March 2012 - tdwg-content - lists.tdwg.org

Re: [tdwg-content] If you need something for referring to a population, then it is probably best to do it as a related class
by Nico Franz 05 Jun '25

05 Jun '25

Hello all: I have a few inserted comments, hopefully with some clarifying effect: On 5/4/2011 10:54 AM, Peter DeVries wrote: > Hi Steve, > > I may have overloaded the term specimen to make the explanation easier > to follow. > > A specimen could be an individual or it could be part of an individual. > > To some extent you need to think about how these models will be used. > > If you subscribe to the model that a species is whatever a taxonomists > says it is then it is difficult to make statements like. > > X% of the world's species will be extinct by 2050. > > If you mean a species as defined by the concept documented at this URI > which is supported by these specimens, images, and DNA then you are on > firmer ground. > > Species in the natural world do a pretty good job recognizing those > individuals that are appropriate mates. In other words members of > their own species. > > Are we modeling species or variations in human conceptualizations of > species? > >> Assuming that there was only one individual organism identified >> there is really one one species (or hybrid). > Aaaaaaaaaaaaaah! Please Nico C., don't take this one up! > > > I stick with this. Assuming you don't have a hybrid individual. That > individual is one species. The fact that human may disagree on what > species it is a human issue. > > Again, Are we modeling species or variations in human > conceptualizations of species? NMF: I believe there is a history of biodiversity database engineering that actually led some people, initially in Australia (Greg Whitbread?) and Europe (Berendsohn's group) to place more emphasis on modeling human conceptualizations of taxa. I understand this happened in the late 80s / early 90s. The motivation was, apparently, that no long-term consensus seemed available to model a single and sufficiently widely accepted taxonomy of, say, Central European vascular plant species or mosses. I believe that projects such as the Euro + Med PlantBase (http://www.emplantbase.org/home.html) are examples of the persistence (success?) of this 20+ year old practice. I think this is the kind of background that Steve is referring to. > > Which of these is of primary importance to decision makers and > non-taxonomist biologists? > Part of the problem with various publications relating to ontologies > and taxonomy is that their species models entail a specific > phylogenetic hypothesis. > > In the real world taxa are not as clean as some would like to make > them out to be. > > Each individual is a unique combination of thousands of separate gene > lineages which often do not follow clean monophyletic paths. > > I would argue that most of those who work with species related data > see them as useful typological constructs which in general follow the > biological species model. NMF: The solution of how to properly model things such as species in RDF, OWL (etc.) should ideally accommodate all "species concepts" (BCS, ESC, PSC, GSC, there's dozens), i.e. it should be neutral towards this issue. The examples below are too simple, ignoring for example cases such as pro parte synonymy, or a concept ("species") that appears unique and monophyletic to one author but (vastly) polyphyletic to another. To do an accurate mapping in that latter case (which is not super-common but it's real), I think one would have to come down on saying we're modeling human conceptualizations. They are not just that, so really it's not a strict dichotomy, meaning that by modeling conceptualizations we do not have to say "the species only exist on our heads", or "well, then anything goes". I agree (sheepishly) that it does come down to what the input data look like, and what the expectations are towards just accommodating the user community versus pushing them in a particular direction. Some of this also on p. 47 of this PDF: https://journals.ku.edu/index.php/jbi/article/view/3927/3852 > > /Aedes triseriatus/ owl:sameAs /Ochlerotatus triseriatus/ > > Others seem to see them as phylogenetic end nodes which entail a > specific phylogenetic history. > > /Aedes triseriatus/ distinctFrom /Ochlerotatus triseriatus/ > / > / > If you are primarily interested in understanding issues of ecology, > disease, diversity and conservation the former model is more > appropriate than the later. > > Respectfully, > > - Pete Regards, Nico Nico M. Franz, Ph.D. Assistant Professor Director, UPRM Invertebrate Collection Department of Biology University of Puerto Rico Call Box 9000 Mayagüez, PR 00681-9000 Phone: (787) 832-4040, ext. 3005 Fax: (787) 834-3673 E-mail: nico.franz(a)upr.edu Laboratory website: http://academic.uprm.edu/~franz/ UPRM-INVCOL: http://uprm-invcol-project.tumblr.com/

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Change genus definition or introduce genericName?
by Peter Desmet 22 Mar '12

