- tdwg-content - lists.tdwg.org

BCI et al. merger
by Bob Morris 10 Aug '12

10 Aug '12

Can anyone tell me authoritatively what is the status of the merger of BCI, Biorepositories.org and Index Herbariorum? In particular, what will the new portal be called and at what URL? I need to update some Audubon Core citations as we near the AC public comment effort. Thanks Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Harvard University Herbaria 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 === The content of this communication is made entirely on my own behalf and in no way should be deemed to express official positions of The University of Massachusetts at Boston or Harvard University.

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Re: [tdwg-content] minimum/maximum elevation and depth - usage and priority?
by Aaike De Wever 09 Jul '12

09 Jul '12

Dear Markus, Dear all, Thanks a lot for your answers so far. I understand that both the use for specifying a range and for reflecting uncertainties on measurements can go in this field, in the later case / for point data I would also be in favor of having elevationInMeters and elevationUncertaintyInMeters. Given the use of min/max to represent uncertainty, I am again puzzled whether it's actually a good idea of having the same value for both fields if you have only one value at hand (as this could be interpreted as 0 uncertainty...) Regarding the location precision, I am also puzzled why there is both coordinateUncertaintyInMeters and coordinatePrecision... With best regards, Aaike De Wever On 3 Jul 2012, at 10:41, Markus Döring (GBIF) wrote: Hi, I always considered the min/max terms for elevation and depth to be useful to express uncertainties. But if that is the main or only use case wouldn't it be less confusing to treat uncertainty the same way across all geospatial terms? I would much prefer to work with elevationInMeters and elevationUncertaintyInMeters than min max. Markus PS: There are actually 4 terms for location precision right now: coordinateUncertaintyInMeters coordinatePrecision pointRadiusSpatialFit footprintSpatialFit

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InstitutionCode - InstitutionID
by Aaike De Wever 03 Jul '12

03 Jul '12

Dear all, While composing a template and recommendations for the Darwin Core fields to supply for the BioFresh project <http://www.freshwaterbiodiversity.eu/>, similar to what Peter Desmet did for herbaria in Apple Core <http://code.google.com/p/applecore/>, I came across a number of terms which I haven't yet completely understood and hope to get some feedback on from this community. Two of these terms are: InstitutionCode - InstitutionID http://rs.tdwg.org/dwc/terms/institutionCode - http://rs.tdwg.org/dwc/terms/institutionID The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record. / An identifier for the institution having custody of the object(s) or information referred to in the record. I guess that the latter term is supposed to be a DOI/GUID for the institute, but am wondering if there is such a thing or whether this field is rather for internal database purposes? Any advise would be appreciated! With best regards, -- Aaike De Wever BioFresh Science Officer Freshwater Laboratory, Royal Belgian Institute of Natural Sciences Vautierstraat 29, 1000 Brussels Belgium tel.: +32(0)2 627 43 90 mobile.: +32(0)486 28 05 93 email: <aaike.dewever(a)naturalsciences.be> skype: aaikew AIM: aaike(a)mac.com LinkedIn: <http://be.linkedin.com/in/aaikedewever> BioFresh: <http://www.freshwaterbiodiversity.eu/> and <http://data.freshwaterbiodiversity.eu/> Belgian Biodiversity Platform: <http://www.biodiversity.be>

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use of the terms dcterms:rightsHolder and dcterms:accessRights in existing databases
by Steve Baskauf 03 Jul '12

03 Jul '12

The terms dcterms:rightsHolder and dcterms:accessRights are "imported" from Dublin Core into the Darwin Core record-level vocabulary. I am interested in them for two reasons: there are several issues with the use of those terms as RDF predicates, and they differ from the terms suggested for use in rights management in the draft Audubon Core vocabulary. What I am wondering is how widely are they actually used in databases by our community? If you maintain a database, do you use them? Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

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Re: [tdwg-content] minimum/maximum elevation and depth - usage and priority?
by Aaike De Wever 03 Jul '12

