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

Re: Summary of Nomenclature and GUIDs
by Yde de Jong 11 Nov '05

11 Nov '05

Dear Sally, One of my Dutch colleagues (Freek Bakker) is member of the Scientific Advisory Board of CBOL. No problem to liaison about relevant outcomes of our name-GUIDs discussions. Kind regards, Yde >Hi all >in response to Yde (and Rod too on a side discussion) - I think >we're straying into discussion of CBOL itself & as I know they are >still in the policy drafting stage, maybe some of these comments >would be best directed straight to the people concerned > >http://www.barcodinglife.org/static/cbol/cbol.html >http://barcoding.si.edu/index_detail.htm > >Not sure which is the 'official' home page out of these two > >Sally

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Re: Summary of Nomenclature and GUIDs
by Yde de Jong 11 Nov '05

11 Nov '05

>>[Yde] A detail I would like to discuss within this context in the >>near future is the best possible way to link species names to >>genetic resources (e.g. DNA barcodes). > >[Sally] This is something that CBOL have been discussing. I think >that their current draft is that barcode sequences should be linked >to the best available name (ie a well defined concept if there's a >checklist, otherwise a name from a nomenclator, & only if there's >nothing available from a nomenclator should they go for just a name, >or even >an unpublished candidate name like sp A, sp. B ). >When CBOL were discussing the link to names earlier this year (in >May) things weren't so well advanced on the GUID front so their >approach may need to be reviewed if we do get a good system of GUIDs >in place for names or concepts. However I know that they are >including GBIF in the discussions so hopefully whatever they come up >with will be compatible with whatever we come up with ... Thanks Sally and Rod (for technical comments). Yes I agree that linking to the best available (checklist/index) concept or (nomenclator) name seems to be the proper way, however, here exactly my fear begins. I simply don't believe that because of the inherent instability of taxon concepts and because of the taxonomical under-education of most molecular workers this will provide a reliable model. I am afraid that when no very strict regulations on identification, voucher typification and naming of used lab-specimen will be established, we will not only end up with a similar bad situation as currently in GeneBank (30% of the sequenced taxa wrongly identified and no vouchers for control), but also an unworkable taxonomic framework because of disintegrating taxon concepts. Especially because the expected expansion of DNA barcodes will be much larger compared to current sequence data, which could enforce fuzzy working. Of course ideally DNA barcoding should proceed from type specimen (not found realistic in our museum) when possible and professional taxonomists should be closely involved. I know CBOL is working on guidelines for vouchering, and so on, but still... Sorry about my sceptics and have a nice weekend! Yde

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Re: Summary of Nomenclature and GUIDs
by Roger Hyam 11 Nov '05

11 Nov '05

Yde, This is not a problem. It doesn't really matter if some one tags data to a TaxonName rather than a TaxonConcept. It just shows that they are ignorant of which concept the specimen they are looking at belongs to or ignorant of concepts all together. But what is important is that it will be obvious what they have done and people can reason from their decision. Probably in a large number of cases it simply won't matter because there will only be one widely accepted concept anyway ... If people really hate TaxonConcepts they will deliberately ignore the whole thing and just link to TaxonNames (which will be bad) but at least it would be a start and it would be clear what they are doing. In the system I put forward earlier everyone can play and use it how they like and it should be possible to work out what is going on. The only things that will mess the system up is people not referring to TaxonNames at all or a whole bunch of nomenclators issuing GUIDs for TaxonNames in the same group and the community not then agreeing to use just one of nomenclators. IMO neither of these things is likely to occur to such an extent as to cause a problem. Hope this helps, All the best, Roger Yde de Jong wrote: >>> [Yde] A detail I would like to discuss within this context in the >>> near future is the best possible way to link species names to >>> genetic resources (e.g. DNA barcodes). >> >> [Sally] This is something that CBOL have been discussing. I think >> that their current draft is that barcode sequences should be linked >> to the best available name (ie a well defined concept if there's a >> checklist, otherwise a name from a nomenclator, & only if there's >> nothing available from a nomenclator should they go for just a name, >> or even >> an unpublished candidate name like sp A, sp. B ). >> When CBOL were discussing the link to names earlier this year (in >> May) things weren't so well advanced on the GUID front so their >> approach may need to be reviewed if we do get a good system of GUIDs >> in place for names or concepts. However I know that they are >> including GBIF in the discussions so hopefully whatever they come up >> with will be compatible with whatever we come up with ... > > Thanks Sally and Rod (for technical comments). Yes I agree that > linking to the best available (checklist/index) concept or > (nomenclator) name seems to be the proper way, however, here exactly > my fear begins. I simply don't believe that because of the inherent > instability of taxon concepts and because of the taxonomical > under-education of most molecular workers this will provide a > reliable model. I am afraid that when no very strict regulations on > identification, voucher typification and naming of used lab-specimen > will be established, we will not only end up with a similar bad > situation as currently in GeneBank (30% of the sequenced taxa wrongly > identified and no vouchers for control), but also an unworkable > taxonomic framework because of disintegrating taxon concepts. > Especially because the expected expansion of DNA barcodes will be > much larger compared to current sequence data, which could enforce > fuzzy working. > Of course ideally DNA barcoding should proceed from type specimen > (not found realistic in our museum) when possible and professional > taxonomists should be closely involved. I know CBOL is working on > guidelines for vouchering, and so on, but still... > > Sorry about my sceptics and have a nice weekend! > > Yde > -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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Re: Summary of Nomenclature and GUIDs
by Sally Hinchcliffe 11 Nov '05

