- tdwg-content - lists.tdwg.org

Proposal to Add a GeoSpatial "Area" to the DarwinCore
by Peter DeVries 22 Nov '10

22 Nov '10

I wrote about this earlier but I never heard anything back. I have made something that uses the geo vocabulary but also allows pointRadiusSpatial fit measure that I call radius. The advantage is that this adds a standard way to deal use something like an extent or pointRadiusSpatial while still benefiting from the widely used geo vocabulary. It also allows these "Areas" to be referenced in a commonly understood urn way that using a ietf standard. For example: "geo:44.86528100,-87.23147800;u=10" There are still some things I need to fix and check with this vocabulary but I am wondering if there is any interest in incorporating this into the DarwinCore. If not I will probably change the name of the ontology. There are also things in the example below that are not part of my proposal. I have what I call "Areas" that look like this: <dwc_area:Area rdf:about="geo:44.86528100,-87.23147800;u=10"> <dcterms:title>44.86528100, -87.23147800 Radius 10 meters</dcterms:title> <dcterms:isPartOf rdf:resource=" http://lod.taxonconcept.org/ontology/void#this"/> <dcterms:identifier>geo:44.86528100,-87.23147800;u=10</dcterms:identifier> <dcterms:created>2010-10-28T00:00:00-0500</dcterms:created> <dcterms:modified>2010-11-09T16:33:34-0600</dcterms:modified> <geo:lat>44.86528100</geo:lat> <geo:long>-87.23147800</geo:long> <dwc_area:radius>10</dwc_area:radius> <txn:elevation>186.54</txn:elevation> <txn:continent>North America</txn:continent> <txn:countryCode>US</txn:countryCode> <txn:country>United States</txn:country> <txn:stateProvince>Wisconsin</txn:stateProvince> <txn:county>Door</txn:county> <txn:localityText>Town of Sevastopol</txn:localityText> <txn:locationName>Shivering Sands Natural Area Woods</txn:locationName> <txn:areaHasOccurrence rdf:resource=" http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurr… "/> <txn:areaHasObservedSpeciesConcept rdf:resource=" http://lod.taxonconcept.org/ses/ICmLC#Species"/> <txn:areaHasIndividual rdf:resource=" http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Indivi… "/> <txn:areaInStateProvince rdf:resource="http://sws.geonames.org/5279468/ "/> <txn:areaInCounty rdf:resource="http://sws.geonames.org/5250768/"/> <wdrs:describedBy rdf:resource=" http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.rdf"/> </dwc_area:Area> I recently added the following predicates, but have not altered my RDF examples. #featureContainsArea #areaWithInFeature http://lod.taxonconcept.org/ontology/dwc_area.owl OWL Doc http://lod.taxonconcept.org/ontology/dwc_area_doc/index.html The predicates are a bit awkward, but I wanted to be clear that this was to link an "Area" like "geo:44.86528100,-87.23147800;u=10" to a Geonames "Feature". I thought a different set of predicates could be created to deal with some other class of "SpatialThing" if needed. Respectfully, - 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/> ------------------------------------------------------------

5 11

Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
by Tony.Rees＠csiro.au 21 Nov '10

21 Nov '10

Just re-sending the message below because it bounced the first time... Markus/all, I guess my point is that (as I understand it) scientificName is a required field in DwC, so the question is what it should be populated with. If it is (e.g.) genus + species epithet + authority, then is it beneficial to supply these fields individually / atomised as well, maybe with other qualifiers as needed? Just looking for an example "best practice" here - or maybe it exists somewhere and you can just point to it. in other words: (a) <scientificName>Homo sapiens</scientificName> <scientificNameAuthorship>Linnaeus, 1758</a> or (b): <scientificName>Homo sapiens Linnaeus, 1758</scientificName> <genus>Homo</genus> <specificEpithet>sapiens</specificEpithet> <scientificNameAuthorship>Linnaeus, 1758</a> if you get my drift... 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

