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Re: [tdwg] [Taxacom] Semantic Web: What is a species?
by Peter DeVries 25 Jan '09

25 Jan '09

Thanks to everyone for posting their comments. ;-) I think that this discussion is illustrative of two issues. Different people often have different ideas of what the same term means and in discussions these subtile differences are not always apparent. When matching or linking two terms or concepts via the Semantic Web, one needs to be aware that they may not actually have the same semantic meaning. If one of my collaborators chooses to tag their specimens with my species concept URI, they are saying that we share a common species concept. What I have been thinking about ,and what prompted the original post, was that I needed a more formal definition of what this species concept is. David Baum has a paper that will be coming out in Systematic Biology that discusses the issue of species concepts, and has some valuable insights. This issue is very complicated and I was not trying to oversimplify it. My goal was to foster thinking about the best way to implement these concepts on the Semantic Web. I had some additional thoughts that I would like to put out there. Animals seem to do a pretty good job of "recognizing" conspecifics through a number of different mechanisms. For them, species act as if they are real. What if species were mainly "real" things with fuzzy borders but our ability as humans to correctly recognize them and and their instances (specimens) is limited. We can only hypothesize that something is a species, but overtime, our hypotheses get closer to approximating the real species. This is a take on Plato's Allegory of the cave http://en.wikipedia.org/wiki/Allegory_of_the_cave And may be best illustrated by an example. We all know what a chair is, right? Now try to write a formal description of a chair that correctly accounts for all the known instances of chairs. Thanks to everyone for posting their thoughts, it has been very helpful. - Pete

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ESA 2008 Talk Using Semantic Web technologies to tie together disparate data about species .. Unique URI for each taxon
by Peter DeVries 25 Jan '09

25 Jan '09

I don't know how many of you are working with Semantic Web technologies, but I did a talk at the2008 Meeting of the Entomological Society of America Meeting in Reno. You can see it here : http://esa.confex.com/esa/2008/webprogram/Paper39190.html One of the issues that I have been struggling with is the need for a unique identifier for a species concept that stays the same despite changes in taxonomic hypotheses. When I brought this up earlier some mentioned that many considered the taxonomic hypothesis to be the species concept. I thought that this approach was wrong because it unnecessarily required me to convince one of my collaborators to adopt my taxonomic hypothesis when it was clear we were talking about the same species. To me a species is a real thing to which different taxonomic hypothesis are applied. With this in mind I implemented a system where each species has a unique URI which resolves according to the recommendations of the linked data community. You can see this service at: http://species.geospecies.org/ Here is the page for Culicidae http://species.geospecies.org/families/Culicidae Here is an example of the URI for Aedes vexans http://species.geospecies.org/spec_concept_uuid/0fcb5b7e-bcfc-4b56-b565-e1e… For a web browser this will resolve to the human readable page, for a semantic web crawler it will respond with RDF data. Here is journal reference marked up using the two major bibliography ontologies that includes what species concepts are included in the article. This allows publications to retain links to species concepts despite changes in nomenclature. http://rdf.geospecies.org/refs/sucaet2008wbr/index.rdf Here is an RDF file of species observation records (the web version is currently password protected) http://rdf.geospecies.org/observations/index.rdf I have chosen the UUID as the mechanism to make unique URI's not because of their inherent beauty, but because the allow anyone on almost any platform to create a unique id without worrying about to identical id's being created. For those interested, I can send you a PDF of my talk slides and text. I would also appreciate any feedback or suggestions :-) - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries(a)wisc.edu Insects of Wisconsin <http://insects.entomology.wisc.edu/> Spiders of Wisconsin <http://spiders.entomology.wisc.edu/> ------------------------------------------------------------

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Re: [tdwg] Semantic Web: What is a species?
by Richard Pyle 25 Jan '09

