- tdwg-content - lists.tdwg.org

Purpose of ResourceRelationship
by Richard Pyle 13 Sep '11

13 Sep '11

On a separate but related issue, I don't think I ever received any feedback on my question some months back regarding the scope of function of the ResourceRelationship class in DwC. I suspect that hardly anyone is using it, and I get the sense that most people assume that it is intended to allow cross-linking instances of DwC classes with objects external to DwC-class items. However, in my mind it serves as the *perfect* mechanism to cross-link instances of DwC classes to each other (e.g., an Occurrence to an Event; an Identification to a Taxon and Organism; a Location to an Event; etc., etc.). It also seems to me to be the perfect mechanism to represent recursive links within a Class. It's this last bit that John's recent email reminded me of. To wit: > Term Name: associatedOrganisms > Identifier: http://rs.tdwg.org/dwc/terms/associatedOrganisms > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: associatedOrganisms > Definition: A list (concatenated and separated) of identifiers of > other Organism records and their associations to this Organism. > Comment: Example: "sibling of MXA-231; sibling of MXA-232". ... as well as associatedOccurrences, associatedTaxa, and possibly other "associated[xxxxx]" terms... Shouldn't these "associations" among instances between and within DwC classes be represented as series of ResourceRelationship instances? Is this not the intended purpose for ResourceRelationship? Or, is it the intended purposes, but the various "associated[xxxx]" terms are there in order to provide a "flattened" or "denormalized" concatenation of identifiers? Aloha, Rich

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dwc: relating dwc:Identification objects to dwc:Taxon objects
by Bob Morris 12 Sep '11

12 Sep '11

As far as I understand for DwC, in order to associate a dwc:Identification with a dwc:Occurrence we need to define a dwc:ResourceRelation analogous to http://rs.tdwg.org/ontology/voc/OccurrenceRecord#identifiedTo (The context is the building of examples of data annotations for the data extensions to the W3 incubation group document Annotation Ontology http://code.google.com/p/annotation-ontology/). The examples will be RDF). a. Am I right? b. Is there one already blessed by TAG? c. If b. is "No", does it make sense to put one on the table? -- 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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multiplicity whine about DwC
by Bob Morris 10 Sep '11

10 Sep '11

Warning: technical DwC whine I am attempting to use DwC in RDF to model something that is functionally like the predicate lsidvoc:identifiesTo in the LSID vocabularies. If I understand correctly, in DwC I must start with an \instance/ of dwc:ResourceRelationship, lets call it x:identifiesTo and use its dwc:resourceID to provide the source Identification and its dwc:relatedResourceID to provide the instance's object Taxon. The problem is, you can't use the same instance x:identifiesTo for two different (Identification, Taxon) pairs because you won't be able to tell which Identification goes with which Taxon. A little more precisely, if you don't have another instance of dwc:Resource Relationship, you will have: x:identifiesTo rdf:type dwc:ResourceRelationship x:identifiesTo dwc:resourceID Identification1 x:identifiesTo dwc:relatedResoruce Taxon1 x:identifiesTo dwc:resourceID identification2 x:identifiesTo dwc:relatedResourceID Taxon2 (This is a generic multiplicity problem about RDF vocabularies that mean to support flat implementation. In some context recently I made that observation on this list. If I were as careful as Steve B I'd go back to the record, find out where and cite it :-) . But I have to rush off and go collect a few weeds from my lawn and get off to a weekend course on botanical printing on fabric sponsored in part by the Arnold Arboretum !) Probably the only solution is to introduce a real predicate outside of DwC that actually looks like lsidvoc:identifiesTo so the graph looks like x:identifiesTo rdf:type rdfs:Property Identification1 x:identifiesTo Taxon1 Identification2 x:identifiesTo Taxon2 This is essentially the approach of http://code.google.com/p/darwin-sw/. Even this has some implementation issues in an environment where you are facing some RDF that has vocabulary from an ontology named by a URI that you can't resolve, which is what we are exploring in the FilteredPush project about the management of annotations of data. I'd love to be shown why I am wrong about the non-reusability of a dwc:ResourceRelation, or whether there is a different way to solve problems like this in DwC 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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Re: [tdwg-content] [tdwg-tag] DwC change review: geo terms
by Hilmar Lapp 09 Sep '11