12 18

Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
by Jim Croft 21 Nov '10

21 Nov '10

There is a subtle difference in in the common but loosely expressed assertion of scientific names having (i.e. Including) authors and name components having authorship (which may or may not be displayed). Jim On Friday, November 19, 2010, John van Breda <john.vanbreda(a)biodiverseit.co.uk> wrote: > I'm coming in a bit late on this conversation so I hope I am not repeating > what has already been said, but botanical names can also have authorship at > both specific and infraspecific levels, e.g. > Centaurea apiculata Ledeb. ssp. adpressa (Ledeb.) Dostál > > And to make it even more complex, you can have subspecies variants, so 2 > infraspecific levels, e.g. > Centaurea affinis Friv. ssp. affinis var. Affinis > > Atomising this properly could be quite complex but necessary to be able to > present the name as it should be written with italics in the correct place. > E.g. in the example above, the author string and rank strings are not > normally italiced, but the rest of the name is. Unless we can include this > formatting information in dwc:scientificName? > > Regards > > John > > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of "Markus Döring > (GBIF)" > Sent: 19 November 2010 09:24 > To: Roderic Page > Cc: tdwg-content(a)lists.tdwg.org; Jim Croft > Subject: Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC > scientificName: good or bad? > > What Darwin Core offers right now are 2 ways of expressing the name: > > A) the complete string as dwc:scientificName > B) the atomised parts: > genus, subgenus, specificEpithet, infraspecificEpithet, > verbatimTaxonRank (+taxonRank), scientificNameAuthorship > > Those 2 options are there to satisfy the different needs we have seen in > this thread - the consumers call for a simple input and the need to express > complex names in their verbatim form. > Is there really anything we are missing? > > > > When it comes to how its being used in the wild right now I agree with Dima > that there is a lot of variety out there. > It would be very, very useful if everyone would always publish both options > in a consistent way. > > Right now the fulI name can be found in once of these combinations: > - scientificName > - scientificName & scientificNameAuthorship > - scientificName, taxonRank & scientificNameAuthorship > - scientificName, verbatimTaxonRank & scientificNameAuthorship > - genus, subgenus, specificEpithet, infraspecificEpithet, taxonRank, > scientificNameAuthorship > - genus, subgenus, specificEpithet, infraspecificEpithet, > verbatimTaxonRank, scientificNameAuthorship > > To make matters worse the way the authorship is expressed is also > impressively rich of variants. > In particular the use of brackets is not always consistent. You find things > like: > > # regular botanical names with ex authors > Mycosphaerella eryngii (Fr. ex Duby) Johanson ex Oudem. 1897 > > # original name authors not in brackets, but year is > Lithobius chibenus Ishii & Tamura (1994) > > # original name in brackets but year not > Zophosis persis (Chatanay), 1914 > > # names with imprint years cited > Ctenotus alacer Storr, 1970 ["1969"] > Anomalopus truncatus (Peters, 1876 ["1877"]) > Deyeuxia coarctata Kunth, 1815 [1816] > Proasellus arnautovici (Remy 1932 1941) > > > On Nov 19, 2010, at 8:50, Roderic Page wrote: > >> I'm with Jm. For the love of God let's keep things clean and simple. >> Have a field for the name without any extraneous junk (and by that I >> include authorship), and have a separate field for the name plus all >> the extra stuff. Having fields that atomise the name is also useful, >> but not at the expense of a field with just the name. >> >> Please, please think of data consumers like me who have to parse this >> stuff. There is no excuse in this day and age for publishing data that >> users have to parse before they can do anything sensible with it. >> >> Regards >> >> Rod >> >> >> On 19 Nov 2010, at 07:06, Jim Croft wrote: >> >>> Including the authors, dates and any thing else (with the exception of >>> the infraspecific rank and teh hybrid symbol and in botany) as part of >>> a thing called "the name" is an unholy abomination, a lexical >>> atrocity, an affront to logic and an insult the natural order of the >>> cosmos and any deity conceived by humankind. >>> >>> In botany at least, the "name" (which I take to be the basic >>> communication handle for a taxo -- _________________ 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

