- tdwg-content - lists.tdwg.org

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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resolvable URIs
by Hilmar Lapp 05 Jun '09

05 Jun '09

Right now the DwC Terms RDF download at http://rs.tdwg.org/dwc/rdf/dwcterms.rdf sets the namespace URI to http://rs.tdwg.org/dwc/terms/ and doesn't seem to otherwise mention the download URI. I may be missing something, but doesn't that mean that DwC Terms referenced in RDF documents using the canonical namespace URI (http://rs.tdwg.org/dwc/terms/ ) can't be resolved? I guess at present that doesn't matter too much as there isn't really anything in the DwC Terms ontology that would tell a client agent something about the term that it wouldn't already know. But it's maybe worth noting that that's different from other well-known vocabularies. For example, the canonical URI for DC Terms (http://purl.org/dc/ terms/) resolves to the RDF for the whole vocabulary. (BTW I'm not sure this is the right list to post DwC questions/issues to - let me know if it's not and where to send instead) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu : ===========================================================

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[tdwg-phylo] phylogenetic tree data
by Yose Widjaja 04 Jun '09

04 Jun '09

Hi, I was just wondering, is it possible to obtain, somewhere from the net, the full phylogenetic tree for life on earth? How big would the data be? How many nodes are there (counting a species, and every split in the graph, as a node)? I'm thinking of fitting it inside the interatctorium (www.interactorium.net) Cheers -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- Yose Widjaja Supreme Emperor @ Jormy Games www.jormy.com yose(a)jormy.com -- -- -- -- -- -- -- -- -- -- -- -- -- --

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[tdwg-spm] e-Biosphere '09 dinner meeting
by Cynthia Parr 01 Jun '09

01 Jun '09

Folks, Apologies to those who are not at the conference. I have made a reservation for 7:30 p.m. dinner for us Tuesday night at the Albert, a pub with an upstairs dining room at 52 Victoria Street, Westminster, London. The cross street is Buckingham Gate. I'm sorry for conflicts that I know that some of you have. We'll use this meeting to get to know each other better and think about future directions for the SPM standard. Come prepared with your experiences and ideas. But we'll save much of the serious discussion for this list and for TDWG in Montpelier. Cyndy -- Cynthia Sims Parr Director of the Species Pages Group Encyclopedia of Life http://www.eol.org Office: 202.633.8730 Fax: 202.633.8742 parrc(a)si.edu Mailing address: National Museum of Natural History P.O. Box 37012 MRC 106 Washington, DC 20013-7012

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[tdwg-spm] SPM side meeting at e-Biosphere
by Cynthia Parr 28 May '09

28 May '09

Thanks for those who responded positively regarding an SPM meeting while at e-Biosphere in London next week. It looks like there may be up to 8 of us. One option is to have dinner together on Tuesday, June 2. The other option is to find a quiet place during Session 12, the afternoon of Wednesday. I have inquired if there is any meeting space available for Session 12, but as requests for that space were due back in April I do not expect we will be accommodated. Please contact me privately at parrc(a)si.edu if you would be able to attend an informal dinner on Tuesday night. I will post the final time and location on a bulletin board at the conference on Monday, and I will also send a message to the group. Thanks in advance, Cyndy -- Cynthia Sims Parr Director of the Species Pages Group Encyclopedia of Life http://www.eol.org Office: 202.633.8730 Fax: 202.633.8742 parrc(a)si.edu Mailing address: National Museum of Natural History P.O. Box 37012 MRC 106 Washington, DC 20013-7012

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[tdwg-spm] Species Profile Model side meeting at e-Biosphere '09
by Eamonn O Tuama (GBIF) 20 May '09

20 May '09

Apologies for repeat posting. From: Parr, Cynthia [mailto:parrc@si.edu] Sent: 15 May 2009 16:51 To: tdwg-spm(a)lists.tdwg.org Subject: Species Profile Model side meeting at e-Biosphere '09 Greetings, We had an informal meeting to discuss SPM at the TDWG meeting in Australia. In order to move the standard forward, I agreed to help coordinate future development of the standard. At the next TDWG meeting we should have a more formal session to do some real work on the standard. However, there are a few things we can do in advance. 1) we can rejuvenate this mailing list, making sure that everyone who wants to be involved is part of the discussion, and 2) we can have a side meeting at the e-Biosphere meeting in London June 1-3. My understanding is that there are free spaces available for this and I will look into availability and timing. How many people on this list would be able (and interested) to attend such a meeting? Those who are not already planning to be at e-Biosphere we could involve via the mailing list. Thanks, Cyndy Cynthia Sims Parr Director of the Species Pages Group Encyclopedia of Life Office: 202.633.8730 Fax: 202.633.8742 <mailto:parrc@si.edu> parrc(a)si.edu Mailing address: National Museum of Natural History P.O. Box 37012 MRC 106 Washington, DC 20013-7012

