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MIAPA Workshop at the TDWG 2011 meeting, New Orleans, LA
by Nico Cellinese 15 Aug '11

15 Aug '11

TDWG MIAPA Workshop Call For Participation: Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard Synopsis Many phylogenetic analysis results are published in ways that present serious barriers to their reuse in numerous research applications that would stand to benefit from them. While some of these barriers are well understood, such as issues with adherence to standard exchange formats, those centering on the associated metadata necessary for researchers to evaluate or reuse a published phylogeny have only recently begun to be articulated. One of the critical next steps towards formalizing these metadata requirements as a minimum reporting standard is to convene meetings of key stakeholder communities with the goal to identify information attributes necessary and desirable for facilitating reuse, and to build consensus on their priority. To this end, we are holding a workshop at the 2011 Biodiversity Information Standards (TDWG) Conference to determine how a future reporting standard for phylogenetic analyses can best serve biodiversity science and related research applications. We invite all interested colleagues to participate. Background The workshop of the Biodiversity Information Standards (TDWG) Phylogenetics Standards Interest Group held at the 2010 TDWG conference included a project focused on how to publish re-usable trees that can be linked into an emerging global web of data. Through follow-up work, this led to the following tangible results: An online draft report of the 2010 TDWG workshop [1], and a corresponding manuscript on best practices for publishing phylogenetic trees (Stoltzfus et al. in preparation); An 2011 iEvoBio presentation on “Publishing re-usable phylogenetic trees, in theory and in practice” [2]; A lighting talk presentation and Birds-of-a-Feather gathering at 2011 iEvoBio, and A survey group that explored barriers to re-use and developed plans for a survey These activities have considerably clarified our understanding of the theory and practice of publishing re-usable phylogenetic trees: how many phylogenies are published each year, the (low) frequency of archiving, what archives and tools are available, what policies are in force, etc. We have identified a number of barriers to re-use involving such aspects as technology, standards, culture, and access. Many of these barriers can be interpreted as a consequence of the lack of a community-agreed standard for what constitutes a well documented phylogenetic record. In the absence of such a standard, trees are often archived as image files rather than in appropriate data exchange formats, and lack important accompanying information (metadata), such as externally meaningful identifiers, that would be needed to make them useful to others. The idea of a Minimum Information About a Phylogenetic Analysis (MIAPA) standard has been suggested [3], but so far there has not been a deliberate process to develop and disseminate a community standard. Meanwhile, a number of systematics and evolution journals have begun to require archiving of the data underlying published research findings [4]. The emerging cultural shift in data archiving and sharing promoted by this policy change offers a unique window of opportunity to move ahead with the development and actual specification of a MIAPA standard. Similar to other minimum reporting standards [5], the primary focus of a future MIAPA standard would be on defining a “checklist” of metadata information attributes that, at a minimum, needs to accompany an archived phylogenetic analysis, and to which standards values for these attributes would need to adhere. The key step in developing community consensus on these elements of the standard is to convene a series of meetings that collectively involve participants from all major groups of stakeholders who would be affected by such a standard, such as users, producers, publishers, or archivists of phylogenetic analyses. To aid this process, the Phylogenetics Standards Interest Group is holding a workshop at the 2011 TDWG conference, with the goal to obtain consensus requirements and priorities for a MIAPA checklist for the purposes of biodiversity science, taxonomy, museum collections, and related research applications. Goals and deliverables The main goal of the workshop is to develop a shared understanding of the role that a MIAPA standard could play in facilitating re-use of phylogenetic analyses for the biodiversity science and related communities, and what the standard would need to specify in order to best fill that role. Possible deliverables include A draft set of information attributes that should or could be included in a provisional MIAPA checklist, with a level of consensus for each of them. A database with use-cases based on exemplifying publications, that report phylogenies to elucidate a broad spectrum of questions relating to biodiversity science. A refined MIAPA survey to be informed by biodiversity science cases for reuse. A plan for further community engagement and consensus-building among biodiversity science stakeholders. Workshop format The workshop will start with a few presentations focused on (i) introducing MIAPA and its potential in facilitating reuse (J. Leebens-Mack); (ii) summarizing recent developments and current status of MIAPA-related efforts (A. Stoltzfus); and (iii) past experiences and resulting best practice recommendations on developing a minimum reporting checklist standard (D. Field). The rest of the workshop will be hands-on. Participants in the workshop will break out into groups to address separate issues according to the anticipated deliverables and best practice recommendations. The workshop will be 1.5 days in duration, and be held during the 2011 Biodiversity Information Standards (TDWG) conference, to take place Oct 17 to 21, 2011 in New Orleans, USA. (http://www.tdwg.org/conference2011/) The workshop will start in the afternoon of Monday, Oct 17, and end on Tuesday. Oct 18. How to participate Participation in the workshop is open to everyone interested. However, space is limited, and we therefore ask that, if you are interested in attending, to please communicate your interest through the MIAPA discussion group [6]. This will also allow us to include you in pre-workshop planning. Since the workshop is part of the TDWG conference, participants will need to register either for the full conference, or for the days of the workshop. The organizers will provide an electronic venue for participants to share ideas and develop plans in advance of the workshop. After the initial presentations, participants will self-organize into task groups. Organizers Nico Celinese, University of Florida Hilmar Lapp, NESCent Jim Leebens-Mack, University of Georgia Enrico Pontelli, New Mexico State University Arlin Stoltzfus, NIST & University of Maryland References [1] Whitacre et al. (2010). Current Best Practices for Publishing Trees Electronically. http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010 [2] O’Meara et al. (2011). Publishing re-usable phylogenetic trees, in theory and practice. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2011.6048.1> [3] Leebens-Mack, J., T. Vision, et al. (2006). "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)." Omics 10(2): 231-7. [4] Whitlock, M., M. McPeek, M. Rausher, L. Rieseberg, and A. Moore (2010). Data Archiving (Editorial). The American Naturalist 175(2): 145. [5] Taylor, C.F., D. Field, S. Sansone, J. Aerts, R. Apweiler, M. Ashburner, C.A. Ball, et al. (2008). Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology 26(8): 889-96. doi:10.1038/nbt.1411 [6] MIAPA discussion group: http://groups.google.com/group/miapa-discuss Published by Google Docs–Report Abuse–Updated automatically every 5 minutes