3 2

Assigned codes in published classifications
by Paul Murray 20 Nov '10

20 Nov '10

Just to toss into the mix a notion of mine that has been deprecated on a number of occasions, but which I stubbornly maintain makes some sort of sense: CSIRO maintains a classification: "Codes for Australian Aquatic Biota" - CAAB codes. CAAB codes actually form a taxonomy: Agassiz's Glassfish (37-310009) falls within group 37 and I think subgroup 37-31. Now, what kind of thing is 'CAAB code 37-310009'? Well: It is an item in a controlled vocabulary - CAAB codes. It has an authority that has created it. It is declared by that authority to be synonymous with certain scientific and common names. It identifies a taxon - a group of individuals. It's possible that the taxon that it identifies - the "taxon concept" - may change a little over time, but hopefully over that time it still means pretty much the same thing. It's stable, but has a history. In short, "CAAB code 37-310009" behaves in many (if not most) respects like a *name*. Not a scientific name, or a cultivar or common name, but a name nevertheless. A persistent identifier for a series of taxon concepts which are intended by the namer to be "the same" - even if they wobble a bit over time. The main reason I like this notion is that one of our databases keeps CAAB and CAVS codes in a special column, and it always seemed a little arbitrary to me. Why these two particular classifications? What if we wanted to incorporate others - would we just have to keep adding columns? Treating these things as another kind of name brings into play all the existing frameworks with which synonymy is managed. To fully recognise these sorts of things as names, there would need to be the idea of a "name space" - after all, if people are assigning numeric codes to things then they are going to collide. "Scientific Names" is a very important namespace, of course, with a number of particular rules that DwC is very interested in. It might be reasonable to treat namespaces as hierarchical, handling the problem that the meaning of the common name "cow" depends on what language you are speaking. The idea of namespaces being hierarchical can also accommodate the notion that some scientific names are managed by ICBN, some by ICZN. _______________________ If "Magic Happens", how come your car runs on petrol?

1 0

EEA use case
by Thomas Bandholtz 20 Nov '10

20 Nov '10

The European Environment Agency has published a use case about networking and aligning species databases all over Europe based on Linked Data: http://svn.eionet.europa.eu/projects/Reportnet/wiki/ContentRegistry/UseCase… I am quite sure they will start working on this quite soon. Cheers, Thomas -- Thomas Bandholtz, thomas.bandholtz(a)innoq.com, http://www.innoq.com innoQ Deutschland GmbH, Halskestr. 17, D-40880 Ratingen, Germany Phone: +49 228 9288490 Mobile: +49 178 4049387 Fax: +49 228 9288491

3 4

Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
by Niels Klazenga 20 Nov '10

20 Nov '10

From the ICBN (Vienna Code): 60F.1. All specific and infraspecific epithets should be written with an initial lower-case letter. Even though this is a recommendation and not an article, translating that into yes an epithet may be capitalised, it is just not done very often, is a bit of a twist. Niels >>> 11/20/10 2:01 AM >>> Actually, yes, in botany a specific or infraspecific epithet may be capitalized. These days it is rarely done and very likely it will disallowed within a few decades. It is very unusual to capitalize an epithet such as affinis; capitalization is reserved for nouns and names. So, in a publication dedicated to Sijfert Koorders one may find names such as Millettia Koordersii, deliberately capitalized. Paul -----Oorspronkelijk bericht----- Van: tdwg-content-bounces(a)lists.tdwg.org namens Dmitry Mozzherin Verzonden: vr 19-11-2010 15:03 > Is it allowed to have capitalized 'var. part' of a name? > I did not know that Dima -- This email and any attachments may contain information that is personal, confidential, legally privileged and/or copyright. No part of it should be reproduced, adapted or communicated without the prior written consent of the sender and/or copyright owner. It is the responsibility of the recipient to check for and remove viruses. If you have received this email in error, please notify the sender by return email, delete it from your system and destroy any copies. You are not authorised to use, communicate or rely on the information contained in this email. Please consider the environment before printing this email. This email was Anti Virus checked by RBG Astaro Mail Gateway.