11 Nov '05

Hi all in response to Yde (and Rod too on a side discussion) - I think we're straying into discussion of CBOL itself & as I know they are still in the policy drafting stage, maybe some of these comments would be best directed straight to the people concerned http://www.barcodinglife.org/static/cbol/cbol.html http://barcoding.si.edu/index_detail.htm Not sure which is the 'official' home page out of these two Sally > >>[Yde] A detail I would like to discuss within this context in the > >>near future is the best possible way to link species names to > >>genetic resources (e.g. DNA barcodes). > > > >[Sally] This is something that CBOL have been discussing. I think > >that their current draft is that barcode sequences should be linked > >to the best available name (ie a well defined concept if there's a > >checklist, otherwise a name from a nomenclator, & only if there's > >nothing available from a nomenclator should they go for just a name, > >or even > >an unpublished candidate name like sp A, sp. B ). > >When CBOL were discussing the link to names earlier this year (in > >May) things weren't so well advanced on the GUID front so their > >approach may need to be reviewed if we do get a good system of GUIDs > >in place for names or concepts. However I know that they are > >including GBIF in the discussions so hopefully whatever they come up > >with will be compatible with whatever we come up with ... > > Thanks Sally and Rod (for technical comments). Yes I agree that > linking to the best available (checklist/index) concept or > (nomenclator) name seems to be the proper way, however, here exactly > my fear begins. I simply don't believe that because of the inherent > instability of taxon concepts and because of the taxonomical > under-education of most molecular workers this will provide a > reliable model. I am afraid that when no very strict regulations on > identification, voucher typification and naming of used lab-specimen > will be established, we will not only end up with a similar bad > situation as currently in GeneBank (30% of the sequenced taxa wrongly > identified and no vouchers for control), but also an unworkable > taxonomic framework because of disintegrating taxon concepts. > Especially because the expected expansion of DNA barcodes will be > much larger compared to current sequence data, which could enforce > fuzzy working. > Of course ideally DNA barcoding should proceed from type specimen > (not found realistic in our museum) when possible and professional > taxonomists should be closely involved. I know CBOL is working on > guidelines for vouchering, and so on, but still... > > Sorry about my sceptics and have a nice weekend! > > Yde *** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk

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Re: GUIDs for Taxon Names and Taxon Concepts
by Roger Hyam 11 Nov '05

11 Nov '05

Hi Rich, I think you are wrong in your conclusions that we do not need GUIDs for TaxonNames and TaxonObjects but I need to do diagrams to illustrate the case so have created a wiki page here: http://wiki.gbif.org/guidwiki/wikka.php?wakka=SeparateNamesAndConcepts I also intersperse some comments below. Richard Pyle wrote: > 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". > > I am not suggesting we leave it fuzzy I am suggesting we leave it up to the nomenclators and that it isn't a GUID issue. I don't leave the maintenance of the brakes on my car fuzzy by not fixing them myself - I delegate it to a mechanic. Just because we are not solving the problem here does not mean that we are not going to get the problem solved. > 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. > Then don't refer to the TaxonName GUIDs issued by nomenclators when you issue your TaxonConcepts. Just ignore the nomenclator bit. If you are correct then everyone will follow your lead. A two GUID system will just degrade to a one GUID system if the names thing is wrong. > 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). > I think you are mixing issues here. The name string probably represents a TaxonConcept sec the dataset - depending on your intent. If you have had people scoring observations to a checklist for an area for a number of years then it would be convenient to treat the names as concepts so that you can reason about how they may be related to other better defined concepts. They are concepts sec your list. If they are just words you found in some books then they are just words till you intend to do something with them. A nomenclator should not be publishing data other than nomenclatural data (debatable what this is I know but no circumscription data anyway). ConceptBank sounds like any indexer (like GBIF) that crawls the people who are defining concepts of taxa and tries to provide sensible query expansion on the basis of the GUIDs or however else it links the objects together. > 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). > > See the wiki page for why I think this is an erroneous conclusion. Here is a definition of the two types of GUID: 1. A TaxonName GUID resolves to a data object that only contains information about nomenclature. The provider does not intend anyone to be able to identify a specimen to this GUID. 2. TaxonConcept GUIDs resolves to a data object that contains information about the delimitation/circumscription/relationships of a taxon. The provider intends people to be able to identify or otherwise related data to this GUID. I think the notion of the intension of the provider is very important as it answers many questions. "Should I attach a GUID to object X?" depends on what you want other people to do with it. I don't think this is very cumbersome definition? There is no 'natural' distinction between these two things. It is a pragmatic split so we produce a series of 'rooted' directed graphs of 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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Re: GUIDs for Taxon Names and Taxon Concepts
by Richard Pyle 11 Nov '05

