- tdwg-content - lists.tdwg.org

dwc:associatedOccurrences
by Mark Wilden 23 Aug '10

23 Aug '10

On Mon, Aug 23, 2010 at 12:07 PM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> wrote: > Bob, > It seems to me that the most semantically clear way to indicate in a > machine-readable way that two herbarium sheets are duplicates would be to > assert that they have the same dwc:individualID. That makes sense for expressing "duplicate of" in a machine-readable way, but what about other associations? For example, Is there a definition somewhere for "reminds me of" or "kinda like"? ///ark Web Applications Developer Center for Applied Biodiversity Informatics California Academy of Sciences

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TDWG 2010 - Cloudy forecast
by John Wieczorek 22 Aug '10

22 Aug '10

Dear all, This year at the TDWG meeting there will be a session on Hardware and Infrastructure. In preparation for that I am interested to know from the community at large if there are particular questions or concerns about public cloud computing solutions such as Amazon Web Services, AppScale, and Google AppEngine. Cheers, John

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Re: [tdwg-content] [tdwg-tag] time and space namespaces in Darwin Core
by Bob Morris 12 Aug '10

12 Aug '10

FWIW, timestamps extracted from EXIF data that a camera put there are typically no more than +- 12 hours accurate, because most devices don't record and/or stamp the timezone. My Android X seems to, but my Canon PowerShot SD750 does not. Your extractions are going to need to add it based on your knowledge about the timezone at the time and location of the bioblitz. Alas, it gets worse, because many people fail to reset their cameras or phones to the local time. To make any kind of educated guess about what time the timestamp \actually/ represents may require knowledge of the device capabilities, what the timezone is where the picture was taken and what it was in the timezone the device thinks its in. The latter might be knowable from specs of the device, e.g. if it can be discovered from those specs that the camera knows its time from a network it is connected to, and if you can deterimine that it actually was connected. But for consumer cameras, this is probably hopeless, and you need metadata from the camera owner. Curiously, the errors from this are not a range, but an enumeration, because timezones worldwide differ from one another by an integral multiple of 1/2 hour. Field biologists of my acquaintance simply keep their cameras always set at GMT. Then at least they know that all their pictures have comparable times. For the bioblitz, participants might consider agreeing to set the cameras to a common time. Aside from the accuracy of hand setting the current time, you would then mainly face social problems about the accuracy of the time: (a) can and will the participants actually do this with the devices they carry; (b)how much will they curse the bioblitz when they forget to set the timezone back to what they intend and (c) do they care whether a picture they took of a pollinator in Massachusetts apparently at high noon, actually was taken in Massachusetts at a time corresponding to high noon in Berlin. At the very least you probably should ask each contributor to record the time on their camera at specified local time each day. All accuracy assertions are about fitness for use. It's not the case that data without accuracy assertions are unfit for any use whatsover. This is because scientific statements are always qualified by either "to the best of current knowledge" or "if we accept the model X into which we put the data". For example, a taxonomic determination may or not be location dependent to the best of current knowledge. For those which aren't, and for the use case "taxonomic determination", geo accuracy is irrelevant. To the best of current knowledge. Bob Morris On Wed, Aug 11, 2010 at 9:52 PM, joel sachs <jsachs(a)csee.umbc.edu> wrote: > On Mon, 9 Aug 2010, Javier de la Torre wrote: > >> Hi, >> >> Ok. That being said, I dont want anybody to die!, > > Me neither. > > I've copied in the tdwg-bioblitz group, which at some point got dropped > from this discussion. If anyone is interested, the full discussion can be > found at http://lists.tdwg.org/pipermail/tdwg-tag/2010-August/thread.html > > For the bioblitz, I think we can do the following: > > i. Since GPS uses WGS84, any smartphone app that's getting coordinates > from the phone's built in GPS can correctly label the coordinates "geo:lat", > and "geo:long". The semantics of the location columns in the Google Fusion > Table will be "WGS84". (see (iii) for the exceptions.) When we publish DwC > from the Fusion Table, we can and should use