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representation of pollen specimens in DwC; current practice?
by Bob Morris 06 Aug '11

06 Aug '11

I'd like to hear the practices of anyone who is actually using (or mapping) DwC to represent pollen specimens that reside in a collection different from the collection from that of the source. Especially: 1. Do you represent the pollen gathering as a different collection event from that of the source specimen. 2. What do you use to link the pollen specimen to the source specimen 3. If you use any DwC values of the source, do you make any attempt to synchronize changes to the source record with those of the pollen record. How? I really, really, would like to first hear answers from people currently doing this before people not doing it weigh in on what they think should be done. If you have service addresses at which I can fetch some pollen and source DwC records, that would help. Thanks Bob Morris -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Department of Organismal and Evolutionary Biology Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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Darwin Core vs. Simple Darwin Core
by joel sachs 04 Aug '11

04 Aug '11

Darwin Core is one of my favourite things. It's simple, elegant, and flexible. I wasn't there at design time, so I don't know if it was designed with the semantic web in mind, but it looks like it. It is, as John put it, primarily a collection of terms [and their definitions]. So if two people/agents use the same terms, they will share the same semantics. (This is why I think that a "more semantic Darwin Core" is not the appropriate goal for a Darwin Core/rdf working group.) I'm concerned that there's so much confusion concerning DwC, since confusion is (typically) a barrier to adoption. One source of confusion is Simple Darwin Core. A huge fraction of DwC records can be expressed as spreadsheets. Since *all* Simple DwC records can be expressed as spreadsheets, many people think Simple Darwin Core = spreadsheet-expressible Darwin Core (which isn't true). This means that if they want to express their data as a spreadsheet, they think they need to conform to Simple Darwin Core. The requirement of Simple Darwin Core is that there be no repeated elements. But the requirement for spreadsheet-expressible Darwin Core is that there be no repeated nested elements. I previously argued (http://lists.tdwg.org/pipermail/tdwg-content/2011-January/002220.html) in favour of using subscripts to represent elements in repeated nests (thereby permitting their use in spreadsheets). Even if we don't permit that, I'm not sure that the benefits of maintaing a separate Simple Darwin Core standard, in addition to the regular Darwin Core standard, are greater than the costs in terms of giving people wrong ideas. (I prefer the presentation at http://rs.tdwg.org/dwc/terms/guides/xml/index.htm, where Simple DwC is presented as simply one of several XML schemas for Darwin Core.) I *think* I see the motivation for Simple DwC. Suppose X wants to use Darwin Core, but doesn't know much about databases, and just wants to put all his data in a spreadsheet. He might not know what a repeated, nested data structure is. So it's easiest to just say to him "don't repeat any elements, and you'll be fine - your records will be spreadsheet-expressible". I agree that that's a benefit. Are there others? Thanks - Joel.

