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Frank Bisby
by Chuck Miller 27 Oct '11

27 Oct '11

Folks, Frank Bisby has passed away unexpectedly. This is quite a loss to our community and the world. Frank was a pioneer in the field now called biodiversity informatics, the first Chairman of TDWG, a colleague and friend. I was glad to be able to spend a lot of time with him in the last few weeks. He was a great man and will be deeply missed. As soon as I get more information about final arrangements I will pass it on. Chuck

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Expressing some relationships in DwC?
by Tony.Rees＠csiro.au 26 Oct '11

26 Oct '11

Hi all, I have a few nomenclatural relationships between name that I would like to express using DwC, and would like to know the preferred way to do this if any. The relationships are as follows: (1) Point a nomen novum to the basionym it replaces. From reading there was formerly a concept basionym/basionymID, apparently this is now replaced with originalNameUsage/originalNameUsageID. So one quesiton is, is this sufficient to infer this is a basionym, when accompanied by noneclaturalStatus = 'nomen novum'? (2) Point an orthographic variant to the name which it is a variant of (whether or not the latter is now the accepted name). In other words, if name A is a variant of name B which is now a synonym of name C, I capture the A=>C relationship with a synonym assertion, but I want a way to capteure the A=>B relationship too. (3) Point a nomen nudum to a validly published instance that comes later (or do the same in reverse, i.e. this name was preceded by xxx as a nomen nudum). Again, this should be independent of whether the validly published name is an accepted name or now a synonym of something else. Advice appreciated, Regards - Tony Rees

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feedback for TCS standard
by Kevin Richards 18 Oct '11

18 Oct '11

Feedback from using TCS in the Global Compositae Checklist, as I mentioned today in the TNC gourp meeting. Apparently there was no doc written up, just a couple of issues put on the TNC wiki, here And these other general issues: * Literature undefined/unstructured * the user defined elements (useful but hard to handle) * active concepts missing (i.e, good to be able to indicate which they are following. could also be provided in user defined elements) * name element on concepts -> define use (is essential for vernacular names) -> what is it supposed to record the orthography in the concept or is this a separate field? Kevin 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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RDF/OWL best practices at TDWG 2011 (and beyond)
by joel sachs 14 Oct '11

14 Oct '11

Everyone, Steve Baskauf and I are convening an RDF/OWL Task Group under the TAG. The main goals of the group will be to i. develop use-cases and competency questions that include tests of biodiversity data discovery, exchange, and semantic reasoning; ii. experiment with a variety of approaches to addressing the use cases; and iii. provide well documented examples of RDF/OWL and SPARQL demonstrated to satisfy the use cases. All are welcome to join the group, and to attend our kickoff meeting on Wednesday, Oct. 19, 2 - 5:30 PM, in New Orleans. Remote access will be available. If you plan on attending, please signup here: http://code.google.com/p/tdwg-rdf/wiki/KickoffSignup (Note: if you participated in the recent discussion about the group on the tdwg-tag list, I added you as a committer to the wiki (http://code.google.com/p/tdwg-rdf/people/list), and you should have edit privileges. All others, please email me first (with your Google ID), so that I can add you.) Looking forward to seeing you all next week - Thanks, Joel.

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Status of Darwin Core Change Requests
by John Wieczorek 03 Oct '11

