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

Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts - Maybe ...
by Kennedy, Jessie 04 Nov '05

04 Nov '05

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: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Chuck Miller 04 Nov '05

04 Nov '05

Rod Page has made some excellent observations today that bear repeating: "we make a mistake if we equate GUIDs with solving all our problems" And "mapping different GUIDs can be tricky, but this is an entirely separate question. I think there's a huge confusion between GUIDs and some sort of global taxonomy -- they are not the same thing." I think it will be a difficult enough task for GBIF/TDWG to standardize and implement the simplest of GUID approaches. To do more risks getting the whole thing bogged down. Can we limit the first round of this work to the simpler, easier-to-do solution? But even then, as Richard pointed out in his very first post, there still exists ambiguity and debate on what constitutes the object to which the GUID applies. At the extreme simplest end of the spectrum, there are many occurrences of a "name string" that are different and unique but are meant to be the same - for instance "aus bus" and "aus bus" (with two spaces) are strictly different to a computer, but are clearly the same thing to a human. >>>From that simplistic variation, there are ever more complex variations on this theme all the way up to "global taxonomy" as Rod calls it. So, precisely deciding even the simplest of name "atoms" for which GUIDs will be standardized and implemented is a significant task. Chuck -----Original Message----- From: Roderic Page [mailto:r.page@BIO.GLA.AC.UK] Sent: Friday, November 04, 2005 4:22 AM To: TDWG-GUID(a)LISTSERV.NHM.KU.EDU Subject: Re: [TDWG-GUID] Topic 3: GUIDs for Taxon Names and Taxon Concepts > >> 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.). > > By "Namestring", do you include author, our just taxonomic > nomenclatural > elements? In either case, why even bother establishing a GUID for > taxonomic > names at all? Why not just use the namestring itself? Oh come on, you can't be serious ;-) Names aren't unique, GUIDs are. > > Moreover, I don't think anyone has suggest that GUIDs be assigned > "solely" > to basionyms. Er, I quote from your earlier post. > I completely agree -- but again, what gets a "Name" GUID? (as opposed to a > "usage" GUID or a "concept" GUID) Only basionyms? (I hope!) Or also > different combinations? (I hope not!) Or also spelling variants? (I *really* > hope not!!) > The point is, there shouldn't be six different "units" to > which GUIDs are assigned to represent "taxon names" [basionyms, > combinations, namestrings, namestrings with authors, concept > definitions, > name usage instances, etc.] > >> 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. > > O.K., my choice of the word "imposing" was bad. I should have said > something like "implementing". The one lesson that the web has taught > us > more vividly than decentralization is the power of standards for > information > exchange. We could have all invented our own version of DarwinCore for > exposing specimen records to the internet, and allowed natural > selection to > take its course such that only the most useful few versions survived > -- but > I don't think that would have been the most effective path to where we > are > now (and where we could be soon, once DarwinCore V2 is ratified and > mapped > against ABCD elements). Yes, standards are nice, but in practise there is usually more than one (like Darwin Core and ABCD), and the winner isn't always decided by committee. But this is a side issue... > >> 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. > > To me, GUIDs are only valuable and serve the information exchange > needs of > our community if they are, to some extent at least, reusable. I do not > understand the value of assigning GUIDs to the records in my taxonomic > database, if I am the only one who will ever use them. I understand the > practical value of establishing "local" GUIDs to my taxon name records > independently from other databases, if the long-term goal is to > eventually > map my GUIDs to the corresponding "equivalent" GUIDs of other > databases. For me the point is that if you have a GUID, I can map to you and add value to my projects. Without a GUID, it's a pain. > > Donald started out this discussion by suggesting that "Taxon Name" > objects > might be thought of as fundamentally different from "Taxon Concept" > objects > (in an analagous way to how publication objects are fundamentally > different > from specimen objects). If you agree with this, then it would be nice > if we > could find a standard line to draw between these two objects, so that > when > we later try to cross-walk our respective datasets, we're mapping > apples to > apples, and oranges to oranges (rather than apples to bananas and then > back > to oranges -- which aptly represents what I'm having to resort to in > mapping > my taxonomic data records to ITIS records). If it hurts don't do it! Put another way, why not make the mapping purely nomenclatural -- this name string also occurs in ITIS, and don't make any claims that whatever ITIS means by that name is what you mean. Alternatively, let users decide what mappings they want to make between you and ITIS. Expertise is rare and widely distributed. I think you're making things harder for yourself than the need to be. > >> 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. > > What is the value of expanding that to potentially hundreds, or > thousands of > GUIDs for each paper -- one GUID from each database that has a table of > literature records? Wouldn't our information exchange be much more > efficient if we all adopted (or at least mapped to) either the DOI or > the > PubMed GUID (or both)? If so, why doesn't this same logic apply to > taxon > names? I guess my point was that this is a case where more than one GUID exists for the "same" thing (a publication), and we manage to cope. Yes, "one GUID to rule them all" might be nice, but I just don't buy that it's going to happen any time soon. Just look at the discussion this topic has generated... Again, I think we make a mistake if we equate GUIDs with solving all our problems. Rather, I suggest they give us an infrastructure on which to build tools for mapping names/concepts/whatever. 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