25 Jan '09

I've said it many times before on this list elsewhere: "A species is what community of taxonomists says it is." It also happens to be the de-facto operational definition ever since the notion of "species" first began, all the way through (and including) today. Until we have another definition that is broadly adopted by the taxonomic community, then it will remain the de-facto operational definition. What Darwin said in the 'Origin of Species' is still true today: "No one definition has as yet satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species." And, by the way, here's how Darwin, in his characteristically overly verbose way, had to say on the matter: "Hence, in determining whether a form should be ranked as a species or a variety, the opinion of naturalists having sound judgement and wide experience seems the only guide to follow. We must, however, in many cases, decide by a majority of naturalists, for few well-marked and well-known varieties can be named which have not been ranked as species by at least some competent judges." In other words, "A species is what community of taxonomists says it is." Aloha, Rich > -----Original Message----- > From: Bob Morris [mailto:morris.bob@gmail.com] > Sent: Sunday, January 25, 2009 7:28 AM > To: Richard Pyle > Cc: tdwg(a)lists.tdwg.org; Taxacom(a)mailman.nhm.ku.edu > Subject: Re: [tdwg] Semantic Web: What is a species? > > Ah, Rich, might I understand your position to be akin to that > of the U.S. Supreme Court Justice the Honorable Potter > Stewart whose concurring opinion in Jacobellis v. Ohio 378 > U.S. 184 (1964) contains the famous words, refering to "obscenity": > > "I shall not today attempt further to define the kinds of > material I understand to be embraced within that shorthand > description; and perhaps I could never succeed in > intelligibly doing so. But I know it when I see it, and the > motion picture involved in this case is not that." > > :-) > > Bob Morris > > > On Sun, Jan 25, 2009 at 6:44 AM, Richard Pyle > <deepreef(a)bishopmuseum.org> wrote: > > > > First, I think the comment that I *most* agree with is the > one made by > > Gurcharan Singh, that these conversations are endless (and will > > probably always be so). There are two reasons I can never seem to > > miss an opportunity to dive in and pontificate (Jim C., > that's your cue...): > > > > 1) I usually have a slightly different perspective at the end these > > conversations, than I had at the beginning (always a good > thing); and > > > > 2) I enjoy the intellectual challenge of trying to make the > same basic > > points each time using a different tact, and coming from a > different > > perspective. > > > > Now, Pete: > > > >> When a medical entomologist states that a species X, breeds in > >> shallow > > ephemeral pools and > >> has a preference for human blood meals do they mean > >> > >> The taxonomic hypothesis A. o. has these properties or > >> > >> the "natural" unit currently called A. o. has these properties ? > > > > Frankly, I don't think most medical entomologists think that deeply > > about it. In fact, I don't think most taxonomists even > think that deeply about. > > I suspect most biologists/scientists/laymen think of > species as "things" > > that exist in nature, and that these "things" have certain > properties > > that are consistent enough to allow predictions and such. > And I would > > wager that, in the vast majority of cases, they would do so > with good > > success. That doesn't make species "real" in my mind (or > even any more > > "real" than other taxonomic units -- in fact I think > populations are > > probably more demonstrably "real" than species). It just makes the > > notion of "species as real" a practical one (as if we > didn't already > > know that, after centuries of people thinking in those terms). > > > >> I think they mean the second and would benefit if the > statements made > > about that natural unit > >> could stay linked to the natural unit species concept over time. > >> > >> Unfortunately under the "species is the taxonomic > hypothesis" system > >> they > > don't. > >> > >> Does this help clarify the distinction I am trying to make? > > > > I'm not sure -- partly because I've never quite understood > what people > > mean by "species are hypotheses". By my reckoning, it's only an > > hypothesis if it's testable & falsifiable. As such, it only makes > > sense in the context of "species are real entities in > nature, and we > > can test whether our circumscriptions (aka taxon concepts) > match those > > real entities". So I've always thought of "species are hypotheses" > > and "species are real, natural entities" as being two sides > of the same coin. > > > > So I guess I don't understand the distinction you're > drawing between > > the two. > > > > Aloha, > > Rich > > > > > > _______________________________________________ > > tdwg mailing list > > tdwg(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg > > > > > > -- > Robert A. Morris > Professor of Computer Science > UMASS-Boston > ram(a)cs.umb.edu > http://bdei.cs.umb.edu/ > http://www.cs.umb.edu/~ram > http://www.cs.umb.edu/~ram/calendar.html > phone (+1)617 287 6466

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Semantic Web: What is a species?
by Peter DeVries 25 Jan '09

25 Jan '09

An interesting side discussion started up from my earlier post and I thought it might beworth discussion on the general list. I expect there will be a number of different opinions on this subject which might prove enlightening. What is a species? The way I have constructed my system I consider species to be real things too which different taxonomic hypothesis are applied. A collector or curator would then decide which species concept they believe is the best match for their specimen or group of specimens. Those individuals would then be tied to a particular species concept. (Not necessarily a specific genus species) Statements or properties could then be associated with particular species concepts. For instance: This Culicidoid species concept is a member of the Anophelinoid Group and thereby inherits the following properties: Maxillary palps about as long as proboscus, not strongly recurved Scutellum evenly rounded Scutellum seta more or less evenly distributed Most like diagram http://..... I am not sure that you could make useful statements like this if specimens are abstracted as an array of names, and if species are not real things that are separate from individual taxonomic hypothesis. Note I use Anophelinoid rather than Anophelinae to avoid tying this group of morphological characters to a specific taxonomic hypothesis. Under this model genera, families and subspecies (as they are now used) are thought of as human constructed clades and are not real in the same sense as species are real. A species exists whether or not a human has chosen to describe and name it. There also seems to be a difference in how ecologists, medical entomologists and taxonomists think of species. The former tend to view species as real things while the later see them as a human constructed grouping, where the taxonomic hypothesis is the species concept. >From the perspective of the semantic web, species concepts defined in these different ways have different meanings and may not be able to be merged directly. At least that is my current thinking .... How do others think of species? --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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Semantic Web Linked Data Validator
by Peter DeVries 22 Jan '09