DwC:decimalLatitude, > DwC:decimalLongitude, and DwC:geodeticDatum (set to WGS84). > > ii. We should record uncertainty. GPS uncertainty > varies with the weather, whether the user is > moving, availability of WAAS, etc. So developers should ensure that > uncertainty is captured each time their app makes a measurement. We'll add > an uncertainty column to the Fusion table. (It will be interesting to see > the range of uncertainty measures in the observations.) > > iii. If someone does precision surveying using a local datum, instead > of WGS84, she must take care that the column names for lat and long in > her Fusion Table are not the same as the column names in the master table. > Thus, when the data is merged, her coordinates won't end up in the columns > with the implied WGS84 semantics. > > Can we agree on that? > > Many thanks! > Joel. > > > > > > why dont we do the same as with dates. We have a verbatimLatitude and > verbatiumLongitude already, why those people dont use that? They should only > use DecimalLatitude if they know they have WGS84. If they use them > incorrectly, well, thats happening all day on the network of GBIF data > providers, and I dont think DWC can changed much on that. What we need is > better tools for them to publish their data, no overcomplicate the standard > just to avoid people using it wrong. >> >> What I want is to help developers using data. If our data will not >> correctly get displayed on a map we have an issue. I would say that >> considering the defacto standard of WGS84 for coordinates we will find lot >> of wrong maps out there because developers think that this is all WGS84 >> (they also dont know what this is), they will just throw them into Google >> Maps and they will be wrong, even if providers set the geodeticDatum. >> >> Probably this discussion is about where to push, the data provider or the >> developer. Beacuse the developer has to deal with thousands of providers, I >> think he has a worst job than the provider, plus is the last on the chain of >> data transformation. We dont want Pumas dissapearing because developers >> didnt handle SRS transformations that he didnt even knew. >> >> Finally, SRS I dont think are standarized, look at the reference you give >> (http://spatialreference.org/) and you will see that you can Upload your >> own. Ok I am a provider and decide to use my own SRS that I have created (or >> more normally, something is wrong) and upload it there... there is no tool >> that will resolve SRS automatically to do transformations. >> >> Now, if the provider knows what an SRS is, which Darwin Core force them to >> declare, I think they should might be able to actually transform previously >> to WGS84 and place their own stuff in Verbatium. >> >> Finally, I am a developer, get data from 100 providers, some got really >> wrong the SRS, how am I gonna know which ones? Now the provider has a good >> tool, visualize his data in Google Maps for example and discover that the >> locations look wrong. I think the second is a much easier place to resolve >> the issue. >> >> But I am a developer and maybe biassed. >> >> Javier de la Torre >> www.vizzuality.com >> >> On Aug 9, 2010, at 4:46 PM, John Wieczorek wrote: >> >>> The reason is simple, we want to help data publishers. It doesn't help >>> data publishers if they can't publish what they have - it would mean there >>> is no room for data improvement tools. That would be sad. Worse, most people >>> haven't a clue what a datum is, or how it can ruin your whole day (or life, >>> in at least one sad case of a crashed helicopter in Patagonia). Given this >>> naiveté, people would simply put whatever geographic coordinates they have >>> into geo:lat/lon and no one would have any way to know that they are >>> incorrect. >>> >>> Note that Darwin Core offers data publishers options to publish event >>> information with year, month, day, startDayOfYear, endDayOfYear, and >>> verbatimEventDate in addition to eventDate and eventTime - same philosophy. >>> >>> On Mon, Aug 9, 2010 at 7:26 AM, Javier de la Torre <jatorre(a)gmail.com> >>> wrote: >>> I am not sure I understand why we can not set DWC fields to conform to >>> WGS84 and then use what everybody else is using. >>> >>> For example in eventDate DWC conforms to ISO 8601, why dont we do the >>> same for location... it would allow to simplify it quite a lot and be more >>> compliant with other standards-existing apps, etc. >>> >>> Just an idea. >>> >>> Javier de la Torre >>> www.vizzuality.com >>> >>> On Aug 9, 2010, at 4:13 PM, John Wieczorek wrote: >>> >>>> The partially good news is that if enough information >>>> (dwc:geodeticDatum) is given in a Darwin Core-based record, geo:lat/lon can >>>> be determined from it. More disturbing to me is that anyone would think >>>> geo:lat/lon