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Re: [tdwg-content] issue tracker?
by John R. WIECZOREK 14 May '09

14 May '09

Dear all, I have surfaced for a few hours, only to head back into the puna before the water freezes solid. I can only address the most important issues right now and I will take the rest of them back with me into the field to work on over the next few days (it doesn't freeze inside the pickup if there is a warm body and a running laptop in there). I think it best that the Issue Tracker is great for public review from the perspective of the Darwin Core Working Group. Having everything there to organize and "track" is exactly what that is for. I have updated the code site "Home" page http://code.google.com/p/darwincore/ to be more explicit about the location and use of the Issue Tracker. I think that is a better place for specific issues about the documents than the tdwg-content list. I think the tdwg-content list is the best place for more philosophical discussions (non-decisive ramblings) that don't point out specific errors or make specific requests. Once the philosophical discussions result in action items, that's when they should go into the issue tracker. What I don't know, and would very much appreciate someone new to try, is to see what submitting public review commentary would be like. It's all too natural to me at this point to have an realistic perspective for new contributors, which almost everyone will be. Also, this is the kind of thing I for which I would have to be connected to the internet to properly visualize from other possible perspectives. I won'thave that luxuryfor another week or so. As I said, I embellished the darwincore Project Home page with respect to the issue tracker. Non-owners and non-project-members will be able to use one of two currently existing issue templates - Report Error (the default) and New Term. These templates can be changed to be more helpful, more can be added if necessary. Anyone with a few spare minutes could give these a try and let us know how it can be made more clear. Don't be afraid to submit a false issue, just note them as such in the summary and/or description. Then, when you have a suggestion, submit it for real as an issue! Thanks, John On Fri, May 8, 2009 at 7:31 AM, Gail Kampmeier <gkamp(a)illinois.edu> wrote: > Regarding the message sent last night on using this list for the > public review, I have now run into another prospective method on > http://code.google.com/p/darwincore/ --the "Issue Tracker" but it has > no link... where is this? Is this it > http://code.google.com/p/darwincore/issues/list ? Is it suitable for > public review or should this be more internal to your working group? > > Would you rather I be using something other than this list to post > questions? I know John is in the field, but please someone else jump > in if you can help. I am hoping to send this to the Exec once I > finish going through it myself. > > Thanks! > Gail > Review Manager, DwC > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content >

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Re: [tdwg-content] Darwin Core review
by Peter Desmet 11 May '09