22 Mar '12

Hi everyone, A spin-off of the discussion regarding canonicalScientificName (and possibly a solution to it as well) concerns the term "genus". As mentioned before, most people probably interpret this term as "The name of the genus of the scientificName." - scientificName: *Aster* simplex var. ramosissimus (Torrey & A. Gray) A. Cronquist - acceptedNameUsage: Symphyotrichum lanceolatum (Willdenow) G.L. Nesom subsp. lanceolatum var. lanceolatum - genus: *Aster* - specificEpithet: simplex - infraspecificEpithet: ramosissimus Even though it is defined as "The full scientific name of the genus in which the taxon is classified.", which leads to this for synonyms: - scientificName: Aster simplex var. ramosissimus (Torrey & A. Gray) A. Cronquist - acceptedNameUsage: *Symphyotrichum* lanceolatum (Willdenow) G.L. Nesom subsp. lanceolatum var. lanceolatum - genus: *Symphyotrichum Nees* - specificEpithet: simplex - infraspecificEpithet: ramosissimus For more background on this issue, please read: http://code.google.com/p/darwincore/issues/detail?id=151 & http://lists.tdwg.org/pipermail/tdwg-content/2012-March/002877.html There are now two possible solutions on the table (by Markus Döring, http://code.google.com/p/darwincore/issues/detail?id=151#c7) for sharing the genus name part we have 2 options: A) consistent dwc approach: We keep the dwc:genus definition as it is to be inline with the other classification terms including subgenus. All of these should contain the accepted classification, not necessarily the part of the name. Two new terms genericName and infragenericEpithet are then proposed to hold the genus part of a name and the infra generic part. This approach keeps the dwc terms consistent and does not mix classification terms with terms for atomized names. B) least change approach: Taking into account that many people already use dwc:genus for the name part we alter the definition of the term as proposed here. This results in the least impact on existing publishers and probably consumers too. But it has the drawback of i) dwc terms are inconsistent with family & subgenus being the classification, not the name part, ii) no option anymore to share the genus classification, iii) no way to share all infra generic names I would hope we can start a vote around those 2 options with A) being my clear favorite We need your opinion and input to move this issue forward. Thanks, Peter -- Peter Desmet Biodiversity Informatics Manager Canadensys - www.canadensys.net Université de Montréal Biodiversity Centre 4101 rue Sherbrooke est Montreal, QC, H1X2B2 Canada Phone: 514-343-6111 #82354 Fax: 514-343-2288 Email: peter.desmet(a)umontreal.ca / peter.desmet.cubc(a)gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet

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Call for Challenge entries for conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Nico Cellinese 21 Mar '12

21 Mar '12

Many trees enter. Fresh analysis ensues. New insights emerge. The conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is again holding a Challenge competition in 2012, on the theme "Synthesizing Phylogenies". Somewhere, buried in large sets of trees, lies a stunning new revelation, a baffling discovery, the answer to a longstanding controversy, or simply something not obvious to the naked eye. The mission of the 2012 iEvoBio challenge is to find those revelations, discoveries and answers within your own data and/or within one of the datasets provided by the challenge. What new scientifically interesting results can you pull from these trees, using any combination of techniques at your disposal? Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website athttp://ievobio.org/challenge.html. Submissions are due by June 25, 2012. Selected candidates will make short oral presentations to demonstrate their work in a "Challenge session" at the conference, and if suitable will automatically be entered into the Software Bazaar track of the conference. Cash prizes will be awarded for first place (USD 1,500) and runner-up entries. The winning entries will be selected by a vote of the iEvoBio meeting participants. Alongside the iEvoBio Challenge, 2012 iEvoBio sponsor Biomatters Ltd is running the Geneious Challenge. The goal of this challenge is to develop a new plugin to Geneious Pro, using the public API, that enables a new and exciting visualization or analysis. The winning entry will receive a $1000 cash prize, and all entrants who submit by the deadline will receive a 12-month subscription license. The Geneious Challenge has the same open and closing dates as the iEvoBio Challenge. See http://ievobio.org/geneious_challenge.html for more information. Separate from iEvoBio, the Encyclopedia of Life (EOL) is leading a Phylogenetic Tree challenge to encourage not only the development of large phylogenies, but their practical use. Together with the Global Names project they will choose two winning entries: one for the best large tree and one for the most promising but not necessarily large tree -- both in Darwin Core Archive format suitable for use in major biodiversity websites such as EOL. The two winners will receive paid trips to the 2012 iEvoBio conference. See http://eol.org/info/tree_challenge for more information. More details about the iEvoBio conference and program are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list athttp://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign <><><><><><><><><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Assistant Curator, Botany & Informatics Adjunct Assistant Professor, Department of Biology Florida Museum of Natural History University of Florida 354 Dickinson Hall, PO Box 117800 Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://cellinese.blogspot.com/

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Re: [tdwg-content] [tdwg-tag] canonicalScientificName
by Peter Desmet 17 Mar '12