alone is sufficient for any application, as it carries no notion >>>> of uncertainty and therefore fitness for use. Add >>>> dwc:coordinateUncertaintyInMeters (or even dwc:coordinatePrecision if you >>>> must) to the mix and I would be much happier. >>>> >>>> >>>> On Sun, Aug 8, 2010 at 11:26 PM, <Garry.Jolley-Rogers(a)csiro.au> wrote: >>>> Hi Jim, >>>> Thanks. Had this aside to read in detail later. I think John is >>>> right... As same value with different constraints mean different >>>> interpretations are possible and seems to be the key thing. How are the >>>> values to be interpreted. >>>> >>>> G >>>> >>>> -----Original Message----- >>>> From: Jim Croft [mailto:jim.croft@gmail.com] >>>> Sent: Monday, 9 August 2010 4:12 PM >>>> To: Alexander, Paul (PI, Black Mountain); Harvey, Paul.W (PI, Black >>>> Mountain); Jolley-Rogers, Garry (PI, Black Mountain); Cawsey, Margaret (CES, >>>> Crace); Greg Whitbread >>>> Cc: tuco(a)berkeley.edu >>>> Subject: Fwd: [tdwg-tag] time and space namespaces in Darwin Core >>>> >>>> Did you catch this thread on tdwg-tag? It is an almost exact mirror >>>> of the conversations we have be having in the taxon profile space, but >>>> involving the specimen locational data. >>>> >>>>> From John's comments it would appear he is not prepared to accept the >>>> >>>> geo: and dwc: lat/long as 'exact match' because, although they are the >>>> same values, they have different constraints (or more precisely one >>>> one has a constraint and one doesn't). >>>> >>>> I wouldn't have picked it but this looks like a case for 'closematch'. >>>> >>>> jim >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: John Wieczorek <tuco(a)berkeley.edu> >>>> Date: Mon, Aug 9, 2010 at 3:56 AM >>>> Subject: Re: [tdwg-tag] time and space namespaces in Darwin Core >>>> To: joel sachs <jsachs(a)csee.umbc.edu> >>>> Cc: tdwg-bioblitz(a)googlegroups.com, tdwg-tag(a)lists.tdwg.org >>>> >>>> >>>> There is actually no equivalency between dwc:decimalLatitude and >>>> geo:lat because geo:lat is specified to represent the latitude in the >>>> WGS84 spatial reference system and dwc:decimalLatitude has no such >>>> such restriction. >>>> >>>> On Fri, Aug 6, 2010 at 10:08 AM, joel sachs <jsachs(a)csee.umbc.edu> >>>> wrote: >>>>> >>>>> On Fri, 6 Aug 2010, Hilmar Lapp wrote: >>>>> >>>>>> Shouldn't the RDF for DwC link DwC:lat to geo:lat (using some subtype >>>>>> or better yet equivalency relation)? And shouldn't hence Linked Data >>>>>> browsers be able to use DwC:lat in the same way as geo:lat? >>>>>> >>>>> >>>>> Yes. But no Linked Data browser I'm aware of applies >>>>> owl:equivalentProperty assetions before rendering the data. (In fact, >>>>> most >>>>> do no reasoning at all.) I agree that, whatever our default display, >>>>> it should include the appropriate mapping statements, either via an >>>>> rdfs:seeAlso or similar link, or directly in the document. >>>>> >>>>> >>>>> Joel. >>>>> >>>>> >>>>>> -hilmar >>>>>> >>>>>> On Aug 6, 2010, at 11:01 AM, joel sachs wrote: >>>>>> >>>>>>> All, >>>>>>> >>>>>>> When representing observation records in RDF, there are advantages >>>>>>> to using Dublin Core and Geo (http://www.w3.org/2003/01/geo/ >>>>>>> wgs84_pos#) >>>>>>> namespaces where possible. For example, if we use DC:date, and >>>>>>> geo:lat, geo:long, instead of DwC:eventDate, DwC:lat, and DwC:long, >>>>>>> then Linked Data browsers can automatically map the records, plot >>>>>>> them on a timeline, etc. >>>>>>> >>>>>>> My question is: What are the disadvantages to doing this? (For >>>>>>> example, is this going to break someone's DwC validator?) >>>>>>> >>>>>>> Thanks - >>>>>>> Joel. >>>>>>> >>>>>> >>>>>> -- >>>>>> =========================================================== >>>>>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>>>>> =========================================================== >>>>>> >>>> >>>> _________________ >>>> Jim Croft ~ jim.croft(a)gmail.com ~ +61-2-62509499 ~ >>>> http://www.google.com/profiles/jim.croft >>>> 'A civilized society is one which tolerates eccentricity to the point >>>> of doubtful sanity.' >>>> - Robert Frost, poet (1874-1963) >>>> >>>> Please send URIs, not attachments: >>>> http://www.gnu.org/philosophy/no-word-attachments.html >>>> >>>> _______________________________________________ >>>> tdwg-tag mailing list >>>> >>>> tdwg-tag(a)lists.tdwg.org >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-tag >>> >>> >> > > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag > > -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: ram(a)cs.umb.edu web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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Proposed Darwin Core term additions and changes: individualRemarks and establishmentMeans
by Steve Baskauf 11 Aug '10