2 1

Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad? [SEC=UNCLASSIFIED]
by Niels Klazenga 20 Nov '10

20 Nov '10

Jim, You are right about the authorship not being part of the name under Art. 46.1. I must have confused ICBN with HISPID or TCS or something, as I have in my head that a scientific name always includes the authorship (as I still believe it should). You are misinterpreting Art. 26.1 though, as that only applies to names of infraspecific taxa that include the type of the specific name. Garovaglia powellii var. muelleri (Hampe) During doesn't. On the other hand, I was wrong as well, as Garovaglia powellii var. muelleri is not strictly an autonym, as infraspecific names that include the type of a subspecies or variety are merely covered by recommendations (26A.1, 26A.3). Can't believe I never saw this before, as I have always wondered how to deal with those things. We have names with multiple infraspecific epithets in our collection as well and I haven't worked out yet how to deal with them. At the moment it is possible to have both Garovaglia powellii subsp. muelleri var. muelleri and Garovaglia powellii var. muelleri and I have a problem with that as these are not just two names that are based on the same type, but are the same name. Garovaglia powellii var. muelleri, by the way, is the only Australian moss name that has ever been given two infraspecific epithets, which is why I keep repeating it as it is the only example I know. For some reason I feel really strongly about not having authors of species names within infraspecific-taxon names, even though I have been guilty of the practice myself. There is no such hierarchy among names as there is among taxa; a name is just a name. The author of a species name has as little to do with the publication of a name of an infraspecific taxon as the author of a genus name has with the publication of a species name. Including the authorship of a species name in the citation of an infraspecific taxon name is just as silly as citing the author of the generic name within a species name citation would be. Also, the aim of a standard (this whole thing started as a discussion on inclusion of authors in scientific names in Darwin Core) is to standardise, right? Just because some botanists think it useful to have authors of species names in infraspecific-taxon names does not mean it should be part of a standard or that it is correct. At any given time and any given context, Acacia dealbata subsp. dealbata indicates a more narrowly circumscribed taxon than Acacia dealbata. Just because taxon concepts change and not everyone has the same taxon concept doesn't mean the 'subsp. dealbata' bit is meaningless. The Pinus pinus thing was a bit careless of me. Let's just say it was late (15:20 in The Netherlands is 1:20 here). Never realised I was arguing with another Dutchman. At this point I am actually not sure who I am arguing with. Niels >>> Jim Croft 11/20/10 9:04 AM >>> One thing I will not buy into is an argument between two Dutchmen... Been there before... ;) Thanks for clarifying the tautonym thing; knew it was there, just could not remember it's name. Strange that one code allows it and the other doesn't. The multiple infraspecific ranks thing is interesting. We took them all out when we learned they were optional and only the lowest was necessary. Then we found we had to put them back in when we realized that the herbarium was curated according the full hierarchy. :) I guess it points out the vale of keeping all the parts and then assembling them according to the needs of the particular context. Jim On Saturday, November 20, 2010, wrote: > > > Van: tdwg-content-bounces(a)lists.tdwg.org namens Niels Klazenga > Verzonden: vr 19-11-2010 15:20 > >> Author citations are not there to make a name look more scientific, >> but are an essential part of a scientific name. They make the name >> unique; without authorship they not necessarily are. Officially, >> a scientific name without authorship is not a scientific name. > > *** > No, they are not part of the name, see Art. 46.1. Also, authorship > does not make a name unique. One and the same name may be rendered > with different authorships in different publications, without this making a difference. Also, to some extent, loosely speaking, there > may be differences even though the authorship is the same. > * * * > >> - Pinus pinus is not an autonym, but a tautonym. In botanical >> nomenclature tautonyms are not valid. > > *** > If precision is the order of the day, Pinus pinus is not a > tautonym. It would be a tautonym if it existed. However, it cannot > be validly published, so it cannot become a name (or a tautonym). > * * * > >> - Autonyms do serve a purpose: Acacia dealbata Link. subsp. >> dealbata indicates a different taxon than Acacia dealbata Link. > > *** > It would, provided these are viewed from the same taxonomic > viewpoint. If this is not assured, it could also be the same taxon. > * * * > >> - Autonyms do in fact have authors, namely the author(s) of >> the earliest infraspecific name of the same rank (with the same >> parent). While authors of infraspecific autonyms are rarely used, >> you'll need to cite them for 'infrainfraspecific' autonyms. So, >> Garovaglia powellii Mitt. subsp. powellii, but Garovaglia powellii >> var. muelleri (Hampe) During (var. muelleri was created as an >> autonym of Garovaglia powellii subsp. muelleri). > > *** > No, this last is not possible, see Art. 26. > Autonyms do not have authors. > * * * > >> - Just because botanists often cite authors after both the >> specific and infraspecific epithets doesn't make it right, >> in fact it's wrong. The authorship of a specific name has got >> nothing to do with the infraspecific name; you might as well >> cite the author of the generic name too. So, Centaurea apiculata >> subsp. adpressa (Ledeb.) Dostál, not Centaurea apiculata Ledeb. >> subsp. adpressa (Ledeb.) Dostál (it is also 'subsp.', not 'ssp.'). >> Unfortunately, also Index Kewensis (in IPNI) cites authors of >> specific names in infraspecific names; TROPICOS (or APNI), >> fortunately, does not. > > *** > Yes, on the "subsp." I do not see support on it being wrong to cite > authorship of a species name; in most circumstances it is superfluous, > but I can think of cases where it would be desirable. > > Sorry for the lecturing, > Paul > > > > -- _________________ 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 -- This email and any attachments may contain information that is personal, confidential, legally privileged and/or copyright. No part of it should be reproduced, adapted or communicated without the prior written consent of the sender and/or copyright owner. It is the responsibility of the recipient to check for and remove viruses. If you have received this email in error, please notify the sender by return email, delete it from your system and destroy any copies. You are not authorised to use, communicate or rely on the information contained in this email. Please consider the environment before printing this email. This email was Anti Virus checked by RBG Astaro Mail Gateway.

