- tdwg-content - lists.tdwg.org

Re: [tdwg-content] Relation of GNA to TDWG vocabularies
by Kevin Richards 15 Nov '10

15 Nov '10

'Effective tools' to do X, Y & Z always seem to be on the agenda, but I'm not sure it is the tools that are the hold up. Unfortunately I think it boils down to funding... I'm sure if we had adequate funding to get people together for the required length of time, working on the right stuff etc, etc, then we would make fantastic progress. I'm thinking a really good session with a basic UML tool would be a big step forward. I have got hold of a UML tool and intend to have a go at a core tdwg model. I think it would be great then if we could organise a session on working on this model. Kevin Sent from my HTC ----- Reply message ----- From: "Lee Belbin" <leebelbin(a)gmail.com> Date: Sat, Nov 13, 2010 3:42 pm Subject: [tdwg-content] Relation of GNA to TDWG vocabularies To: "tdwg-content(a)lists.tdwg.org" <tdwg-content(a)lists.tdwg.org> Well stated Stan, but I'd add a third- 3. Effective tool/s for viewing (graph, sub-graph, tables, properties etc.), add/delete/modify with adaptable governance control (e.g., assigned management to sub-graph domains), annotate (with full logging of who did what, when and how...). This is in effect a collaboration tool. Until we have a tool (preferable to tools) that can be intuitive and effective for building, managing and deploying /exporting vocabs or ontologies, we will struggle with this socially and technically tough, but very necessary task. The social issues are the hardest, but an effective collaboration tool would be a big help. A tool that will be readily embraced by #2 (the domain specialists) seems far more important than the tools I've seen so far that are embraced by #1 (e.g. Protégé). That we don't have a TDWG ontology is an increasing worry. Lee Lee Belbin Geospatial Team Leader Atlas of Living Australia -----Original Message----- From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Blum, Stan Sent: Saturday, 13 November 2010 9:43 AM To: tdwg-content(a)lists.tdwg.org Subject: Re: [tdwg-content] Relation of GNA to TDWG vocabularies Progress on the TDWG ontology seems to require: 1) one or more people with good sense of what can be done with ontologies, both in the near-term and long-term; and 2) one or more people who understand the way information is partitioned in this domain and how it could fit together. I think we have a lot of #2, but not many of #1. FYI, we have seed money to bring these categories together. -Stan On 11/12/10 2:25 PM, "Bob Morris" <morris.bob(a)gmail.com> wrote: > On Fri, Nov 12, 2010 at 4:57 PM, Richard Pyle > <deepreef(a)bishopmuseum.org> > wrote: > >> [...] the current status of the TDWG-Ontology efforts. The Google >> Code website seems a bit anemic, > > Ooh, I love that line. I think I'll put it in the script of my next > animation, to be titled: "Alpha and Beta discuss the current status of > of the TDWG-Ontology efforts" > > Thanks for correcting the URL. > > Bob > > > Robert A. Morris > Emeritus Professor of Computer Science UMASS-Boston > 100 Morrissey Blvd > Boston, MA 02125-3390 > Associate, Harvard University Herbaria > email: morris.bob(a)gmail.com > web: http://bdei.cs.umb.edu/ > web: http://etaxonomy.org/mw/FilteredPush > http://www.cs.umb.edu/~ram > phone (+1) 857 222 7992 (mobile) > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

7 6

Background for the Individual class proposal. 3. Should an Individual also be a Collecting Unit?
by Steve Baskauf 15 Nov '10