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Yde de Jong 04 Nov '05

04 Nov '05

Dear Sally, >>>[Yde] For practical reasons I think the starting point for >>>assigning GUIDs should be basically nomenclatural. >> >>[Richard] I completely agree -- but again, what gets a "Name" GUID? >>(as opposed to a "usage" GUID or a "concept" GUID) Only basionyms? >>(I hope!) Or also different combinations? (I hope not!) Or also >>spelling variants? (I *really* hope not!!) There is also a problem >>of how to deal with autonyms (=nominotypical names in zoology). >>One GUID, or two? Logically, only one -- but most people don't do >>it that way. > >[Sally] I agree that name guids are probably a good place to start, >partly because they're one of the areas where the rules have been >fairly thoroughly thrashed out over the past 200 years ... I would >argue (after all the debate that went on in the TCS-LC mailing list) >that a new combination _should_ get a GUID, (after all, as has been >said >before, GUIDs are cheap...) because there is a good mechanism in the >LC part of the TCS to resolve from a new combination to the base >name. However if the zoologists don't like to treat new combinations >as names in their own right, I see no problem with them not doing it >... as long as whatever system we come up with will allow both >approaches side by side. Zoologists should establish a central nomenclator to keep their combinations. 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. >[Sally] Obviously the zoologists have always had the problem that they don't >have a comprehensive nomenclator but now that they're working on that >with registration - are there any other significant gaps that aren't >covered by a nomenclator of some sort that could be used to issue >ids? I don't agree. Obviously botanist don't have real nomenclators and probably will never be able to establish one on short term because of their problems with homonyms, pro parte synonymy, etcetera. I discussed this issue with Frank Bisby and his team in St Petersburg and they agreed that while zoologists can try to set up a central nomenclator (like ZooBank), botanist should look for other solutions. This could be one or more concept based lists like IOPI. Kind regards, Yde

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Two kinds of GUIDs?
by Yde de Jong 04 Nov '05

04 Nov '05

Dear all, Considering the last messages. In my understanding (sorry for repeating part of your input) we can distinguish two kinds of GUIDs: (1) Universal GUIDs like the ISBN numbers of publications and the GeneBank codes of sequences. (2) Local GUIDs, which are uniquely linked to objects in your (local) database, however, which metadata and metadata structure is standardised (in our case by GBIF). The Universal GUIDs we need for unambiguous cross-linking of databases, because we can't match databases efficiently otherwise (e.g. semantically). Indeed in the future everyone should add a column to its taxon table and cross-reference to a universal GUIDs system (=nomenclator) which keep the standard GUIDs for each name (let's leave 'what's in the name' for the moment). For me its clear that there is a difference between the use of a name within a concept and the name itself. Such a universal GUIDs system doesn't need to deal with the use of names and therefore not with concepts. Actually names within a nomenclator should never change, only the content should grow through time (like sequence data in GeneBank). Local GUIDs are important for GBIF to show the origin of data. This is essential not only for a proper acknowledgement, but also to identify possible duplications (e.g. Fauna Europaea data sets are being implemented in many other databases, GBIF needs to have a tool to detect such duplications). In addition those local GUIDs can be used, when cross-mapped with universal GUIDs, to provide concepts for the GBIF portal in a workable way. Meaning that a GBIF portal user can chose which species concept (e.g. that of the CoL) he/she would like to use for connecting the requested biodiversity data. Kind regards, Yde

