November 2005 - tdwg-tag - lists.tdwg.org

Re: GUIDs for Taxon Names and Taxon Concepts
by Richard Pyle 10 Nov '05

10 Nov '05

Hi Roger, > Rich - yes. I think you sum up the difference between new combinations > in ICZN and ICBN well. But... just because the ICZN does not consider > the usage of a name in a different genus as a nomenclatural act does not > stop us creating a data object (TaxonName object) to represent what that > name looks like in the new genus - perhaps with its new ending and > possibly different author string (ICZN Recommendation 51G). I agree that nothing is stopping us, but I forsee headaches down the road as a result of doing so. In your next message, you wrote: "1. We have two kinds of GUID (one for TaxonNames and one for TaxonConcepts)." >>>From this I interpret that TaxonName GUIDs are different with TaxonConcept GUIDs -- is that correct? If so, the problem is that a botanist would assign a new TaxonName GUID to a new combination, and a zoologist would assign a TaxonConcept GUID to the same entity, because "genus combination" is a property of a name in botany, and a properyy of a usage (~concept) in zoology. Yes, you could certainly force-treat zoological names as though they were botanical names (treating new combinations as "new names"), just as you could easily force-treat botanical names as though they were zoological names (assigning TaxonName GUIDs only to basionyms, and representing new combincations via Usage/TaxonConcept GUIDs). I just believe that we will come to regret it if we leave the distinction "fuzzy". My point has always been, and continues to be, that *IF* you have separate "kinds of GUID" for TaxonNames and TaxonConcepts, the line between the two should be unambigious (and ideally be consistent for both botany and zoology). After thinking about it some more, in the context of what has been written on this thread, I find myself coming back to that first "IF". Given that there seems to be a need and a desire to leave the definition of a "name unit" (to which a GUID is assigned) loose and flexible, then perhaps it would be premature to establish a GUID system for Name-Objects at all. Instead, I think we can both simplify *and* disambiguate taxonomic objects if there is only *ONE* GUID system -- which represents a Name-Usage instance. In the case of datasets consisting of only namestrings, with no specific implied concept objects, the names can be interpreted as "NameString SEC Nobody" (=Nominal TaxonConcept in TCS). Nomenclators could use whichever subset of these Name-usage GUIDs that they wish to refer to their own version of a name-object. For example, ZooBank can concern itself only with those GUIDs attached to original basionym usage instances, and IPNI can manage both basionyms usage instances and new-combination usage instances. ConceptBank could expand the scope of GUIDs to all those usage instances that represent defined concepts. Name indexers could use the broadest set of GUIDs (effectively all name-usage instances). So, in summary, my feeling is that if we are to think of "two kinds of GUID" for taxon objects, then we need an unambiguous (and cross-Code) distinction between the two. If such a distinction is too cumbersome to draw (as it seems to be, based on the current thread), then we should only go with one kind of GUID -- and by default it should be the one kind that is most flexible (=usage instance). Aloha, Rich P.S. > Is there a parallel with autonyms under ICBN? People use autonyms so > should they have a GUID? But they are automatically created and mean > different things in different circumstances. "Autonyms" is the term that botanists use; "Nominotypical Names" is the term zoologists use. I'm pretty sure they mean the same thing (or something very similar). They add a layer of complexity no matter whether you represent a name as a botanical-style unit, or a zoological-style unit.

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Summary of Nomenclature and GUIDs
by Roger Hyam 10 Nov '05