15 Nov '10

In the first and second installment of this series, I have tried to show that the class Individual as I have proposed it is a central part of a fully denormalized Darwin Core model. It's connective role allows for one-to-many relationships between itself and both the Occurrence and Identification classes (see http://bioimages.vanderbilt.edu/pages/full-model.jpg) I have also pointed out that in that role, it has very few properties. The reason for this is described in detail on p.26 of my Biodiversity Informatics paper (https://journals.ku.edu/index.php/jbi/article/view/3664) but in summary the only way we can actually find out anything about an individual organism is through some kind of observation or collection, which is exactly what happens in an Occurrence. Thus things that we "know" about Individuals generally are directly or indirectly associated with Occurrences, not with the instances of Individual themselves. Rich has suggested that we should consider whether some properties that are currently properties of Occurrence should be moved into the proposed Individual class. It is good to think about this, because we do want to have an economy of classes and terms (no point in having two classes for something when one would do), and because the mental image that we have about an individual organism does include aspects of both the proposed Individual class and the part of the ASC diagram called "Collecting Unit". There are a number of ways of approaching this problem. The first approach, which is the way the discussion developed on the email list, is to just try moving terms from Occurrence to the proposed Individual class and to see whether that would "work" or not. As the discussion progressed, I began to feel increasingly uncomfortable with this process, but wasn't sure why. After I went back to the ASC diagram, it became clear to me what was the problem was. I believe that the question is really being framed incorrectly. What I have proposed for the class Individual is precisely what I have described in the previous posts: for it to serve as a node connecting Occurrences to Identificaitons. What I think Rich wants to recognize is the section of the ASC model called Collecting Unit and the boxes below it: Unsorted Lot, Lot, Specimen, and Specimen Component (I'm not sure exactly what "Derived Object" is - maybe things like images of specimens?). If I am correct in understanding what Rich wants, then the question boils down to: can or should my proposed class be the same as (or possibly include) the section on the ASC diagram called Collecting Unit. I think that I have a pretty clear idea in my mind what Individual as I have defined it means, so my task has been to try to understand what exactly is a CollectingUnit and what properties should it have. The I can approach the question of congruence with "my" Individual. If all things that we would want to fold within CollectingUnit share properties that can be placed within the Individual class, then they are congruent and should be the same thing. If some or most properties that we want to fit within CollectingUnit don't fit the defined purpose of the Individual class, then they should be two separate classes. Because the ASC model was developed by the museum community, I think that its creators were primarily concerned with handling dead specimens. However, as Rich has correctly pointed out, the distinction between dead and living CollectingUnits is probably artificial. Rather, both living and preserved specimens may be instances of the same class which have a different value for some "live/dead" property (see http://code.google.com/p/darwincore/issues/detail?id=91) So for the moment, I'm assuming that a CollectingUnit can be either living or preserved. The case of preserved specimens is fairly straightforward. The have their origin in a single Occurrence that happens at a single Event (what I called a "resource creation event" in my Biodiversity Informatics paper). Living specimens are more complex. They may originate when the whole organism is collected from the wild and moved to a zoo or botanical garden (John's wildebeest calf). In that case there is a clear "resource creation event" if we call the living specimen a resource that is distinct from the organism when it was in the wild. In some cases, the living specimen is born in captivity, grown from a seed, or propagated vegetatively from a cutting. In that case, there is also a definable event when the living specimen originated. What was really driving me crazy was this: http://bioimages.vanderbilt.edu/vanderbilt/7-314 The Bicentennial oak is a tree that is growing in Vanderbilt's arboretum. It seemed to me that it was a living specimen because it is now a part of a collection of trees (the arboretum). But it is over 230 years old and Vanderbilt itself is only 137 years old. So clearly nobody captured, moved, or planted it to make it a part of the arboretum. For a while I tried to define it out of being a living specimen, but then I realized that the thing that made it different from other old trees that are standing around Nashville is that it has been accessioned. In other words, when the tree was claimed as a part of the arboretum, assigned an identifier (7-314), and added to the arboretum database, it became a living specimen in addition to being just a normal tree. The event of calling the tree a part of the arboretum, assigning it an identifier, and adding it to the arboreutm database is the Occurrence that marks the creation of the thing "living specimen". At that point it can have any attribute that other Occurrences have and it is then capable of serving as evidence for the Occurrence because anybody can examine it at will. The "claimed as a part of the arboretum" part is important, because I can go out into the woods and collect information about a tree there, assign it an identifier, and add it to my database, but that doesn't make it a living specimen because I don't assert that I have any control over it or that I can guarantee anyone that I can verify its status at will. If I band a bird and release it, I have assigned it an identifier and hopefully will be able to track it over time, but I can't claim it is a living specimen because I don't claim to exert control over it. That's different from John's wildebeest calf which is in a pen and be observed at will. It is similar to a maize plant in a field in Iowa which was cultivated by a human, but has no curator who is making sure that it can be found again and that it won't be harvested and ground up into wildebeest food without his or her knowledge. If I think about all of the kinds of things that I would like to put into the spot on the ASC diagram labeled "Collecting Unit" (including things like the Bicentennial Oak that was never "collected" by anybody), the one thing that they all seem to have in common is this aspect of being "accessioned". So I would assert that in a general model, "AccessionedUnit" would be a better name than "CollectingUnit". Some of the terms that I think should come out of Occurrence (such as preparations and disposition) could apply to any AccessionedUnit. So that brings me back to the question of whether this thing that I'm calling AccessionedUnit (which is sitting in the spot on the ASC diagram where Collecting Unit was originally) can or should be considered the same as what I have proposed to be the class dwc:Individual. The decision on this should not be made based on what we "think" an Individual should be, but rather on what we need it to be to fulfill the role that we have assigned it in our model. With that in mind, it might be better for the moment to change the name dwc:Individual to dwc:ResamplingUnitHavingDetermination because that is what it needs to do according to its current definition and location in the model diagram (I'm considering resampling to be the documentation of multiple Occurrences). The question them becomes: should AccessionedUnit be considered the same as ResamplingUnitHavingDetermination because they share the same properties (i.e. are described by the same terms)? To me the answer is clearly "no". It is very likely that an AccessionedUnit will never be associated with more than one Occurrence (i.e. be resampled), particuarly if it is