2 1

Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
by Jonathan Giddy 19 Nov '10

19 Nov '10

On 19/11/10 11:15, John van Breda wrote: > I'm coming in a bit late on this conversation so I hope I am not repeating > what has already been said, but botanical names can also have authorship at > both specific and infraspecific levels, e.g. > Centaurea apiculata Ledeb. ssp. adpressa (Ledeb.) Dostál > > And to make it even more complex, you can have subspecies variants, so 2 > infraspecific levels, e.g. > Centaurea affinis Friv. ssp. affinis var. Affinis > > Atomising this properly could be quite complex but necessary to be able to > present the name as it should be written with italics in the correct place. > E.g. in the example above, the author string and rank strings are not > normally italiced, but the rest of the name is. Unless we can include this > formatting information in dwc:scientificName? > > > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of "Markus Döring > (GBIF)" > > > Is there really anything we are missing? > > I'd like to back this "requirement" up. It would be useful to record which name parts should be emphasised (italicized), so that a human editor or smart software can apply the appropriate Code, and less-smart software such as browser Javascript can display the name correctly formatted. Jon.

5 4

Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
by Gregor Hagedorn 19 Nov '10

19 Nov '10

> I'm coming in a bit late on this conversation so I hope I am not repeating > what has already been said, but botanical names can also have authorship at > both specific and infraspecific levels, e.g. > Centaurea apiculata Ledeb. ssp. adpressa (Ledeb.) Dostál > > And to make it even more complex, you can have subspecies variants, so 2 > infraspecific levels, e.g. > Centaurea affinis Friv. ssp. affinis var. affinis you are correct and it is relevant that such names are in use. However, the first is, according to the code redundant and not recommended. A name has only one authority. The second is an expression of hierarchical arrangement, not a "name". It is similar to including expressions about subgenus grouping in a string like: Rosa (Rosa) hemisphaerica This means, it is not possible to have: Centaurea affinis Friv. ssp. affinis var. affinis Centaurea affinis ssp. dissimilis var. affinis Breda Gregor

1 0

Re: [tdwg-content] Inclusion of authorship in DwC scientificName: good or bad? [SEC=UNCLASSIFIED]
by Niels Klazenga 19 Nov '10