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Darwin Core XML data using class terms
by Donald.Hobern＠csiro.au 04 Aug '11

04 Aug '11

I've been giving some thought to the class terms and the examples of class-based DwC data in the Darwin Core XML Guide (http://rs.tdwg.org/dwc/terms/guides/xml/index.htm - see the Classes and Containment section). As this list has recently been discussing Simple DwC and the restrictions it imposes, I'd be interested in knowing of the experience of any projects that have sought to use the class terms as a mechanism for streaming richer data using Darwin Core. Can anyone provide examples of projects sharing data in this way? Are there any findings on the success of exporting and consuming class-based DwC data, in particular on the consistency of how such data are interpreted? Has anyone given thought to how a consumer would derive the equivalent of a set of best-fit Simple DwC records from the kind of class-based DwC presented in the guide's examples? Thanks, Donald [cid:image001.png@01CC4ADE.F6E045F0] Donald Hobern, Director, Atlas of Living Australia CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au<mailto:Donald.Hobern@csiro.au> Web: http://www.ala.org.au/

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New terms need resolution: "Evidence"
by John Wieczorek 03 Aug '11

03 Aug '11

None of this was entered as an issue in the Darwin Core Issue tracker. Rather, it arose from the discussion on DigitalStillImage (Issue 68). The Darwin Core simplifies the representation of concepts related to the occurrence of life in nature. Specifically, there is a Darwin Core Occurrence class, but no separate class to explicitly represent the physical evidence for the Occurrence. This is problematic when trying to be explicit about the attributes of physical or digital objects in the semantic world. Various names have been given to this concept, including "PhysicalObject", "Evidence", "PhysicalEvidence", "Sample", "Specimen", "CollectionObject" in the ASC model, "DataSets/DataSet/Units/Unit/..." in ABCD, "Representation" (Baskauf 2010) and "Token" as a preferred alternative to "Representation" in tdwg-content (http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001742.html) Open Issues: Determine if there is a general consensus on the need for new class for this concept. Decide the best name for this class. Create a new Type Vocabulary term referring to this new class. Change the Darwin Core Type Vocabulary terms that refine Occurrence (FossilSpecimen, PreservedSpecimen, LivingSpecimen) to refine the new Type Vocabulary term referring to this new class. Decide which properties currently organized under Occurrence should instead be organized under this new class. As a seed for further discussion, here is a complete proposal. ============== Term Name: CollectionObject Identifier: http://rs.tdwg.org/dwc/terms/CollectionObject Namespace: http://rs.tdwg.org/dwc/terms/ Label: CollectionObject Definition: The category of information pertaining to persistent evidence of a biological entity (specimen, sample, image, sound, drawing, etc.). Comment: For discussion see http://code.google.com/p/darwincore/wiki/CollectionObject Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: CollectionObject-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: {DataSets/DataSet/Units/Unit/CultureCollectionUnit or DataSets/DataSet/Units/Unit/MycologicalUnit or DataSets/DataSet/Units/Unit/HerbariumUnit or DataSets/DataSet/Units/Unit/BotanicalGardenUnit or DataSets/DataSet/Units/Unit/PlantGeneticResourceUnit or DataSets/DataSet/Units/Unit/ZoologicalUnit or DataSets/DataSet/Units/Unit/PalaeontologicalUnit or DataSets/DataSet/Units/Unit/MultimediaObjects/MultimediaObject} Term Name: CollectionObject Identifier: http://rs.tdwg.org/dwc/dwctype/CollectionObject Namespace: http://rs.tdwg.org/dwc/dwctype/ Label: CollectionObject Definition: A resource describing an instance of the CollectionObject class. Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Member Of: http://rs.tdwg.org/dwc/terms/DwCType Has Domain: Has Range: Version: CollectionObject-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: not in ABCD Term Name: collectionObjectID Identifier: http://rs.tdwg.org/dwc/terms/collectionObjectID Namespace: http://rs.tdwg.org/dwc/terms/ Label: collectionObjectID Definition: An identifier for the CollectionObject. 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 collectionObjectID globally unique. Comment: For a specimen in the absence of a bona fide global unique identifier, for example, use the form: "urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]. Examples: "urn:lsid:nhm.ku.edu:Herps:32", "urn:catalog:FMNH:Mammal:145732". For discussion see http://code.google.com/p/darwincore/wiki/CollectionObject Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/identifier Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: collectionObjectID-2011-07-04 Replaces: Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/CollectionObject ABCD 2.06: DataSets/DataSet/Units/Unit/UnitGUID Term Name: collectionObjectRemarks Identifier: http://rs.tdwg.org/dwc/terms/collectionObjectRemarks Namespace: http://rs.tdwg.org/dwc/terms/ Label: collectionObjectRemarks Definition: Comments or notes about the Collection Object. Comment: Example: "custody transferred in 1995 from National Park Service". For discussion see http://code.google.com/p/darwincore/wiki/CollectionObject Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2009-07-04 Has Domain: Has Range: Version: collectionObjectRemarks-2011-07-04 Replaces: SampleRemarks-2009-01-18 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/CollectionObject ABCD 2.06: DataSets/DataSet/Units/Unit/Notes Note that with the addition of CollectionObject, the InstitutionCode, CollectionCode, CatalogNumber triplet would no longer apply to an Occurrence. This is a big, non-backward compatible change. Terms to be organized under CollectionObject rather than Occurrence: catalogNumber preparations disposition otherCatalogNumbers Terms that might have to be added to under CollectionObject to retain capabilities currently achieved under Occurrence: associatedCollectionObjectMedia associatedCollectionObjectReferences associatedCollectionObjects associateSequences