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Richard Pyle 04 Nov '05

04 Nov '05

Hi Chuck, > I think it will be a difficult enough task for GBIF/TDWG > to standardize and implement the simplest of GUID approaches. > To do more risks getting the whole thing bogged down. Can > we limit the first round of this work to the simpler, easier-to-do solution? I can certainly agree to that (and to Ricardo's similar plea)! My original point, as you repeated in your post, was the issue of understanding what "object" gets a Name-GUID (distinguished from a Specimen-GUID or a Publication-GUID). The discussion about the degree to which GUIDs are shared vs. created anew was a tangent discussion that easily can (and should) be postponed to another time. > So, precisely deciding even the simplest of name "atoms" for > which GUIDs will be standardized and implemented is a significant task. Agreed (of course)...but do you mean that it is a "significant task" in the sense of overwhelming (e.g., that we should defer it for a later time)? Or do you mean "significant" as in "important" (e.g., that we should spend some time discussing it before getting too far ahead)? Aloha, Rich

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DNA barcoding analogy
by Vince Smith 04 Nov '05

04 Nov '05

Dear all, Perhaps a real world analogy might be useful. There are comparisons between this discussion and the DNA barcoding debate, particularly on the question of ascribing identity and separating notions of identity from concepts about that identity. In DNA barcoding a string of DNA bases can be generated from a biological specimen, much in the same way that a taxonomist might generate or apply a taxonomic name. The DNA barcode (like a taxonomic name) might not be unique, but quite separately we can apply concepts to these strings that add meaning (e.g. these DNA barcodes / taxonomic names do / do not refer to the same 'thing', what ever that 'thing' [e.g. a species] might be). The first step to doing this is to uniquely identify all the elements (DNA barcodes or taxonomic names) by applying GUID's to them. Keeping up with the DNA barcoding analogy, NCBI already do this with Genbank accession numbers that uniquely identify DNA sequences. Genbank will give any DNA sequence an identifier independently of any taxon concept ascribed to a particular sequence or even if a DNA sequence is a duplicate (although they try to avoid the latter). The number is just an identifier. Given that generating GUID's is easy, and can be done in a distributed manner (e.g. with LSID's) there is no reason why we can't do this for taxonomic names. As in DNA barcoding the hard part will be in ascribing concepts to taxonomic names (e.g. does this group of DNA barcodes / taxonomic names identify the same concept). Some of this can be automated by applying rules across the metadata (i.e DNA sequences or authority data for a taxon name) identified by GUID's. There will always be disputes about these rules, and to some extent there are real question over how much of this can be automated for taxonomic names (uBio seem to be making a lot of headway with this). For me the real debate is over these rules and the concepts behind them, not the (Globally Unique) identifiers. Regards, Vince Smith ____________________________________________________ Dr. Vincent S. Smith Illinois Natural History Survey 607 East Peabody Drive Champaign, IL 61820-6970 USA Tel: +1 (217) 265-0831 Fax: +1 (217) 333-4949 E-mail: vsmith(a)inhs.uiuc.edu Web: http://darwin.zoology.gla.ac.uk/~vsmith/ iChat Video Conferencing: vsmithuk(a)mac.com (invitation only) Skype: vsmithuk; or try SkypeIn (call whichever is nearer you) SkypeIn London: 020-755-88950; or Chicago: (312)-239-0950 ____________________________________________________