17 Mar '12

Hi all, Since most of the discussion happened on this tdwg-content and tdwg-tag mailing lists already, can't we continue here? I created a link to both from the issue page: http://code.google.com/p/darwincore/issues/detail?id=150#c2 I have been stuck in a meeting all day, while Tim Roberston wrote some convincing arguments against creating a canonicalScientificName term ( http://code.google.com/p/darwincore/issues/detail?id=150#c1) as did Rich Pyle (email March 14 17:20 GMT-10:00). I will need some time to think about these. :-) I will try to write a coherent response tomorrow. Peter On Thu, Mar 15, 2012 at 06:38, Tim Robertson [GBIF] <trobertson(a)gbif.org>wrote: > Hi all, > > Now that a "formal" proposal for a new term has been added [1], should > this discussion continue here or on the issue tracker? To my knowledge > that is the only forum that will be used for a new term when considering if > it will get accepted. > > > When records doesn't fit in standard terms and you cannot afford losing > > the information, the only solution is to add your own custom field. I > > am clearly happier when I find the term I need in the standard. > > I'm, not sure this not applies in this case Simon. Is there really a > scenario where you would put something in canonicalScientificName that you > *could not* put in dwc:scientificName and would require a new term? > > > As canonicalScientificName is both useful enough and clearly defined I > vote for adding it to the standard. > > I've actually challenged this and believe it is not clearly defined [1], > as it does not deal detail what to do when you are filling both, nor how a > consumer would deal with apparently conflicting information. While the > same is true for dwc:genus etc, this one is *so close* to > dwc:scientificName and in many cases could legitimately have the same > content, guidelines are going to be needed for consistent use. I fear a > repeat of the consumption mess dealing with conflicting abcd:catalogNumber > and abcd:catalogNumberNumeric unwittingly being used inconsistently across > resources. > > >> I suspect that the vast majority of names do not present > >> these problems. Why do we let edge cases determine what we do? > > Rod, for the vast majority of names a couple of regular expressions > suffice anyway - right? We don't need a new term to deal with the easy > stuff, and for the hard stuff this term doesn't help anyway. > > Cheers, > Tim > > > [1 ] > http://code.google.com/p/darwincore/issues/detail?id=150&colspec=ID%20Type%… > > > > On Mar 15, 2012, at 10:22 AM, Simon Chagnoux wrote: > > > Sure, for prototypes and proof of concept things, edge cases can be left > > apart. But some people and institutions also use Darwin Core for > > exchanging data between big databases. It is a simple and powerful tool > > for that, especially coupled with DwC/A. > > > > When records doesn't fit in standard terms and you cannot afford losing > > the information, the only solution is to add your own custom field. I > > am clearly happier when I find the term I need in the standard. > > > > As canonicalScientificName is both useful enough and clearly defined I > > vote for adding it to the standard. > > > > Regards, > > > > Simon. > > > > > > > > Le 14/03/2012 20:17, Roderic Page a écrit : > >> Apart from the fact that I can barely bring myself to care about > >> plants ;) I suspect that the vast majority of names do not present > >> these problems. Why do we let edge cases determine what we do? > >> > >> Regards > >> > >> Rod > > > > > > _______________________________________________ > > 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 > -- Peter Desmet Biodiversity Informatics Manager Canadensys - www.canadensys.net Université de Montréal Biodiversity Centre 4101 rue Sherbrooke est Montreal, QC, H1X2B2 Canada Phone: 514-343-6111 #82354 Fax: 514-343-2288 Email: peter.desmet(a)umontreal.ca / peter.desmet.cubc(a)gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet

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Re: [tdwg-content] [tdwg-tag] Canonical name parsing
by Paul van Rijckevorsel 15 Mar '12

15 Mar '12

----- Original Message ----- From: "Paul Kirk" <p.kirk(a)cabi.org> Sent: Wednesday, March 14, 2012 7:34 PM and ... an infraspecific name in ICNAFP (previously ICBN) without an infraspecific rank-indicator is NOT a name, so less than useless ... :-) *** Surely this is not right. The "connecting term" denoting the rank is not part of the name. However, its use is mandatory. In higher ranks a similar problem may occur, where a non-standard termination is used or where a name may be used in more than one rank. Anyway, it never hurts to have a rank-indicating term for names in higher ranks, for those users who are not familiar with the standard terminations. Paul P.S. I would guess "ICNafp"?

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Re: [tdwg-content] [tdwg-tag] Canonical name parsing
by Peter Desmet 14 Mar '12