11 Aug '10

In http://code.google.com/p/darwincore/issues/detail?id=70 I proposed addition of the class Individual to Darwin Core. In the discussion of that proposal, the question was raised as to which existing DwC terms should be a part of this class if it were added. After considerable thought and some work in developing RDF representations for Individuals, I believe that the term establishmentMeans should be a member of the proposed class. It has also become clear to me that if the class is introduced, there is a need for the term individualRemarks which would serve a parallel purpose to other xxRemarks terms in DwC. I have provided implementation examples in the recommendations, which can be found at http://code.google.com/p/darwincore/issues/detail?id=80 and http://code.google.com/p/darwincore/issues/detail?id=81 If you would like to discuss these proposals, please post on the tdwg-contents list or add comments to the Google Code wiki. I have cross-posted to the tdwg-tag list, but I think any discussion would be better held on the tdwg-content list, so please post there. Steve Baskauf -- 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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Latest DwC as TAPIR output model?
by Tim Robertson (GBIF) 10 Aug '10

10 Aug '10

Hi all, This thread started as a query about the availability of the latest DwC in TAPIR output models, and specifically for use with TAPIRLink. John correctly points out that the TDWG list should have been copied from the start, and I am remedying that now. I have condensed the thread to only the main points to make it easy to digest, and suggest we continue the discussion here. The current point in the discussion relates to the SimpleDarwinCore being flat in nature, and therefore why it holds a subset of all the DwC terms documented in the standard. Thanks, Tim On Aug 7, 2010, at 7:59 AM, John Wieczorek wrote: > Hi folks, > > I wish that this conversation had taken place on the tdwg-content > list so that others might take advantage of the discussion, but I > don't feel comfortable moving someone else's conversations there. Good point John. Sorry all, this was my mistake. > > The Simple Darwin Core Schema is up to date. It does not contain the > MeasurementOrFact terms, nor the ResourceRelationship terms, > precisely because, as Renato said, the Simple Darwin Core is flat > and the other terms in those two sets make little sense in a flat > schema because they would allow you to share no more than one > MeasurementOrFact and one ResourceRelationship. > > There is a Generic Darwin Core schema that provides a model for > building other schemas from the Darwin Core, but it is not an > application schema as the SimpleDarwinCore schema is. At least two > groups are using the Generic Darwin Core schema imported into other > schemas to extend the capabilities of the Generic Darwin Core - the > germ plasm folks and the Apiary folks. The former have a published > schema at http://code.google.com/p/darwincore/source/browse/#svn/ > trunk/xsd/profiles/germplasm, while the latter are working on one > for herbarium sheet data entry, for which they are interested in > many more types of annotations than just the Identification class > found in Darwin Core presently. > > If there is more that you want to share than just the Simple Darwin > Core, but don't actually need a more complex structure, one simple > way to do it would be to use the dynamicProperties term from Simple > Darwin Core. The description is at http://rs.tdwg.org/dwc/terms/index.htm#dynamicProperties > and further explanation on its use can be found at in the "Do More > with Simple Darwin Core" section (http://rs.tdwg.org/dwc/terms/simple/index.htm#domore > ) of the Simple Darwin Core page. > > Hope that helps, > > John > > Renato, > Simple Darwin Core is almost what I want but looking at the schema > here http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd > it is lacking the auxillary terms that occur that are listed here http://rs.tdwg.org/dwc/terms/index.htm > - which are the Measurement of Fact terms and the Resource > Relationship terms. > > So ideally I would like all the terms listed here http://rs.tdwg.org/dwc/terms/index.htm > included however if that is too difficult or would take too long > then I would be happy with the Simple Darwin Core schema as > described here http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd > Paul > > I'm not sure if the simple DwC schema is up-to-date, but it seems to > contain more than 150 elements. I think the idea behind "simple" > resides > in the fact that the schema defines a flat structure, not that it only > contains a subset of DarwinCore. > > I can check if that schema is up-to-date and then build the output > model, > but first I would just need to know from you guys if this kind of > schema > will suit your needs. > Renato > > > > I was hoping the whole schema :-) > > > > Here in Australia the OZCAM community (all Australian museums) has > just > > migrated it's schema to the new standard - using about 60 or 70 of > the > > fields so we would like to be able to expose all of them. > > > > With my TDWG exec hat on I'd like to think that any data providers > could > > expose their data using the new DwC schema and GBIF being the > largest > > consumer of data should be doing their utmost to facilitate that > being > > possible. > > TapirLink is the ideal way to do that as many are using it already > and so > > upgrading providers to the new schema using Tapirlink should be > relatively > > easy. > > Paul > >> I would think an output based on the simple DwC should be made > available > >> and GBIF will promote that with TAPIRLink, but I leave it to Paul > to > >> shout if he anticipates something else? > >> Tim > >>> You're right. There's no output model for the latest DwC, but it > should > >>> be > >>> easy to make one. Is there a specific XML Schema for the data > structure > >>> or > >>> are you planning to use the simple DwC? > >>> > >>> http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd > >>> > >>> If you want, just let me know the schema and I can quickly build a > >>> model > >>> for it. > >>> Renato > >>>> Do you know if anyone put together output models for the TAPIR > using > >>>> the latest DwC? > >>>> http://rs.tdwg.org/tapir/cs/dwc/ does not appear to have any > and the > >>>> folks in Australia are looking into this. Just want to make sure > >>>> there aren't any floating around already. > >>>> Tim