19 Nov '10

Never thought I would be able to contribute to this list, but since we're talking botanical nomenclature, and since we're being pedantic... If you want to standardise botanical names you want to follow the standard that matters most in botanical nomenclature, the ICBN, including its recommendations. - Author citations are not there to make a name look more scientific, but are an essential part of a scientific name. They make the name unique; without authorship they not necessarily are. Officially, a scientific name without authorship is not a scientific name. - Pinus pinus is not an autonym, but a tautonym. In botanical nomenclature tautonyms are not valid. - Autonyms do serve a purpose: Acacia dealbata Link. subsp. dealbata indicates a different taxon than Acacia dealbata Link. - Autonyms do in fact have authors, namely the author(s) of the earliest infraspecific name of the same rank (with the same parent). While authors of infraspecific autonyms are rarely used, you'll need to cite them for 'infrainfraspecific' autonyms. So, Garovaglia powellii Mitt. subsp. powellii, but Garovaglia powellii var. muelleri (Hampe) During (var. muelleri was created as an authonym of Garovaglia powellii subsp. muelleri). - Just because botanists often cite authors after both the specific and infraspecific epithets doesn't make it right, in fact it's wrong. The authorship of a specific name has got nothing to do with the infraspecific name; you might as well cite the author of the generic name too. So, Centaurea apiculata subsp. adpressa (Ledeb.) Dostál, not Centaurea apiculata Ledeb. subsp. adpressa (Ledeb.) Dostál (it is also 'subsp.', not 'ssp.'). Unfortunately, also Index Kewensis (in IPNI) cites authors of specific names in infraspecific names; TROPICOS (or APNI), fortunately, does not. - One also should only use the lowest-ranked infraspecific epithet: Garovaglia powellii var.muelleri (Hampe) During, not Garovaglia powellii subsp. muelleri (Hampe) During var. muelleri. Centaurea affinis Ledeb. subsp. affinis var. affinis is not a name but a classification, albeit a very shallow one. Sorry for the lecturing. Niels Niels Klazenga Pacific Dunlop Research Fellow/Bryologist National Herbarium of Victoria, Royal Botanic Gardens Birdwood Avenue South Yarra, VIC 3141 Australia Tel: (03) 9252 2369 Fax: (03) 9252 2350 e-mail: Niels.Klazenga(a)rbg.vic.gov.au >>> Jim Croft 11/19/10 4:17 PM >>> Also gently, botanists generally don't do Pinus pinus or Pinus pinus pinus. We do Pinus patula var. patula (or Pinus patula subsp. patula). These are autonyms that are not published as such but come into existence 'automagically' when another variety or subspecies is described. They do not actually serve any useful purpose other than to alert you that there are other varieties or subspecies in this species to be aware of and that you are not dealing with them in this case. In the hypothetical instance above, you could assume that 'Pinus patula' referred to Pinus patula var. patula and you might be right. But it might also refer to the the range of variation covered by the other varieties as well. To resolve this you really need some other contextual information such as whether you are dealing with broader concept or the narrower one before or after the other components were excised from or added to the mix. If you were goign to invent a taxonomic and nomenclatural system from scratch, with the benefit of hindsight and the absence of legacy practice, there is no way on earth you would ever do it like this... :) jim On Fri, Nov 19, 2010 at 3:06 PM, Paul Murray wrote: > It has just been gently explained to me the Pinus pinus is not an autonym, although Pinus pinus pinus is. I suppose this underscores the point that IT people building systems and webpages out of this data will tend not to get it right if just given the data fields. > > On 19/11/2010, at 1:08 PM, Paul Murray wrote: > >>> some quick additions to my previous mail in haste: >>> >>> I am referring to the new Darwin Core as referred to be Tony, not the ontology/tdwg vocabulary which predates the latest Darwin Core. >>> >>> When dealing with hybrid formulas and informal conceptual hints like