dead and has been put in a museum collection. It is possible that the thing referred to by an AccessionedUnit might be documented by multiple Occurrences if it is alive (like the Bicentennial Oak), but that is not an intrinsic property of an AccessionedUnit in the same way that preparations or disposition would be. On the other hand it is also quite clear that many "ResamplingUnitHavingDetermination"s will never become accessioned. That would include the banded bird, a tree photographed in the forest, or a whale observed swimming in the ocean. The longer I think about this, the more convinced I am that making a distinction between AccessionedUnit and ResamplingUnitHavingDetermination is the best course of action. Having made a decision about this based on functional need and shared properties, it is still helpful for me to try to develop a mental image of what these two things are. In my mind, I imagine the ResamplingUnitHavingDetermination (which I will henceforth return to calling dwc:Individual) to be an entity having a homogeneous taxonomic identity. It has some moment when it came into existance as a living thing (by being born, planted, or founded) although we will never know when that moment was unless an Occurrence happens that allows us to document that Event. The Individual remains an entity as long as it has the potential to be documented as an Occurrence. That doesn't necessarily means that it must be alive. But if it decomposes, or is preserved and put into a collection, it no longer is capable of being resampled (i.e. documented by an Occurrence). Thus a fossil that is dead for a million years and is sitting in some stratum still fits my mental image of an Individual. If it gets chipped out of the rock and put in a museum, there would no longer be any point in documenting another Occurrence for it since there would be no useful Location or GeologicalContext information to be gained from that. A roadside population of herbaceous plants having homogenous taxonomic identity would be an Individual from the first time it was capable of being sampled (when it was founded) and would end being an Individual when it was extirpated by some road construction crew and was no longer capable of being documented by an Occurrence. A wolf pack would be a similar case. My mental image of AccessionedUnit is an entity that comes into existence when some human person or institution takes control of it, assigns it an identifier, and keeps records of it. I think I would never see it as coming to an end. Even if it is lost or destroyed, it would continue to exist as long as the person or institution maintains its record. It would just have dwc:disposition "lost" or "destroyed". It could be a dead, preserved specimen in a jar or glued to a sheet of paper, a living wildebeest calf in a zoo, or even a field sampling plot in a park as long as the park exerts control and ownership over it and maintains records about it. It could not be any wild, free-ranging animal or plant. It could not be roadkill left on the side of the road to decompose. It could not be a photograph of a wildebeest calf in the zoo, or the sound recording of the wildebeest calf's grunt. It COULD be a tissue sample from the wildebeest calf or from the roadkill. The critical thing is that it is a physical artifact originating from a living thing that has been cataloged and placed under human control. I think this is the kind of thing that Rich wanted to be able to define when he wanted to broaden the definition of Individual. For any entity having an origin as a living thing (in my mental image), its status as an Individual is independent of its status as an AccessionedUnit. If the entity is removed and preserved in its entirety (fish killed and put in a jar of formaldehyde), it ceases to exist as a dwc:Individual and begins to exist as an AccessionedUnit. If a branch is removed from a tree or one plant pulled from a roadside population to become specimens, the removed part becomes an AccessionedUnit while the dwc:Individual continues to exist. In the case of the Bicentennial Oak or a permanent sampling plot, the entity simultaneously exists as both an AccessionedUnit and a dwc:Individual. In terms of metadata records, the establishment of any AccessionedUnit is an Occurrence (grouped under the Individual) having a property of recordedBy. Whether or not subsequent Occurrences are possible for the Individual depends on whether the act of creating the AccessionedUnit has rendered subsequent sampling irrelevant. I agree with the point that was made previously that no specific taxonomic level should be placed in the definition of Individual. That would allow for the possibility that Individuals could contain several different lower level taxa as long as the Individual is homogeneous at the taxonomic level at with the determination is applied. I am open to suggestion for how this could be accomplished. Somehow there needs to be a value for a term like "individualScope" that allows one to make the kind of inferences about duplicates that I described previously. Maybe one controlled value for "individualScope" should be "DuplicateLevel" meaning that the Individual is homogeneous in taxonomic identity to the level at which a taxonomist would collect multiple specimens and call them duplicates. That would get us out of the problem of deciding whether the several grass stems we collect and send off to different herbaria are actually the same biological individual or clones connected by underground stems. Other possible levels could be "BiologicalIndividual" for things known to be single biological individuals, and "Heterogeneous" for things that are know or suspect to be mixtures of lower level taxa but for which it is convenient to assign a determination at a higher taxonomic level at which we know the mixture to be homogeneous. For AccessionedUnit, I think there should also be an accessionedUnitScope term. I defer to the museum people on this, but the boxes in the ASC diagram (unsorted lot, lot (presumably homogeneous), specimen (presumably one biological individual), and specimen component) could be a starting point. The "partOf" and "hasPart" properties could be used to related AccessionedUnits that are related to each other. Relating these various levels of AccessionedUnits to levels of Individual above "DuplicateLevel" is going to be tricky, but if people want to do this, I'm sure there is a way to represent the relationships in RDF. THE BOTTOM LINE I believe that the proposed definition for the DwC class Individual should stand as it is (i.e. as a node to connect multiple Occurrences to multiple Identifications). To allow Identifications for Individuals that are homogeneous at higher taxonomic levels, we also need a term like dwc:individualScope. I believe that there needs to be a separate class that represents what I've described here as "AccessionedUnit" which also has some kind of scope property. I am not going to propose a name for this thing or propose what properties belong with it. Rich and the herbarium/museum/botanical garden/zoo people need to decide and propose that. AccessionedUnit then becomes one of several types of evidence that can be used to support an Occurrence, with dctype:StillImage, dctype:Sound, dctype:Text as other possibilities. Darwin Core does not need to define their properties and types since others (MRTG, DCMI) have already done so. We then need two more terms: one to relate the evidence to the Occurrence and one to relate the Occurrence to the evidence (I would suggest "hasEvidence" and "isEvidenceFor" as possibilities). If we can do these things, I think we could say that a general (i.e. denormalized enough to satisfy everyone who is dissatisfied at the present moment) Darwin Core model is "complete" to the "left" of Identification on the http://bioimages.vanderbilt.edu/pages/full-model.jpg diagram. I'm not going to touch the Taxon side right now. Whether or not action is taken on creating a class for what I'm calling "AccessionedUnit", there is no reason to hold up action on my Individual class proposal if people agree with the points I've made here. Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 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) 343-6707 http://bioimages.vanderbilt.edu

