August 2011 - tdwg-content

Re: [tdwg-content] If you need something for referring to a population, then it is probably best to do it as a related class
by Nico Franz 05 Jun '25

05 Jun '25

Hello all: I have a few inserted comments, hopefully with some clarifying effect: On 5/4/2011 10:54 AM, Peter DeVries wrote: > Hi Steve, > > I may have overloaded the term specimen to make the explanation easier > to follow. > > A specimen could be an individual or it could be part of an individual. > > To some extent you need to think about how these models will be used. > > If you subscribe to the model that a species is whatever a taxonomists > says it is then it is difficult to make statements like. > > X% of the world's species will be extinct by 2050. > > If you mean a species as defined by the concept documented at this URI > which is supported by these specimens, images, and DNA then you are on > firmer ground. > > Species in the natural world do a pretty good job recognizing those > individuals that are appropriate mates. In other words members of > their own species. > > Are we modeling species or variations in human conceptualizations of > species? > >> Assuming that there was only one individual organism identified >> there is really one one species (or hybrid). > Aaaaaaaaaaaaaah! Please Nico C., don't take this one up! > > > I stick with this. Assuming you don't have a hybrid individual. That > individual is one species. The fact that human may disagree on what > species it is a human issue. > > Again, Are we modeling species or variations in human > conceptualizations of species? NMF: I believe there is a history of biodiversity database engineering that actually led some people, initially in Australia (Greg Whitbread?) and Europe (Berendsohn's group) to place more emphasis on modeling human conceptualizations of taxa. I understand this happened in the late 80s / early 90s. The motivation was, apparently, that no long-term consensus seemed available to model a single and sufficiently widely accepted taxonomy of, say, Central European vascular plant species or mosses. I believe that projects such as the Euro + Med PlantBase (http://www.emplantbase.org/home.html) are examples of the persistence (success?) of this 20+ year old practice. I think this is the kind of background that Steve is referring to. > > Which of these is of primary importance to decision makers and > non-taxonomist biologists? > Part of the problem with various publications relating to ontologies > and taxonomy is that their species models entail a specific > phylogenetic hypothesis. > > In the real world taxa are not as clean as some would like to make > them out to be. > > Each individual is a unique combination of thousands of separate gene > lineages which often do not follow clean monophyletic paths. > > I would argue that most of those who work with species related data > see them as useful typological constructs which in general follow the > biological species model. NMF: The solution of how to properly model things such as species in RDF, OWL (etc.) should ideally accommodate all "species concepts" (BCS, ESC, PSC, GSC, there's dozens), i.e. it should be neutral towards this issue. The examples below are too simple, ignoring for example cases such as pro parte synonymy, or a concept ("species") that appears unique and monophyletic to one author but (vastly) polyphyletic to another. To do an accurate mapping in that latter case (which is not super-common but it's real), I think one would have to come down on saying we're modeling human conceptualizations. They are not just that, so really it's not a strict dichotomy, meaning that by modeling conceptualizations we do not have to say "the species only exist on our heads", or "well, then anything goes". I agree (sheepishly) that it does come down to what the input data look like, and what the expectations are towards just accommodating the user community versus pushing them in a particular direction. Some of this also on p. 47 of this PDF: https://journals.ku.edu/index.php/jbi/article/view/3927/3852 > > /Aedes triseriatus/ owl:sameAs /Ochlerotatus triseriatus/ > > Others seem to see them as phylogenetic end nodes which entail a > specific phylogenetic history. > > /Aedes triseriatus/ distinctFrom /Ochlerotatus triseriatus/ > / > / > If you are primarily interested in understanding issues of ecology, > disease, diversity and conservation the former model is more > appropriate than the later. > > Respectfully, > > - Pete Regards, Nico Nico M. Franz, Ph.D. Assistant Professor Director, UPRM Invertebrate Collection Department of Biology University of Puerto Rico Call Box 9000 Mayagüez, PR 00681-9000 Phone: (787) 832-4040, ext. 3005 Fax: (787) 834-3673 E-mail: nico.franz(a)upr.edu Laboratory website: http://academic.uprm.edu/~franz/ UPRM-INVCOL: http://uprm-invcol-project.tumblr.com/

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An individual identified to a higher group like Order, is still an instance of a species - just a species that is currently unspecified
by Peter DeVries 25 Sep '11

25 Sep '11

What I would recommend is that you treat a specimen that is identified to an order (Perciformes) with something like the following. Species => Order Perciformes species undetermined. The individual is still an instance of a species, however that species has yet to be determined. What would work best is to have some standard way of writing the green string above. This would allow the occurrences that are of individuals identified only to the Order Perciformes, to be interpreted as a species that falls somewhere within the Order Perciformes. - 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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Darwin Core change request status
by John Wieczorek 30 Aug '11

30 Aug '11

Hi folks, This is just a brief update to let you know that I'm now concentrating on resolving the open change requests to Darwin Core. Some of it is quite straightforward. For example, the following additions have support without objection: yearOfPublication georeferencedDate identificationVerificationStatus dcterms:StillImage dcterms:MovingImage dcterms:Sound while the following has been accepted for removal from consideration: DigitalStillImage And the following changes have been accepted: remove subclassing from Darwin Core Type Vocabulary terms XML schema changes for extension eventDate validation Open issues remain (or at least I need to discover in the vast discussion if there was a consensus) on the following: dcterms:source Individual Organism Evidence IndividualRemarks occurrenceDetails/recordUri recordClass

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Collections and Digitization Specialist position available at Florida State University
by Greg Riccardi 18 Aug '11

18 Aug '11

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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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