10 Nov '05

Hi Everyone, Can I hope to summarize the GUID debate with regard to TaxonNames and TaxonConcepts and suggest a way forward? (This borrows from Rod's post and various conversations with others) 1. We have two kinds of GUID (one for TaxonNames and one for TaxonConcepts). 2. Anyone can set up a system issuing either type of GUID. 3. Big central initiatives (nomenclators like IPNI & ZooBank) will issue TaxonName GUIDs but they will not have a monopoly on these enforced by the system. 4. 'sensible' taxonomists and institutions will generate TaxonConcept GUIDs for the concepts they want to broadcast. Each of these TaxonConcepts will refer to a TaxonName held in a major nomenclator (using it's GUID). They may also refer to other TaxonConcepts from other institutions and their own via GUIDs. 5. Indexers and users of the system can crawl the graph of TaxonConcept relationships (for query expansion etc) but they know that the vast majority of concepts should be linked to a GUID generated by the major nomenclators. The indexer does not have to string match to try and figure out how the TaxonConcepts are related (i.e. whether they are different delimitations of the same name). 6. Not so sensible taxonomists and institutions will not refer to a major nomenclator. Their TaxonConcepts will be difficult to relate to others globally. 7. If nomenclators do not do their job well they could, theoretically, be replaced by some one else setting one up. *The important thing to note here is it doesn't matter what a name is!* All the nomenclatural stuff is up to the nomenclator and not the GUID system. If, for example, ZooBank decided it wouldn't issue GUIDs for new combinations and it did not meet the needs of the community then the community would be free to set up another nomenclator or try and force ZooBank to change. Likewise IPNI and autonyms or whatever. But all these discussions about gender, spelling etc are separate from the GUID issues. Basically the taxonomist would go to the nomenclator and say "I want to describe something you haven't issued a GUID for." Either the nomenclator would issue the GUID or the taxonomist would have to start a revolution to get something changed. So debates about what the nomenclators issue GUIDs for can spin out to the relevant nomenclator lists (does ZooBank have one yet?). The second important thing to note is that no one is *forced *to do anything. If people don't like a nomenclator or system they can simply go their own way so there is no restriction on scientific freedom or anything. There is a great deal to flesh out on this but is it something we could agree on as a basic plan? If people don't object to this line of progression I could make up a page on the wiki that looks like we have agreed on it and we could spin out to discuss things like how we differentiate between name and concept GUIDs, central services for issuing GUIDs for those who may not want to run the resolution thing, what you get back in the meta data etc etc. All the best, Roger -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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GUIDs for Taxon Names and Taxon Concepts
by Roger Hyam 09 Nov '05

09 Nov '05

Hi, I have been rattling off messages in between meetings over the last couple of days responding to points on the list only to find later that they have been bouncing. I will try again and respond to Rich's point here and Yde's in another post - and hope one of them get onto the list! Rich - yes. I think you sum up the difference between new combinations in ICZN and ICBN well. But... just because the ICZN does not consider the usage of a name in a different genus as a nomenclatural act does not stop us creating a data object (TaxonName object) to represent what that name looks like in the new genus - perhaps with its new ending and possibly different author string (ICZN Recommendation 51G). Data structures can be used to represent things in life that have the same structure not that necessarily have the same meaning. So two types of names: 1. Really honest to God nomenclatural acts ( zoological basionyms). 2. New combinations we want to talk about (with references to basionyms). but both represented with the same data structure. Both could have GUIDs. Is there a parallel with autonyms under ICBN? People use autonyms so should they have a GUID? But they are automatically created and mean different things in different circumstances. Hope this is helpful. Roger -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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Re: AW: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Yde de Jong 09 Nov '05