5 13

Ontology
by Lee Belbin 14 Nov '10

14 Nov '10

Re (0) - fair point Roger, but as I said (implied maybe) in my last post, surely the most significant use case is the harmonization of old and new TDWG standards?! Your 'stool' analogy is currently missing at least one leg. Lee Lee Belbin Geospatial Team Leader Atlas of Living Australia

3 2

Relation of GNA to TDWG vocabularies
by Bob Morris 13 Nov '10

13 Nov '10

What will be the relationship of the GNA to the TDWG ontologies now managed at http://code.google.com/p/tdwg-ontology/source/ (or at least to those parts concerned with names) ? Thanks Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

5 8

Background for the Individual class proposal. 2. Classes and types
by Steve Baskauf 13 Nov '10

13 Nov '10

I'm going to start this post with two comments about RDF. I think some people think they have a phobia of RDF (I know that I did at first). What I really think is that they have a phobia of RDF represented as XML or RDF represented in N3 notation. This point has been made before: RDF is a system for describing properties of and relationships among resources (i.e. things that can be assigned identifiers) but it does not have only one particular way that these properties and relationships must be specified. It is perfectly correct to represent RDF entirely in pictures (i.e. as an RDF "graph", see http://www.w3.org/TR/rdf-primer/ and ignore all of the text - just look at the figures). RDF graph notation wouldn't be of much use to a computer, but that graph could easily be translated into one of the other notations (XML or N3) and then a computer would understand it perfectly. Since RDF is something that is specifically designed to represent relationships among classes of resources, it is the perfect thing to clearly lay out what we mean when we have a discussion of the sort that we are having here. One of the reasons why I am so keen to make diagrams of the sort I posted in the first message in this series is because once you have the diagram, it is a relatively simple matter to change the shapes of the boxes and add arrows instead of triangles or lines with crow's feet and voila! you have an RDF graph. It then becomes an academic exercise to have an RDF model in XML or whatever format you like. I am of the opinion that we are actually pretty close to a consensus about what the diagram should be, which means that we are also pretty close to a simple RDF model for Darwin Core. The other comment about RDF is that we need to work out a basic model now. Partly this is because there are already several people who have been contributing to this discussion who are already writing RDF or who intend to do so in the near future. If we have any delusions about doing even the most simple kind of machine reasoning in the future, we all need to be using the same basic diagram (i.e. model). The other reason why we need to work this out now is that if we don't, we will impede the process of utilizing GUIDs/Persistent Identifiers. The draft TDWG GUID Applicability Statement (http://www.tdwg.org/stdtrack/article/download/150/51 recommendation 10) says clearly that a proper GUID should be able to be dereferenced to provide an RDF/XML representation (did I use "dereferenced" right, Bob?). If we don't agree on how to represent the classes of resources that are of interest to the DwC community in RDF then we are setting up the situation where TDWG makes a recommendation (on how GUIDs are implemented) that is impossible for people to follow. I believe that it is best to settle on a basic model now rather than at an indefinite point in the future for this reason. Having given this rationale, I'm going to talk about how we look at classes and types in Darwin Core and how the need for an RDF representation of DwC should influence our view on this topic. In Darwin Core as it stands (see the "Audience" section of http://rs.tdwg.org/dwc/terms/index.htm) classes are simply categories that group terms that describe instances of the class. The description specifically states that the terms are intended to be properties of the class (i.e. properties of instances of the class). When DwC terms are used as column headings in a database table, there isn't any "rule" that say that one must specify the type of thing to which that term applies. On the other hand, I think that it is considered a Bad Thing in RDF to apply properties to a resource having an unspecified type. It's not impossible to do so, but specifying the rdf:type of a resource is one of the most fundamental things that one does in creating a description of the resource. This is recognized in the TDWG GUID Applicability Statement (recommendation 11) which says that objects identified by GUIDs should be typed using a well-known vocabulary. One "well-known vocabulary" is the Darwin Core Type Vocabulary (http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm) There isn't any formal relationship between the Darwin Core classes in the dwc: (http://rs.tdwg.org/dwc/terms/) namespace and the types in the dwctype: (http://rs.tdwg.org/dwc/dwctype/) namespace. We could use the dwctypes to describe resources that we want to say are instances of dwc: classes (and meet the GUID guidelines), but that would raise problems that I will get into later. The point is that as Darwin Core is currently set up, there isn't a formal relationship between the dwc: classes that are used to group the terms and the dwctype: types that could be used to rdf:type them. As it is described, the dwctype vocabulary is simply stated to be used as values for basisOfRecord and as I pointed out in the previous post, basisOfRecord only really works when Occurrences are limited to having a single token. In RDF, the relationship between classes and types is different from the way it currently stands in Darwin Core. RDF classes and types are tied together by definition (http://www.w3.org/TR/2004/REC-rdf-schema-20040210/#ch_type) If you assert that a resource has an rdf:type of X, you are simultaneously asserting that the resource is an instance of class X. The relationship between a class in RDF and the declaration of rdf:type is so entwined that naming a XML container element by the class of the resource is an instance is identical to an explicit declaration of type. The following two examples produce exactly the same result if you paste them into an RDF validator like http://www.w3.org/RDF/Validator/ : <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <rdf:Description rdf:about="http://bioimages.vanderbilt.edu/baskauf/10692#occ"> <rdf:type rdf:resource="http://rs.tdwg.org/dwc/terms/Occurrence"/> </rdf:Description> </rdf:RDF> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dwc="http://rs.tdwg.org/dwc/terms/"> <dwc:Occurrence rdf:about="http://bioimages.vanderbilt.edu/baskauf/10692#occ"> </dwc:Occurrence> </rdf:RDF> Even though there is no explicit declaration of rdf:type in the text of the second example (i.e. the dwc:Occurrence container element is empty), the validator treats the code as if a type property were stated explicitly - you can see that the resulting triple and graph created by the validator shows the RDF as having made an explicit declaration of rdf:type=dwc:Occurrence. So my point is that to enable people to follow the TDWG GUID recommendations and provide RDF that tells people