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Re: Two kinds of GUIDs?
by Roderic Page 04 Nov '05

04 Nov '05

In my view we do this: 1.If you create a database you have your own primary keys for whatever information is "yours" 2. If you expose your data to the outside world, you do so as GUIDs, e.g. <my database server>:<my data type>:<my id> (see, it's easy) 3. If you refer to any external data you store the GUID for that data. That way if you and I refer to a GenBank sequence in our databases, we both store the same GUID. GUIDs in the above format automatically show provenance (where they came from). The notion of a local GUID is nonsensical (by definition). The notion of "Universal" GUIDs confound inference (do you and I mean the same thing) with having a globally unique, actionable identifier. I guess I'm trying to say that I don't this is as hard as it's being made out to be. GUIDs enable you to explicitly identify objects, that's all. This is a huge step towards integrating databases, but doesn't solve the mapping issue. Yes, mapping different GUIDs can be tricky, but this is an entirely separate question. I think there's a huge confusion between GUIDs and some sort of global taxonomy -- they are not the same thing. So, if you want to refer to a taxon in your database what do you do, you use a GUID from your favourite taxonomic database. If GBIF set up a project to map GUIDs from different databases (good luck to them), you could use that. This is a separate question -- but by using GUIDs I know what you are referring to (as an object), and so do others. Regards Rod On 4 Nov 2005, at 10:55, Yde de Jong wrote: > Dear all, > > Considering the last messages. > > In my understanding (sorry for repeating part of your input) we can > distinguish two kinds of GUIDs: > > (1) Universal GUIDs like the ISBN numbers of publications and the > GeneBank codes of sequences. > > (2) Local GUIDs, which are uniquely linked to objects in your (local) > database, however, which metadata and metadata structure is > standardised (in our case by GBIF). > > The Universal GUIDs we need for unambiguous cross-linking of > databases, because we can't match databases efficiently otherwise > (e.g. semantically). Indeed in the future everyone should add a > column to its taxon table and cross-reference to a universal GUIDs > system (=nomenclator) which keep the standard GUIDs for each name > (let's leave 'what's in the name' for the moment). > > For me its clear that there is a difference between the use of a name > within a concept and the name itself. Such a universal GUIDs system > doesn't need to deal with the use of names and therefore not with > concepts. Actually names within a nomenclator should never change, > only the content should grow through time (like sequence data in > GeneBank). > > Local GUIDs are important for GBIF to show the origin of data. This > is essential not only for a proper acknowledgement, but also to > identify possible duplications (e.g. Fauna Europaea data sets are > being implemented in many other databases, GBIF needs to have a tool > to detect such duplications). > > In addition those local GUIDs can be used, when cross-mapped with > universal GUIDs, to provide concepts for the GBIF portal in a > workable way. Meaning that a GBIF portal user can chose which species > concept (e.g. that of the CoL) he/she would like to use for > connecting the requested biodiversity data. > > Kind regards, > > Yde > > ------------------------------------------------------------------------ ---------------------------------------- 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

