July 2009 - tdwg-content - lists.tdwg.org

FW: [STDTRK] Request for a Decision for Public Review of DarwinCore Draft Standard
by Donald Hobern 26 Aug '09

26 Aug '09

At Gail's request, I'm forwarding some discussion between Renato and myself on the Darwin Core draft Thanks, Donald Renato, You are quite right - domains and ranges may cause us more problems. At very least it may be sensible for these to be things which get asserted within other OWL files used within specific projects to govern their own application models and inference rules. In the end my concerns are really around the need for more clarity on the way that the dcTerms:type values are to be used and how this relates to past use of Darwin Core. I'm not sure I ultimately disagree with any of the decisions made. However I still cannot find any actual definition for the Occurrence and Event cases to explain what situations they are intended to cover. Unless we take the time to define the intended scope for all our terms and property values, it is hard to predict whether data from multiple sources can be expected to be suitable for combination. The scientific name case is one example. I would like an explicit statement that it means nothing more than "the name of a taxon (somehow) associated with this record" rather like a Dublin Core subject. If, e.g. in the case of an Occurrence record, it is meant to be a statement that a taxon was actually recorded at the location on the given date, we may need to be more explicit. I'm still not comfortable with leaving these things unstated. I must however emphasise that I am very happy to see how much work has gone into this revision and the level of forethought in addressing many important issues. Donald -----Original Message----- From: renato(a)cria.org.br [mailto:renato@cria.org.br] Sent: Friday, 24 July 2009 7:04 AM Subject: RE: [STDTRK] Request for a Decision for Public Review of DarwinCore Draft Standard Hi Donald, Scientific name is precisely the kind of term that I feel should be generic. There's an ancient search interface at CRIA that illustrates the use case "give me everything you have related with this scientific name": http://names.cria.org.br/index?lang=en (check all checkboxes at the bottom of the page) In SPARQL I think the query would simply look like: SELECT ?x WHERE { ?x <http://rs.tdwg.org/ont/scientificName> "some name" } instead of repeating the same condition for every possible combination of domain#property. Most id properties (collectionID, locationID, etc.) should also probably be "domainless" since they can appear in objects from many different classes. Best Regards, -- Renato > Looking at what is in the DwC document, I think my concerns are with > plans to use DwC for checklist data rather than the DwC proposal itself, > but the problem issue may be in there somewhere. Here are some comments I > sent earlier: > > I need to take some time and provide some comments on the use of Darwin > Core for non-occurrence data. In general I believe we need to be moving > towards simple class properties with tightly defined explanations of the > expected content and format. This use of DwC seems to me to be a > significant dilution of the semantic content of these properties. If DwC > is an object property just for a taxon occurrence, the explanation of > dwc:ScientificName would be something like "The scientific name assigned > to the taxon to which the recorded organism was identified". If we extend > it to cover taxon occurrences, checklist entries and all the other things > that people seem to have in mind, the explanation would reduce to "The > scientific name which is associated with this record". In practice few > people will be stumbled, but I really don't like it. It would be so easy > just to have chk:ScientificName as well as dwc:ScientificName and to keep > the semantics explicit. This becomes particularly problematic when we > play with RDFS and OWL. We could choose to define the "dwc:ScientificName" > property to have a domain restricted to TaxonOccurrence, allowing a > reasoner > to infer that objects with this property can be treated as > TaxonOccurrence records. With the diluted dwc:ScientificName all we can > infer is that the object is a > ThingWithSomethingToDoWithTheBiologicalDomain. > > Donald -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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assertions in DwC terms
by Hilmar Lapp 24 Aug '09