03 Jul '12

Dear John, Dear all, Thanks a lot for the answers so far. I am still curious about a good example of the min/max use, at first I thought the trawl sampling was a good example as well, but I guess it rather applies if you sampled an area with a certain radius around the provided coordinates. As most data we will encounter will come from a single point/elevation/depth, I am just a little worried that it may puzzle data providers that they have to provide both min and max. With best regards, Aaike Hi Aaike, These values are indeed meant to capture the range of possible elevation/depth or the extent of them. If there upper and lower bounds are the same, then the values in the minimum and maximum should be the same. Cheers, John On Mon, Jul 2, 2012 at 8:38 AM, Aaike De Wever <aaike.dewever(a)naturalsciences.be> wrote: Dear all, Following on my previous email, I also had a question on the following terms: * minimumElevationInMeters - maximumElevationInMeters http://rs.tdwg.org/dwc/terms/minimumElevationInMeters - http://rs.tdwg.org/dwc/terms/maximumElevationInMeters The lower limit of the range of elevation (altitude, usually above sea level), in meters. * minimumDepthInMeters - maximumDepthInMeters http://rs.tdwg.org/dwc/terms/minimumDepthInMeters - http://rs.tdwg.org/dwc/terms/maximumDepthInMeters The lesser/greater depth of a range of depth below the local surface, in meters. Both for elevation and depth there are two terms representing the minimum and maximum, which I figure are meant to provide a range. As in most cases, for point data, there will be only one elevation and depth value, I was wondering what is the recommended best practice for these terms. Should one use minimum or maximum or provide the same value for both terms? Any advise on this would be appreciated! With best regards, -- Aaike De Wever BioFresh Science Officer Freshwater Laboratory, Royal Belgian Institute of Natural Sciences Vautierstraat 29, 1000 Brussels Belgium tel.: +32(0)2 627 43 90 mobile.: +32(0)486 28 05 93 email: <aaike.dewever(a)naturalsciences.be> skype: aaikew AIM: aaike(a)mac.com LinkedIn: <http://be.linkedin.com/in/aaikedewever> BioFresh: <http://www.freshwaterbiodiversity.eu/> and <http://data.freshwaterbiodiversity.eu/> Belgian Biodiversity Platform: <http://www.biodiversity.be> _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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minimum/maximum elevation and depth - usage and priority?
by Aaike De Wever 03 Jul '12

03 Jul '12

Dear all, While composing a template and recommendations for the Darwin Core fields to supply for the BioFresh project <http://www.freshwaterbiodiversity.eu/>, similar to what Peter Desmet did for herbaria in Apple Core <http://code.google.com/p/applecore/>, I came across a number of terms which I haven't yet completely understood and hope to get some feedback on from this community. The terms I am referring to are: * minimumElevationInMeters - maximumElevationInMeters http://rs.tdwg.org/dwc/terms/minimumElevationInMeters - http://rs.tdwg.org/dwc/terms/maximumElevationInMeters The lower limit of the range of elevation (altitude, usually above sea level), in meters. * minimumDepthInMeters - maximumDepthInMeters http://rs.tdwg.org/dwc/terms/minimumDepthInMeters - http://rs.tdwg.org/dwc/terms/maximumDepthInMeters The lesser/greater depth of a range of depth below the local surface, in meters. Both for elevation and depth there are two terms representing the minimum and maximum, which I figure are meant to provide a range. As in most cases, for point data, there will be only one elevation and depth value, I was wondering what is the recommended best practice for these terms. Should one use minimum or maximum or provide the same value for both terms? Any advise on this would be appreciated! With best regards, -- Aaike De Wever BioFresh Science Officer Freshwater Laboratory, Royal Belgian Institute of Natural Sciences Vautierstraat 29, 1000 Brussels Belgium tel.: +32(0)2 627 43 90 mobile.: +32(0)486 28 05 93 email: <aaike.dewever(a)naturalsciences.be> skype: aaikew AIM: aaike(a)mac.com LinkedIn: <http://be.linkedin.com/in/aaikedewever> BioFresh: <http://www.freshwaterbiodiversity.eu/> and <http://data.freshwaterbiodiversity.eu/> Belgian Biodiversity Platform: <http://www.biodiversity.be>

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minimum/maximum elevation and depth - usage and priority?
by Aaike De Wever 02 Jul '12

