properties can be inherited up or down the hierarchy, depending on the properties and their associated logical constraints. At some point, I will assemble a set of other specific use cases, and how we manage them through our use of the "Individual" instance (although I will probably not use the word "Individual", as this seems to cause too much confusion in these discussions). Aloha, Rich -- John Deck (541) 321-0689 <tel:%28541%29%20321-0689>

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Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
by Richard Pyle 29 May '13

29 May '13

Thanks, Ramona this is an *extremely* helpful email! It helps clear things up a lot in my mind. Just to be clear, what I am looking for is the notion of a defined physical object (what I think you mean by material entity), and I explicitly mean the material entity itself. Yes, there is information (properties) that relate to that material entity, but to me that is a separate issue. What I would like to see clearly defined is the class representing the material (physical) entity which seems to me to be a superclass of what materialSample is intended to represent. Perhaps our (TDWG/DWC) community is not yet ready to deal with this level of abstraction (unfortunately, I absolutely have to, because Occurrence is simply way too overloaded a class for me to use independently of what I have been calling individual and what I have been calling Evidence). In that case, I guess the best thing to do is accept materialSample as a basisOfRecord for Occurrence and move on. But this is more or less the same thing that happened the last time we engaged in this conversation (2 years or so ago), and I was hoping this conversation about materialSample could leverage progress on the larger issue. As Ive said before, the last thing I want to do is confuse or otherwise slow down the process of incorporating the term materialSample into DWC. Its just that I saw enough overlap with that other issue, that I was hoping we could find a reasonable pathway forward on both. Thanks again for the very helpful comments. Aloha, Rich From: Ramona Walls [mailto:rlwalls2008@gmail.com] Sent: Wednesday, May 29, 2013 9:14 AM To: Richard Pyle Cc: John Deck; Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Rich, I now understand more fully what you are asking for ( a clear definition goes a long way!). A material sample, as we discussed it at the Kansas and Oxford workshops, does indeed need to be physically removed from its environment. This is also the case with the OBI term material sample, which, as a subclass of OBI:specimen is the output of some collecting process. It is true that concept of material sample could be defined to include sampling in an observational sense, but that is not how it is defined at this point. Based on this, material sample is NOT the term you are looking for or defined as : "The category of information pertaining to the physical basis of a sampling, subsampling, or observational event. In biological collections, the [SuperclassTerm] is typically a defined group of organisms, a single whole organism, or a part of a whole organism that is collected or otherwise documented in nature, and either preserved, destructively processed, or documented through some form of Evidence (such as images or reported visual observations)." What you have defined is a category of information (whatever that may be) that pertains to some material entity. Not the material entity itself, but information about that entity. The "SuperclassTerm" you refer to in the definition sounds an awful lot like a material entity from the Basic Formal Ontology, which is used for defining material sample in OBI and the Bio-collections Ontology. Ramona On Wed, May 29, 2013 at 11:51 AM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Many thanks, John. This is extremely helpful! First of all, in the context of a distinct term for basisOfRecord, I see absolutely no problem with adding the term MaterialSample. I fully support your proposal (although if this is simply a basisOfRecord term to be used alongside Occurrence, PreservedSpecimen, LivingSpecimen, FossilSpecimen, HumanObservation, MachineObservation; does it need a defined ID term? Do all the others have defined ID terms?). However, Im excited by this conversation because I think we are very close to solving a bigger problem (which was the focus of the 2010 discussion on this list around IndividualOrganism). This bigger problem involves the need for a defined concept (Im hesitating to say class), and an associated ID, in dwc that refers to the physical/material basis of an Occurrence. We dont yet have a term for this concept in dwc (IndividualID hinted at the need for one, but that term was not well-defined, and the term itself seems to cause confusion). As Steve Baskauf and I have both been advocating for the establishment of new class in dwc for exactly this purpose, I just want to make sure that were on the same page about what each concept is. The more I understand about what you need for materalSample, the more convinced I am that both of our needs can be met with the same concept. I am perfectly happy to adopt the term MaterialSample, but I guess it all boils down to this: In order for something to be a MaterialSample, must it necessarily be removed from nature? If the answer is No, then I think we can merge the two concepts into one. If the answer is Yes, then I think materialSample is best characterized as a subclass of what Steve and I have been pushing for (setting aside, for the moment, the additional complexity of taxonomically homogeneous vs. heterogeneous). In the latter case, I would define the superclass (whatever term is used for it), along the lines of: "The category of information pertaining to the physical basis of a sampling, subsampling, or observational event. In biological collections, the [SuperclassTerm] is typically a defined group of organisms, a single whole organism, or a part of a whole organism that is collected or otherwise documented in nature, and either preserved, destructively processed, or documented through some form of Evidence (such as images or reported visual observations)." Aloha, Rich From: jdeck88(a)gmail.com [mailto:jdeck88@gmail.com] On Behalf Of John Deck Sent: Wednesday, May 29, 2013 4:01 AM To: Richard Pyle Cc: Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton; Ramona Walls Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples 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 In the text of the issue submitted for MaterialSample ( <https://code.google.com/p/darwincore/issues/detail?id=167> https://code.google.com/p/darwincore/issues/detail?id=167) we noted cases where the current basisOfRecord terms pertaining to the Occurrence class (Occurrence, PreservedSpecimen, LivingSpecimen, FossilSpecimen, HumanObservation, MachineObservation) do not adequately cover certain cases, including: environmental sample (for metagenomic analysis), transcriptomes (measuring genes but not taxa), and destructive samples (e.g. tissues destructively sampled in order to generate genomic DNA). The term we borrowed from OBI (http://purl.obolibrary.org/obo/OBI_0000747) is broad enough to be utilized across various cases that fulfill our criteria while still maintaining a consistent, clear and human understandable meaning. For our purposes, we can think of Material Sample as any type of matter that we can use in order derive further evidence needed for identifications, and taxa, whether it is taxonomically homogenous, heterogenous, a single individual, sets of individuals, or populations. 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 this material entity is an individual (sensu individualID in DwC) is an independent axis of classification. As was already pointed out, 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. We maintain our position on the proposal for MaterialSample as a value for the basisOfRecord, with an associated materialSampleID to identify instances of them. Per Steves initial comments, we have already withdrawn the proposal for a MaterialSample class distinct from that in the Darwin Core type vocabulary, which should make it easier to evaluate the implications of what were discussing. ******************** NOTES, MaterialSample from OBI: OBI has fairly broad definitions of samples & specimens that are meant to be utilized across many different scientific activities. Material Sample is defined as a material entity that has the material sample role, while a material sample role is defined as a specimen role borne by a material entity that is the output of a material sampling process, and a material sampling process is a specimen gathering process with the objective to obtain a specimen that is representative of the input material entity. On Mon, May 27, 2013 at 11:59 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Hi Markus, Great question! Particularly because this is exactly the sort of use case we designed our model around. > if you take a tissue sample of the same tree every year, would the identifier > in individualID be the same for all of them or be different? WIth the current > dwc:individualID definition it would be the same for all samples. If I > understand you correct each sample would have its own "individual" > identifier in your proposal? It can't see how you can collapse these