11 Nov '05

Hi Roger, Many thanks! This is helpful. > I think you are wrong in your conclusions that we do not need > GUIDs for TaxonNames and TaxonObjects You are mistaken if you believe that I don't think we need GUIDs for TaxonName objects. I *do* think we need them. I just believe that we will do more harm than good if we encourage a proliferation of separate Name-GUIDs and Concept-GUIDs, when there is not a clear distinction between them. If we recognize two distinct "kinds" of GUIDs, with the realization that the same informational object (e.g., a new combination) would be represented by one data provider as one "kind" of GUID, and by another data provider as the other "kind" of GUID, then I think we are setting ourselves up for some really thorny data management issues down the road. > I need to do diagrams > to illustrate the case so have created a wiki page here: > > http://wiki.gbif.org/guidwiki/wikka.php?wakka=SeparateNamesAndConcepts This is excellent and I will expand upon it in the Wiki to reflect the point I am trying to make as soon as I have time. > > 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". > > I am not suggesting we leave it fuzzy I am suggesting we leave it up to > the nomenclators and that it isn't a GUID issue. It is a GUID issue if there are two different "kinds" of GUID established, without a clear distinction between them. And I think the current distinction between whether a data provider sould establish a TaxonConcept GUID or a TaxonName GUID for a given data record is "fuzzy". > Just because we are not solving the problem here does not mean that > we are not going to get the problem solved. Yes, but we may be creating a new problem, or exacerbating an existing problem, by introducing different kinds of GUIDs without a clear understanding of which types of GUIDs apply to which kinds of data objects. > Then don't refer to the TaxonName GUIDs issued by nomenclators when you > issue your TaxonConcepts. Just ignore the nomenclator bit. If you are > correct then everyone will follow your lead. A two GUID system will just > degrade to a one GUID system if the names thing is wrong. It's not about "right" or "wrong" -- it's about optimizing the efficiency and effectiveness of information exchange. Encouraging the creation of ill-defined GUIDs carries with it a risk of impeding information exchange, because of ambiguities about mapping records in one dataset to records in another dataset. > Here is a definition of the two types of GUID: > > A TaxonName GUID resolves to a data object that only contains > information about nomenclature. The provider does not intend > anyone to be able to identify a specimen to this GUID. > > TaxonConcept GUIDs resolves to a data object that contains information > about the delimitation/circumscription/relationships of a taxon. > The provider intends people to be able to identify or otherwise > related data to this GUID. As a vocal and long-standing commentator on the difference between a taxonomic "name" and a taxonomic "concept", I feel I have a strong grasp of this distinction. What concerns me on this GUID discussion is that I believe that ill-defined GUID "domains" ("kinds") have the potential of doing more harm than good. We don't all agree on what a "name" is. We don't all agree on what a "concept" is. But we probably can agree on what a usage instance is. This is why I now advocate focusing on this broadest, most flexible, and unambiguous of taxonomic entities to start with in applying TDWG-standard GUIDs to, because ALL datasets can conform to it (especially if the "SEC" part of the usage instance can be set to "Nobody in particular"). I'll try to articulare this more effectively on the Wiki page you started. Aloha, Rich

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Re: GUIDs for Taxon Names and Taxon Concepts
by Vince Smith 11 Nov '05