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use cases and competency questions
by Steve Baskauf 28 Jul '11

28 Jul '11

For the benefit of the uninitiated (that would be me and possibly others), could someone please post definitions of "competency question" and "use case" along with a couple of examples of each? 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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Of Evidence and Individuals (Was Plea for competency questions)
by Richard Pyle 27 Jul '11

27 Jul '11

Hi All, I, too, am just back from an extended trip with limited internet access, and am catching up on this discussion. I think Steve's two recent posts are extremely helpful -- for me in particular. I very-much like the way he's framed the discussion around "competency questions" (however correctly the term is applied). I started off giving a detailed reply to the "Individual" (="BiologicalEntity") class post, but then decided to read through the "Evidence" post as well; and this lead me to deleting everything I had written and start from scratch. In summary, I largely agree with most of what Steve says in both posts, but I'm still more than a little bit nervous about the distinction between the two new proposed classes. In particular, this passage from Steve's post about the "Evidence" (="CollectionObject") class freaks me out a little bit: > So then what IS an actual individual organism like the wildebeest calf? > It is a BiologicalEntity if it has been documented as an Occurrence or > assigned an Identification. It is a CollectionObject if it was > collected for a zoo, or shot and mounted in a museum. Or it can be > both simultaneously if it is both documented and collected. If none > of these things were done, then it's neither a BiologicalEntity nor a > CollectionObject - it's simply a wildebeest calf. Define the > class/type of the thing by the properties that you wish to assert for > it (or the competency questions that you can answer for it). I think I get where you are coming from here, but I'm very queasy about this notion that the same "thing" (a mass of flesh & bones) can be represented as an instance of two different DwC classes, depending merely on what attributes about the "thing" are emphasized. For example, during my recent trip to South Africa, we took the opportunity of one of our non-diving days to visit a game park where we saw (among other things), numerous wildebeest (coincidentally enough). I took video images of these wildebeest with my GPS-enabled camera, and therefore documented the presence of a specific individual wildebeest at a particular date and time. Clearly there is a dwc:Occurrence record there, so it's certainly a BiologicalEntity (by your definition; i.e., documented as an Occurrence and assigned an Identification). But does a Game Park constitute the same thing as a zoo? There are electric fences around the perimeter of the park, so I'm inclined to think so. Is it also a CollectionObject? Would this be an example of something that is both? The more I think about it, the less confident I am that we really need *both* new classes. With such potential overlap between them, should we not simply generalize them both into the same class, and provide whatever properties are known/relevant in a DwC instance of it? You said that the CollectionObject class is fully capable of doing much of what I want to accomplish with my vision of "Individual". Could I not say the exact same thing that a broader definition of CollectionObject (i.e., one that doesn't attempt to distinguish the disposition of the same mass of flesh & bones in the context of human-mitigated captivity/preservation vs. nature) could be fully capable of accomplishing what you want to accomplish with Individual? Namely, the three competency questions you established for the "Individual" (=BiologicalEntity) class. > An actual single, live organism can serve both as a unit for > resampling and "attachment" of Identifications, AND as an > organizational unit that is part of and which has parts that are > biological samples. Some other entities, such as cohesive pack/herds > and clonal organisms can also serve both purposes. Other entities > cannot: it doesn't make sense to resample dead organisms or pieces of > organisms, I guess it depends on what you mean by "resample". Surely a tissue sample can be removed from a dead organism, and used for DNA sequencing that can lead to a new Identification instance. I agree that a dead organism cannot represent the basis for future Occurrence instances, but I don't really see the relevance of that. > Personally, I would like for the third function ("inferring > duplicates"; linking multiple Identifications to the same entity and > being assured that all Identifications of the same Individual would > apply to all artifacts associated with that Individual) to be > accommodated by the definition, I definitely support this, and on this basis, I am willing to abandon my earlier defense for what you would call taxonomic heterogeneity. I still feel the need to not limit the rank at which a taxon identification may be applied, but I am ready to abandon my original notion that a rock with multiple phyla of organism attached should ever be represented as a single instance with Identification "Animalia". In other words, I've come around to your perspective on this. I think the power of implied "taxon identification inheritance" that you advocate in your function #3 overrides my advocacy for taxonomically heterogenous organisms to be lumped together with the same instance of the class. Thus, I now agree with you on the following: > When I used that term, I intended for it to mean that the entity is > believed to be homogeneous to the lowest possible level in the way > that one knows that two branches from the same tree or two parts of > the same clonal organism are guaranteed to have the same taxonomic identify at every level. So, from my perspective, we can put that part of the debate to rest. > This email is now at or has exceeded the length of an email that many > people will take the time to read. So I will draw it to a close and > post a separate email on the topic of competency questions for John's > proposed class "CollectionObject" which I believe address Rich's > desire to track "real-world" objects (samples, re-samples, etc.). Rather than respond separately to the other post, I've just made this single response with the new subject heading, because I think we're narrowing down the scope of the debate in such a way that we should now focus on the difference between the two proposed new classes ("Individual"/"BiologicalEntity", and "Evidence"/"CollectionObject"). For a while, I thought I saw the difference as being the "Evidence" was more like an instance of "Documentation" (e.g., an image, a label on a preserved specimen, etc.); rather than the flesh-and-bones organism itself. But with your suggestion that this class may serve the function(s) of my desires for the "Individual" class, the waters have been muddied a bit in my own mind. I guess if there are to be two separate classes, then I would favor a more generalized "Organism" class to serve the functions of what Steve has described for both the "CollectionObject" and "BiologicalEntity" classes, but then define a separate "Documentation" class that serves as the basis of "proof" for an Occurrence. On a semi-related topic, I don't think it's appropriate to create a DwC class simply to establish a Many-to-Many relationship between instances of other classes. That function (in my mind) is already elegantly fulfilled by the existing dwc:ResourceRelationship class (another major discussion that will need to take place on this list). While it's true that certain DwC classes do serve a M:M function (e.g., Occurrence), I think that classes should represent "things" that are unambiguously different, with very specific sets of properties. On a final, somewhat encouraging note, I *really* like the diagram represented in the link that Cam sent earlier: http://code.google.com/p/darwin-sw/ During one of our non-diving days in South Africa, Rob Whitton and I spent some time thinking about the BiSciCol project (BCC'd on this post), and we studied this diagram and both agreed it represents an *excellent* foundation to both this discussion on proposed new DwC classes, and the BiSciCol project in particular. Aloha, Rich