14 Mar '12

Hi Paul, Higher taxon: "Magnoliidae Novák ex Takhtajan" (a subclass). - scientificName: Magnoliidae Novák ex Takhtajan - taxonRank: subclass But there are no terms to share the canonical name "Magnoliidae". The only available options are kingdom, phylum, class, order, family, genus, subgenus, specificEpithet, infraspecificEpithet, none of which are appropriate. Solution: - canonicalScientificName: Magnoliidae Infrageneric taxon: "Abies sect. Amabilis (Matzenko) Farjon & Rushforth" (a section) - scientificName: Abies sect. Amabilis (Matzenko) Farjon & Rushforth - taxonRank: section - genus: Abies But there are no terms to share "Abies Amabilis", "Abies sect. Amabilis", "Abies section Amabilis" or even "Amabilis". The only available options are kingdom, phylum, class, order, family, genus, subgenus, specificEpithet, infraspecificEpithet, none of which are appropriate. Why we have subgenus, but not *infragenericEpithet* is another issue. I would at least be able to share "Amabilis". Solution: - canonicalScientificName: Abies Amabilis - taxonRank: section Peter There is no place to share the canonical name "Magnoliidae" for this taxon. On Wed, Mar 14, 2012 at 14:37, Paul Kirk <p.kirk(a)cabi.org> wrote: > 'For higher taxa or infrageneric taxa, these terms are not sufficient' > ... why? > > > > Paul > > > > ------------------------------ > > *From:* tdwg-tag-bounces(a)lists.tdwg.org [tdwg-tag-bounces(a)lists.tdwg.org] > on behalf of Peter Desmet [peter.desmet(a)umontreal.ca] > *Sent:* 14 March 2012 18:26 > *To:* Richard Pyle > *Cc:* TDWG content mailing list; Donald Hobern (GBIF); dev Developers; > Christian Gendreau; TDWG TAG mailing list > > *Subject:* Re: [tdwg-tag] [tdwg-content] Canonical name parsing > > Rich, > > I wished those terms were sufficient, but as mentioned in the > justification for http://code.google.com/p/darwincore/issues/detail?id=150 > : > > genus, specificEpithet, infraspecificEpithet: concatenated, this terms are identical to the canonicalScientificName for genera, species and infraspecific taxa. For higher taxa or infrageneric taxa, these terms are not sufficient. In addition, there is some ambiguity regarding the genus definition: for synonyms, is it the accepted genus or the genus that is part of the synonym name? See: http://lists.tdwg.org/pipermail/tdwg-content/2010-November/002052.html. In the former case, the genus cannot be used to concatenate a canonicalScientificName. > > To give an example for a higher taxon: > scientificName: Magnoliidae Novák ex Takhtajan > taxonRank: subclass > > There is no place to share the canonical name "Magnoliidae" for this > taxon. > > Peter > > On Wed, Mar 14, 2012 at 14:13, Richard Pyle <deepreef(a)bishopmuseum.org>wrote: > >> >> I guess the parts that confuse me are: >> >> 1) What providers are able to produce a canonicalScientificName as per >> Peter’s definition, but are unable to provide the pre-parsed elements of >> genus | subgenus | specificEpithet | infraspecificEpithet? >> >> 2) What consumers could make use of a canonicalScientificName as per >> Peter’s definition, but are unable to make (even better) use of the >> pre-parsed elements of genus | subgenus | specificEpithet | >> infraspecificEpithet? >> >> Aloha, >> Rich >> >> >> >> >> From: tdwg-content-bounces(a)lists.tdwg.org [mailto: >> tdwg-content-bounces(a)lists.tdwg.org] On Behalf Of Peter Desmet >> Sent: Wednesday, March 14, 2012 7:03 AM >> To: Donald Hobern (GBIF) >> Cc: TDWG content mailing list; Christian Gendreau; Tim Robertson [GBIF]; >> TDWG TAG mailing list; dev Developers >> Subject: Re: [tdwg-content] Canonical name parsing >> >> Hi Donald, >> >> scientificName, with its current definition [1] is a great term and >> should be continued to used as such. As with most Darwin Core terms, it >> offers flexibility, so its not an impediment for publishing data. In the >> GBIF context, this term is considered mandatory: records without it are >> ignored during indexing (I believe). All of this can stay. >> >> canonicalScientificName would be an additional term with a clear rule >> (see my proposed definition [2]). This is the case for other Darwin Core >> terms as well, such as >> decimalLatitude [3], minimalElevationInMeters [4] or countryCode [5]. >> They serve as an ready-to-use addition/alternative to verbatimLatitude [6], >> verbatimElevation [7] and country [8] respectively. These terms don't stop >> anyone from publishing data, but data publishers who can provide this kind >> of information have the choice to do so. It would be the same for >> canonicalScientificName. >> >> And yes, an aggregator like GBIF can play an important role in providing >> consistent data to its users and figuring out what they really need, but >> not all data is consumed that way. In addition, I hope a user would be able >> to download cleaned data from the GBIF portal as Darwin Core. Wouldn't it >> be nice that the parsed canonicalScientificName created by GBIF can be >> provided in its proper term? There are users out there who want this! >> >> Regards, >> >> Peter >> >> [1] http://rs.tdwg.org/dwc/terms/index.htm#scientificName >> [2] http://code.google.com/p/darwincore/issues/detail?id=150 >> [3] http://rs.tdwg.org/dwc/terms/index.htm#decimalLatitude >> [4] http://rs.tdwg.org/dwc/terms/index.htm#minimumElevationInMeters >> [5] http://rs.tdwg.org/dwc/terms/index.htm#countryCode >> [6] http://rs.tdwg.org/dwc/terms/index.htm#verbatimLatitude >> [7] http://rs.tdwg.org/dwc/terms/index.htm#verbatimElevation >> [8] http://rs.tdwg.org/dwc/terms/index.htm#country >> >> On Wed, Mar 14, 2012 at 11:19, Donald Hobern (GBIF) <dhobern(a)gbif.org> >> wrote: >> > >> > Hi Peter. >> > >> > I certainly agree that aggregators only represent one use case here >> but, having seen a lot of the mess of real-world data, I don't believe that >> simply adding a new term will fix this problem for the users you describe. >> To get the results you want, we would need a sufficiently large majority >> of data sets to follow the rules perfectly that we could ignore those that >> were non-conformant. This would mean we should mandate that every data set >> must use the new element (with or without the existing scientificName >> element) and that they must present scientific names in the expected way >> (or else have their data considered non-compliant). Until now, the >> philosophy on publishing Darwin Core data has been to make it as easy as >> possible for data providers to expose their data, even at the expense of >> greater complexity for consumers. I suspect that we would have a lot less >> data available for use now if we had taken a more stringent approach. >> > >> > In some ways, this proposal reminds me of the structures in ABCD which >> seek to offer users verbatim and more normalised ways to represent several >> types of information. This actually makes consuming all the possible forms >> of such data very complex, since a record may contain all variant forms or >> just any one of them. If multiple forms are available, which one should be >> considered the primary version? >> > >> > I suspect that things may also get complicated as soon as you discuss >> botanical subspecies, varieties, subvarieties, forms and subforms. There >> are recommended ways to abbreviate the rank markers in these cases but some >> variation can be expected. >> > >> > Of course aggregators should be providing more robust services for >> accessing exactly what you want in a consistent, predictable way and I >> would suggest that the best place to attack the problem is to define >> exactly what a typical user needs to see and then for GBIF and similar >> projects to work on delivering predictable data downloads and web services >> that clean out all of these nomenclatural inconsistencies - and perhaps >> also add value in other ways such as augmenting the data with associated >> environmental values (as the Atlas of Living Australia does). This would >> allow us all to work together on developing a consistent and predictable >> algorithm for handling interpretation of name strings, including synonymy, >> misspellings, virus names and everything else that makes this such a >> difficult problem. >> > >> > Best wishes, >> > >> > Donald >> > >> > ---------------------------------------------------------------------- >> > Donald Hobern - GBIF Director - dhobern(a)gbif.org >> > Global Biodiversity Information Facility http://www.gbif.org/ >> > GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark >> > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 >> > ---------------------------------------------------------------------- >> > >> > >> > -----Original Message----- >> > From: peter.desmet.cubc(a)gmail.com [mailto:peter.desmet.cubc@gmail.com] >> On Behalf Of Peter Desmet >> > Sent: Wednesday, March 14, 2012 3:41 PM >> > To: Tim Robertson [GBIF] >> > Cc: Donald Hobern (GBIF); dev Developers; TDWG content mailing list; >> TDWG TAG mailing list; Christian Gendreau >> > Subject: Re: Canonical name parsing >> > >> > Hi Tim, >> > >> > I agree, aggregators like GBIF and Canadensys will have to deal with >> clean and dirty data in each field anyway: they need code libraries to deal >> with this and it is good that these are being developed. But, that doesn't >> help someone who wants to use data from a Darwin Core Archive with his data >> in Excel or a Roderic Page who wants to get things done for a prototype. >> > Having to use Java libraries or even the Name Parser [1] (though both >> > great) is a barrier to data use. Darwin Core (Archives) is not only >> used for machine to machine interaction, humans use it too, and I think we >> should allow easy hacking (I mean this in the good sense), especially for >> something as important as the scientific name. >> > In addition, as a data publisher (e.g. for our VASCAN checklist) I >> > *do* have the information to provide a clean and simple to use >> canonicalScientificName, but I just can't share it via the otherwise >> excellent biodiversity sharing standard Darwin Core. I think that's a pity. >> > >> > Peter >> > >> > [1] http://tools.gbif.org/nameparser/ >> > [2] http://data.canadensys.net/vascan >> > >> > PS: Yes, Canadensys will use the GBIF interpretation libraries. Since >> we develop in Java as well, using those libraries is as easy as the >> proverbial "one line of code". We're looking forward in testing them and >> providing patches to enhance them. Open source FTW! :-) >> > >> > >> > On Wed, Mar 14, 2012 at 07:32, Tim Robertson [GBIF] < >> trobertson(a)gbif.org> wrote: >> > > Hi Peter, >> > > >> > > I'm replying off the TDWG list, since it is a bit of a tangent to >> your discussion. If you feel it is relevant, please CC the list again. >> > > >> > > At GBIF as you know, we have to interpret all kinds of quality