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Yde de Jong 04 Nov '05

04 Nov '05

Dear Richard, >I have a couple of comments/questions: > >>The taxon concept is considered the use of a species concept in >>literature, so that equals your definition, however, the issue of >>taxon concepts is very much a botanic subject. > >I'm not sure I understand the difference between a "species concept" and a >"taxon concept", in your quote above. > >If I understand your prior remark: "but in general we understand as species >concept the species name plus the associated subjective synonyms" -- I think >this is the same as the "taxon concept", but taken to a resolution involving >only name-bearing type specimens. I do not see any difference between a >zoologist's "species concept" and a botanist's "taxon concept" -- they are >all taxon concepts. In all cases, a "concept" is a set of multiple >individual organisms, representing a subjective scope of biodiversity to >which a scientific name is applied. How that scope is communicated (e.g., >via synonym names as surrogates of their respective name-bearing types; or >by a broader spectrum of non-type specimen material; or by character >descriptions; or whatever) is necessarily variable, but they are just >different ways of defining the boundaries of a circumsctiption of organisms. >Same for botany and zoology. Also, the connection with literature is not so >much (in my mind) a definitive attribute of a taxon concept. Rather, it is >the easiest way to *refer* to an implied taxon concept. So the literature >is not part of the concept -- just part of a convenient way of representing >a concept in short-hand notation (and also representing a cross-reference to >documentation that will in most cases further describe the boundaries of the >concept). From a zoological perspective I fully agree with your comment that species concept and taxon concept are equivalent; in zoology there is indeed no difference how the scope of a concept is communicated (therefore I said that in zoology the taxon concept is more implicit and often merged to the species concept). From a botanical perspective I am not so sure if species concept and taxon concept can be understand as fully equivalent because from the work of Mark Geoffroy I remember that in botany every observation counts, meaning that even when the taxonomy (synonymy) in two publications is similar, but both publications include dissimilar observations both publication can be understood to cover different taxon concepts. >>- 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). > >By this, do you mean that combinations *other* than the original combination >are stored in Fauna Europaea? If so, then are they simply indicated as a >direct link between two naked names; or is the link qualified in some way >with a "source" (e.g., some publication or expert's assertion that the genus >name and species epithet are linked)? The 'other' combinations stored in Fauna Europaea aside the original combinations are the currently accepted species names. >>For practical reasons I think the starting point for assigning >>GUIDs should be basically nomenclatural. > >I completely agree -- but again, what gets a "Name" GUID? (as opposed to a >"usage" GUID or a "concept" GUID) Only basionyms? (I hope!) Or also >different combinations? (I hope not!) Or also spelling variants? (I *really* >hope not!!) There is also a problem of how to deal with autonyms >(=nominotypical names in zoology). One GUID, or two? Logically, only one -- >but most people don't do it that way. > >These are some of the most fundamental questions that need to be addressed >before any universal GUID system can be implemented. I think zoologists would like to focus on basionyms (and for them a basionym is already a concept proceeding from the name elements), botanist would like to focus on concepts (and for them basionym are already the really minimal name units). Kind regards, Yde

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Can we break down GUID problem into 2 hierarchical sub-problems?
by Ricardo Scachetti Pereira 04 Nov '05

04 Nov '05

Hello all, Based on the excellent exchange of ideas we had during the last few days, I have a suggestion to move forward. From what Roderic said, I think it makes total sense to break down the problem into more manageable pieces: 1) Assigning and resolving identifiers (that includes identifying objects of any type in any granularity); and 2) Mapping uniquely identified data objects into a rich semantic web (per and cross domain, i.e, specimens, names and concepts, observations, ecological experiments, etc, along the lines of Donald's ontology idea). In my opinion, once we solve the problem of uniquely and globally identifying objects (at any granularity), then we will have a nice framework to develop a rich semantic mapping infrastructure. The strategy of breaking the problem into 2 components nicely matches Donald's initial approach of breaking down the discussions into topic: Donald's topic 1 is equivalent to problem 1 stated above and topics 2 and 3 are equivalent to problem 2 above for two particular subdomains (specimens and taxonomic names and concepts). So the question is: do we all agree that those two problems can be solved hierachically (first solve #1 then use the solution to solve #2)? At least to make the problem more manageable? Cheers, Ricardo Roderic Page wrote: > ... > GUIDs enable you to explicitly identify objects, that's all. This is a > huge step towards integrating databases, but doesn't solve the mapping > issue. Yes, mapping different GUIDs can be tricky, but this is an > entirely separate question. I think there's a huge confusion between > GUIDs and some sort of global taxonomy -- they are not the same thing. > > So, if you want to refer to a taxon in your database what do you do, > you use a GUID from your favourite taxonomic database. If GBIF set up a > project to map GUIDs from different databases (good luck to them), you > could use that. This is a separate question -- but by using GUIDs I > know what you are referring to (as an object), and so do others. > > Regards > > Rod _______________________________________________________ Yahoo! Acesso Grátis: Internet rápida e grátis. Instale o discador agora! http://br.acesso.yahoo.com/