two things > into one definition. No, that is not how we would handle it. In our model, there would be one IndividualID to represent the tree, spanning the time period beginning (more or less) when the seed was germinated, until the time at which the entire physical structure of the tree was disintegrated. It is an individual tree. There would be multiple Occurrence instances, for each time that someone observed or sampled or otherwise wished to document some condition of that tree. All of these Occurrence instances would refer to the same individualID value (i.e., the "tree"). In the example above, this means there would be a different Occurrence instance for each year that a sample is taken -- because in each case, an assertion that the full tree existed at a certain time and place can be made (I understand that trees tend not to move around very much, so the Location for each event associated with each Occurrence would, in this case, remain the same; but the other Event properties -- such as eventID, samplingProtocol, samplingEffort, eventDate, eventTime, startDayOfYear, endDayOfYear, year, month, day, verbatimEventDate, habitat, fieldNumber, fieldNotes, eventRemarks -- would be documented accordingly for each sampling Occurrence instance). Suppose that the tree is visited every month, but only sampled once per year. In that case, there would be an Occurrence record for every monthly visit. In other words, an Occurrence instance exists regardless of whether a physical sample was made or not. Any in-situ images made of the tree would likewise be associated with the specific Occurrence instance, and each image would represent a separate instance of "Evidence". Now, let's focus on the annual samplings. Every time a new sample is taken from the tree, at least one new instance of Individual (with a unique individualID value) is created to represent the sample. This sample (individual instance) may be a "gathering" (set of multiple individual specimens gathered at the same time), or it may be a single specimen, or it may be simply a tissue sample intended for destructive analysis. In any case, it's a new individual instance derived from the "parent" individual instance representing the whole tree. In our implementation, "Individual" can be hierarchical, such that a whole-organism tree can be sub-sampled with many "child" instances of "gatherings" (say, one gathering each year), and each gathering may have multiple child "specimen" individuals (e.g. individual botanical sheets created from the multiple items of a single gathering), and each specimen may have further "child" subsamples extracted for DNA analysis (or whatever), and the hierarchy can continue on down to whatever derivatives that people feel a need to keep track of (e.g., aliquot). The point is, all Individual instances are well-defined physical objects (or well-defined sets of physical objects), and they can be arranged in a n-tiered hierarchy. Moreover, each Individual that can be characterized as a "sample" (what we refer to as a "CollectionObject") may also have a property value for "CollectionOccurrenceID" -- which refers to the specific Occurrence instance at which the sample was obtained. So, for example, if the tree is visited on May 27, 2013 and a specimen (sample) is taken, then: 1) An Event instance is generated to represent the event where the tree was visited; 2) An Occurrence instance is generated, which refers to the new EventID, and the existing IndividualID for the whole tree, and includes whatever other Occurrence properties are relevant for the tree at the time of this Occurrence 3) An Individual instance is generated for the specimen, which has a property value for parentIndividualID that refers to the individualID for the whole tree, and a property value for collectionOccurrenceID that refers the Occurrence instance where the specimen was collected. So, to summarize the answer to your question: - There are multiple Occurrence instances that refer to the same Individual instance representing the whole tree (and, hence can be collapsed to the same IndividualID value). - Any Individual can have derivatives that are themselves unique Individual instances. - Individuals are arranged hierarchically, and certain properties can be inherited up or down the hierarchy, depending on the properties and their associated logical constraints. At some point, I will assemble a set of other specific use cases, and how we manage them through our use of the "Individual" instance (although I will probably not use the word "Individual", as this seems to cause too much confusion in these discussions). Aloha, Rich -- John Deck (541) 321-0689 <tel:%28541%29%20321-0689>