03 Oct '11

Dear all, This is an update to let you know that I have just submitted a summary with a request to the TDWG Executive Committee for authorization to make changes to the Darwin Core terms. The specific changes requested are those that have achieved an unopposed consensus on this list during the public review period that began 4 July 2011 (and ended when I sent the message to the Executive today). For reference, the specific changes for which authorization was sought are those having the status "Vote" on the Darwin Core Issue Tracker and listed below: Issue 84: new term namePublishedInYear Issue 96: new term dcterms:references, deprecate dwc:occurrenceDetails Issue 104: new term georeferencedDate Issue 105: new term identificationVerificationStatus Issue 109: remove subclassing from dwctype:Occurrence Issue 110: remove subclassing from dwctype:PreservedSpecimen Issue 111: remove subclassing from dwctype:FossilSpecimen Issue 112: remove subclassing from dwctype:LivingSpecimen Issue 113: remove subclassing from dwctype:HumanObservation Issue 114: remove subclassing from dwctype:MachineObservation Issue 115: new term dcmitype:StillImage to Darwin Core Type Vocabulary (value for basisOfRecord) Issue 116: new term dcmitype:MovingImage to Darwin Core Type Vocabulary (value for basisOfRecord) Issue 117: new term dcmitype:Sound to Darwin Core Type Vocabulary (value for basisOfRecord) In addition, there have been requests to add two attributes to all Darwin Core terms to facilitate applications: Issue 121: add English term label attribute Issue 122: add term alias attribute For details on these and all other open issues for the Darwin Core, see http://code.google.com/p/darwincore/issues/list. Cheers, John

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Recruiting members of the iEvoBio 2012 Organizing Committee
by Hilmar Lapp 02 Oct '11

02 Oct '11

iEvoBio, the conference on Informatics for Phylogenetics, Evolution, and Biodiversity, is a recently founded satellite conference held in conjunction with the Evolution meetings. iEvoBio aims to be a forum bringing together biologists working in evolution, systematics, and biodiversity, with software developers, and mathematicians, both to catalyse the development of new tools, and to increase awareness of the possibilities offered by existing technologies (ranging from mega- scale data analysis to rich visualization). The inaugural meeting was held in 2010 (see http://ievobio.org/2010) and received wide acclaim; the second one, held in 2011 (see http://ievobio.org/2011), was similarly successful and productive. The conference is poised to establish itself as a self-sustaining annual event and a must-attend for researchers, developers, and users of informatics resources in our fields. For the 2012 iEvoBio conference, to be held in junction with the 2012 Evolution Meetings in Ottawa, Canada, we are seeking new members to join us on the organizing committee. Aside from being enthusiastic about the conference itself, we are particularly interested in people with research pursuits that involve integrative, interdisciplinary, and synthetic questions, and a commitment to promoting the reuse of data, information, and software. Serving on the iEvoBio organizing committee entails attending weekly conference calls, and sharing responsibility for making the conference happen at all stages, including crafting communications such as calls for abstracts, managing content contributions from participants, and budgeting. The iEvoBio organizing committee shapes and manages the entire event, from start to finish. As such, participating in the committee provides ample opportunities for people with ideas, wild or not, to conceive innovative program elements towards iEvoBio’s social objectives of fostering participation, interaction, and collaboration, and to make those happen. The committee has been marked by an open- minded, highly constructive, but also deeply professional climate. Serving on the committee is actual work, but also provides a unique opportunity to collaborate with like-minded people who one may not otherwise get to work with, on a product for the benefit of our community and the advancement of our science. To apply, fill out a short online application form at http://bit.ly/okxqS1 by October 15th, 2011. We expect the organizing committee to have at least 6-7 members, and thus currently at least 4-5 seats are available to be filled through this call. This call is open to people at all professional “grades” and our hope is that at least one, and hopefully more, seats will be filled with graduate or postdoctoral students. We (see the undersigned below) will sort through the applications and reach a decision within one week after close of applications. If you have any questions about the conference or the committee, we encourage you to resolve these before applying by contacting us (see email addresses below). Please feel free to re-send, tweet (http://bit.ly/qyYT0s), or share this message as needed. Thanks! On behalf of the future 2012 iEvoBio Organizing Committee, Rob Guralnick (robert.guralnick(a)colorado.edu), University of Colorado at Boulder Hilmar Lapp (hlapp(a)nescent.org), National Evolutionary Synthesis Center (NESCent)

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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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Occurrences, Organisms, and CollectionObjects: a review
by John Wieczorek 19 Sep '11