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Roderic Page 04 Nov '05

04 Nov '05

> >> 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.). > > By "Namestring", do you include author, our just taxonomic > nomenclatural > elements? In either case, why even bother establishing a GUID for > taxonomic > names at all? Why not just use the namestring itself? Oh come on, you can't be serious ;-) Names aren't unique, GUIDs are. > > Moreover, I don't think anyone has suggest that GUIDs be assigned > "solely" > to basionyms. Er, I quote from your earlier post. > I completely agree -- but again, what gets a "Name" GUID? (as opposed to a > "usage" GUID or a "concept" GUID) Only basionyms? (I hope!) Or also > different combinations? (I hope not!) Or also spelling variants? (I *really* > hope not!!) > The point is, there shouldn't be six different "units" to > which GUIDs are assigned to represent "taxon names" [basionyms, > combinations, namestrings, namestrings with authors, concept > definitions, > name usage instances, etc.] > >> 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. > > O.K., my choice of the word "imposing" was bad. I should have said > something like "implementing". The one lesson that the web has taught > us > more vividly than decentralization is the power of standards for > information > exchange. We could have all invented our own version of DarwinCore for > exposing specimen records to the internet, and allowed natural > selection to > take its course such that only the most useful few versions survived > -- but > I don't think that would have been the most effective path to where we > are > now (and where we could be soon, once DarwinCore V2 is ratified and > mapped > against ABCD elements). Yes, standards are nice, but in practise there is usually more than one (like Darwin Core and ABCD), and the winner isn't always decided by committee. But this is a side issue... > >> 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. > > To me, GUIDs are only valuable and serve the information exchange > needs of > our community if they are, to some extent at least, reusable. I do not > understand the value of assigning GUIDs to the records in my taxonomic > database, if I am the only one who will ever use them. I understand the > practical value of establishing "local" GUIDs to my taxon name records > independently from other databases, if the long-term goal is to > eventually > map my GUIDs to the corresponding "equivalent" GUIDs of other > databases. For me the point is that if you have a GUID, I can map to you and add value to my projects. Without a GUID, it's a pain. > > Donald started out this discussion by suggesting that "Taxon Name" > objects > might be thought of as fundamentally different from "Taxon Concept" > objects > (in an analagous way to how publication objects are fundamentally > different > from specimen objects). If you agree with this, then it would be nice > if we > could find a standard line to draw between these two objects, so that > when > we later try to cross-walk our respective datasets, we're mapping > apples to > apples, and oranges to oranges (rather than apples to bananas and then > back > to oranges -- which aptly represents what I'm having to resort to in > mapping > my taxonomic data records to ITIS records). If it hurts don't do it! Put another way, why not make the mapping purely nomenclatural -- this name string also occurs in ITIS, and don't make any claims that whatever ITIS means by that name is what you mean. Alternatively, let users decide what mappings they want to make between you and ITIS. Expertise is rare and widely distributed. I think you're making things harder for yourself than the need to be. > >> 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. > > What is the value of expanding that to potentially hundreds, or > thousands of > GUIDs for each paper -- one GUID from each database that has a table of > literature records? Wouldn't our information exchange be much more > efficient if we all adopted (or at least mapped to) either the DOI or > the > PubMed GUID (or both)? If so, why doesn't this same logic apply to > taxon > names? I guess my point was that this is a case where more than one GUID exists for the "same" thing (a publication), and we manage to cope. Yes, "one GUID to rule them all" might be nice, but I just don't buy that it's going to happen any time soon. Just look at the discussion this topic has generated... Again, I think we make a mistake if we equate GUIDs with solving all our problems. Rather, I suggest they give us an infrastructure on which to build tools for mapping names/concepts/whatever. 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

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