the type of the resource, TDWG bears a responsibility to provide GUID users with terms that are suitable for use as an rdf:type property for every class of resource that we can reasonably be expected to want to assign a GUID. In my book, that's every box shown on the summary diagram http://bioimages.vanderbilt.edu/pages/full-model.jpg except for tokens (and excluding Time if we agree that we will always denormalize it out of existence as a class). I exclude token as a group because they are not a single class of resource. Any type of resource that provides evidence that an Occurrence happened can be a token. In some cases (such as images and sounds) those types are already defined in Dublin Core. Darwin Core would only need to define types for things that aren't defined elsewhere, such as the Collecting Units in the ASC model (but this is the topic of the third installment). One way to do this (and the way that I favor) is to make sure that there is a Darwin Core class for every category of resource for which one would reasonably expect to assign a GUID. Referring to the full model diagram, the only categories that don't have classes at the moment are Individual (which I have proposed to add), Time (which may or may not be necessary), and Collecting Unit (again, more on this in the final installment). The first category could be created by voting to accept my proposal about the class Individual. The last would require a new recommendation, but I think that Rich has pretty much suggested that this should happen when he says that there are a lot of terms in the Occurrence category that don't belong there (i.e. they belong with Collecting Units). So it would make sense from the point of view of a more logical organization of terms to do this anyway. As Bob has pointed out, in RDF making a declaration of rdf:type=X is the same thing as declaring that class X exists. So why not make the rdf:types BE the Darwin Core classes so we will be declaring something that actually does already exist instead of conjuring up virtual classes from types that we make up? There have been some people who have questioned my proposal for adding Individual as a DwC class on the basis that it is not clear that anybody "needs" it. What I am stating here is that anybody who plans to write RDF following recommendations based on a fully normalized Darwin Core RDF model (which should be EVERYONE who writes RDF using Darwin Core!) "needs" all of the classes that connect resources they plan to describe. That means that anybody who plans to connect Occurrence metadata to Identifications should be doing it in their RDF through named instances of the dwc:Individual class. Another alternative would be to fix the dwctype vocabulary, but that would be messier. The dwctype vocabulary is designated as the controlled vocabulary for basisOfRecord, so it is a bit dangerous to mess with it without breaking basisOfRecord. The other problem as was noted earlier on the list is that currently certain types in the DwC type vocabulary are declared as subClasses of other types, and that these declarations will cause unintentional assertions that don't make sense in the context of the general model that we've been discussing (namely that every PhysicalSpecimen is an Occurrence which is also an Event). It seems to me that there is more "fixing" required here than is worth the effort given that we can just use the classes as the rdf:types as I described in the previous paragraph. The final alternative would be to make the TDWG Ontology functional and use it to type resources. Although there has been some recent discussion on the list about working on the Ontology, at the present moment there isn't a clear plan or timeline to finish it. Telling people to wait for something that may never happen is not an acceptable alternative to me. I think it is clear that there are multiple people and institutions that are either ready to write RDF in support of GUIDs or are already doing it now. Six months is about the longest timeframe that I think is reasonable for coming up with a solution to the typing problem discussed above and to have some kind of basic guidelines for the structuring of RDF. A general model based on the existing Darwin Core classes is the only path forward that I can see as feasible in that time frame and a general model could always be build into a more sophisticated model (i.e. the Ontology) at liesure if anyone cared to take the time. If TDWG doesn't get its act together on a six-month to one year time scale, people will simply give up and write Darwin Core-based RDF without any TDWG guidelines. It has been suggested that a Task Group be formed to draft a DwC RDF Guide. I would be very keen to see that happen and would be willing to be involved in the process, but I'm not interested in it if the process doesn't start out with some version the consensus model we've discussed here and with some quick decision from the TAG about how to handle the rdf:typing problem. Without those two things, there would just be endless unproductive debate about how to go about building the model from scratch and I've got better things to do than that. I will end this with one final comment about the proposed Individual class in this context. I have stated clearly in several earlier posts that I don't think that the Individual class really has many properties and that it functions primarily as a named node to facilitate one-to-many relationships with other classes. This may strike some people as odd, given that the primary purpose of classes in the existing Darwin Core seems to be to group similar terms that can act as properties for the class. What became apparent to me when I was creating the diagrams for the first post was that if the Time terms are pulled out of the Event class (as they probably should be in a fully normalized model) and the "Collecting Unit" terms are pulled out of the Occurrence class (as I think must happen if we separate tokens from Occurrences), there are also very few property terms left in the Event and Occurrence classes. Most of the terms that remain are "housekeeping) ones used for remarks, or to make note of the person who documented the instance and when. Most of the terms that actually describe measurable properties are found in the peripheral classes like Location, Time, and Collecting Unit. Just as in the case of the proposed Individual class, the Event and Occurrence classes are primarily named nodes that connect other classes. The only reason they have very many terms at the present is because we have some of the terms in the "wrong" place for a fully normalized model. I think that it is also no coincidence that these three classes (Event, Occurrence, and Individual) are also the three that we have had the most trouble defining. I think that's precisely because they have very few properites of their own. They do roughly correspond to things for which we have conceptual images, which is why we are able to come up with meaningful names for them. But as I have argued, it is better to define them according to what we want them to DO rather than by our mental image of them. And that is a lead-in to the third and final post. -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 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) 343-6707 http://bioimages.vanderbilt.edu