24 Aug '09

The current DwC Terms version (at http://rs.tdwg.org/dwc/rdf/dwcterms.rdf) defines the domain for (at least some) object properties. Unless I am missing something this means that when I use DwC Terms for properties I implicitly assert the class of the subject, which means that either I can use DwC terms only for subjects of the type they are intended for (and why would one want to limit DwC's use in this way?), or reasoning based on RDF or OWL extractions of leads to problems. For example, in the Phenoscape project [1] we would like to link characters, states, or OTUs to the specimens based on which a systematist defined a (or all) character(s) or state(s). The specimens would be described in a NeXML document [2] with embedded RDFa annotation by institutionCode, collectionCode, and catalogNumber. The RDF extracted from that when run in a reasoner (which we will do) would implicitly assert that the specimen is a DwCTerms:Occurrence. Right now that probably doesn't hurt much in this case, but it might in the future, and I'm not sure what is gained from forcing those implicit assertions in the vocabulary. Should I post this as an issue to the tracker on Google Code, too? -hilmar [1] http://phenoscape.org [2] http://nexml.org -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu : ===========================================================

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Re: [tdwg-content] Public Review of the Darwin Core 'standard'
by Kevin Richards 07 Aug '09

07 Aug '09

I'm not sure if this is my misunderstanding of RDF and ontologies, so correct me if I am wrong... I noticed that the http://rs.tdwg.org/dwc/terms/geoReferencedBy property has domain http://purl.org/dc/terms/Location. Is this the standard way of working with Dublin Core? I would have though it would be better to define a "common" person/agent type property (or better still reuse FOAF or DC Agent types - http://purl.org/dc/terms/Agent) This property has no range and can therefore be applied to any RDF class/element. This would remove the need for repetitive elements that refer to Agent type properties, eg geoReferenceBy, identifiedBy, measurementDeterminedBy, etc. This was part of the intention of the TDWG Common Vocab. (http://rs.tdwg.org/ontology/voc/Common.rdf) which brings me to my next question - how do the DwC terms relate to the TDWG ontology? - do we need a "mapping" to them? I suppose, because the DwC ontology needs to be ratified as a standard, it can't really rely on an un-ratified ontology - but it would be good to specify how the two should work together, or map to each other. Otherwise I think this is looking excellent - a fantastic step towards an overarching ontology for TDWG data objects. Kevin -----Original Message----- From: tdwg-bounces(a)lists.tdwg.org [mailto:tdwg-bounces@lists.tdwg.org] On Behalf Of Lee Belbin Sent: Saturday, 11 July 2009 11:09 a.m. To: tdwg(a)lists.tdwg.org; Taxacom(a)mailman.nhm.ku.edu Subject: [tdwg] TDWG: Public Review of the Darwin Core 'standard' Apologies for cross posts - and please feel free to distribute this announcement to all relevant communities. TDWG is pleased to announce the commencement of the Public Review of Darwin Core - a standard for sharing biodiversity information. You will find the proposed standard is a living document with a history, an anchor in the Dublin Core, and mechanisms to grow and change. Since being officially put forward as a draft standard in February 2009, Darwin Core has undergone a peer review, a review by the TDWG Executive, and multiple revisions. Open Invitation: We invite all who may contribute and/or consume biodiversity information to examine this proposed standard during the Public Review period from 11th July through at least 10th August 2009. How to Participate: Visit the Darwin Core Progress site (http://code.google.com/p/darwincore/wiki/DarwinCoreProgress) for the latest background information on the process and critical links to content (http://rs.tdwg.org/dwc/index.htm) and participation. To discuss ideas with others or offer comments that are not targeted for action, please subscribe (http://lists.tdwg.org/mailman/listinfo/tdwg-content) and contribute to the tdwg-content mailing list (tdwg-content(at)lists.tdwg.org) Recommended actions or issues should be submitted to the Issue Tracker of the Darwin Core (http://code.google.com/p/darwincore/wiki/SubmittingIssues) so that they may be assigned, prioritized, and tracked. This Public Review process will be archived along with all other documentation in the TDWG Standards Track. Questions about the process should be directed to the Review Manager, Gail Kampmeier (gkamp(at)illinois.edu) Please share this opportunity for public comment and review with others you think may be interested. Acknowledgements: As Review Manager, I would like to express my gratitude to the authors, John Wieczorek, (MVZ), Markus Döring (GBIF), Renato De Giovanni (CRIA), Tim Robertson (GBIF), Dave Vieglais (KUNHM) for the enormous efforts made in bringing the Darwin Core standard to this point; to the initial anonymous peer reviewers, and to Lee Belbin and the rest of the TDWG Executive for their advice, support, and encouragement in this process; and to GBIF for tipping the scales by bringing together the authors in a workshop that led to this submission. Links expanded: Darwin Core Progress - http://code.google.com/p/darwincore/wiki/DarwinCoreProgress Darwin Core content - http://rs.tdwg.org/dwc/index.htm Subscribe to tdwg-content - http://lists.tdwg.org/mailman/listinfo/tdwg-content Issue Tracker - http://code.google.com/p/darwincore/wiki/SubmittingIssues Related Links: TDWG: http://www.tdwg.org/ Other TDWG Standards: http://www.tdwg.org/standards/ TDWG Standards Track (in OJS): http://www.tdwg.org/stdtrack/index Dublin Core's Metadata Initiative in Science: http://ils.unc.edu/spaces/sam/index.php/Main_Page Sincerely, Gail E. Kampmeier, Review Manager Illinois Natural History Survey, Institute of Natural Resource Sustainability, University of Illinois at Urbana-Champaign, 1816 South Oak St., Champaign, Illinois 61820 USA email: gkamp(at)illinois.edu Lee Belbin TDWG Secretariat _______________________________________________ tdwg mailing list tdwg(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