09 Nov '05

Dear Roger, Firstly thanks to Richard for answering most of the question and sorry for my delayed reply. The principal difference in how new combinations are considered in zoology compared to botany is indeed also reflected in how zoologists deal with the authorship. A botanical taxonomic treatment like: Eupogodon spinellus (C.Agardh) Kützing Dasya spinella C.Agardh = Dasyopsis spinella (C.Agardh) Zanardini ...would -with respect to the authorship(!)- be rewritten by a zoologist like: Eupogodon spinellus (C.Agardh 1827) Dasya spinella C.Agardh 1827 = Dasyopsis spinella (C.Agardh 1827) So the parentheses shows that the species name not shows the original combination, that's all, the authorship of new combinations is not kept. I have to add that, in contrast to botany, the zoological community is very heterogeneous and split into many more or less isolated subgroups. Between all those zoological subgroups different interpretations of the ICZN and different nomenclatural practices exists. Most vertebrate groups for instance are bookkeeping combinations in a way more or less similar to botany. Some nematode taxonomists (especially those working on plant parasites) deal with the authorship in a botanical way, and so on. I should check whether the use of the genus-group name to handle objective synonymy is 'just' a practise (in most insects groups) to economize taxonomic work or governed by the code. I think it's a practise, however, please don't forget that zoologists are (also) absolutely free to extensively preserve used combinations if they prefer. If I am right some zoological database systems like those of Richard (Taxonomer) and Chris Lyall also keep the authorship of new combinations (like in botany). Kind regards, Yde >Hi Roger, > >I'm not sure what you're specifically asking, but there is definitely a >difference between ICBN and ICZN Codes in terms of what constitutes a >nomenclatural act. Under the ICBN code, combining a species epithet with a >different genus name (i.e., creating a new combination) is a Code-governed >act. Under ICZN, it is not. There are some ICZN rules that affect >subsequent combinations (e.g., gender agreement, secondary homonyms, etc.), >but the point is, ICZN-governed "names" are limited to what more or less >corresponds to botanical basionyms. > >These differences between the two Codes have led to the different >perspectives of: > >Botanical -- subsequent genus combination constitutes a new name, and thus >genus combination is an attribute of a name object. > >Zoological -- genus combination (other than original genus combination) >considered an attribute of *usage* of a name; therefore not creating a "new" >name object. > >The difference is also reflected in the different styles of attributing >authorship of names. > >As I said in a previous post, it all boils down to whether genus combination >is an attribute of a name object (botanical), or of a name-usage instance >(zoological). > >Maybe you're asking about something altogether different, in which case I >apologize for adding mud to the water.... > >Aloha, >Rich > > > >>Yde, >> >>Could you say which articles in the code (http://www.iczn.org/iczn/) >>support the usage examples you are giving here. >> >>My understanding of this is that it is a matter of presentation within >>publications and not a matter of different use of the nomenclatural >>codes. The authors are simply assuming that the specific epithets are >>well enough known (in combination with the author string) for them not >>to have to quote the genus part of the binomial. It seems to me to be >>merely a presentation convention like abbreviating the genus name to a >>single letter. >> >>If it is significantly different way of treating names (and therefore >>relevant to the GUID debate) why isn't in the code? Perhaps we should >>approach the ICZN 2000 editorial committee for their comments? But this >>would definitely be outside the scope of GUIDs and should perhaps be >>moved to a different list. >> >>Quoting article numbers nearly always clarifies these debates. >> >>Hope this helps, >> >>Roger

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Patricia Mergen 07 Nov '05

07 Nov '05

Sorry if I send comments to the various mails and if some points were further discussed later, but coming back from meetings I have some time now to go through the many postings of this last days. Pat Roderic Page <r.page(a)BIO.GLA.AC.UK> wrote: I'm a bit concerned that some may have conflated "Global" with "Centralised". GUIDs do not need to be centrally issued, indeed I'd argue that this is counter productive. To my mind the lesson from the web is decentralisation is the only way to cope with the issue of scale. Attempts at grandiose centralisation tend to fail. Hence, we should plan for GUIDs to be issued by more than one data source. After all, we are talking about GUIDs for digital objects, not ideas. I agree here with Rod that for the GUID decentralisation is a better solution, that a "grandiose centralisation option" will tend to fail in this case, not only for technical but also for "social" reasons. The idea that only the resolution system needs to be able to distinguish between specimens, taxon names, etc., seems unfortunate. With LSIDs the GUID has a namespace element, which can be readily used to distinguish between types of record (e.g., a PubMed record and a DNA sequence record from NCBI have different namespaces). Assigning GUIDs solely to basionyms strikes me as crazy -- I'd suggest most taxa aren't known by their basionyms. I'd advocate GUIDs for every name string (with the possible exception of orthographic variants, spelling mistakes, etc.). I don't really think this is about taxonomy, it's about information retrieval and stability of identifiers for digital objects. Here also I tend to agree, what we need is a technical GUID that enable to identify what is out there, the compliance with nomenclatural, taxonomical rules has to and is already dealt with elsewhere I believe ? Lastly, "imposing standards" is the wrong way to think about this. Standards win support if they work, and are adopted. I'd suggest this stuff will happen if people make compelling applications that others make use of, not because TDWG decides what should be done. So, my final question is, what is wrong with having each taxonomic database serve their own GUIDs for their own data (using an agreed format, such as RDF), and where possible GUIDs from different sources are mapped (e.g., a name string in IPNI to one in uBio). Users employ whatever GUID they find useful -- at least we then know what digital object they are referring to. If we think of the scientific literature, many paper have at least two GUIDs (DOI and PubMed), both of which are useful, and which serve different purposes. This may seem like a recipe for anarchy, but we can do this now (and, in effect we already have, my Taxonomic Search Engine serves LSIDs for the major taxonomic name databases). If we think the solution rests with a central authority (and ZooBank) then I think we are fooling ourselves. Regards Rod ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species at http://ispecies.org --------------------------------- Yahoo! FareChase - Search multiple travel sites in one click.