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Background for the Individual class proposal. 1. Denormalization of models and correspondence to the ASC model
by Steve Baskauf 13 Nov '10

13 Nov '10

This is part 1 of three messages that attempt to summarize the issues that we have been discussing over the last month and to suggest a solution and a way forward. If you zone out when you get emails longer than three lines, please erase the messages and go on with your life. Unfortunately this is a complicated topic and I'm trying to lay out the issues in the simplest and most straightforward way that I can. The first email (this one) describes how a fully normalized model of Darwin Core can arise from modifying the ASC model to meet articulated needs of the Darwin Core constituency. The second email will describe why we need to come to a consensus on this and the criteria that I think should be considered before a decision is reached. The third email discusses the issue that Rich has raised as to whether the proposed Individual class should have a rather narrow scope (as I have advocated) or if it should be broadened to include other functions. I have separated this material into three emails because they are really separate but related issues and may each spawn threads relating to the particular issue. ---------------------------------------------------------------------- To try to get a better understanding of the issues we have been discussing, I went back to the Association of Systematics Collections (ASC) information that Stan posted at http://wiki.tdwg.org/twiki/bin/view/TAG/HistoricalDocuments - in particular, the chart http://wiki.tdwg.org/twiki/bin/viewfile/TAG/HistoricalDocuments?rev=1;filen… I have cut out a section of that chart that will fit on one screen and have created several images that have various models involving Darwin Core classes pasted at the top. Each subsequent Darwin Core class model is more normalized than the previous one. Below each model I show how that denormalization maps to the ASC model. The first diagram is the ASC model itself http://bioimages.vanderbilt.edu/pages/asc-model.jpg There are several differences in names between ASC and DwC. dwc:Location corresponds to Locality in ASC, dwc:Event corresponds to Collecting Event in ASC, dwc:Identification corresponds to Determination in ASC, and Collecting Unit in ASC corresponds to a subset of what I have been calling the "token" (evidence), that is limited to organisms, their pieces, and their conglomerations. One may quibble about exact correspondence, but I think that fundamentally those things are congruent. In the ASC model, the lines with crow's feet correspond to one-to-many relationships, with the foot at the "many" end. In my diagram a triangle does the same thing with the point of the triangle representing the "one" end. As you can see, the subset of the ASC model shown here can summarized in simplified form using DwC classes (excluding for the time being the parts of the model that fall into the DwC Taxon class). The ASC model reflects the "museum" perspective: in many or most cases the whole organism is collected, or if only part of the organism is collected (e.g. tree branch) the organism is rarely re-visited for additional collections. So this model is denormalized (flattened) to the extent that it doesn't allow for multiple types of tokens per organism and resampling of the organism over time. The second diagram represents Darwin Core at the time it became a standard in 2009. http://bioimages.vanderbilt.edu/pages/darwin-core-model.jpg The difference from the previous diagram is the creation of the Occurrence class. This class recognizes the needs of the observation community because it allows one to connect Events to Determinations directly without forcing them to be associated with a physical object (token). This modification was beneficial because terms describing the act of documenting the presence of a taxon during an Event are shared between observations and specimen collection. This model presupposes that there is no more than one token per Occurrence. dwc:basisOfRecord is used to describe the nature of that one token. Terms for handling tokens other than specimens are not well developed. The third diagram is a slight modification of the second and is what I've been calling the "explicit token" model: http://bioimages.vanderbilt.edu/pages/dwc-explicit-token-model.jpg The only difference between it and the previous model is that there is now recognition that the token is a separate thing from the Occurrence. Types of tokens other than specimens (such as images and sounds) are recognized explicitly as means of documenting Occurrences. The lines connecting Occurrence to tokens have "crow's feet" on the token side, allowing that there may be one to many tokens that act as evidence for a single Occurrence. When I complain that basisOfRecord "doesn't work", it is with this model in mind. In this model, there is not one single "basis" (token) for a record - under this model there would need to be the possibility to have multiple basisOfRecord values for an Occurrence, which I don't really think is supported currently in DwC. The fourth diagram, which I call the "full model" adds one more component to the explicit token model: http://bioimages.vanderbilt.edu/pages/full-model.jpg This model is what I consider to be the fully normalized version of Darwin Core (excluding the Taxon parts). This model introduces the Individual class exactly as I have defined it in my proposed term addition: as a node that connects Occurrences to Identifications (a.k.a. Determinations). This is not really an addition to the existing Darwin Core standard because the term individualID already exists in the Occurrence class. My proposal simply gives a name to the thing that is the object of individualID - in fact my original justification for the term addition says exactly that. The fundamental purpose that Individual serves is to accommodate the "crow's foot" on the Occurrence side of the line that connects Individual to Occurrence, i.e. to allow re-sampling over time and space. That is all. The line going to Identification/Determination has to be connected somewhere and it makes sense to connect it to Individual rather than Occurrence since the resampled entity is not going to change its identity from one sampling to another. I have done one more thing in this model to make it more denormalized. It's a spin-off from Paul Murray's post http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001771.html which got me to thinking that if we were to treat time in the same way we are treating Locations and other entities a fully normalized model would have a class for Time since time can have varying degrees of specificity (just like Location and Taxon) and there is a one-to-many relationship between Time and Event (i.e. there can be many Events going on at different Locations at a given Time, just like there can be many Events at different Times at a given Location). We almost always denormalize the Time class out of our models because in most cases it can be represented as a single ISO 8601 string. But as Paul points out, Time can be a complicated thing that one might want to model in a more sophisticated way than a single string. I'm not suggesting that we should do this in Darwin Core if nobody needs it, but the point is that it COULD be done. There probably already is a class for Time defined by somebody else (does anyone know about this?). In summary, the fully normalized model that I have presented seems to be consistent with almost all of the discussion that has taken place on the list recently. Although the ASC model is "more normalized" than this in some parts, I haven't heard many of the participants in the discussion advocating for a general Darwin Core model that is more complex than what I've presented in the last link. Obviously, individuals (humans) could add many more classes of things in their own personal models, but I think the classes in this last model can acommodate nearly all of the resources people have said that they want to describe using Darwin Core. End of part 1 -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 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) 343-6707 http://bioimages.vanderbilt.edu