22 Jan '09

For those interested in making their data available on the Semantic Web, check out Vapour http://validator.linkeddata.org/vapour It provides a way to test if your URI's properly resolve. - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries(a)wisc.edu Insects of Wisconsin <http://insects.entomology.wisc.edu/> Spiders of Wisconsin <http://spiders.entomology.wisc.edu/> ------------------------------------------------------------

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FW: Database job
by Lee Belbin 07 Jan '09

07 Jan '09

Lee Belbin TDWG Secretariat From: Gary Rosenberg [mailto:rosenberg@ansp.org] Sent: Thursday, 8 January 2009 9:21 AM To: Lee Belbin Subject: Database job Hi Lee, I don't know if you've heard that the Academy of Natural Sciences is looking for a biodversity database manager. The ad was posted on taxacom, but some TDWG members might not have seen it. Could you circulating the link to the TDWG distribution list? http://www.ansp.org/about/employment.php#983 People can contact me if they have questions about the position. Best wishes, Gary Rosenberg """""""""""""""""""""""""""""""""""""""""""""""""""""""" Gary Rosenberg, Ph.D. Pilsbry Chair of Malacology Academy of Natural Sciences 1900 Benjamin Franklin Parkway Philadelphia, PA 19103-1195 USA Phone: 215-299-1033, Fax: 215-299-1170 Email: rosenberg(a)ansp.org http://clade.acnatsci.org/rosenberg http:///www.malacolog.org/ <http://www.malacolog.org/>

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Reminder: deadline for abstract submission to EGU Biodiversity Informatics Session
by Eamonn O Tuama (GBIF) 06 Jan '09

06 Jan '09

Dear Colleagues, We kindly remind you that the deadline for submitting an abstract to the European Geosciences Union (EGU) General Assembly 2009 is 13 January 2009! We cordially invite you to submit an abstract for the Biodiversity Informatics session, the main objective of which is to highlight the value of adopting informatics standards for both Biodiversity and Earth and Space Science disciplines thereby promoting interoperability across heterogeneous systems and, in particular, demonstrating how the kinds of observational data mobilised by the Global Biodiversity Information Facility network can be integrated with other geospatial data to address issues relating to climate change, protected area management, invasive species, etc. General information: http://meetings.copernicus.org/egu2009/index.html Biodiversity Informatics Session: http://meetingorganizer.copernicus.org/EGU2009/session/380 Guidance on abstract submission: http://meetings.copernicus.org/egu2009/abstract_management/index.html If you have any questions, please do not hesitate to contact one of the organisers: Convenor: Eamonn O Tuama; eotuama at gbif.org Co-convenor: Hannu Saarenmaa; hannu.saarenmaa at helsinki.fi Co-convenor: Jeremy Kerr; Jeremy.Kerr at uottawa.ca _______________________________________________ Éamonn Ó Tuama, Ph.D. (eotuama(a)gbif.org), Senior Programme Officer, Inventory, Discovery, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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The Club of Rome: biodiversity / technology: call for contributions
by Lee Belbin 14 Dec '08

14 Dec '08

This looks like it should be a very interesting meeting and one where it would seem appropriate for TDWG to be 'raised'. Is anyone planning to attend? Would anyone consider representing TDWG and possibly reporting back (v.)briefly? We do have a number of prepared PowerPoint presentations on TDWG, a poster and brochures that could be used (see http://www.tdwg.org/about-tdwg/resources-for-outreach/). I'd be happy to help tailor a brief presentation. Help! Lee Lee Belbin TDWG Secretariat From: Club of Rome - ESC [mailto:agenda@clubofrome.at] Sent: Tuesday, 9 December 2008 1:52 AM To: agenda(a)clubofrome.at Subject: biodiversity / technology: call for contributions <http://www.clubofrome.at> The Club of Rome - European Support Centre Dear Ladies and Gentlemen, we are searching for contributions to an event which will discuss the usage of Information Technology for Biodiversity Conservation and Management and Information Technology in Agriculture. This implies database processing, sensor technologies, and also networking of organisations and activists. The event will be held on January 15th at UNESCO in Paris and is organized by the European Support Centre of the Club of Rome ( http://www.clubofrome.at ) and the project ICT Ensure ( http://ict-ensure.tugraz.at ). We would be very grateful if you forwarded this mail to persons in your organisation who are dealing with the topics and who might be interested to participate or to contribute with a statement. Please don't hesitate to contact us for further information. Best regards Thomas Schauer -- Dr. Thomas Schauer Director European Support Centre of the Club of Rome Tuchlauben 8/15, 1010 Vienna, Austria Tel.: +43-1-5125770 Fax: +43-1-5125770-10 http://www.clubofrome.at