19 Sep '11

Dear all, Prepare yourself mentally. After more than a year of discussions, prototypes, scholarly papers, bar room brawls, etc., we are very near having a path forward for two new, related classes for Darwin Core that attempt to remove ambiguity inherent in the Occurrence class as it currently stands. Adding classes is quite a bit more complicated than adding properties (as you'll see if you manage to get through this message), and so it is important to be as thorough as possible to make sure we get it right. I'll try here to synthesize the rough consensus and the remaining issues. Basically, the idea is to pull two distinct concepts out of Occurrence and give them their own classes. Maybe not surprisingly, one of the hardest things to agree upon has been the names for these classes. The class that was proposed first as "Individual" has seen no less than 12 alternate names, none of them satisfying to everyone. The closest thing to an acceptable name was "Organism", with caveats that the definition should make it abundantly clear what is to be included in the class and what is not. I'll use "Organism" here to refer to the class in the hopes of offending the fewest people. The rough consensus on "Organism" is that is should include viruses, symbionts, individuals, colonies, groups of individuals, and even populations, but that there should be taxonomic homogeneity to an instance of an "Organism". There has been some concern about how and where to draw the line on homogeneity. No attempt has yet been made to write a definitive description of the class, though many examples of representatives of the class have been given. What we need to move forward on the "Organism" class are an official definition and an official comment, the combination of which should be sufficient for someone previously unfamiliar with the term and the arguments leading to its existence to understand. Some existing terms (individualCount, sex, lifeStage, reproductiveCondition, behavior, previousIdentifications, associatedTaxa) will have to be reorganized to be under this new class. These terms may require updated definitions for consistency. New terms (organismID, associatedOrganisms, organismRemarks) and an Organism Darwin Core Type vocabulary term will have to be added. Following is an updated proposal for changes related to the adoption of a new "Organism" class: Term Name: Organism Identifier: http://rs.tdwg.org/dwc/terms/Organism Namespace: http://rs.tdwg.org/dwc/terms/ Label: Organism Definition: The category of information pertaining to a specific instance of an organism (virus, symbiont, individual, colony, group of individuals, population) reliably be known to taxonomically homogeneous. Comment: For discussion see http://code.google.com/p/darwincore/wiki/Organism Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-09-09 Date Modified: 2011-09-09 Has Domain: Has Range: Version: Organism-2011-09-09 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: Organism Identifier: http://rs.tdwg.org/dwc/dwctype/Organism Namespace: http://rs.tdwg.org/dwc/dwctype/ Label: Organism Definition: A resource describing an instance of the Organism 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: 2011-09-09 Date Modified: 2011-09-00 Member Of: http://rs.tdwg.org/dwc/terms/DwCType Has Domain: Has Range: Version: Organism-2011-09-09 Replaces: Is Replaced By: Class: ABCD 2.06: not in ABCD Term Name: organismID Identifier: http://rs.tdwg.org/dwc/terms/organismID Namespace: http://rs.tdwg.org/dwc/terms/ Label: organismID Definition: An identifier for the set of information associated with an Organism. May be a global unique identifier or an identifier specific to the data set. Comment: For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity 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: 2011-09-09 Date Modified: 2011-09-09 Has Domain: Has Range: Version: organismID-2011-09-09 Replaces: individualID-2009-09-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/Organism ABCD 2.06: DataSets/DataSet/Units/Unit/UnitID Term Name: organismRemarks Identifier: http://rs.tdwg.org/dwc/terms/organismRemarks Namespace: http://rs.tdwg.org/dwc/terms/ Label: organismRemarks Definition: Comments or notes about the Organism. Comment: Example: "seen several times in Tilden Park before capture". 