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[tdwg-phylo] NSF INTEROP proposal
by Hilmar Lapp 31 Jul '09

31 Jul '09

FYI, a group of collaborators (Arlin Stoltzfus, Karen Cranston, Sheldon McKay, Enrico Pontelli, Nico Cellinese, and myself) under the leadership of Arlin recently pulled together a grant application for the NSF Interop solicitation. The ideas for the grant emerged mostly from the recent Database Interoperability Hackathon (for which I posted the announcement and Call for Participation here back in Jan). Proposal summary and full text are public at the following URL: http://evoinfo.nescent.org/NSF_Interop_Proposal It was submitted July 22. If funded, TDWG and this Interest Group will play a significant role in the proposed activities. We probably won't hear about reviews or funding before Feb/March next year, so keep fingers crossed until then. Cheers, -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu : ===========================================================

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InstitutionCode Issue - ownership vs. custodianship
by John R. WIECZOREK 31 Jul '09

31 Jul '09

This Darwin Core Issue (http://code.google.com/p/darwincore/issues/detail?id=34) is being brought into this forum for further discussion in the hopes of a definitive recommendation. ==New Term Recommendation== Submitter:Ann Hitchcock Justification: The evolution, from 2003 to the present, of the term "Institution Code" has resulted in a change from property ownership ("the institution to which the collection belongs") to administrative or management responsibility ("the institution administering the collection or data set"). We need to be able to separately identify the owning institution when that institution differs from the managing institution. Such a situation occurs when the owning party lends the collection to a repository for long-term management. The catalog numbers that both institutions may assign to the same specimen are addressed by the Catalog Number and "Other Catalog Numbers," but property ownership is not addressed. Definition: The name (or acronym) in use by the owner of the collection or data set if different from the InstituionCode. Comment:Examples: "NPS", "INBio". For discussion see http://code.google.com/p/darwincore/wiki/Occurrence Refines:InstitutionCode Has Domain:http://rs.tdwg.org/dwc/terms/Occurrence Has Range: Replaces: ABCD 2.06:DataSets/DataSet/Units/Unit/SourceInstitutionID Comment 1 by gtuco.btuco, Today (3 hours ago) Interesting. Do you think that dc:rights (http://rs.tdwg.org/dwc/terms/index.htm#dcterms:rights) and dc:rightsHolder (http://rs.tdwg.org/dwc/terms/index.htm#dcterms:rightsHolder) might fulfill the needs you are recommending? Status: Accepted Labels: Priority-Medium Milestone-Release1.0 Delete comment Comment 2 by ann_hitc...(a)nps.gov, Today (14 minutes ago) "Rights" and "Rights Holder" do address part of the issue, especially if a second example on "Rights" could be given that refers to physical property in addition to intellectual property. For example "Specimens are U.S. Government Property." Although these definitions are helpful, they still do not address the issue that the occurrence of the specimens or data set may be recorded in both the collection of the institution with custody and the collection of the institution with ownership. Perhaps the term "administering" in the definition for Institution Code should be replaced with "with custody of" and the proposed definition for Institution Code should be bifurcated as follows: InstitutionOwnership Code: The name (or acronym) in use by the institution that owns the collection or data set in which the Occurrence is recorded. InstitutionCustody Code: The name (or acronym) in use by the institution with custody of the collection or data set in which the Occurrence is recorded, if different from the InstitutionOwnership Code. Comment 3 by gtuco.btuco, Today (moments ago) Since this has moved into the realm of discussion and away from a definitive recommendation, I need to move it to the tdwg-content list for open discussion. If you have not yet joined that list, please do so to continue the conversation there in an open forum.