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Re: Topic 3: (Fauna Europaea and gender agreement) GUIDs for Taxon Names and Taxon Concepts
by Yde de Jong 07 Nov '05

07 Nov '05

Dear Donald, >Just catching up. There is one small practical >point I'd like to understand about Fauna >Europaea. You wrote the following: > >>How is Fauna Europaea organised? >>- Basically we have a list of 'naked' taxon >>names (from the infraspecific level to Kingdom) >>including full authorship for at least the >>generic and (infra)specific levels. All those >>taxon names (read: name elements) have unique >>id's. >>- All epithets are linked to their original >>genus, so original combinations can be >>reconstructed. This is nearly, but not >>completely similar to basionyms in botany >>because gender unequivalencies are not >>necessarily corrected. >>- Species names are created by recursively >>linking species-group names to genus-group >>names. Genus names are parents of specific >>epithets, and specific epithets are parents of >>infraspecific epithets. >>- Subjective synonyms are specific epithets >>recursively linked as childs to 'accepted' >>specific epithets. For objective synonymy genus >>names synonyms are recursively linked as childs >>to 'accepted' genus names. >>- Conclusion: Names (=naked name >>element/author/year plus original genus for >>epithets) are for eternity. Species names (so >>your taxon names) are temporary concepts (if >>they are not basionyms) which don't have >>identifiers and which are not kept in the >>database after taxonomic changes else then by >>version control. >>- However, an unique species name id can be >>easily artificially created by merging both >>generic and epithet id's (a trick we also use >>for Species2000). >- Taxon concepts are not explicitly covered. > >Can you explain a little more about how you >handle epithet agreement ("gender >unequivalencies") in this system? I realise >this is tangential from the main GUID >discussion, but it does seem to be a >complication to the task of treating the epithet >as the primary unit. We asked our experts to provide the original genera of all included epithets. We had a hard time in the beginning to convince especially the Coleoptera and Diptera experts for the need of this additional details, because it is not part of their standard practice to keep this kind of information. For synonyms there are hardly gender unequivalencies, because for the epithets mainly the original spellings are included which (by definition) follow the gender of the original genus. For accepted species names we don't keep the original spellings of epithets when the endings of epithets shift because of combinations with counter-gendered genus names. So we can have the situation: Bruchela pygmaea Gyllenhal 1833 [Original genus Urodon] (see: http://www.faunaeur.org/full_results.php?id=186668) Very likely the real original combination has been: Urodon pygmaus Gyllenhal 1833, but we don't keep 'pygmaus' as gender variant. For Fauna Europaea this is not a principal (taxonomic) issue, only a technical issue in how to implement fuzzy search facilities (e.g. by trunking all taxon name endings and replace them by wild cards) to lead users to the relevant currently accepted species name. However, personally I would prefer to include all original spellings of epithets in Fauna Europaea the near future. ------ An interesting additional story on the subject of gender endings: Years ago most Lepidopterist's gave up the effort of trying to harmonize the genders of genus names and adjectives. It was expected during the last years that at some moment the ICZN would accept this practise. Recently the European Society of Lepidopterist did accept this practice, however, the ICZN did not. Because the ICZN was our holy book in Fauna Europaea and the zoological code commission much represented within our committees the Lepidopterist's were forced strictly to follow the code and to adapt their data as such. Due to this fact now the absurd situation exists that the Fauna Europaea data are incongruent with Lepidoptera data in other resources with respect to adjectives endings. Therefore within the next version of Fauna Europaea we will (explicitly) include two variant gender spellings of Lepidoptera species. ------ Next week I will meet the ZooBank people in London and ask about their opinion on keeping orthographic variants for genus names (e.g. shifts from 'Dasia' to 'Dasya'), adjectives (gender endings) and author names ('Müller' and 'Mueller'). Kind regards, Yde