of >> content. I tend to agree with Donald that this would not really help in >> consumption, as in my experience we will have to deal with both clean and >> dirty data in each field *anyway* when this is used at network scale. I >> would rather see us evolve the interpretation libraries to handle all the >> corner cases, which we need to develop anyway. We already do a pretty >> decent job at extracting canonicals. This is further enhanced when you >> couple the extracted canonical with a fuzzy match against the >> "authoritative names" we can now index thanks to the availability of >> checklists in DwC-A format. >> > > >> > > I know you are a Java shop. Are you using the GBIF interpretation >> libraries [1] at the moment? If not, is there a reason why you don't? >> > > They are used in all GBIF projects (portal, checklistbank etc), and >> the more we enhance them, the better it is for everyone. We have a >> significant test coverage [2,3] and there have been quite some man months >> (years?) spent already in their development and with some real regular >> expression experts (most notably Markus D. and Dave M.). All our work is >> Maven-ized, versioned and available in our Maven repository [4]. >> > > >> > > I hope these are interesting to you. We would welcome any patches to >> enhance them, or assistance in identifying the corner cases and capturing >> those as unit tests. >> > > >> > > Hope this helps, >> > > Tim >> > > >> > > [1] >> > > >> http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src >> > > /main/java/org/gbif/ecat/parser/NameParser.java >> > > [2] >> > > >> http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src >> > > /test/java/org/gbif/ecat/parser/NameParserTest.java >> > > [3] >> > > >> http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src >> > > /#src%2Ftest%2Fresources [4] >> > > http://repository.gbif.org/index.html#nexus-search;quick~ecat-common >> > > >> > >> > >> > >> > -- >> > Peter Desmet >> > Biodiversity Informatics Manager >> > Canadensys - www.canadensys.net >> > >> > Université de Montréal Biodiversity Centre >> > 4101 rue Sherbrooke est >> > Montreal, QC, H1X2B2 >> > Canada >> > >> > Phone: 514-343-6111 #82354 >> > Fax: 514-343-2288 >> > Email: peter.desmet(a)umontreal.ca / peter.desmet.cubc(a)gmail.com >> > Skype: anderhalv >> > Public profile: http://www.linkedin.com/in/peterdesmet >> > >> > >> > _______________________________________________ >> > tdwg-content mailing list >> > tdwg-content(a)lists.tdwg.org >> > http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> >> >> >> -- >> Peter Desmet >> Biodiversity Informatics Manager >> Canadensys - www.canadensys.net >> >> Université de Montréal Biodiversity Centre >> 4101 rue Sherbrooke est >> Montreal, QC, H1X2B2 >> Canada >> >> Phone: 514-343-6111 #82354 >> Fax: 514-343-2288 >> Email: peter.desmet(a)umontreal.ca / peter.desmet.cubc(a)gmail.com >> Skype: anderhalv >> Public profile: http://www.linkedin.com/in/peterdesmet >> >> >> This message is only intended for the addressee named above. Its >> contents may be privileged or otherwise protected. Any unauthorized use, >> disclosure or copying of this message or its contents is prohibited. If >> you have received this message by mistake, please notify us immediately by >> reply mail or by collect telephone call. Any personal opinions expressed >> in this message do not necessarily represent the views of the Bishop Museum. >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> > > > > -- > Peter Desmet > Biodiversity Informatics Manager > Canadensys - www.canadensys.net > > Université de Montréal Biodiversity Centre > 4101 rue Sherbrooke est > Montreal, QC, H1X2B2 > Canada > > Phone: 514-343-6111 #82354 > Fax: 514-343-2288 > Email: peter.desmet(a)umontreal.ca / peter.desmet.cubc(a)gmail.com > Skype: anderhalv > Public profile: http://www.linkedin.com/in/peterdesmet > > P Think Green - don't print this email unless you really need to** ** > > ************************************************************************ > The information contained in this e-mail and any files transmitted with it > is confidential and is for the exclusive use of the intended recipient. If > you are not the intended recipient please note that any distribution, > copying or use of this communication or the information in it is > prohibited. > > Whilst CAB International trading as CABI takes steps to prevent the > transmission of viruses via e-mail, we cannot guarantee that any e-mail or > attachment is free from computer viruses and you are strongly advised to > undertake your own anti-virus precautions. > > If you have received this communication in error, please notify us by > e-mail at cabi(a)cabi.org or by telephone on +44 (0)1491 832111 and then > delete the e-mail and any copies of it. > > CABI is an International Organization recognised by the UK Government > under Statutory Instrument 1982 No. 1071... > > ************************************************************************** > **** > > > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag > > -- Peter Desmet Biodiversity Informatics Manager Canadensys - www.canadensys.net Université de Montréal Biodiversity Centre 4101 rue Sherbrooke est Montreal, QC, H1X2B2 Canada Phone: 514-343-6111 #82354 Fax: 514-343-2288 Email: peter.desmet(a)umontreal.ca / peter.desmet.cubc(a)gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet