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Darwin Core vernacularName field
by Geoffrey Allen 27 Jul '11

27 Jul '11

Greeting, I have recently begun the process of digitising the 60,000 specimen vouchers from the UNB herbarium. The textual data for 40,000+ of those has already been entered into a database, and I am now trying to map those values to DwC so that we may share the data with other collections. I have some concern over the fact that simple DwC does not allow the repetition or extension of certain fields. The vernacularName field is a particular problem. New Brunswick is Canada's only officially bilingual province, as such, our specimens are all identified with both their English and French common names in the database. It would be very useful if we could extend DwC, creating something along the lines of <vernacularName lang=en>, or allow nesting of elements, perhaps in the form: <vernacularName> <English>Chives</English> <French>Ciboulette, brulotte</French> </vernacularName> The other option, as I see it, is that we store the English and French common names in our own fields, and then concatenate the two to create the DwC:vernacularName field. I see this option as less than ideal since it may hinder search/browsability. It may also cause a host of other problems from interpreting to storing the data. The herbarium with whom we first intent to share the data has already expressed a concern that their system cannot handle the diacritics found in many of the French names (!). They would like the Eng. common names, but not the French. This is more difficult to achieve if we concat the values. One additional thought is that the herbarium's imprint, _Flora of New Brunswick_, also includes common names in Maliseet and Mi'kmaq wherever possible. Although these two aboriginal languages do not currently exist in the dataset we are using, there is the potential that they may be added at some point in the future. It seems to me that the repetition of fields may be necessary in other instances too. I am having some difficulty figuring out how to record all the location data we have for the specimens, which are indicated using verbal descriptions, Lat/Long, UTM, and NTS coordinates - in many cases using all 4 for a single sample, but I will save the details for another posting. I will watch for the group's thoughts on this problem. Many thanks, Geoffrey -------------------------------------------- Geoffrey Allen Digital Projects Librarian Electronic Text Centre Harriet Irving Library University of New Brunswick Fredericton, NB E3B 5H5 Tel: (506) 447-3250 Fax: (506) 453-4595 gsallen(a)unb.ca

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Plea for competency questions. Was Re: New terms need resolution: "Individual"
by Bob Morris 26 Jul '11

26 Jul '11

There is a series of jokes, and an entire TV quiz show, essentially starting from the meme "What is the question to which the answer is <X>". Now, I am not a biologist (surprise!), so it is likely that domain ignorance leaves me unable to understand whether all the postings in the thread about new DwC term resolution are arguing from the same set of questions their authors hope to have answered by a resolution of the term "Individual". (It's even a little unclear to me whether everybody has the same notion of "resolution of a term", but that's a whole different discussion, which would contain a lot of uses of "rdf:type" and the contentious "rdfs:domain"). I speculate that lengthy term definition debates would be shorter if they started with agreement on competency questions for the term. Competency questions are sort of usage scenarios cast as questions. See http://marinemetadata.org/references/competencyquestionsoverview . Bob Morris On Thu, Jul 14, 2011 at 2:41 AM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: > My turn to disagree (strongly, in this case). It's not an instance of a > taxon, it's an instance of an Organism. A taxon is merely a non-factual > (i.e., opinion-based) attribute of an organism, secondarily associated via > an Identification instance. > > I could probably be comfortable with "OrganismInstance"; but in that case, > why not just "Organism" as Paul suggested? Isn't "Instance" sort of implied > by all the classes? > > I am certainly open to debate about where the "upper boundary" of an > instance of this class, and I agree that "population" could be interpreted > more as a low level of "taxon", rather than a high level of "organism". But > I certainly don't think that instances of this class should be limited to a > singular organism. Would a coral head then constitute thousands of > instances of this class? Surely such colonies could be collapsed into a > single instance of this class. And the same would likely also be useful for > colonies of insects (ants, termites, bees, etc.), as well as small groups > (pack of wolves, pod of whales, etc.); not to mention a specimen "lot" in a > Museum collection. > > I agree it should have only *one* taxon, but that there should be no upper > limit on the rank of this taxon. If more than one taxon is identified, then > there needs to be a separate instance of this class for each identified > taxon. But this only applies when multiple taxa are acknowledged -- it does > NOT restrict multiple taxa being linked to the same instance via multiple > identifications when there is a difference of opinion about what the correct > taxon identity should be. In other words, an instance of this class may be > identified as "A" *or* "B", but could not legitimately be identified as "A" > *and* "B" simultaneously (except, perhaps in the case of hybrids, but that's > another situation altogether). > > More later. > > Aloha, > Rich > >> -----Original Message----- >> From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content- >> bounces(a)lists.tdwg.org] On Behalf Of Gregor Hagedorn >> Sent: Tuesday, July 12, 2011 10:09 AM >> To: Steven J. Baskauf >> Cc: tdwg-content(a)lists.tdwg.org >> Subject: Re: [tdwg-content] New terms need resolution: "Individual" >> >> > represent a single taxon. I think that Individual is probably not a >> > good name due to confusion with the technical use of that term >> elsewhere. >> >> TaxonInstance seems to me to be perhaps most precise. >> Personally I have a problem merging individual with population, since >> population -> metapopulation -> subspecies form a continuum in my >> understanding. But I am quite willing to be pragmatical :-) >> >> Gregor >> _______________________________________________ >> 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 > > -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Department of Organismal and Evolutionary Biology Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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Plea for competency questions. Was Re: New terms need resolution: "Evidence"
by Steve Baskauf 26 Jul '11