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Donald Hobern 07 Nov '05

07 Nov '05

Rich, I never meant my post to come across as a criticism of your level of detail (or anyone else's). I believe that all of the messages that have been sent contribute to an understanding of the problem space that a GUID solution must address. I just wanted to limit expectations as to what we could hope to solve within these discussions. Best wishes, Donald --------------------------------------------------------------- Donald Hobern (dhobern(a)gbif.org) Programme Officer for Data Access and Database Interoperability Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 --------------------------------------------------------------- -----Original Message----- From: Taxonomic Databases Working Group GUID Project [mailto:TDWG-GUID@LISTSERV.NHM.KU.EDU] On Behalf Of Richard Pyle Sent: 07 November 2005 10:37 To: TDWG-GUID(a)LISTSERV.NHM.KU.EDU Subject: Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts Thanks, Donald -- and my apologies for interpreting too much detail in your request. The question of whether concepts need their own GUIDs, vs. being represented by Name-GUID+Publication-GUID, as posed in your original Post on this "Topic 3", seemed to me a more specific question than the issue of what a "Name" object is or should be -- so I had calibrated my level of specificity in my response too precisely. I understand and agree that the focus should be broader at this stage, and I will re-calibrate the level of specificity of my comments accordingly. > For example, Yde's suggestions about > fundamentally different expectations among zoologists and > botanists need to be addressed in the TCS group. It was discussed among the TCS group -- at GREAT length. There seems no easy answer, other than "different solutions for different Codes", which seems to me to be the genesis of a terrible future legacy.... It all boils down to the distinction of which attributes apply to a Name object, vs. which apply to usage instances. The botanical approach stacks more attributes on the Name object, whereas the zoological approach tends to put them more on the usage instances. But as you suggest, this is something best saved for a Taxonomy GUID subgroup discussion. In any case, thanks for your clarification of the focus. Aloha, Rich Richard L. Pyle, PhD Database Coordinator for Natural Sciences Department of Natural Sciences, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Donald Hobern 07 Nov '05