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canonicalScientificName
by Peter Desmet 14 Mar '12

14 Mar '12

Hi everyone, In a recent tweet [1] Roderic Page reminded me that in Darwin Core, we don't have a ready-to-use scientificName field. The definition for scientificName [2] asks for the full verbose name, including authors. I think this is a good definition (see below), but it also means that in a lot of use cases, names need to be parsed before they can be used or matched. I am currently helping collections publish their data for Candensys [3] and as a data producer I am happy we can provide all the information we have in scientificName, but as a data user, I get frustrated every time I see those long verbose botanical names with multiple authors. I am convinced that our data would be more usable if we had an additional canonicalScientificName term. Which is why I am now officially requesting it on the Darwin Core code site: http://code.google.com/p/darwincore/issues/detail?id=150 (see below). This has been discussed in detail before [4], but no consensus was reached. I hope we can get our act together this time! Regards, Peter Desmet -- [1] https://twitter.com/#!/rustyrussell22/status/179500954901692417 [2] http://rs.tdwg.org/dwc/terms/index.htm#scientificName [3] http://www.canadensys.net [4] http://lists.tdwg.org/pipermail/tdwg-content/2010-November/thread.html#1976 ==New Term Recommendation== Submitter: Peter Desmet Justification: The scientific name is probably the most used element of an occurrence/taxon, but currently Darwin Core does not provide a single ready-to-use-field for this. A canonicalScientificName with the scientific name as a uninomial, binomial or trinomial could solve this problem. The current terms are not sufficient: - scientificName: verbose, used to record all components of a scientific name (if available), including authorship(s) and rankmarker(s). It is critical to keep this definition, as this term is sometimes the only place to share certain information, e.g.: quadrinomials, intermediate botanical authors, hybrid formulas, etc. The disadvantage of only having this verbose notation is that the user needs to parse the name before he/she can use or match it. - genus, specificEpithet, infraspecificEpithet: concatenated, this terms are identical to the canonicalScientificName for genera, species and infraspecific taxa. For higher taxa or infrageneric taxa, these terms are not sufficient. In addition, there is some ambiguity regarding the genus definition: for synonyms, is it the accepted genus or the genus that is part of the synonym name? See: http://lists.tdwg.org/pipermail/tdwg-content/2010-November/002052.html. In the former case, the genus cannot be used to concatenate a canonicalScientificName. The need for this term has been discussed thoroughly already (see: http://lists.tdwg.org/pipermail/tdwg-content/2010-November/thread.html#1976) but no consensus was reached. I'd like to reopen the discussion and I hope that a consensus can be reached quickly, so our data can be used more easily. Definition: The scientific name as a uninomial, binomial or trinomial. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined. This term should not contain authorship(s), rankmarker(s) or identification qualifications. If the scientific name cannot be expressed as a uni-, bi- or trinomial (e.g. hybrid formulas), do not use this term (use scientificName instead). Comment: Examples: "Carex" (genus), "Vulpes vulpes" (species), "Anaphalis margaritacea occidentalis" (plant variety) Refines: Has Domain: Has Range: Replaces: ABCD 2.06: -- Peter Desmet Biodiversity Informatics Manager Canadensys - www.canadensys.net Université de Montréal Biodiversity Centre 4101 rue Sherbrooke est Montreal, QC, H1X2B2 Canada Phone: 514-343-6111 #82354 Fax: 514-343-2288 Email: peter.desmet(a)umontreal.ca / peter.desmet.cubc(a)gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet

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Re: [tdwg-content] Canonical name parsing
by Peter Desmet 14 Mar '12

14 Mar '12

Hi Tim, I agree, aggregators like GBIF and Canadensys will have to deal with clean and dirty data in each field anyway: they need code libraries to deal with this and it is good that these are being developed. But, that doesn't help someone who wants to use data from a Darwin Core Archive with his data in Excel or a Roderic Page who wants to get things done for a prototype. Having to use Java libraries or even the Name Parser [1] (though both great) is a barrier to data use. Darwin Core (Archives) is not only used for machine to machine interaction, humans use it too, and I think we should allow easy hacking (I mean this in the good sense), especially for something as important as the scientific name. In addition, as a data publisher (e.g. for our VASCAN checklist) I *do* have the information to provide a clean and simple to use canonicalScientificName, but I just can't share it via the otherwise excellent biodiversity sharing standard Darwin Core. I think that's a pity. Peter [1] http://tools.gbif.org/nameparser/ [2] http://data.canadensys.net/vascan PS: Yes, Canadensys will use the GBIF interpretation libraries. Since we develop in Java as well, using those libraries is as easy as the proverbial "one line of code". We're looking forward in testing them and providing patches to enhance them. Open source FTW! :-) On Wed, Mar 14, 2012 at 07:32, Tim Robertson [GBIF] <trobertson(a)gbif.org> wrote: > Hi Peter, > > I'm replying off the TDWG list, since it is a bit of a tangent to your discussion. If you feel it is relevant, please CC the list again. > > At GBIF as you know, we have to interpret all kinds of quality of content. I tend to agree with Donald that this would not really help in consumption, as in my experience we will have to deal with both clean and dirty data in each field *anyway* when this is used at network scale. I would rather see us evolve the interpretation libraries to handle all the corner cases, which we need to develop anyway. We already do a pretty decent job at extracting canonicals. This is further enhanced when you couple the extracted canonical with a fuzzy match against the "authoritative names" we can now index thanks to the availability of checklists in DwC-A format. > > I know you are a Java shop. Are you using the GBIF interpretation libraries [1] at the moment? If not, is there a reason why you don't? > They are used in all GBIF projects (portal, checklistbank etc), and the more we enhance them, the better it is for everyone. We have a significant test coverage [2,3] and there have been quite some man months (years?) spent already in their development and with some real regular expression experts (most notably Markus D. and Dave M.). All our work is Maven-ized, versioned and available in our Maven repository [4]. > > I hope these are interesting to you. We would welcome any patches to enhance them, or assistance in identifying the corner cases and capturing those as unit tests. > > Hope this helps, > Tim > > [1] http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src/main… > [2] http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src/test… > [3] http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src/#src… > [4] http://repository.gbif.org/index.html#nexus-search;quick~ecat-common > -- Peter Desmet Biodiversity Informatics Manager Canadensys - www.canadensys.net Université de Montréal Biodiversity Centre 4101 rue Sherbrooke est Montreal, QC, H1X2B2 Canada Phone: 514-343-6111 #82354 Fax: 514-343-2288 Email: peter.desmet(a)umontreal.ca / peter.desmet.cubc(a)gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet