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: 2011-09-09 Date Modified: 2009-09-09 Has Domain: Has Range: Version: organismRemarks-2011-09-09 Replaces: Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/Organism ABCD 2.06: DataSets/DataSet/Units/Unit/Notes 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". For discussion see http://code.google.com/p/darwincore/wiki/Organism Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-09-09 Date Modified: 2011-09-09 Has Domain: Has Range: Version: associatedOrganisms-2011-09-09 Replaces: associatedOccurrences-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/Organism ABCD 2.06: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceInstitutionCode + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceName + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitID The class proposed as "CollectionObject" has seen fewer alternate name proposals than "Organism", but the same call for clarity on inclusion and exclusion has been voiced. The basic idea is to use this class to cover information that could be considered "persistent evidence" that an organism occurred, and that the concept is distinct from both "Organism" and Occurrence. Evidence might include collection-based materials, digital media, written materials, and literature. "Evidence" may be a bit vague as a name for the class, providing no real indication that the "Evidence" should apply to an "Organism" rather than to an Occurrence, Taxon, Identification, or any other class. Nor does it convey the idea that the evidence should be persistent. "PersistentEvidenceThatAnOrganismExisted" gets the idea across pretty well, but it is a bit lengthy (and no one actually proposed this name). ABCD isn't shy about vague term names - it uses "Unit" for roughly this concept. The long-standing term "CollectionObject" is less vague than the proposed alternatives, but it might lead people to assume that the object must be physical, and that it must be housed within a collection, neither of which is strictly required. No one objected to this name for the term, however, so I will continue to use it here to illustrate the proposed changes and additions to accommodate this concept. Some existing terms (institutionID, institutionCode, collectionID, collectionCode, ownerInstitutionCode, catalogNumber, preparations, disposition, otherCatalogNumbers, associatedSequences) will have to be organized under this new class. These terms may require updated definitions for consistency. Note that with the addition of the "CollectionObject" class, the institutionCode, collectionCode, catalogNumber triplet would no longer apply to an Occurrence. New terms (collectionObjectID and collectionObjectRemarks) and an CollectionObject Darwin Core Type vocabulary term will have to be added. Following is an updated proposal for changes related to the adoption of a new "CollectionObject" class: 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 that an organism existed (specimen, sample, image, sound, drawing, field notes, publication), including digital forms. 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: 2011-09-09 Date Modified: 2011-09-09 Has Domain: Has Range: Version: CollectionObject-2011-09-09 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: 2011-09-09 Date Modified: 2011-09-09 Member Of: http://rs.tdwg.org/dwc/terms/DwCType Has Domain: Has Range: Version: CollectionObject-2011-09-09 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: 2011-09-09 Date Modified: 2011-09-09 Has Domain: Has Range: Version: collectionObjectID-2011-09-09 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 CollectionObject. 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: 2011-09-09 Date Modified: 2009-09-09 Has Domain: Has Range: Version: collectionObjectRemarks-2011-09-09 Replaces: SampleRemarks-2009-01-18 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/CollectionObject ABCD 2.06: DataSets/DataSet/Units/Unit/Notes Because of these changes for "Organism" and "CollectionObject", the definition of the Occurrence class will have to change and quite a different set of terms organized under it, namely: occurrenceID, occurrenceRemarks, recordNumber, recordedBy, establishmentMeans, and occurrenceStatus The Occurrence definition will change from "The category of information pertaining to evidence of an occurrence in nature, in a collection, or in a dataset (specimen, observation, etc.)." to something more akin to "The category of information pertaining to evidence of an occurrence of an Organism in nature." The term occurrenceDetails will be deprecated in favor of the Dublin Core term dcterms:references at the record level. Also, associatedMedia, which was organized under Occurrence, would become a record level term, as it could apply as easily to Occurrences, "Organisms", and "CollectionObjects". If you made it this far, I congratulate you on your dedication to the cause. Please let's clear up the remaining issues as a community and put these new terms to good use. Cheers, John

