November 2010 - tdwg-content

"Individual" use case
by Dean Pentcheff 02 Nov '10

02 Nov '10

Count me in as another late entry to this discussion, lurking under the rumbling flight paths of the VLPs (Very Large Postings). Here's a potential case to consider in the whole "how to file all the parts" issues that seem to be arising. It's a parent/child scheme that we're implementing for our marine invertebrate specimen database. We think we are being reasonable in the way we thought of this. We hope that this concept could be accomodated by DwC. That's the sum of the contribution for consideration: we hope DwC can/will cope with this. It may well be that it happily does so under all of the "Individual" interpretations that are bouncing around. But hey, we thought we'd toss it in just to make sure. With marine invertebrates, we very often find ourselves subsampling collected things (yes, "thing" is deliberately vague to avoid misusing any heavy-baggage words). It is intrinsic to the nature of the collections. Things often arrive as unsorted lots (think of a jar full of coral rubble in 95% alcohol, sitting on our shelf). We want to have a record for that jar in our database, so it gets one, with a recordID. Months later, we sort the jar to phylum level, and each of those jars gets a record, each with a recordID, and those jars go on a shelf. We treat those records as children of the unsorted-lot-record, and they each have a pointer back to that unsorted-lot parent record. Then we later sort one of those phylum-level jars into species jars. Those, in turn, each get a record with a recordID, and point to their parent phylum-level-jar record. And so forth down to individuals in jars, and tissue samples of individuals, and DNA extracts of those tissues. To complete the picture: many specimens do, of course, come in simply as an individual in a jar. Those just get a record, and that's that: no parent, no child (no child yet... until there's a tissue sample). Key points: 1. We never know how many levels of subsorting there will be. That differs from the "preparation" orientation of many vertebrate collections (for example), where there's a predefined set of preps that can come from each collected individual. We very often don't start with individuals. 2. Each thing, whether it comes in the door directly or is derived from something that did, gets a first-class catalog record, and the sole unifying feature that gets us the full information on a thing are the parent-child relationships of the data records. Information has to continue to reside in those records and be accessible from the "children" (an example would be a transfer to a different preservative when pulling one individual into a specimen jar from a lot jar: you need to know the preservative this thing is in now, and you also need to know what preservative its parent thing was in). 3. One field of each record has to document whether the item still exists: a thing may be completely subdivided into subparts leaving nothing left over to put back on the shelf. But in that case, we still keep the data record since it's still the parent of the subsorted things and still holds the relevant historical information. So one day when we push these data out into the Wild World in a DwC context, the thing we'd like to see accomodated is the ability of systems outside our own walls to resolve back up that chain of subsorting to build the whole information set for a thing, including the relevant information from its logical "parents". OK, now we'll be delighted to hear that this scheme was obviously accomodated all along, or alternately, that this whole concept is a pretty dumb way of cataloging our holdings. -Dean -- Dean Pentcheff Research Associate, Natural History Museum of LA County pentcheff(a)gmail.com dpentche(a)nhm.org

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Updated TaxonConcept Occurrence Examples
by Peter DeVries 02 Nov '10

02 Nov '10

I have updated a number of the examples. The RDF representation creates, or makes statements about several separate entities. http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.html(S… to Bottom) * Now includes a way to document the original occurrence and id labels Here is the RDF http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.rdf TXN_FCT < http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f…> *The Occurrence*: http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurr… TXN_FCT < http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f…> URIburner < http://linkeddata.uriburner.com/about/html/http/ocs.taxonconcept.org/ocs/f5…> Sindice < http://sig.ma/search?pid=3e0bb912d2ab43e0efd7baa0bbcd1a4e > *The Individual * http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Indivi… TXN_FCT < http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f…> *An Identification * http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Identi… TXN_FCT < http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Focs.taxonconcept.org…> *The Species Concept* http://lod.taxonconcept.org/ses/ICmLC.html TXN_FCT < http://lsd.taxonconcept.org/describe/?url=http://lod.taxonconcept.org/ses/I…> Area geo:44.86528100,-87.23147800;u=10 < http://lsd.taxonconcept.org/describe/?url=geo:44.86528100,-87.23147800;u%3D…> Also there seem to be several OWL validators, some which are for OWL 1 others for OWL 2 OWL 1 http://www.mygrid.org.uk/OWL/Validator OWL 2 http://owl.cs.manchester.ac.uk/validator/ Updated the ontologies, but they are not 100% yet. Beware of Protege !!!, You can create things that look correct and validate in Protege but the actual .owl file is not correct. http://lod.taxonconcept.org/ontology/txn.owl 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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newbie comments on Individual
by Nate Flesness 02 Nov '10

02 Nov '10

This is a tough list to join - lots of specialized vocabulary and concepts (its purpose of course) - I've been "lurking" awhile, and this is the first time I think I understand and might have something small to add from the live collections point of view. Speaking from 30+ years at ISIS working with biodiversity data from 800+ institutions (zoos, aquariums, etc) on live animal individuals and groups, I'd expand Steve Baskauf's comment to say people need BOTH the ability to handle individual animals (a wolf) and ALSO the situation Where your data does not distinguish individuals but you track a group identity and some kind of count (a wolf pack... we do that, and/or by life stage, and/or by sex). Some live fish can be practically tracked as individuals, and sometimes obviously not because there are ~5000 in that tank. Some of our groups are too big to count individuals even as estimates (beehives, ant colonies), so we change the units and count colonies. I hope this was faintly relevant and look forward to meeting more of you in person when opportunity allows, Nate Flesness Director of Science International Species Information System (ISIS) www.isis.org<http://www.isis.org>

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Request for withdrawal of proposal to move dwc:establishmentMeans to proposed the DwC class Individual
by Steve Baskauf 02 Nov '10

02 Nov '10

In my previous understanding of Occurrence in which a single token was incorporated as a part of an Occurrence, I considered an Individual to have ceased to exist and to have become an Occurrence of type LivingSpecimen when it was collected to be part of a collection (e.g. zoo). Given this understanding, I felt that there were few or no cases where the establishmentMeans of an Individual would change (excluding its capture and incorporation in a collection) and therefore it made sense for having a single establishmentMeans value for the individual. However, under the apparent consensus opinion that the token documenting an Occurrence is a separate entity, I no longer believe that there is any purpose in recognizing an entity called "LivingSpecimen". A living specimen is simply an individual with curation information. The token for an Occurrence that involves the collection of a living specimen is the Individual itself (in the case of removal of the entire organism) or a different Individual (i.e. in the case where a new individual is propagated vegetatively from the Individual being documented by the Occurrence). Given this understanding, the establishmentMeans of an Individual can change over time, so it is not possible for every Individual to have a single value for establishmentMeans. The consensus that seems to have emerged from the tdwg-content discussion is that dwc:establishmentMeans is a complex thing that describes the relationship of an Individual to a Location that can change over time. I do not see how establishmentMeans is a property of an Occurrence - in fact it is not clear to me exactly how one applies establishmentMeans as a property to an instance of any existing DwC class. But in any case, there does not now seem to be any advantage to moving it from the class Occurrence to the proposed class Individual, so I officially withdraw my proposal if that is possible. Alternatively, the TAG could take a vote and vote the proposal down, but I think that would be a waste of time. 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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