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Evidence/Token Class [was: New Darwin Core terms proposed relating to material samples]
by Richard Pyle 27 May '13

27 May '13

Thanks, Dan. I changed the subject line because I think your comment: > tissue converted to DNA extract is still tissue (the tissue is still > "material sample" after "destructive sampling", and still part of > the event, just as is a photograph of the beast in the museum. Relates to part of what Steve wrote: > We defined a class for evidence, but we also considered not having evidence > being an explicit class. Not defining an explicit Token class would have simplified > the diagram at the bottom of the page - one could just say that there should be > evidence and it should be linked to the resource it documents. > Token and THeE/IndividualOrganism are not disjoint classes - the physical entity > can be the evidence if somebody "owns" it and makes it available for people to examine. > However, in DSW, Token and THeE are not synonymous because we allow evidence > to include things that are not physically derived from the entity (e.g. images, sounds, > string data records) in addition to physical specimens. This is an area that at first seems subtle, but once we actually started working with data, starts to became more and more intuitive (at least to me, anyway). I first started thinking about this seriously during a 2007 meeting of ICZN Commissioners, when we were contemplating the question of what could/should, and what could/should not, fulfill the role of a type specimen under the ICZN Code. Needless to say, we did not come up with a complete answer to the question, but the discussion did help frame in my mind the question in much better detail. Under the ICZN Code (which differs in a few respects from the ICNafp Code in this area), the definition of a type specimen s fairly straight-forward: 1) It must be biological material. An image (e.g., illustration or photograph) cannot be a type specimen (I believe the ICNafp accommodates "iconotypes"). Rather, the organism depicted in an image is regarded as being the type specimen. 2) A type specimen consists of the entire organism. For example, in the case of a mammal that is captured and separated into its fur, skeleton, alcoholic-preserved tissues, and tissue samples for DNA analysis, all of these things together constitute the type specimen. In other words, the whole specimen is the type. This is in contrast to ICNafp, where a single specimen from a tree (for example) is the type, whereas other specimens taken from the same tree are isotypes, and the remainder of the tree is not a type at all. 3) It is understood that the community of organisms inhabiting a type specimen (e.g., parasites and commensals) do not form part of the type specimen. There are other issues as well (especially for ichnotaxa, colonies, and other specific cases), but the general point is that under the ICZN Code, a type specimen consists of the sum of all cells that contain the same DNA material that were part of the same biological individual (i.e., identical twins, clones, and parthenogenic and other asexually reproducing organisms potentially contain the same DNA material, but are different "individuals"). Most of the above is pretty straight-forward. Where it gets a bit squishy is when you go down below the "tissue sample" level into smaller and smaller subunits. Can a single cell containing intact DNA be a type specimen for a multicellular organism? Can a single DNA molecule be a type specimen? Can a single chromosome be a type specimen? Can a PCR product be a type specimen? ...you can add as many hair-splitting examples as you wish. Conversations like this let me to draw a distinction between matter that is actually from an organism, vs. stuff that is representative of the organism but lacks any material connection to the organism. Coming back to Dan Janzen's comment; I would conclude that most things that would full under the term "materialSample" include actually matter from a biological organism. A PCR product is borderline, because it presumably does contain actual matter from the organism, but the vast majority of matter in the PCR product was not from the organism. Once you lose all the matter from the organism, you are no longer talking about the "individual", but instead are now talking about "Evidence of the Individual". This applies to images of the individual (whether taken in-situ, or in a lab), DNA "sequences" (rendered as text), images of the results of DNA sequencing analysis (in various forms), and various other non-biological derivatives. So, this leads me to the comment from Steve about "Evidence" (which, if I understand correctly, is conceptually the same as the DSW "Token": https://code.google.com/p/darwin-sw/wiki/ClassToken) In our model, a specimen is *not* a Token or Evidence -- it is an individual. This has proven (in my mind at least -- Rob W. still has reservations) to be a MUCH more practical way to think of, and manage data for, specimens. This email will be WAY too long if I try to explain all the subtleties of this, so I'll just leave it at that. But clearly there are some differences between our notion of "Evidence", and the DSW concept of "Token" -- although both seem to be intended to solve the same problem. Enough for now.... Aloha, Rich

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Fwd: SANBI Post Doctoral Fellowships
by John Wieczorek 08 May '13

08 May '13

Forwarding relevant opportunity announcement from South Africa. ---------- Forwarded message ---------- From: Gloria Cupido <G.Cupido(a)sanbi.org.za> Date: Wed, May 8, 2013 at 5:17 AM Subject: SANBI Post Doctoral Fellowships To: Paula Hathorn <P.Hathorn(a)sanbi.org.za> Dear all **** ** ** Please see on the SANBI website adverts for the two biodiversity informatics post doctoral fellowships based at the University of the Western Cape http://www.sanbi.org/jobs/post-doctoral-fellowship-interrogation-biodiversi… http://www.sanbi.org/jobs/post-doctoral-fellowship**** ** ** Please circulate these adverts to potential candidates who will add value to the programme we are establishing.**** ** ** Kind regards**** ** ** Paula**** ** ** ** ** Paula Hathorn**** Learning Network Manager**** Biodiversity Information Management **** South African National Biodiversity Institute **** Tel: +27 21 799 8885**** Cell: +27 82 2608584**** Fax2email: 0865208130**** ** ** ------------------------------ Please visit our website www.sanbi.org for more information about the South African National Biodiversity Institute . Think before you print. Please consider the environment before printing this email. NOTE: This email and any attachments are intended for the addressee only, and contain information that may be legally privileged and / or confidential and / or the subject of copyright that is protected by law. Any unauthorised usage, disclosure, alteration or dissemination is prohibited. The SANBI accepts no responsibly for any loss whether it be direct, indirect or consequential, arising from information made available and actions resulting there from. No liability is accepted by the SANBI or the sender. The views or opinion expressed in this email message may not necessarily be that of the SANBI or the SANBI Management. The SANBI reserves the right to monitor all email communication. Please consider the environment before printing this email. The disclaimer is located at http://www.sanbi.org/node/5672

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