11 May '09

Thanks Marküs, Would it be possible for you to answer the two following questions? - Is Darwin Core now officially in public review? - If yes, how should people comment on DwC (see also emails from Gail Kampmeier): through this mailing list or using the (better suited?) issue tracker on Google Code, where more than 130 term pages are missing for discussion (404 errors)? In other words, can I forward DwC for review to the Canadensys community now or do you want us to wait? Peter On Mon, May 11, 2009 at 8:43 AM, "Markus Döring (GBIF)" <mdoering(a)gbif.org> wrote: > thanks for this mail, peter! > john is currently on fieldwork in argentina, so he is offline for lots of > time, so please excuse his silence over long periods. > He will be glad to see your comments I will imagine. > > cheers, > Markus > > > On May 7, 2009, at 9:11 PM, Peter Desmet wrote: > >> Hi everyone, >> >> As Marküs informed me last time, I should post all my Darwin Core >> remarks on this list. >> Most of my remarks are about missing information in the complete >> historical record (see below), except the following: >> >> 1. Great work!! I haven't had time to read the full documentation yet, >> but I'm very glad everything is so well documented now. It answers a >> lot of questions and it will greatly facilitate the adoption of the >> standard. Over the last 2 years I have given several presentations >> about Darwin Core to data publishers, but with all the current >> improvements, it will be a blast to do this! Especially the use of >> classes (instead of core and extentions) makes it much easier to grasp >> conceptually. >> >> 2. Is Darwin Core now officially in public review? Will we receive an >> invitation email to review (which I could forward)? >> >> 3. What is the reasoning behind changing all the term names from >> UpperCamelCase to lowerCamelCase? >> >> 4. HABITAT >> http://rs.tdwg.org/dwc/terms/index.htm#habitat >>> >>> I don't think I agree the best practice for this term is to use a >>> controlled vocabulary. This field can contain plenty of text information >>> that may be lost if one switches to a controlled vocabulary. >> >> 5. GEODETICDATUM >> http://rs.tdwg.org/dwc/terms/index.htm#geodeticDatum >>> >>> So you need to use the same geodetic datum for the verbatim coordinates >>> as for the decimal lat & long? >> >> 6. PREVIOUSIDENTIFICATIONS >> >> http://rs.tdwg.org/dwc/terms/history/index.htm#previousIdentifications-2009… >>> >>> Under the current definition (and examples) of previousIdentifications, >>> this list can include person names and dates. This is significantly >>> different from the previous definition: "A list (concatenated and separated) >>> of previous ScientificNames to which the sample was identified". In my >>> opinion this old definition should be kept in the complete historical >>> record, with a "replaced by" link. >> >> >> ------------ MISSING/INCORRECT INFORMATION ------------ >> >> 1. The following historical classes cannot be found (anymore) in the >> complete historical record. If added, they should have a "replaced by" >> link and the new term should have a "replaces link" (except if new >> term is part of Dublin Core). >> >>> Sample (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#Occurrence-2009-04-24) >>> SamplingEvent (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#Event-2008-11-19) >>> SamplingLocation (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#Location-2009-04-24) >>> SampleAttribute (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#MeasurementOrFact-2009-04-24) >>> EventAttribute (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#MeasurementOrFact-2009-04-24) >>> AccessConstraints (now >>> http://dublincore.org/documents/dcmi-terms/#terms-accessRights) >>> Generalizations (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#dataGeneralizations-2009-04-…) >>> SampleRemarks (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#occurrenceRemarks-2009-04-24) >>> SamplingEventID (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#eventID-2009-04-24) >>> SamplingEventRemarks (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#eventRemarks-2009-04-24) >>> SamplingEventAttributes (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#dynamicProperties-2009-04-24) >>> SamplingLocationID (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#locationID-2009-04-24) >>> SamplingLocationRemarks (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#locationRemarks-2009-04-24) >>> SamplingAttributeID and EventAttributeID (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#measurementID-2009-04-24) >>> SamplingAttributeType and EventAttributeType (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#measurementType-2009-04-24) >>> SamplingAttributeValue and EventAttributeValue (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#measurementValue-2009-04-24) >>> SamplingAttributeAccuracy