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TaxonConcept Ontology, Test Data Set, SPARQL Endpoint, HTML and RDF representations
by Peter DeVries 11 Nov '10

11 Nov '10

I have cleaned up my ontology* at : http://lod.taxonconcept.org/ontology/txn.owl <http://lod.taxonconcept.org/ontology/txn.owl>It validates here: http://owl.cs.manchester.ac.uk/validator/ Here is a small sample of species concepts, occurrences and related data in one gzipped .rdf http://lod.taxonconcept.org/txn_base.rdf.gz It includes these examples: http://lod.taxonconcept.org/examples.html This small file should allow people to test inferencing etc. I expect and would encourage people to try it to see if they can find something wrong, or some utility that they would like. I have a sparql endpoint that is described here: http://www.taxonconcept.org/sparql-endpoint/ The data set should also be available on the LOD Cloud Endpoint http://lod.openlinksw.com/sparql http://lod.openlinksw.com/isparql/ * This is live most of the time except when I am updating the server or data. The HTML and RDF representations have changed since my last update. Here is are two examples: http://lod.taxonconcept.org/ses/iuCXz.html http://lod.taxonconcept.org/ses/iuCXz.rdf <http://lod.taxonconcept.org/ses/iuCXz.rdf> http://lod.taxonconcept.org/ses/dwAmr.html <http://lod.taxonconcept.org/ses/dwAmr.html> http://lod.taxonconcept.org/ses/dwAmr.rdf <http://lod.taxonconcept.org/ses/dwAmr.rdf>* Once I have this worked out I have no problem with TDWG/GBIF/EoL taking this over. I just need a live namespace in which changes can be made quickly. Respectfully, - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

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TDWG and the Darwin Core
by Jim Croft 11 Nov '10

11 Nov '10

"Alpha and Beta discuss the lack of a semantically rich version of the Darwin Core." you are a bad man Bob Morris... :) http://www.xtranormal.com/watch/7632561/ -- _________________ Jim Croft ~ jim.croft(a)gmail.com ~ +61-2-62509499 ~ http://www.google.com/profiles/jim.croft 'A civilized society is one which tolerates eccentricity to the point of doubtful sanity.' - Robert Frost, poet (1874-1963)

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Request for vote on proposals to add Individual as a Darwin Core class and to add the term individualRemarks as a term within that class
by Steve Baskauf 11 Nov '10

11 Nov '10

I am pleased with the significant and thoughtful discussion that has taken place on the tdwg-content email list regarding the relationships among Occurrences, Individuals, and other entities that are a part of the community's thinking about biodiversity metadata and the way that those metadata are structured. It appears from the discussion that there is widespread acceptance of the idea that Individual as a concept has a place in the structuring of biodiversity metadata and that there is some consensus of what "Individual" means (i.e. an entity ranging from actual biological individuals to small coherent populations that can reliably be asserted to represent a single taxon). Whether that acceptance and consensus constitutes a compelling need for adding two new terms (the class dwc:Individual and dwc:individualRemarks) to the Darwin Core standard or not is the point of a TAG "vote". Given the discussion that has occurred, it seems to me that there are two reasons why there is an actual need for those terms. One reason is that if members of the Darwin Core constituency intend to structure their metadata in a fully normalized manner that includes grouping Occurrences by Individuals (and it appears that there are at least several who intend to do this), the term dwc:individualRemarks is needed to provide a means indicate the nature of the individual (i.e. is it a biological individual, clonal individuals, a small population, etc.?) and the class dwc:Individual is needed as the category within which to put individualRemarks so as to indicate that individualRemarks is a property of Individuals. The second reason for explicitly recognizing Individual as a class is that it would place a term representing the concept of "Individual" within a "well-known vocabulary". I feel that would be critical for facilitating the ultimate development of a recommendation for the representation of Darwin Core as RDF. At this point, it is not clear to me that there are any other existing DwC terms that should be moved to a new Individual class. Originally, I suggested that individualCount should be placed in that class, but I no longer think so. Counting the number of individuals is really something that happens when an Occurrence takes place and a small cohesive group of a single taxon (e.g. wolf pack or plant population) could have an individualCount that changes over time. As was discussed earlier in on the email list, the xxxxxxID terms probably really belong in the Record-level terms category rather than being listed within particular classes. So I don't believe that dwc:individualID should be in the proposed class either. As I detailed in my Biodiversity Informatics paper, an Individual is really an entity that serves primarily as a node that allows the grouping of other resources (namely Occurrences and Identifications). As such, it really has few (or no) properties that can be known outside of Occurrences. Thus I would like to "call the question" on the issue of the proposal. I would suggest that the issue of adding the class dwc:Individual and the term dwc:individualRemarks within it be addressed in a single vote, since there little point in having one term without the other. I would also hope that those on the TAG who choose to vote would review the list discussion carefully first. Given that the question of "what exactly is an Individual?" came up a few times after that question was clearly answered in the thread is an indication that some people entered the thread later on without the benefit of having read some of the earlier posts. Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 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) 343-6707 http://bioimages.vanderbilt.edu