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Re: [tdwg-content] Latest DwC as TAPIR output model?
by Paul Flemons 09 Aug '10

09 Aug '10

Great, thanks Renato! - once again Id like to thank everyone for their prompt responses on this matter - Ive been impressed! Best Regards to you all Paul ________________________________ From: Ajay Ranipeta [ajay.ranipeta(a)gmail.com] Sent: 10 August 2010 11:47 To: renato(a)cria.org.br Cc: Markus Döring (GBIF); Paul Flemons; Tim Robertson (GBIF); tdwg-content(a)lists.tdwg.org; Dave Martin Subject: Re: [tdwg-content] Latest DwC as TAPIR output model? Thanks all. Will use the updated url's from Renato for the Australian node. Cheers, [a] On Tue, Aug 10, 2010 at 11:35 AM, <renato(a)cria.org.br<mailto:renato@cria.org.br>> wrote: Markus, Thanks for pointing out those files. I didn't remember them. I just had to make a few changes to get everything working properly. I also updated the file that maps terms from the new DarwinCore to the older versions, so that TapirLink providers can easily migrate. I took the liberty to copy most files to rs.tdwg.org/tapir<http://rs.tdwg.org/tapir> just to keep tapir-related things together. More specifically I copied: cns: http://rs.tdwg.org/tapir/cns/dwc_terms_2009_09_23.xml simple output model: http://rs.tdwg.org/tapir/cs/dwc/terms/2009-09-23/model/dwc_simple.xml simple darwin schemas: http://rs.tdwg.org/tapir/rs/ Please let me know if you think the corresponding files still need to remain in darwincore.googlecode.com<http://darwincore.googlecode.com> because in this case I should better add it as a new default trusted domain for TapirLink providers. Best Regards, -- Renato > Paul, > you only need to change some configuration in TapirLink to enable the new > darwin core terms for configuration. > In addition to the output model for tapir we also host the official CNS > (concept name server) file that tells tapir software which concepts/terms > are available for mapping. You can find it next to the output model here: > http://darwincore.googlecode.com/svn/trunk/tapir/dwc_terms.cns > > In TapirLink the best option is to update the tapirlink/config/schemas.xml > file like this, so the new terms become available for any new resource: > > <?xml version="1.0" encoding="utf-8" ?> > <schemas> >  > <schema alias="DarwinCore 1.4"> > <namespace>http://rs.tdwg.org/dwc/dwcore/</namespace> > <location>http://rs.tdwg.org/tapir/cns/dwc_1_4.xml</location> > <handler>CnsSchemaHandler_v2</handler> > </schema> > <schema alias="DarwinCore 1.4 curatorial extension"> > <namespace>http://rs.tdwg.org/dwc/curatorial/</namespace> > <location>http://rs.tdwg.org/tapir/cns/dwcur_1_4.xml</location> > <handler>CnsSchemaHandler_v2</handler> > </schema> > <schema alias="DarwinCore 1.4 geospatial extension"> > <namespace>http://rs.tdwg.org/dwc/geospatial/</namespace> > <location>http://rs.tdwg.org/tapir/cns/dwgeo_1_4.xml</location> > <handler>CnsSchemaHandler_v2</handler> > </schema> > <schema alias="ABCD 2.06"> > <namespace>http://www.tdwg.org/schemas/abcd/2.06</namespace> > <location>http://rs.tdwg.org/tapir/cns/abcd_2_06.xml</location> > <handler>CnsSchemaHandler_v2</handler> > </schema> >  > <schema alias="DarwinCore"> > <namespace>http://rs.tdwg.org/dwc/terms/</namespace> > <location>http://darwincore.googlecode.com/svn/trunk/tapir/dwc_terms.cns</location> > <handler>CnsSchemaHandler_v2</handler> > </schema> > </schemas> > > > With this the new terms become available in the tapir link configurator. > Alternatively you can insert the link to the cns file manually for every > resource you want to configure in step5 (Mapping) at the bottom under > "Location of additional schema:" enter > http://darwincore.googlecode.com/svn/trunk/tapir/dwc_terms.cns and select > CNS XML file. > > > I am checking in this schema.xml change into the trunk of TapirLink at > sourceforge now. > > Markus > > > On Aug 8, 2010, at 13:38, Paul Flemons wrote: > >> Tim, >> I think we will use TapirLink for now in which case we need to have the >> Simple Darwin Core schema implemented in TapirLink. >> Any volunteers for doing that? >> >> We will be interested in the IPT version at RC5. >> >> Ta >> Paul -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ##################################################################################### This e-mail message has been scanned for Viruses and Content and cleared by MailMarshal ##################################################################################### ALIVE UNTIL 19 SEPTEMBER 2010 A dynamic program of events celebrating the International Year of Biodiversity TALKS TOURS WORKSHOPS KIDS ACTIVITIES MUSIC DISPLAYS www.australianmuseum.net.au/biodiversity The Australian Museum. 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Fwd: Taxon Concept dilemma
by Mark Wilden 09 Jul '10