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Re: [tdwg-content] Occurrences, Organisms, and CollectionObjects: a review
by Chuck Miller 19 Sep '11

19 Sep '11

"the [controlled] vocabularies can be quite dynamic, variable, and/or contentious" Indeed they can. But, avoiding them I think is not the solution for the community. Avoiding them proliferates even more dynamics, variability and contention. However, the standardization of controlled vocabularies needs to be a separate activity, one that TDWG has been somewhat absent from of late and one we need to add to the mix of issues for TDWG to address. I suspect there is a lot of programming time being spent on discovering the dynamics and variability of the vocabularies currently in use and remediating them repeatedly in separate and far corners of the world. Even some small effort to consolidate a few variations or at least sort them out once rather than repeatedly by every new programmer that comes into this community would be beneficial to the biodiversity informatics world. Chuck -----Original Message----- From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Kevin Richards Sent: Tuesday, September 13, 2011 3:40 PM To: tuco(a)berkeley.edu Cc: TDWG Content Mailing List Subject: Re: [tdwg-content] Occurrences, Organisms, and CollectionObjects: a review Thanks John, the ResourceRelationship does satisfy my concerns! 1 person satisfied, 10 to go. :-) Kevin -----Original Message----- From: gtuco.btuco(a)gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of John Wieczorek Sent: Wednesday, 14 September 2011 8:22 a.m. To: Kevin Richards Cc: TDWG Content Mailing List Subject: Re: [tdwg-content] Occurrences, Organisms, and CollectionObjects: a review Let's see if I can catch up. On Thu, Sep 8, 2011 at 2:20 PM, Kevin Richards <RichardsK(a)landcareresearch.co.nz> wrote: > Great job John. > > 1 comment - I feel a little uncomfortable about the unstructured nature of the associatedOrganisms term. If I was writing some software to read and import some DwC data, I would be interested in capturing the associations that have been defined (in some structured way). I understand your discomfort. That proposed term is to take the place of the corresponding associatedOccurrences. As with the other "associatedX" terms, it is meant to allow useful information to be retained as part of flat records, not necessarily to be rigorously interpretable for the contents of the list, which would require data content standards as well. > There is possibly a few ways to improve this: > - define a structured way of filling this field, eg "[relationship type (from controlled vocabulary), eg host]:[related Organism ID]" > - add another field for just associatedOrganismIDs, that just has the > IDs and not free form text - not sure how this will help though > - add another class for AssociatedOrganism, that has fromOrganismID, > toOrganismID and relationshipType This is really the realm of more relational representations, in which you could use the ResourceRelationship class to good effect. > I also notice with a few of the DwC terms that it is recommended to use a controlled vocabulary for setting the value of the term, but the controlled vocabulary itself is not provided. Is it not the place for the DwC vocabulary to provide these? Or has the work just not been done to define them? No Darwin Core term enforces controlled vocabularies. Only recommendations are made, and that's on purpose. One of the biggest reasons is that the vocabularies can be quite dynamic, variable, and/or contentious, and we did not want that distraction in the management of the Darwin Core terms. > Kevin > > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of John > Wieczorek > Sent: Thursday, 8 September 2011 1:05 p.m. > To: TDWG Content Mailing List > Subject: [tdwg-content] Occurrences, Organisms, and CollectionObjects: > a review > > Dear all, > > Prepare yourself mentally. After more than a year of discussions, prototypes, scholarly papers, bar room brawls, etc., we are very near having a path forward for two new, related classes for Darwin Core that attempt to remove ambiguity inherent in the Occurrence class as it currently stands. Adding classes is quite a bit more complicated than adding properties (as you'll see if you manage to get through this message), and so it is important to be as thorough as possible to make sure we get it right. I'll try here to synthesize the rough consensus and the remaining issues. > > Basically, the idea is to pull two distinct concepts out of Occurrence and give them their own classes. > Maybe not surprisingly, one of the hardest things to agree upon has been the names for these classes. The class that was proposed first as "Individual" has seen no less than 12 alternate names, none of them satisfying to everyone. The closest thing to an acceptable name was "Organism", with caveats that the definition should make it abundantly clear what is to be included in the class and what is not. I'll use "Organism" here to refer to the class in the hopes of offending the fewest people. > > The rough consensus on "Organism" is that is