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Re: [tdwg-content] tdwg-content Digest, Vol 20, Issue 17
by Nico Cellinese 10 Nov '10

10 Nov '10

Steve is using Species as ranks in his definition and I think this is the wrong approach. Let's make all this rank agnostic please! Use the word taxon! What if I have a group of organisms that represents a polyphyletic species and I want to name a lineage (group of organisms) within this traditionally recognized species that I am not recognizing as species per se (as in rank of species). In other words, Identifications and ranks are two different things, so let's abandon ranks for a more objective discussion on taxa. Individuals are definitively not species. Nico (the other one) > > On Wed, Nov 3, 2010 at 7:24 AM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> wrote: > > John, > I'm not sure that I agree with your analysis that the definition prevents the possibility of making an Identification at a rank less specific than a species. My revised definition says that the Individual should only include groups of organisms that are reliably known to be of a single species - it doesn't say that we need to know what that species is (i.e. an identification to genus or family can be made with the hope that someone down the line would be able to refine the identification to species). Clarification on this point could be added to the comment or the Google Code page, but I don't think there is a problem with the definition per se. However, if there is a consensus that the definition is too restrictive, I would not object to changing the wording of the definition from "species (or lower taxonomic rank if it exists)" to "taxon" if there were clarification added to the comments or Google Code page that Individual was not intended to include aggregations of mult > > iple species. > > I agree that there is a need for a term that represents "collections", "bags", "aggregations", or whatever you want to call an aggregation that includes multiple species. But I have never intended that Individual should be that term. If we expand Individual to include aggregates, then it becomes unusable for its original intended purpose. I would prefer for someone to propose a different term for aggregates of individuals instead of adding that function to Individual. Then define the relationship of this new thing to Individual as a one:many relationship (one aggregation:many Individuals). > > Steve > > > John Wieczorek wrote: > Most of you probably do not receive postings from the Google Code site for Darwin Core. Steve B. updated the proposal for the new term Individual, and then commentary ensued on the Issue tracker. Since there remains an unresolved issue, I'm bringing the discussion back here by adding the commentary stream below. The unresolved issue is Steve's amendment is the restriction in the definition to "a single species (or lower taxonomic rank if it exists)." > > > > Rich argues that we should not obviate the capability of applying an Identification to an aggregate (e.g., fossil), where the aggregate consists of multiple taxa. > > Steve argues that Identifications should be applied only to aggregates of a single taxon. > > > > > Steve, aside from the aggregate issue (which should be solved satisfactorily), your suggestion is too restrictive, because it would obviate the possibility of making an Identification (even for a single organism) to any rank less specific than a species. That is a loss of capability, and therefore unreasonable. > > > > > > Comment 7 <http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%2…> by baskaufs <http://code.google.com/u/baskaufs/> , Today (8 hours ago) > As a result of the discussion that has taken place on the tdwg-content email list during 2010 October and November, I am updating the term recommendation for Individual as follows: > > Definition: The category of information pertaining to an individual organism or > a group of individual organisms that can reliably be known to represent a single species (or lower taxonomic rank if it exists). > > Comment: Instances of this class can serve the purpose of connecting one or more instances of the Darwin Core class Occurrence to one or more instances of the Darwin Core class Identification. > > Refines: N/A > > Please note that as a precautionary measure, I have removed the statement that Individual refines http://purl.org/dc/dcmitype/PhysicalObject because the definition of PhysicalObject specifically mentions that the object is inanimate. I am not currently aware of any well-known term that defines living things. > > Steve Baskauf > > > > > Delete comment <http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%2…> > > Comment 8 <http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%2…> by deepreef(a)hawaii.rr.com <http://code.google.com/u/deepreef@hawaii.rr.com/> , Today (8 hours ago) > I think the definition should be "...represent a single taxon". We shouldn't restrict it to members of the same species (or lower), because then we technically can't include things that may represent more than one species, yet would best be treated within the scope of an Individual. > > Also, I'm slightly partial to the term "Organism" for this class, rather than "Individual", because it's more clearly tied to the biology domain, and less likely to collide with the word "Individual" in other domains. I know such collision is not a technical problem, but it might lead to some confusion. > > > > Delete comment <http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%2…> > > Comment 9 <http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%2…> by baskaufs <http://code.google.com/u/baskaufs/> , Today (8 hours ago) > Well, the reason that I defined it to be members of the same species is to ensure that the term Individual can serve the primary function that I perceived was needed: to make the connection from occurrences to identifications. When I said one or more identifications, I meant one or more opinions about what that single species (or lower) was, not that there could be multiple identifications of several different species that happened to be in the same "bag" such as the contents of a pitfall trap containing multiple species, an image that contained several species, or a specimen that contained parasites of a different species. I think that there is a need for a term for this other kind of thing, (a heterogeneous "lot", "batch", or something), but I think that including this in definition of Individual defeats the purpose for which I proposed it. If there were several different species in the "Individual", then > one would have to specify which identification went with which biological individual within the "lot", which would result in actually breaking down the "lot" into single species "Individuals" anyway. > >

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