02 Jul '12

Dear all, Following on my previous email, I also had a question on the following terms: * minimumElevationInMeters - maximumElevationInMeters http://rs.tdwg.org/dwc/terms/minimumElevationInMeters - http://rs.tdwg.org/dwc/terms/maximumElevationInMeters The lower limit of the range of elevation (altitude, usually above sea level), in meters. * minimumDepthInMeters - maximumDepthInMeters http://rs.tdwg.org/dwc/terms/minimumDepthInMeters - http://rs.tdwg.org/dwc/terms/maximumDepthInMeters The lesser/greater depth of a range of depth below the local surface, in meters. Both for elevation and depth there are two terms representing the minimum and maximum, which I figure are meant to provide a range. As in most cases, for point data, there will be only one elevation and depth value, I was wondering what is the recommended best practice for these terms. Should one use minimum or maximum or provide the same value for both terms? Any advise on this would be appreciated! With best regards, -- Aaike De Wever BioFresh Science Officer Freshwater Laboratory, Royal Belgian Institute of Natural Sciences Vautierstraat 29, 1000 Brussels Belgium tel.: +32(0)2 627 43 90 mobile.: +32(0)486 28 05 93 email: <aaike.dewever(a)naturalsciences.be> skype: aaikew AIM: aaike(a)mac.com LinkedIn: <http://be.linkedin.com/in/aaikedewever> BioFresh: <http://www.freshwaterbiodiversity.eu/> and <http://data.freshwaterbiodiversity.eu/> Belgian Biodiversity Platform: <http://www.biodiversity.be>

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Beginner's Guide to RDF now available
by Steve Baskauf 01 Jul '12

01 Jul '12

The Beginner's Guide to RDF is now available at the TDWG-RDF Task Group's website via the RRL http://code.google.com/p/tdwg-rdf/wiki/Beginners The guide is intended to serve as an introduction for persons who are not already familiar with RDF and OWL, and as a reference for those who would like organized access to reference material on those topics. The information is presented with minimal formal language and includes functional examples from the biodiversity informatics community. Thanks to the members of the Task Group who provided clarification and examples during discussion prior to writing the guide and especially to Paul Murray and Bob Morris who provided helpful feedback on drafts of the guide. Steve Baskauf TDWG-RDF Task Group co-convener -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

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Job announcement: Biodiversity Informatics Manager for Canadensys
by Peter Desmet 28 Jun '12

28 Jun '12

Dear colleagues, The Université de Montréal Biodiversity Centre is seeking to hire a Biodiversity Informatics Manager for the Canadensys network (http://www.canadensys.net) An excerpt from the position description: The Biodiversity Informatics Manager will maintain, improve and expand the Canadensys biodiversity network, to ensure its relevance, usefulness and visibility. He/she will design and implement innovative tools to publish, synthesise and display biodiversity data, building upon the current infrastructure, which includes a community portal (http://www.canadensys.net) blog (http://www.canadensys.net/blog) explorer (http://data.canadensys.net/explorer) repository (http://data.canadensys.net/ipt) and checklist database (http://data.canadensys.net/vascan) ... The full description - including how to apply - can be found attached or at http://www.canadensys.net/job-announcement.pdf. Evaluation of applications will begin July 15, 2012. Best regards, Peter Desmet p.p. Anne Bruneau PS: Apologies for cross-posting.

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Re: [tdwg-content] LSID Resolution Service using DDDS/DNS
by Julien Cigar 20 Jun '12