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Re: [tdwg-content] InstitutionCode Issue - ownership vs. custodianship
by John van Breda 31 Jul '09

31 Jul '09

Sorry if this is a bit of a noob question and this has been covered elsewhere as this is my first step into the foray at tdwg. Why is this only being split into separate ownership and custodianship terms? It strikes me that a collection (or specimen for that matter) may have multiple related institutions so if we allow multiple institution codes but tag each with a relationship type then it is more flexible. For example we could have a "current custodian" as well as a "usual custodian" for something that is not in its normal place. I also wonder whether by describing this as Institution rather than an Agent this limits the type of entity that can be tagged - a custodian or owner might be a private collector. John van Breda Biodiverse IT +44 20 3239 5810

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Darwin Core Collection-related terms
by John R. WIECZOREK 24 Jul '09

24 Jul '09

I have taken the content of the Darwin Core Issues 32 and 33 to post here as they both require discussion before an unambiguous recommendation can be made. >>>From http://code.google.com/p/darwincore/issues/detail?id=32 Reported by ren...(a)cria.org.br Term Name: collectionID Recommendation: Reuse the term which is already defined in NCD (on the other hand, the NCD term defined in the corresponding RDF file should probably not be restricted to a specific domain). Submitter: Renato De Giovanni Comment 1 by gtuco.btuco This is indeed intended to be the same term. Can you provide the URI to the term in NCD? Status: Accepted Labels: Milestone-Release1.0 Priority-Critical Comment 2 by ren...(a)cria.org.br Currently the URI is: http://rs.tdwg.org/ontology/voc/Collection#collectionId But I think that relationship terms like this one should probably not be bound to a domain since they can be used by objects from many different classes. I'm not sure if it's possible to change NCD and if the NCD creators would agree with this change. Perhaps a better URI for this term would be: http://rs.tdwg.org/ontology/voc/collectionId Comment 3 by gtuco.btuco, Today (1 minute ago) Since this issue no longer has a single defensible concrete solution I think it should be moved to the discussion list tdwg-content until one can be proposed. I'll copy the whole issue thread there. ----- >>>From http://code.google.com/p/darwincore/issues/detail?id=33 Reported by ren...(a)cria.org.br Term Name: collectionCode Recommendation: Reuse existing term from NCD, but I would probably also suggest to change the NCD term from http://rs.tdwg.org/ontology/voc/Collection#acronymOrCoden to http://rs.tdwg.org/ontology/voc/collectionCode (without a domain). It would be nice to know Markus' or Roger's opinion about this, since they participated in the NCD group. Submitter: Renato De Giovanni Comment 1 by gtuco.btuco Also moving this issue to tdwg-content for discussion.

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