sensu strictu/latu a full namestring is also useful. For determination derived artifacts like cf. or aff. darwin core has an identificationQualifier term: http://rs.tdwg.org/dwc/terms/index.htm#identificationQualifier >>> >>> And there really is no need for a canonicalName term as I suggested below as we have the 3 parts (Genus, specificEpithet, infraspecificEpithet) already as atoms. >>> >> >> This is an issue we are struggling with now. Getting from the data items and flags to a correctly laid out name string is not at all trvial. >> >> For botanical names, if the third term of the name is not a ssp, then you need the rank: >> A-us b-us var. d-us >> >> There may also be a hybrid mark, which may appear .... actually, I need to confirm this: I think it may appear right at the front, or it may appear in front of the terminal epithet - I'm not sure whther it replaces the rank code or has to appear on one side of it: >> X A-us b-us var. d-us >> A-us b-us var. X d-us >> A-us b-us X var. d-us >> >> To correctly compose botanical names, there is a rule that is different from the zoological rule: for autonyms, the botanists prefer that the authority string appear after the "root" name, not after the whole name: >> zoological - Vombatus ursinus ursinus Mike >> botanical - Pinus L. pinus >> >> And so you need to know a) is the name an autonym? and b) is it botanical? >> >> Cultivar names may be introduced with a psudeo-rank of "cv." or by putting the cultivar name in quotes. Cultivar names are not italicised. And this is not even to begin discussing hybrids and grafts. Oh - and I believe that sometimes zoologists like the family name in square brackets in front of the name. And there's also nomenclatural status/qualifier: "nom. cons." etc. >> >> And so on and so forth. Lord only knows how virologists name their taxa. >> >> The difficulty is: we want our data to be useable by web applications, which is why we produce JSON. It's not sensible to expect that every javascript programmer is going to get this stuff right. We cannot simply give enough data that - if you know all the rules - you can get it correct. What we have concluded is that our data needs to have an item in it that will permit a programmer to easily render the name correctly, and that this needs to be separate from the fields as data. >> >> There are a couple of options so far: >> >> * an array or RDF "list" of components, each component being an object with a string and some sort of indicator as to whether it should be italicised or not >> >> * a format string into which the components of the name are substituted. >> For instance: the format string for a subspecies might be "{G} {s} {e}" (e for epithet), wheras that for a form or variety would be "{G} {s} {r} {e}". We would wind up with - hopefully - a manageable list of formats. >> >> * an XHTML literal (rdf:parseType="literal"), making use of span elements and css classes to permit finer control over formatting. XHTML is the applcable standard for formatted text. >> We would use tags where appropriate, so that with no css at all the scientific name still comes out correctly. Thus: >> >> Vombatus >> ursinus >> ursinus >> >> >> >> >> > > > If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. > > Please consider the environment before printing this email. > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > -- _________________ 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-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content -- This email and any attachments may contain information that is personal, confidential, legally privileged and/or copyright. No part of it should be reproduced, adapted or communicated without the prior written consent of the sender and/or copyright owner. It is the responsibility of the recipient to check for and remove viruses. If you have received this email in error, please notify the sender by return email, delete it from your system and destroy any copies. You are not authorised to use, communicate or rely on the information contained in this email. Please consider the environment before printing this email. This email was Anti Virus checked by RBG Astaro Mail Gateway.

2 1