07 Nov '05

Rod, Your straw man is just about exactly where I hope we will go with the TDWG standards as we fit GUIDs into the picture. Thanks, Donald --------------------------------------------------------------- Donald Hobern (dhobern(a)gbif.org) Programme Officer for Data Access and Database Interoperability Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 --------------------------------------------------------------- -----Original Message----- From: Taxonomic Databases Working Group GUID Project [mailto:TDWG-GUID@LISTSERV.NHM.KU.EDU] On Behalf Of Roderic Page Sent: 04 November 2005 10:40 To: TDWG-GUID(a)LISTSERV.NHM.KU.EDU Subject: Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts Perhaps to try and clarify my previous post (not a good idea to write before the coffee has kicked in), as a straw man what's wrong with the following approach: 1. Data providers serve up their own records, each identified by a GUID 2. At a minimum a "record" is metadata about that object, using existing vocabulary as much as possible. This means Dublin Core for basic stuff (title, creator, etc.), Prism for bibliographic details, Basic Geo (WGS84 for geographic co-ordinates, Darwin Core for other specimen stuff, etc. 3. Such records may refer to other objects (e.g., a sequence may refer to a publication and a museum voucher specimen), all by way of GUIDs. 4. Each record carries a Creative Commons license specifying what you can do with the data. The present system where museums have some text saying what can and can't be done is too clumsy, and putting the GBIF data usage agreement in the way of searching GBIF is way too cumbersome. If we do this (and we're pretty close to this already), then I think we've got the core of a useful resource. Partly because all of this is technically easy to do, and is already being done in other areas. So, why not just do it? ---- I think the role of GUIDs is to (a) unambiguously identify digital objects, and (b) tell us where to get that digital record. Many of the issues that crop up here are, in my opinion, not really about GUIDs. Regarding the issue of taxonomic concepts, I think this is something of a red herring. If concepts are essentially a pairing of name and use, then given a GUID for a name and a publication, there will be huge numbers of these, and they will occur in all sorts of domains (taxonomy, ecology, development, conservation, medicine, etc.). They will also exist in databases (e.g., GenBank, TreeBASE, etc.). But if they are pairings of names and usage (e.g., publication, database), then given a name GUID and a usage GUID, do we need anything else, really? Names, publications, and specimens are primary, concepts are secondary. It seems to me the core notion of a concept is knowing what somebody meant when using a name. This is (a) a problem of inference, and (b) probably intractable in most cases (who knows what ecologist "x" meant by species "y" in 1910, regardless of what classification he or she may have claimed to be using). One example where this inference is more straightforward, especially given 1-4 above, is if observations are linked to specimens. For example, in TreeBASE there are various occurrences of "Apomys datae" in different studies. Given that these names are linked to sequences, which are linked to specimens, we can infer that these different occurrences are the same thing. This kind of inference is made much easier when data is openly available. I also think that inference of concepts will be domain-specific, localised to particular questions, and not necessarily something taxonomic databases need to themselves support. Do we seriously think we can build a database of the usage of all names and what they meant? I suggest this knowledge will emerge over time on the foundations of 1-4 above. Since taxonomists don't control how names are used, and probably use names a lot less than other biologists (after all, we provide names so biologists can communicate), I don't think it is the role of taxonomists to document every concept. The KISS principle (Keep It Simple Stupid) would seem to apply here. Why not focus on something that is achievable, has value, and can be linked to what people in other areas are doing (such as bioinformatics, the Semantic Web, etc.). In other words, maybe it's time to stop thinking like taxonomists... ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species at http://ispecies.org ___________________________________________________________ To help you stay safe and secure online, we've developed the all new Yahoo! Security Centre. http://uk.security.yahoo.com

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts - Maybe ...
by Donald Hobern 07 Nov '05