09 Jul '10

On Tue, Jul 6, 2010 at 6:10 AM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: > This is why the only way we're going to be able to establish > RelationshipAssertions (sensu TCS) is via third-party assertions. In other > words, someone is going to have to assert an opinion over whether the > implied members of Smith's Aus bus would have included the population in > Hawaii, and whether the implied set of Jones' Aus cus would have included > the population in the Marshall Islands. I think that a "someone" is always asserting such an opinion - Smith and Jones included. There is no Platonic ideal of a particular species. Every single classification is a matter of educated opinion. Smith has one opinion and Jones has another opinion. Brown may step in and decide that Smith's opinion is the correct one - but that's just another opinion. Consumers of the classification choose whose opinions are the most useful. A taxon is always related to a taxon-assigner. In this sense, "circumscription" is perhaps not the best way to think about it, because very few assigners actually determine taxa by enumerating organisms. The idea of researchers creating taxa, and third parties adjudicating them to arrive at the "true" classification, is too limited. It's third parties all the way down. ///ark

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TDWG Presentation for biologists
by David Remsen (GBIF) 09 Jul '10

09 Jul '10

Hi, On short notice I have been invited to give a presentation on TDWG and the Sept. meeting to the monthly meeting of the Woods Hole Oceanographic Institution biology department on Monday morning. I have looked at the presentations on the TDWG outreach site but they seem a bit too technical for biologists. MIght anyone have any TDWG materials geared toward non-technical biologists? Best, David Remsen ---------------------------------------------------------------------------- David Remsen, Senior Programme Officer Electronic Catalog of Names of Known Organisms Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321472 Fax: +45-35321480 Mobile +45 28751472 Skype: dremsen ----------------------------------------------------------------------------

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Re: [tdwg-content] [tdwg-tag] WPS for Names
by Matt Jones 08 Jul '10