26 Jul '11

John Wieczorek has made an additional proposal (http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002574.html) to resolve the issue of "Evidence" by creating a class called "CollectionObject". I believe that his intended meaning for the term is exactly what I have intended in the past when I used the term "token". I believe that the proposal for the CollectionObject class is intimately related to the question of the definition of Individual/BiologicalEntity because I think that the competency questions Rich wants to address through the Individual/BiologicalEntity class are a subset of what I would consider to be the competency questions for the CollectionObject class. Because of TDWG's historical roots in the collections community, "occurrences" have been subconsciously or even explicitly linked with the evidence that documents them. For example, PreservedSpecimens have been considered a subclass of Occurrence in the Darwin Core type vocabulary. But in the lengthy tdwg-content discussion of 2009-10 (summarized at http://code.google.com/p/darwin-sw/wiki/TdwgContentEmailSummary) there seemed to be a consensus that an Occurrence is a record of an Individual at a particular Time and Location. That Occurrence is an independent entity from the evidence that serves to document it, which could include one (or perhaps zero) to many PreservedSpecimens, Images, text files recording MachineObservations, etc. Separating the Occurrence from its documenting evidence makes it easier to be explicit about the number and types of evidence that document the Occurrence. So I would define competency question #1 for the proposed CollectionObject class as to: 1. document an Occurrence (which I will refer to as the "Occurrence" use of evidence). However, I would also assert that CollectionObject need not be restricted to documenting an Occurrence, but that it may also: 2. document the existence of an Individual/BiologicalEntity, aggregates that include it, and pieces that came from it (which I will refer to as the "Provenance" use of evidence) and 3. support an Identification to a particular Taxon (the "Identification" use of evidence). [note: see http://code.google.com/p/darwin-sw/wiki/ClassToken for further discussion of this] If the CollectionObject is a whole dead organism serving as a museum specimen, then it might simultaneously address all three of these questions. The time and place listed on the specimen label provide the information about the Occurrence, the dead organism serves as proof of its own existence, and determinations typed or written on the label are vouched for by the presence of the dead organism. In this case the need to separate these three uses of CollectionObject may not be obvious. But consider a more complex situation of the sort that BiSciCol would like to be able to handle. A wildebeest calf is digitally photographed in South Africa as it is being captured. The calf is shipped to a zoo in England where a blood sample is taken. Part of this tissue sample is stored in liquid nitrogen, but part is used for a DNA extraction. The DNA is sequenced and used in a molecular phylogeny project. Here we have 5 pieces of evidence (each of which could be assigned GUIDs): the digital StillImage, the calf itself in the zoo (a LivingSpecimen), the blood sample, the DNA sample, and the DNA sequence in digital text form. All five of these pieces of evidence could potentially reside as CollectionObjects in different physical or electronic repositories. *Competency question 1 (Occurrence) * StillImage: timestamp and embedded GPS metadata associated with the image document the time and place where the calf was located at the time of capture. LivingSpecimen: the collection record that the zoo keeps for the calf document the time and place where the calf was located at the time of capture. (the other three pieces of evidence do not provide information about any time and place where the calf was located) *Competency question 2 (Provenance)* StillImage: a foaf:depiction of the calf (Individual/BiologicalEntity) LivingSpecimen: owl:sameAs the calf (Individual/BiologicalEntity) blood sample: dcterms:isPartOf the calf (Individual/BiologicalEntity) DNA sample: dcterms:isPartOf the blood sample which dcterms:isPartOf the calf (Individual/BiologicalEntity) DNA sequence: [sequencedFrom] the DNA sample which dcterms:isPartOf the blood sample which dcterms:isPartOf the calf (Individual/BiologicalEntity) (all five pieces of evidence support the existence of the calf, and the provenance of each piece of evidence can be traced back to the calf) *Competency question 3 (Identification)* As part of the phylogenetic analysis, the DNA sequence could serve as evidence for assigning the calf to a particular taxon. A mammal expert in Australia might examine the digital StillImage via the web and assert that the calf is a wildebeest. Another mammal expert in England might examine the calf at the zoo and assert that the calf is a wildebeest (or perhaps look at the calf in the zoo when it is full grown and also look at the StillImage taken at the time it was captured and make the assertion based on two forms of Evidence). (the DNA sample itself apart from the sequence probably wouldn't be used as evidence for an Identification; the blood sample might if the cytology were distinctive) ----------- I would assert that the bottom line here is that an entity that falls within the proposed CollectionObject class would need to address at least one of these three competency questions. It would not be necessary for it to address all three. The properties of instances of the CollectionObject class would be that they could be connected through object properties to Occurrences, Individuals/BiologicalEntities, or Identifications; and that they could have data properties that we typically assign to collected items such as catalogNumber, collectionCode, preparation, etc. John has suggested moving DwC terms for such properties from under Occurrence to the proposed CollectionObject class (http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002574.html) As John has noted, this is a significant change, but I believe that it is an important one if one is to accept the distinction between Occurrences and the evidence that documents them - an imperative in more complex cases such as I outlined above. ---------- I want to end this email by returning to Rich's outlook on the "Individual" issue. In his various posts, it seems to me that much of what he wants to accomplish through the "Individual" class falls within what I've defined here as competency question 2 (tracking provenance of resources, in particular physical things that are, include, or are taken from living organisms). It seems like the CollectionObject class is fully capable of doing much of what he wants to accomplish. Just get rid of the term "Individual" - as Paul Murray has noted (http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002615.html) it already has a different meaning. Use "CollectionObject" to address Rich's provenance competency questions (tracking and connecting collected objects) and "BiologicalEntity" to address mine (joining zero-to-many Occurrences to zero-to-many forms of evidence to zero-to-many Identifications). So then what IS an actual individual organism like the wildebeest calf? It is a BiologicalEntity if it has been documented as an Occurrence or assigned an Identification. It is a CollectionObject if it was collected for a zoo, or shot and mounted in a museum. Or it can be both simultaneously if it is both documented and collected. If none of these things were done, then it's neither a BiologicalEntity nor a CollectionObject - it's simply a wildebeest calf. Define the class/type of the thing by the properties that you wish to assert for it (or the competency questions that you can answer for it). With regard to the issue of taxonomically heterogeneous entities: tracking the provenance of taxonomically heterogeneous CollectionObjects and CollectionObjects that are pieces of organisms is not really a big deal. A fish fin isPartOf an individual fish isPartOf a jar of a mixed fish isPart of a marine trawl. However, tracking and reconciling Identifications of taxonomically heterogeneous collections of things and their subsamples (the second part of what Rich wanted to accomplish) is more complex task that I cannot at this point wrap my head around (see the "Additional Comments" at http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity for more commentary on this). 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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