should include viruses, symbionts, individuals, colonies, groups of individuals, and even populations, but that there should be taxonomic homogeneity to an instance of an "Organism". There has been some concern about how and where to draw the line on homogeneity. No attempt has yet been made to write a definitive description of the class, though many examples of representatives of the class have been given. > > What we need to move forward on the "Organism" class are an official definition and an official comment, the combination of which should be sufficient for someone previously unfamiliar with the term and the arguments leading to its existence to understand. Some existing terms (individualCount, sex, lifeStage, reproductiveCondition, behavior, previousIdentifications, associatedTaxa) will have to be reorganized to be under this new class. These terms may require updated definitions for consistency. New terms (organismID, associatedOrganisms, organismRemarks) and an Organism Darwin Core Type vocabulary term will have to be added. Following is an updated proposal for changes related to the adoption of a new "Organism" > class: > > Term Name: Organism > Identifier: http://rs.tdwg.org/dwc/terms/Organism > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Organism > Definition: The category of information pertaining to a specific > instance of an organism (virus, symbiont, individual, colony, group of individuals, population) reliably be known to taxonomically homogeneous. > Comment: For discussion see > http://code.google.com/p/darwincore/wiki/Organism > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: recommended > Date Issued: 2011-09-09 > Date Modified: 2011-09-09 > Has Domain: > Has Range: > Version: Organism-2011-09-09 > 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: Organism > Identifier: http://rs.tdwg.org/dwc/dwctype/Organism > Namespace: http://rs.tdwg.org/dwc/dwctype/ > Label: Organism > Definition: A resource describing an instance of the Organism 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: 2011-09-09 > Date Modified: 2011-09-00 > Member Of: http://rs.tdwg.org/dwc/terms/DwCType > Has Domain: > Has Range: > Version: Organism-2011-09-09 > Replaces: > Is Replaced By: > Class: > ABCD 2.06: not in ABCD > > Term Name: organismID > Identifier: http://rs.tdwg.org/dwc/terms/organismID > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: organismID > Definition: An identifier for the set of information associated > with an Organism. May be a global unique identifier or an identifier specific to the data set. > Comment: For discussion see > http://code.google.com/p/darwincore/wiki/BiologicalEntity > 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: 2011-09-09 > Date Modified: 2011-09-09 > Has Domain: > Has Range: > Version: organismID-2011-09-09 > Replaces: individualID-2009-09-24 Is Replaced By: > Class: http://rs.tdwg.org/dwc/terms/Organism > ABCD 2.06: DataSets/DataSet/Units/Unit/UnitID > > Term Name: organismRemarks > Identifier: http://rs.tdwg.org/dwc/terms/organismRemarks > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: organismRemarks > Definition: Comments or notes about the Organism. > Comment: Example: "seen several times in Tilden Park before capture". > 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: 2011-09-09 > Date Modified: 2009-09-09 > Has Domain: > Has Range: > Version: organismRemarks-2011-09-09 > Replaces: > Is Replaced By: > Class: http://rs.tdwg.org/dwc/terms/Organism > ABCD 2.06: DataSets/DataSet/Units/Unit/Notes > > 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". For > discussion see http://code.google.com/p/darwincore/wiki/Organism > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: recommended > Date Issued: 2011-09-09 > Date Modified: 2011-09-09 > Has Domain: > Has Range: > Version: associatedOrganisms-2011-09-09 > Replaces: associatedOccurrences-2009-04-24 Is Replaced By: > Class: http://rs.tdwg.org/dwc/terms/Organism > ABCD 2.06: > DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUni > tSourceInstitutionCode > + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedU > + ni > + tSourceName > + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedU > + ni > + tID > > > The class proposed as "CollectionObject" has seen fewer alternate name proposals than "Organism", but the same call for clarity on inclusion and exclusion has been voiced. The basic idea is to use this class to cover information that could be considered "persistent evidence" that an organism occurred, and that the concept is distinct from both "Organism" and Occurrence. Evidence might include collection-based materials, digital media, written materials, and literature. > > "Evidence" may be a bit vague as a name for the class, providing no real indication that the "Evidence" should apply to an "Organism" > rather than to an Occurrence, Taxon, Identification, or any other class. Nor does it convey the idea that the evidence should be persistent. "PersistentEvidenceThatAnOrganismExisted" gets the idea across pretty well, but it is a bit lengthy (and no one actually proposed this name). ABCD isn't shy about vague