20 Jun '12

Thank you all for those clarifications, I'll not go further with LSID and rather use the usual URLs. On 06/19/2012 23:41, Jonathan A Rees wrote: > Sadly nobody ever registered urn:lsid: with IETF, or even specified it > well enough that it would be able to pass IETF NID review if > submitted. LSIDs aren't URNs or URIs in any standards sense. Jonathan > > On Mon, Jun 18, 2012 at 10:51 AM, Julien Cigar<jcigar(a)ulb.ac.be> wrote: >> Hi Roderic, >> >> Thanks for your reply. >> >> But I've almost the same feeling. The more I read about LSIDs, the more I >> feel that there are no real huge benefits over URLs, .. although it looks >> like different concept to me: I see more an URL as the location of the >> resource, and the LSID the identifier of that resource. >> >> It's frustrating because at first glances all the models and the "to be >> compliant you must ..." rules that come with the spec seemed pretty >> >> Some advantages I see compared to URLs: >> - the separation of data and metadata (through the .getData / .getMetadata >> methods and the WSDL files), .. although you could achieve more or less the >> same by playing on the Accept header of the HTTP request >> - the versioning >> - the resolution services/discovery services.. although there are a lot of >> "assuming that..." in the spec >> - protocol independent >> - other things ... ? >> >> Best regards, >> Julien >> >> >> On 06/18/2012 15:15, Roderic Page wrote: >>> Hi Julien, >>> >>> Firstly, let me say "run, run away now". Unless you need to support >>> resolving existing LSIDs (e.g., Index Fungorum, IPNI) then I can see no >>> reason to use LSIDs. The future landscape of identifiers is essentially URLs >>> and DOIs. The difference between the two boils down to whether you want your >>> identifiers to have a degree of management or not (you can add management to >>> URLs but the DOI infrastructure for this seems more established). >>> >>> My understanding has been that querying the DNS for the SRV record is >>> enough. This is what my LSID tester >>> http://darwin.zoology.gla.ac.uk/~rpage/lsid/tester/ >>> <http://darwin.zoology.gla.ac.uk/%7Erpage/lsid/tester/> does. Reading the >>> LSID spec I get the sense that, had it been more widely adopted, there was a >>> mechanism to resolve LSID authorities centrally at a server >>> "lsidauthority.org<http://lsidauthority.org>" (option [a]). If this >>> mechanism didn't exist, we would do a regular DNS lookup of the domain in >>> the LSID we were trying to resolve (option [b]). Option (a) was never >>> implemented, so it's option (b). >>> >>> >>> That said, >>> >>> Regards >>> >>> Rod >>> >>> On 18 Jun 2012, at 13:04, Julien Cigar wrote: >>> >>>> Hello, >>>> >>>> I'm reading the LSID spec and there are some things that are some things >>>> that are a little cloudy to me. >>>> >>>> The spec says that the client should query the DNS for NAPTR records for >>>> the domain name "lsid.urn.arpa", but it seems that the URN NID part "lsid" >>>> has not been established at IANA (lsid.urn.arpa is unresolvable) ? Why ? >>>> I wondered if it's enough to query the DNS of the "authority >>>> identification" part of the LSID (domain name) for a _lsid._tcp SRV record >>>> and assume that this entry is a valid resolution service for the given LSID >>>> ? If not, what's the proper way to find a resolution service for, let's say, >>>> "urn:lsid:blah.my.domain:foo:12345" ? >>>> >>>> Thank you >>>> >>>> Best regards, >>>> Julien >>>> >>>> -- >>>> No trees were killed in the creation of this message. >>>> However, many electrons were terribly inconvenienced. >>>> >>>> <jcigar.vcf>_______________________________________________ >>>> tdwg-content mailing list >>>> tdwg-content(a)lists.tdwg.org<mailto:tdwg-content@lists.tdwg.org> >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>> >>> --------------------------------------------------------- >>> Roderic Page >>> Professor of Taxonomy >>> Institute of Biodiversity, Animal Health and Comparative Medicine >>> College of Medical, Veterinary and Life Sciences >>> Graham Kerr Building >>> University of Glasgow >>> Glasgow G12 8QQ, UK >>> >>> Email: r.page(a)bio.gla.ac.uk<mailto:r.page@bio.gla.ac.uk> >>> >>> Tel: +44 141 330 4778 >>> Fax: +44 141 330 2792 >>> Skype: rdmpage >>> AIM: rodpage1962(a)aim.com<mailto:rodpage1962@aim.com> >>> >>> Facebook: http://www.facebook.com/profile.php?id=1112517192 >>> Twitter: http://twitter.com/rdmpage >>> Blog: http://iphylo.blogspot.com >>> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html >>> >> >> -- >> No trees were killed in the creation of this message. >> However, many electrons were terribly inconvenienced. >> >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> -- No trees were killed in the creation of this message. However, many electrons were terribly inconvenienced.

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