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Re: [tdwg-content] canonicalScientificName
by Donald Hobern 14 Mar '12

14 Mar '12

Hi Peter. I certainly sympathise with the desire for a readily-consumed naked scientific name field. However, unless the canonicalScientificName element is enforced as a mandatory field (which would in itself impact some data publishers and may prevent them validly sharing their data without extra work to provide clean scientific names), it will be yet another element which data consumers must check. If canonicalScientificName is supplied, consumers will still need to handle cases where it is malformed. If is not supplied, they will need to ignore the record or else do precisely what they do today with the scientificName field. I therefore worry that adding this field could in fact make the task more complex, rather than simpler, for data consumers. Thanks, Donald ---------------------------------------------------------------------- Donald Hobern - GBIF Director - dhobern(a)gbif.org Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 ----------------------------------------------------------------------

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Applications open for iEvoBio 2012 Travel Awards
by Nico Cellinese 13 Mar '12

13 Mar '12

The 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is offering limited funds for travel expenses for the 2012 iEvoBio meeting in Ottawa, Canada. Preference will be given to participants lacking sources of funding for meeting attendance, such as graduate students, emerging professionals, and participants from underrepresented groups and countries. Please explain in an attached document the need for funding, the benefit that attending iEvoBio will afford you and how you will contribute to the meeting (max 350 words). We are looking for do-ers! A brief letter of support from your advisor, supervisor, or professional mentor should be submitted to the organizing committee (electronically), together with the application headed by the information below, to travelaward(a)ievobio.org by the deadline of 15 April 2012. Participants are required to make all their own travel arrangements, including visas and lodging, if required. Application format: Name: Contact information (address/phone/email): Academic Institution: Role (student, researcher, etc.): Origination of travel (if different from home institution) and estimated travel expenses: Explain the benefit that attending iEvoBio will afford you and what you will bring to the meeting (350 words or less):

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Call for Abstracts open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Nico Cellinese 03 Mar '12

03 Mar '12

The Call for Abstracts for full talks is now open for the 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs2/index.php/ievobio/2012. See below for instructions. Accepted talks will be 15 minutes in length and will be presented during the full talk session of the conference. Because the number of program slots for full talks is limited, some talks may be moved to the Lightning Talk session (5 minutes in length). Submitted talks should be in the area of informatics aimed at advancing research in phylogenetics, evolution, and biodiversity, including new tools, cyberinfrastructure development, large-scale data analysis, and visualization. Submissions should be 1 page long at most and include a title, a list of contributors, and an abstract. The abstract should provide an overview of the talk's subject, and give enough detail to allow reviewers to decide whether the submission merits a full talk, or whether it should be moved to a Lightning Talk session. If the subject of the talk is a specific software component for use by the research community, the abstract must state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. The deadline for submission is April 2, 2012. We intend to notify authors of accepted talks before early registration for iEvoBio (and Evolution) ends. Further instructions for submission are at the following URL: http://ievobio.org/ocs2/index.php/ievobio/2012/schedConf/cfp Full talks are one of the five kinds of contributed content that feature in iEvoBio. The other four are: 1) Lightning talks (5 mins long), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of-a-Feather gatherings. The Call for Challenge entries is already open (see http://ievobio.org/challenge.html) The calls for contribution to the other three sessions will open later, and will remain open until shortly before the conference or until the respective track fills up. In addition, 2012 iEvoBio sponsor Biomatters Ltd will be running the Geneious Challenge alongside this year’s iEvoBio Challenge, see http://ievobio.org/geneious_challenge.html for more information. More details about the conference and program are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida and Florida Museum of Natural History Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign (*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see http://www.opensource.org/docs/definition.php) and reuse within the research community. For this reason, if a submitted talk concerns a specific software system for use by the research community, that software must be licensed with a recognized Open Source License (see http://www.opensource.org/licenses/) and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial. Authors of full talks who cannot meet this requirement at the time of submission should state their intentions, and are advised that the requirement must be met by July 9, 2012, at the latest.

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iEvoBio conference, July 10-11, 2012
by Nico Cellinese 02 Mar '12

02 Mar '12

Dear All, The official website of iEvoBio 2012 is now open (www.ievobio.org) The 2 days conference will be held in conjunction with the annual Evolution meeting in Ottawa on the 10-11 July, 2012. Note that the program includes two exciting challenges and much more! We hope to see you in Canada! Cheers, NIco <><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Assistant Curator, Botany & Informatics Adjunct Assistant Professor, Department of Biology Florida Museum of Natural History University of Florida 354 Dickinson Hall, PO Box 117800 Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://cellinese.blogspot.com/

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