term names - it uses "Unit" for roughly this concept. The long-standing term "CollectionObject" is less vague than the proposed alternatives, but it might lead people to assume that the object must be physical, and that it must be housed within a collection, neither of which is strictly required. No one objected to this name for the term, however, so I will continue to use it here to illustrate the proposed changes and additions to accommodate this concept. > > Some existing terms (institutionID, institutionCode, collectionID, collectionCode, ownerInstitutionCode, catalogNumber, preparations, disposition, otherCatalogNumbers, associatedSequences) will have to be organized under this new class. These terms may require updated definitions for consistency. Note that with the addition of the "CollectionObject" class, the institutionCode, collectionCode, catalogNumber triplet would no longer apply to an Occurrence. > > New terms (collectionObjectID and collectionObjectRemarks) and an CollectionObject Darwin Core Type vocabulary term will have to be added. Following is an updated proposal for changes related to the adoption of a new "CollectionObject" class: > > 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 that an organism existed (specimen, sample, image, sound, drawing, field notes, publication), including digital forms. > 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: 2011-09-09 > Date Modified: 2011-09-09 > Has Domain: > Has Range: > Version: CollectionObject-2011-09-09 > 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: 2011-09-09 > Date Modified: 2011-09-09 > Member Of: http://rs.tdwg.org/dwc/terms/DwCType > Has Domain: > Has Range: > Version: CollectionObject-2011-09-09 > 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: 2011-09-09 > Date Modified: 2011-09-09 > Has Domain: > Has Range: > Version: collectionObjectID-2011-09-09 > 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 CollectionObject. > 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: 2011-09-09 > Date Modified: 2009-09-09 > Has Domain: > Has Range: > Version: collectionObjectRemarks-2011-09-09 > Replaces: SampleRemarks-2009-01-18 Is Replaced By: > Class: http://rs.tdwg.org/dwc/terms/CollectionObject > ABCD 2.06: DataSets/DataSet/Units/Unit/Notes > > > Because of these changes for "Organism" and "CollectionObject", the definition of the Occurrence class will have to change and quite a different set of terms organized under it, namely: > > occurrenceID, occurrenceRemarks, recordNumber, recordedBy, > establishmentMeans, and occurrenceStatus > > The Occurrence definition will change from "The category of information pertaining to evidence of an occurrence in nature, in a collection, or in a dataset (specimen, observation, etc.)." to something more akin to "The category of information pertaining to evidence of an occurrence of an Organism in nature." > > The term occurrenceDetails will be deprecated in favor of the Dublin Core term dcterms:references at the record level. Also, associatedMedia, which was organized under Occurrence, would become a record level term, as it could apply as easily to Occurrences, "Organisms", and "CollectionObjects". > > If you made it this far, I congratulate you on your dedication to the cause. Please let's clear up the remaining issues as a community and put these new terms to good use. > > Cheers, > > John > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > 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 > 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 _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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Inclusion of geo:lat, geo:long, geo:alt in Darwin Core unresolved
by John Wieczorek 15 Sep '11

15 Sep '11

Dear all, I have reviewed both the recent and ancient discussions regarding the proposal to include geo:lat, geo:long, and geo:alt among the recommended terms from Darwin Core. This particular proposal is not being voted on for inclusion by the TAG at this point, because further research has revealed some issues that need to be addressed. I'll include here the issues I raised to the TAG in the hope of stimulating further discussion in pursuit of a public consensus. The proposal is to recommend 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 at 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:long 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:long 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, having so many spatially-related terms. 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 geographic coordinates in decimal degrees and only a datum transformation has to be done on them to get geo_lat and geo:long. 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 before we abandon the terms and make millions of georeferenced records less readily usable? 3) A request was expressed by one reviewer that the term geo:alt should 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, but related to the Darwin Core elevation terms. No discussion of these issues has yet taken place. Cheers, John

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