07 Nov '05

Jessie, Many thanks for this valuable response. For reference, I agree with all of Jessie's judgments below. Donald --------------------------------------------------------------- Donald Hobern ( <mailto:dhobern@gbif.org> dhobern(a)gbif.org) Programme Officer for Data Access and Database Interoperability Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 --------------------------------------------------------------- _____ From: Taxonomic Databases Working Group GUID Project [mailto:TDWG-GUID@LISTSERV.NHM.KU.EDU] On Behalf Of Kennedy, Jessie Sent: 04 November 2005 14:18 To: TDWG-GUID(a)LISTSERV.NHM.KU.EDU Subject: Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts - Maybe ... Dear All Sorry for coming in so late into the discussion in this list - I have a bit of catching up to do..but have been reading the listings on this Topic with great interest and agreeing with much of what has been said by everyone but still seeing misunderstandings or disagreements between people on what we mean and what we should do which is inevitable given that people have different reasons for wanting GUIDs etc. To summarise my take on what's been said and if I misquote anyone please forgive me and feel free to correct me.. I agree with Donald (and Rich) about needing Taxon_Name_GUIDs and Taxon_Concept_GUIDs. I agree with Donald that a shorthand to referring to a Taxon_Concept is the combination of Taxon_Name and the Taxon_Publication. This is slightly but importantly different to Rich here in that the publication should be seen as a taxonomic publication (for another discussion elsewhere) rather than any publication - i.e. not simply usage of a name which could include an observation or identification - this interpretation opens up Taxonomic_Concepts too widely to cover potential taxa rather than those which have been defined, described and published in some scientific manner.) I agree with the principle that GUIDs do not have to be issued from a central repository BUT.. I do not agree that we should be issuing GUIDs for every taxonomic record - be that for Taxonomic_Name or Taxonomic_Concept. There needs to be some control - even if the control is self imposed. I agree with Sally that we should have Nomenclators provide GUIDs for Taxon_Names but would be more strict and say that these names should have only one GUID and that the GUID should always resolve to exactly the same name. So IPNI would be plant names, Index fugorum fungi names, zoobank when available animal names etc. and that we should share the resource of fixing this rather than duplicating effort (if I had any resource to give;-) ) IPNI and IF wouldn't overlap in names. I agree that anyone should be able to assign GUIDs but for their "own" Taxonomic_Concepts, (so for example a provider like say Mammal species of the world (or Bergey's manual for bacteria) which has well described concepts, could issue GUIDs for all of the concepts they recognise and other users of concepts could use their GUID in their database to record observations etc if they agreed with their concept. If they didn't agree with the MSW concept they could publish their own Taxonomic_Concept and GUID and relate it to some MSW Taxonomic_Concept GUID) BUT.. I would argue that we should try to avoid generating GUIDs multiple times for legacy concepts. For example, as mentioned by Rich the original descriptions of names are original concepts - we wouldn't want ITIS, GBIF, Species 2000, SEEK and whomever else creating different GUIDS of their own to represent this concept if possible or we would never move towards knowing we're talking about the same thing (- how this might be managed is probably for another discussion topic). I agree with Rod to the extent that moving forward with a distributed GUID publication system is easy where providers publish GUIDs for their own digital objects BUT.. I don't think it's helpful or in the spirit of GUIDs to take a digital object and republish it with another GUID without managing the replication of the GUIDs for the object - which could effectively be what happens if every data provider just issues GUIDs for the data they hold which is effectively the same as what someone else has already published. I think we do want to move towards reuse of GUIDs as much as possible and therefore sharing of work and easier and more accurate data integration. Also, what's the point of having millions of unique GUIDs if I don't know which one to put in "my" database to represent the Taxon_Name or Taxonomic_Concept I want to refer to? Rod would suggest this be self selecting (use your favourite provider, or the one you're told to - but I don't think it's that simple and doesn't get us towards a good solution - unless the one you're told to use does it properly!) I don't agree with Rod that we should do only purely nomenclatural mappings - as for most of the projects I'm involved with and people I've spoken to this will not solve their problems - we do need to know what the name means. However nomenclatural mapping is useful and a part of solving the overall problem. I agree with Rod that GUIDs will not solve all our problems but if managed and planned in a sensible way they will help us on our way to solving the problem. What providers of GUIDs need to decide is what they are providing a GUID for - in our area is it a Taxon_Name, a Taxonomic_Concpet, a Taxonomic_Observation, a Specimen, a Description (of a specimen or Taxonomic_Concept), a Taxonomic_Publication or whatever. Each of these things can probably refer to some to the other things and these should be using GUIDs. For example if you're an ecologist you might record survey data and issue- a GUID for a Taxonomic_Observation which contains a GUID to a Taxonomic_Concept which contains a GUID to a Taxonomic_Name which in turn will contain a GUID to a Specimen - the type specimen a GUID to a Taxonomic_Name maybe the basionym a Description which in turn will contain GUIDs to the Specimen(s) or Taxonomic_Concept described The ecologist may only want to know about their observation of the Taxonomic_Concept and not concern themselves with the embedded detail. So hopefully you'll see that we really want commonality in usage of GUIDs as much as possible so I think we need to think a bit about how we manage this - possibly another topic for discussion and certainly one that GBIF could lead. I agree with Rod the idea of a local GUID as being nonsensical - GUID meaning Globally Unique Identifier. The issue is about global uniqueness and resolvability which are separate things but related in this discussion. And as Rod says about whether we mean the same thing. Now as Rod says sorting out the name part is a huge step forward I think sorting out the Concept part is a bigger step forward - but won't EVER solve the issue of whether or not someone identified something properly or whether they're thinking the same as me but if we have Taxonomic_Concepts (with GUIDs) we're nearer to knowing what we mean. Isn't this what the semantic web people are saying - you can't assume that because the name is the same we're talking about the same thing... So I do believe we need Taxonomic_Concepts and Taxonomic_Names and all we're trying to do is sort out the terminology and semantics for what concepts of organisms exist or have existed in the world. Jessie Prof. J B Kennedy School of Computing Napier University 10 Colinton Road Edinburgh EH10 5DT Tel: +44 (0)131 455 2772 Fax: +44 (0)131 455 2727 Email: j.kennedy(a)napier.ac.uk WWW: http://www.soc.napier.ac.uk/jessie This message is intended for the addressee(s) only and should not be read, copied or disclosed to anyone else outwith the University without the permission of the sender. It is your responsibility to ensure that this message and any attachments are scanned for viruses or other defects. Napier University does not accept liability for any loss or damage which may result from this email or any attachment, or for errors or omissions arising after it was sent. Email is not a secure medium. Email entering the University's system is subject to routine monitoring and filtering by the University.