and EventAttributeAccuracy (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#measurementAccuracy-2009-04-…) >>> SamplingAttributeUnit and EventAttributeUnit (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#measurementUnit-2009-04-24) >>> SamplingAttributeDeterminedDate and EventAttributeDeterminedDate (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#measurementDeterminedDate-20…) >>> SamplingAttributeDeterminedBy and EventAttributeDeterminedBy (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#measurementDeterminedBy-2009…) >>> SamplingAttributeRemarks and EventAttributeRemarks (now >>> http://rs.tdwg.org/dwc/terms/history/index.htm#measurementRemarks-2009-04-24) >> >> 2. There are plenty of missing discussion pages on the Google Code >> website. See attachment for full list. >> >> 3. See remarks per term. >> >> OCCURENCE >> http://rs.tdwg.org/dwc/terms/index.htm#Occurrence >>> >>> Details links to 2008-11-19, not to the more recent 2009-04-24. >> >> http://rs.tdwg.org/dwc/terms/history/index.htm#Occurrence-2009-04-24 >>> >>> Date modified: 2008-11-19? >>> No "replaces" link to 2008-11-19 >> >> http://rs.tdwg.org/dwc/terms/history/index.htm#Occurrence-2008-11-19 >>> >>> Date modified: 2008-04-24? >>> Status: recommended? >>> No "replaced by" link to 2008-04-24 >> >> ----- >> LOCATION >> http://rs.tdwg.org/dwc/terms/history/index.htm#Location-2009-04-24 >>> >>> Status: recommended? >>> No "replaced by" link to dcterms:Location >> >> ----- >> TAXON >> http://rs.tdwg.org/dwc/terms/index.htm#Taxon >>> >>> Details link to 2008-11-19, not to the more recent 2009-01-23. >> >> http://rs.tdwg.org/dwc/terms/history/index.htm#Taxon-2008-11-19 >>> >>> No "replaced by" link to 2009-01-23 >>> Status: recommended? >> >> http://rs.tdwg.org/dwc/terms/history/index.htm#Taxon-2009-01-23 >>> >>> No "replaces" link to 2008-11-19 >> >> ----- >> INFORMATIONWITHHELD >> Some of the examples in >> http://rs.tdwg.org/dwc/terms/index.htm#informationWithheld are better >> placed in >> http://rs.tdwg.org/dwc/terms/index.htm#dataGeneralizations >> ----- >> RELATEDINFORMATION >> >> http://rs.tdwg.org/dwc/terms/history/index.htm#RelatedInformation-2007-04-17 >>> >>> No "replaces" link to >>> http://rs.tdwg.org/dwc/terms/history/index.htm#RecordURL-2005-07-10 >> >> ----- >> CONDITION >> http://rs.tdwg.org/dwc/terms/index.htm#reproductiveCondition >>> >>> The reproductive condition of the biological individual(s): should >>> include plural? >> >> ----- >> BEHAVIOR >> http://rs.tdwg.org/dwc/terms/history/index.htm#behavior-2009-04-24 >>> >>> The decision >>> (http://rs.tdwg.org/dwc/terms/history/decisions/index.htm#Decision-2009-03-0…) >>> mentions SamplingEvent and Sample, two now historical classes. >> >> ----- >> CATALOGNUMBERNUMERIC >> >> http://rs.tdwg.org/dwc/terms/history/index.htm#CatalogNumberNumeric-2003-06… >> Is now historical, but there is no "replaced by" link (probably to: >> >> http://rs.tdwg.org/dwc/terms/history/index.htm#otherCatalogNumbers-2009-04-…) >> ----- >> EVENTDATE >> http://rs.tdwg.org/dwc/terms/history/index.htm#eventDate-2009-04-24 >>> >>> Split the replaces link in two: EarliestDateCollected & >>> LatestDateCollected >> >> ----- >> EVENTTIME >> http://rs.tdwg.org/dwc/terms/history/index.htm#eventTime-2009-04-24 >>> >>> Split the replaces link in two: StartTimeOfDay & EndTimeOfDay >> >> ----- >> BINOMIAL >> http://rs.tdwg.org/dwc/terms/history/index.htm#binomial-2008-11-19 >>> >>> Is not used in the DwC terms, but has the status: recommended. >> >> ----- >> RELATEDRESOURCETYPE >> >> http://rs.tdwg.org/dwc/terms/history/index.htm#relatedResourceType-2009-04-… >>> >>> Is not used in the DwC terms, but has the status: recommended. >> >> ----- >> RELATEDBASISOFRECORD >> >> http://rs.tdwg.org/dwc/terms/history/index.htm#RelatedBasisOfRecord-2008-11… >>> >>> Is not used in the DwC terms, but has the status: recommended. >> >> >> Regards, >> >> Peter >> >> >> -- >> Peter Desmet >> Biodiversity Informatics Manager / Directeur de l'informatique de la >> biodiversité >> Montréal Biodiversity Centre / Centre sur la biodiversité de Montréal >> Canadensys - www.canadensys.net >> >> Institut de recherche en biologie végétale >> Université de Montréal >> 4101 Rue Sherbrooke Est >> Montréal, Québec, H1X2B2 >> Canada >> >> Télé / Phone: 514-872-5249 >> Télécopie / Fax: 514-872-9406 >> Email: peter.desmet.cubc(a)gmail.com >> <missing_discussion_pages.txt> > > -- Peter Desmet Biodiversity Informatics Manager / Directeur de l'informatique de la biodiversité Montréal Biodiversity Centre / Centre sur la biodiversité de Montréal Canadensys - www.canadensys.net Institut de recherche en biologie végétale Université de Montréal 4101 Rue Sherbrooke Est Montréal, Québec, H1X2B2 Canada Télé / Phone: 514-872-5249 Télécopie / Fax: 514-872-9406 Email: peter.desmet.cubc(a)gmail.com

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