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Biodiversity Informatics session at European Geosciences Union meeting: call for participation
by Eamonn O Tuama (GBIF) 08 Dec '08

08 Dec '08

Dear Colleagues, You are invited to submit an abstract for the Biodiversity Informatics session in the forthcoming Earth and Space Sciences Informatics programme of the European Geosciences Union General Assembly to be held in Vienna, 19-24 April 2009. The main objective of this session is to highlight the value of adopting informatics standards for both Biodiversity and Earth and Space Science disciplines thereby promoting interoperability across heterogeneous systems and, in particular, demonstrating how the kinds of observational data mobilised by the Global Biodiversity Information Facility network can be integrated with other geospatial data to address issues relating to climate change, protected area management, invasive species, etc. General information: http://meetings.copernicus.org/egu2009/index.html Biodiversity Informatics Session: http://meetingorganizer.copernicus.org/EGU2009/session/380 Guidance on abstract submission: http://meetings.copernicus.org/egu2009/abstract_management/index.html Authors are invited to submit abstracts by Tuesday 13 January 2009. If you have any questions, please do not hesitate to contact me or one of the co-convenors of the session, and please feel free to forward this message to others who may be interested. Convenor: Éamonn Ó Tuama; eotuama at gbif.org Co-convenor: Hannu Saarenmaa; hannu.saarenmaa at helsinki.fi Co-convenor: Jeremy Kerr; Jeremy.Kerr at uottawa.ca With regards, Éamonn Ó Tuama _______________________________________________ Éamonn Ó Tuama, Ph.D. (eotuama(a)gbif.org), Senior Programme Officer, Inventory, Discovery, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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Project Officer Required
by Charles Hussey 21 Oct '08

21 Oct '08

Project Officer PESI project Fixed-term appointment, 22 months full-time. Based at the Natural History Museum, South Kensington, Salary £28,000 p.a. The Natural History Museum is leading a Work Package within a project funded through the EU Framework 7 Capacities Work Programme, entitled "A Pan-European Species-directories Infrastructure" (http://www.eu-nomen.eu/pesi <http://www.eu-nomen.eu/pesi> ). This 3-year project, which commenced in May 2008, is led by the University of Amsterdam and involves 40 partner organisations from 26 countries. PESI will integrate the infrastructural components of four major community networks on taxonomic indexing, namely those of marine life, terrestrial plants, fungi and animals, into a joint work programme. In addition, PESI will set up networks of both taxonomic experts and regional focal points and will work to address the issues of pooling resources, standardisation, sustainability, accessibility and international cooperation. Work Package 4, led by the NHM deals with the development, integration and application of taxonomic standards. We shall be working closely with relevant standards organisations and nomenclators (such as GBIF, ZooBank, IPNI, Index Fungorum and Algaebase). Work will include development of management classification schemes, a controlled terminology for species status and utilisation of globally unique identifiers for names (GUIDs). Required deliverables will take the form of four reports to the EU Commission. You will be working under the direction of the Work Package Leader and will have responsibility for undertaking the NHM programme of work. You will be liaising closely with the five other partners in the work package and with other work packages. There will be a small amount of foreign travel to attend meetings. You will be expected to have the ability both to work on your own initiative and as part of a collaborative team. You will be good at assessing facts and making reasoned judgements. A working knowledge of databases (preferably to do with biodiversity informatics), and of a European language, would be useful. You will have experience of producing technical reports. You will be able to demonstrate a familiarity with biological nomenclature and taxonomic classification. You must have a degree in a biological science or a computing discipline, preferably at PhD level, together with substantial experience as a professional or academic natural scientist or computer scientist. For a full job description and to apply online please visit the Natural History Museum website at www.nhm.ac.uk/jobs <http://www.nhm.ac.uk/jobs> Closing date: Sunday 16 November 2008. Posted by: Charles Hussey, Science Data Co-ordinator, UK Biodiversity Programme, Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD United Kingdom Tel. +44 (0)207 942 5213 Fax. +44 (0)207 942 5529 e-mail c.hussey(a)nhm.ac.uk Species Dictionary project: www.nhm.ac.uk/nbn/ <http://www.nhm.ac.uk/nbn/> Nature Navigator: www.nhm.ac.uk/naturenavigator/ <http://www.nhm.ac.uk/naturenavigator/>

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