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Re: AW: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Roger Hyam 07 Nov '05

07 Nov '05

Yde, Could you say which articles in the code (http://www.iczn.org/iczn/) support the usage examples you are giving here. My understanding of this is that it is a matter of presentation within publications and not a matter of different use of the nomenclatural codes. The authors are simply assuming that the specific epithets are well enough known (in combination with the author string) for them not to have to quote the genus part of the binomial. It seems to me to be merely a presentation convention like abbreviating the genus name to a single letter. If it is significantly different way of treating names (and therefore relevant to the GUID debate) why isn't in the code? Perhaps we should approach the ICZN 2000 editorial committee for their comments? But this would definitely be outside the scope of GUIDs and should perhaps be moved to a different list. Quoting article numbers nearly always clarifies these debates. Hope this helps, Roger On Fri, 4 Nov 2005 15:31:19 +0100, Yde de Jong <yjong(a)SCIENCE.UVA.NL> wrote: >Dear Robert, > >What I mean is that most entomologists will >summarize a taxonomic treatment like: > >Eupogodon spinellus (C.Agardh 1827) > >† Dasya spinella C.Agardh 1827 >= Dasyopsis spinella (C.Agardh 1827) >= Dasya cervicornis J.Agardh 1841 >= Dasyopsis cervicornis (J.Agardh 1841) >= Eupogodon cervicornis (J.Agardh 1841) >= Gigartina flabellata Schousboe 1892 >= Larnacea flabellata (Schousboe 1892) >= Eupogodon flabellatus (Schousboe 1892) > >‰ Dasya acanthophora Montagne 1840 >‰ Rodonema spinella Naccari 1828 >‰ Eupogonium spinellum Kützing 1879 > >-------- > >....in either this way: > >Eupogodon Kützing 1845 >= Dasyopsis Zanardini 1843 > >Eupogodon spinellus (C.Agardh 1827) - originally in Dasya >= cervicornis J.Agardh 1841 - originally in Dasya >= flabellata Schousboe 1892 - originally in Gigartina > > >....or this way: > >Eupogodon Kützing >= Dasyopsis Zanardini > >Eupogodon spinellus (C.Agardh) >† Dasya spinella C.Agardh >= Dasya cervicornis J.Agardh 1841 >= Gigartina flabellata Schousboe 1892 > > >And when some generic names are frequently >associated with certain species-group names >within a genus also: > >Eupogodon Kützing >= Dasyopsis Zanardini >= Gigartina auct. >= Larnacea auct. > >Eupogodon spinellus (C.Agardh) >† Dasya spinella C.Agardh >= Dasya cervicornis J.Agardh 1841 >= Gigartina flabellata Schousboe 1892 > > >Kind regards, > >Yde > > > > > >>Dear Yde, >> >>>I have to check if the TCS can deal with >>>objective synonymy in a zoological sense. >>>Species2000 for instance can't not deal either >>>with objective synonymy nor with basionyms and >>>is therefore missing a crucial part of >>>information. >> >>Just asking: What exactly do you mean with 'objectice sysnonymy in >>zoological sense' ? >> >>regards, >>Robert Huber > -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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