08 Jul '10

Kevin, Also of relevance would be the work that iPlant is sponsoring on a Taxonomic Name Resolution Service (TNRS) -- see: https://pods.iplantcollaborative.org/wiki/display/iptol/TNRS+Workshop for background on a recent workshop for this activity. I'm sure they'd be interested in collaborating. I think Brian Enquist would have a good idea of progress on the project and would be able to provide more details. Matt On Wed, Jul 7, 2010 at 1:49 PM, Evgeniy Meyke <evgeniy(a)earthcape.com> wrote: > Hi Kevin, Tony, and all > > > > As one of the very likely consumers of such a service I’ll be following > this with great interest. > > > > A quick question at this point. Is anything like this planned for GNA ( > www.globalnames.org)? or GBIF? > > > > Evgeniy > > > > *From:* tdwg-tag-bounces(a)lists.tdwg.org [mailto: > tdwg-tag-bounces(a)lists.tdwg.org] *On Behalf Of *Kevin Richards > *Sent:* 8. heinäkuuta 2010 0:32 > *To:* Tony.Rees(a)csiro.au; tdwg-tag(a)lists.tdwg.org > > *Cc:* tdwg-content(a)lists.tdwg.org > *Subject:* Re: [tdwg-tag] WPS for Names > > > > Thanks Tony. I would be interested in any collaboration we can do in this > area (assuming I find 5 minutes to work on it :-)) > > > > There seems to be several approaches to name matching/integration – one > working with the name strings, and one working with more structured data. > It would be good to clarify and perhaps standardise these approaches. (the > second approach is discussed in a recent paper of mine). > > > > It does indeed become a slippery slope, and this is one of the reasons I am > keen to promote some sort of infrastructure/configurability of a matching > system, so that end users can configure a matching algorithm/workflow to > suit their particular data. > > > > Kevin > > > > > > *From:* Tony.Rees(a)csiro.au [mailto:Tony.Rees@csiro.au] > *Sent:* Wednesday, 7 July 2010 7:06 p.m. > *To:* Kevin Richards; tdwg-tag(a)lists.tdwg.org > *Cc:* tdwg-content(a)lists.tdwg.org > *Subject:* RE: WPS for Names > > > > Dear all (actually: I’m not sure who are the recipients currently on > tdwg-tag, maybe I will now find out!!) > > > > As some on this list may be aware, this is an area that has been of > interest to me for quite some time (for example see: > http://taxacom.markmail.org/message/ywq7ijiaeks7heiv ), so happy to see > what can be done in this space. > > > > Currently my algorithm is web accessible and tests designated genus names > against genus names held, and genus+species combinations against both genus > only, and genus+species combinations as held in my “IRMNG” reference > database (search entry point is at > http://www.cmar.csiro.au/datacentre/irmng/ if interested). I am also > planning to implement a degree of cross-rank matching shortly, e.g. if a > subgenus is supplied, test this as a possible genus against genus+species > combinations (as this often turns out to be the reason for a direct mismatch > in practice), same with infraspecies vs. subspecies (my current interface > does not yet handle infraspecies, and just detect then “parks” apparent > subgenera, but the intention is to handle these as testable components in > due course). > > > > Maybe I will set up the above options and let you know as available for > testing. Also I may look for genus+species concatenated (think Homosapiens), > genus+subgenus+species with missing brackets around subgenus, and maybe > other things, as per my somewhat extensive exposure to otherwise > non-resolved namestrings floating around in OBIS/GBIF data provider space. > Of course it is a slippery slope; other examples are family in genus field > and vice versa, or common name similar; genus and species reversed; > truncated names not flagged as such; abbreviated genera (which I already > handle as exact, but not fuzzy matches at this time, at least as “H. > sapiens” etc.); more.. > > > > Any comments on the above welcome, > > > > Regards - Tony > > > > Tony Rees > Manager, Divisional Data Centre, > CSIRO Marine and Atmospheric Research, > GPO Box 1538, > Hobart, Tasmania 7001, Australia > Ph: 0362 325318 (Int: +61 362 325318) > Fax: 0362 325000 (Int: +61 362 325000) > e-mail: Tony.Rees(a)csiro.au > Manager, OBIS Australia regional node, http://www.obis.org.au/ > Biodiversity informatics research activities: > http://www.cmar.csiro.au/datacentre/biodiversity.htm > Personal info: > http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566 > > > ------------------------------ > > *From:* tdwg-tag-bounces(a)lists.tdwg.org [mailto: > tdwg-tag-bounces(a)lists.tdwg.org] *On Behalf Of *Kevin Richards > *Sent:* Wednesday, 7 July 2010 11:55 AM > *To:* tdwg-tag(a)lists.tdwg.org > *Cc:* tdwg-content(a)lists.tdwg.org > *Subject:* [tdwg-tag] WPS for Names > > > > I have been pondering taxon name matching type services lately… > > > > I wonder if the OGC WPS (Web Processing Service) would make a good platform > for integrating the various name matching algorithms that are being worked > on lately. > > > > I was imagining something like a web interface where you can go to and view > a list of the available algorithms and select different algorithms in > different orders to get the best set of match results your own list of name > strings/data. > > If everyone set up their algorithms as a WPS then this interface would call > each WPS in the appropriate order until then end of the configured workflow > path. > > > > UI something like (in diagram): > > > > > > Where the bottom part is configurable by the user. Each box being a > representation of a WPS service for doing the match. > > > > Any thoughts? > > Perhaps something that could be discussed at TDWG? > > > > One issue would be how to define/specify the list of names to match against > – then when you pass the processing of a match routine how would it access > the names list to match?? Perhaps it could all be based on one server and > people could submit algorithm/WPS services to it? > > > > Hmmmm, will keep dreaming … > > > > 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 > > > ------------------------------ > > 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-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag > >

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Re: [tdwg-content] WPS for Names
by Kevin Richards 07 Jul '10

07 Jul '10

Thanks Tony. I would be interested in any collaboration we can do in this area (assuming I find 5 minutes to work on it :-)) There seems to be several approaches to name matching/integration - one working with the name strings, and one working with more structured data. It would be good to clarify and perhaps standardise these approaches. (the second approach is discussed in a recent paper of mine). It does indeed become a slippery slope, and this is one of the reasons I am keen to promote some sort of infrastructure/configurability of a matching system, so that end users can configure a matching algorithm/workflow to suit their particular data. Kevin From: Tony.Rees(a)csiro.au [mailto:Tony.Rees@csiro.au] Sent: Wednesday, 7 July 2010 7:06 p.m. To: Kevin Richards; tdwg-tag(a)lists.tdwg.org Cc: tdwg-content(a)lists.tdwg.org Subject: RE: WPS for Names Dear all (actually: I'm not sure who are the recipients currently on tdwg-tag, maybe I will now find out!!) As some on this list may be aware, this is an area that has been of interest to me for quite some time (for example see: http://taxacom.markmail.org/message/ywq7ijiaeks7heiv ), so happy to see what can be done in this space. Currently my algorithm is web accessible and tests designated genus names against genus names held, and genus+species combinations against both genus only, and genus+species combinations as held in my "IRMNG" reference database (search entry point is at http://www.cmar.csiro.au/datacentre/irmng/ if interested). I am also planning to implement a degree of cross-rank matching shortly, e.g. if a subgenus is supplied, test this as a possible genus against genus+species combinations (as this often turns out to be the reason for a direct mismatch in practice), same with infraspecies vs. subspecies (my current interface does not yet handle infraspecies, and just detect then "parks" apparent subgenera, but the intention is to handle these as testable components in due course). Maybe I will set up the above options and let you know as available for testing. Also I may look for genus+species concatenated (think Homosapiens), genus+subgenus+species with missing brackets around subgenus, and maybe other things, as per my somewhat extensive exposure to otherwise non-resolved namestrings floating around in OBIS/GBIF data provider space. Of course it is a slippery slope; other examples are family in genus field and vice versa, or common name similar; genus and species reversed; truncated names not flagged as such; abbreviated genera (which I already handle as exact, but not fuzzy matches at this time, at least as "H. sapiens" etc.); more.. Any comments on the above welcome, Regards - Tony Tony Rees Manager, Divisional Data Centre, CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, Tasmania 7001, Australia Ph: 0362 325318 (Int: +61 362 325318) Fax: 0362 325000 (Int: +61 362 325000) e-mail: Tony.Rees(a)csiro.au<mailto:Tony.Rees@csiro.au> Manager, OBIS Australia regional node, http://www.obis.org.au/ Biodiversity informatics research activities: http://www.cmar.csiro.au/datacentre/biodiversity.htm Personal info: http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566 ________________________________ From: tdwg-tag-bounces(a)lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of Kevin Richards Sent: Wednesday, 7 July 2010 11:55 AM To: tdwg-tag(a)lists.tdwg.org Cc: tdwg-content(a)lists.tdwg.org Subject: [tdwg-tag] WPS for Names I have been pondering taxon name matching type services lately... I wonder if the OGC WPS (Web Processing Service) would make a good platform for integrating the various name matching algorithms that are being worked on lately. I was imagining something like a web interface where you can go to and view a list of the available algorithms and select different algorithms in different orders to get the best set of match results your own list of name strings/data. If everyone set up their algorithms as a WPS then this interface would call each WPS in the appropriate order until then end of the configured workflow path. UI something like (in diagram): [cid:image001.gif@01CB1E7E.666E0530] Where the bottom part is configurable by the user. Each box being a representation of a WPS service for doing the match. Any thoughts? Perhaps something that could be discussed at TDWG? One issue would be how to define/specify the list of names to match against - then when you pass the processing of a match routine how would it access the names list to match?? Perhaps it could all be based on one server and people could submit algorithm/WPS services to it? Hmmmm, will keep dreaming ... 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 ________________________________ 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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