09 Sep '11

(Sorry if you receive this twice - John asked to repost here.) Where is adopting these terms now going to put us with respect to OGC standards, which, I think, will ultimately be more authoritative than an informal W3C vocabulary. I don't have enough insight into OGC standards for vocabularies for describing geolocations, but I have also learned earlier this year from Flip Dibner (copied here) that there are efforts underway within OGC to create RDF vocabularies (presumably corresponding to OGC's XML standards?). -hilmar On Sep 6, 2011, at 6:33 PM, Javier de la Torre wrote: > Hi John, > > As you mention from previous discussion I would still adopt option > number 1 as I believe there is enough tools out there to handle > transformations. The current situation I think is much worst on the > consumer part and I think is time to think more on data use than on > data mobilization. > > Best, > > Javier. > > On 07/09/2011, at 00:00, John Wieczorek <tuco(a)berkeley.edu> wrote: > >> Perhaps my message was too long for easy digestion and action, as >> I've >> received no responses. I will take the initiative to initiate option >> 3. No further action from the TAG on this at this point. Be prepared >> though, VOTES by the TAG on publicly resolved issues are forthcoming >> very soon. >> >> On Sat, Sep 3, 2011 at 9:34 AM, John Wieczorek <tuco(a)berkeley.edu> >> wrote: >>> Hi TAGers, >>> >>> I am deep in the review process for the proposed changes to Darwin >>> Core, trying to do due diligence. Some of the change requests are >>> challenging to summarize to determine if there is consensus, in >>> spite >>> of, or because of the discussions. One of the requests on which I’d >>> like some TAG help before proposing a solution is the request for >>> the >>> inclusion of the terms from the geo: namespace >>> (xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#"). >>> >>> Support in tdwg-content for this request comes from multiple >>> independent sources. There has been a long history of discussion >>> (http://lists.tdwg.org/pipermail/tdwg-tag/2010-August/000050.html), >>> beginning in anticipation of the 2010 TDWG BioBlitz. The proposal >>> has >>> gone through the minimum 30-day public review and discussion on the >>> forum tdwg-content(a)lists.tdwg.org: >>> >>> http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002581.html >>> >>> There seems to be general support for the additions, however, after >>> reviewing the discussions and the references. I have the following >>> observations/concerns: >>> >>> 1) The discussions presented geo:lat and geo:lng as W3C standards. >>> This is not actually the case. These terms were created by the W3C >>> Semantic Web Interest Group in 2003. The documentation for these >>> terms >>> (http://www.w3.org/2003/01/geo/) states: >>> >>> "This document was created as an informal collaboration within W3C's >>> Semantic Web Interest Group. This work is not currently on the W3C >>> recommendation track for standardization, and has not been subject >>> to >>> the associated review process, quality assurance, etc. If there is >>> interest amongst the W3C membership in standards work on a >>> location/mapping RDF vocabulary, this current work may inform any >>> more >>> formal efforts to follow." >>> >>> These terms do seem to have widespread usage in the semantic web. >>> Should we be concerned that they are not part of a standard? >>> >>> 2) geo:lat and geo:lng are not semantically equivalent to the >>> existing >>> Darwin Core terms decimalLatitude and decimalLongitude, which have >>> been a part of the Darwin Core since it 2003 (or before, if we >>> ignore >>> the missing Datum term in earlier versions). The addition of the >>> geo: >>> terms as a third set of geolocation terms for Darwin Core raised >>> concerns about confusion. I share this concern. An option would be >>> to >>> adopt these terms and deprecate dwc:decimalLatitude, dwc:Longitude, >>> and dwc:geodeticDatum. Data that would have occupied these terms >>> would >>> go instead to dwc:verbatimLatitude dwc:verbatimLongitude, and >>> dwc:verbatimSRS. I see a couple of problems with this. First, most >>> of >>> the time the data in the decimal coordinate fields are not the >>> verbatim originals, so this would be a misuse of the Darwin Core >>> terms. Second, this change would make it more difficult for data >>> consumer’s to use existing georeferences. Here’s how. Right now the >>> verbatim fields are meant to hold the original coordinate >>> information, >>> which means they have a wide variety of content - everything from >>> UTMs >>> to custom-encoded coordinates, in any conceivable format. Meanwhile, >>> the data in the decimal coordinates fields can be much more readily >>> transformed into the desired standardized spatial reference system >>> afforded by the geo: terms, because the values are at least >>> standardized on decimal degrees and only a datum transformation >>> has to >>> be done on them. >>> >>> Do we abandon the dwc: terms decimalLatitude, decimalLongitude, and >>> geodeticDatum? Do we abandon them now? Do we build the simplest >>> possible tools necessary for anyone to do the transformations so >>> that >>> these terms are no longer needed? If so, do we wait until those >>> tools >>> exist? >>> >>> 3) Additional concern was expressed that the term geo:alt should >>> also >>> be added. No one has made a formal request for this. However, if the >>> other geo: terms were adopted, it might be silly not to adopt this >>> one >>> as well. Doing so would raise a host of issues similar to those >>> raised >>> for lat and lng. >>> >>> I don’t have a good solution. The best short-term one, in my >>> opinion, >>> is to leave Darwin Core as it is, and to recommend that if >>> applications (or aggregators) want to share “cleansed” point-based >>> georeferences, that they do so with the geo: tags, the values for >>> which they derive through transformations to WGS84 of the DwC >>> decimal >>> coordinates and geodeticDatum. >>> >>> Options: >>> >>> 1) Accept the proposal, adding geo:lat, geo:lng, and geo:alt to the >>> list of recommended terms for DwC. >>> >>> 2) Reject the proposal pending further directed research into a >>> comprehensive solution that considers all geospatial terms in Darwin >>> Core (including footprintWKT, for example). >>> >>> 3) Reject the proposal for now, reopening the public discussion with >>> these concerns. >>> >>> Others? >>> >> _______________________________________________ >> tdwg-tag mailing list >> tdwg-tag(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-tag > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.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 03 Aug '11

03 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 03 Aug '11

03 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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