11 Nov '05

Dear Roger, Many thanks for developing the taxon concept wiki. You might want to take a look at Nadia Anwa's work at the Univ. of Glasgow. She has developed a taxon name warehouse that attempts to automate the mapping of related taxonomic names to build potential taxon concepts (http://spira.zoology.gla.ac.uk/ - be patient with the server, it is a little slow). Each search generates a map showing these relationships. In this scenario GUID's would be associated with the component names and the map (or rather the potential taxon concept derived from the map). Nadia's approach is perhaps less refined than what some people envisage but is a first step toward automation. Regards, Vince ____________________________________________________ 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 ____________________________________________________ On 11 Nov 2005, at 07:26, Roger Hyam wrote: > Hi Rich, > > I think you are wrong in your conclusions that we do not need GUIDs > for TaxonNames and TaxonObjects but I need to do diagrams to > illustrate the case so have created a wiki page here: > > http://wiki.gbif.org/guidwiki/wikka.php?wakka=SeparateNamesAndConcepts > > I also intersperse some comments below. > > Richard Pyle wrote: >> 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". >> >> > I am not suggesting we leave it fuzzy I am suggesting we leave it > up to the nomenclators and that it isn't a GUID issue. I don't > leave the maintenance of the brakes on my car fuzzy by not fixing > them myself - I delegate it to a mechanic. Just because we are not > solving the problem here does not mean that we are not going to get > the problem solved. >> 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. >> > Then don't refer to the TaxonName GUIDs issued by nomenclators when > you issue your TaxonConcepts. Just ignore the nomenclator bit. If > you are correct then everyone will follow your lead. A two GUID > system will just degrade to a one GUID system if the names thing is > wrong. >> 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). >> > I think you are mixing issues here. The name string probably > represents a TaxonConcept sec the dataset - depending on your > intent. If you have had people scoring observations to a checklist > for an area for a number of years then it would be convenient to > treat the names as concepts so that you can reason about how they > may be related to other better defined concepts. They are concepts > sec your list. If they are just words you found in some books then > they are just words till you intend to do something with them. > > A nomenclator should not be publishing data other than > nomenclatural data (debatable what this is I know but no > circumscription data anyway). > > ConceptBank sounds like any indexer (like GBIF) that crawls the > people who are defining concepts of taxa and tries to provide > sensible query expansion on the basis of the GUIDs or however else > it links the objects together. > >> 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). >> >> > See the wiki page for why I think this is an erroneous conclusion. > > Here is a definition of the two types of GUID: > A TaxonName GUID resolves to a data object that only contains > information about nomenclature. The provider does not intend anyone > to be able to identify a specimen to this GUID. > TaxonConcept GUIDs resolves to a data object that contains > information about the delimitation/circumscription/relationships of > a taxon. The provider intends people to be able to identify or > otherwise related data to this GUID. > I think the notion of the intension of the provider is very > important as it answers many questions. "Should I attach a GUID to > object X?" depends on what you want other people to do with it. I > don't think this is very cumbersome definition? There is no > 'natural' distinction between these two things. It is a pragmatic > split so we produce a series of 'rooted' directed graphs of > > 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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Re: Summary of Nomenclature and GUIDs
by Sally Hinchcliffe 11 Nov '05

11 Nov '05

Yde wrote (among other things) > A detail I would like to discuss within this context in the near > future is the best possible way to link species names to genetic > resources (e.g. DNA barcodes). > This is something that CBOL have been discussing. I think that their current draft is that barcode sequences should be linked to the best available name (ie a well defined concept if there's a checklist, otherwise a name from a nomenclator, & only if there's nothing available from a nomenclator should they go for just a name, or even an unpublished candidate name like sp A, sp. B ) When CBOL were discussing the link to names earlier this year (in May) things weren't so well advanced on the GUID front so their approach may need to be reviewed if we do get a good system of GUIDs in place for names or concepts. However I know that they are including GBIF in the discussions so hopefully whatever they come up with will be compatible with whatever we come up with ... Sally *** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk

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Re: Summary of Nomenclature and GUIDs
by Roderic Page 11 Nov '05

11 Nov '05

> > A detail I would like to discuss within this context in the near > future is the best possible way to link species names to genetic > resources (e.g. DNA barcodes). > Well, the simplest way is if the genetic resources themselves have GUIDs (such as an LSID, Biopathways.org provides some for NCBI, and I'm playing with this as well). Then one simply adds one or more tags to the metadata associated with the resource. For example, using RDF a DNA sequence could have a tag such as <dc:source rdf:resource="urn:lsid:ncbi.nlm.nih.gov:TaxId:345788" /> indicating it comes from the taxonomy with NCBI's TaxId 345788. For the taxon one could use a tag like <dcterms:isReferencedBy rdf:resource="urn:lsid:ncbi.nlm.nih.gov:genbank:AF234577" /> indicating that sequence AF234577 comes from this taxon [both LSIDs are made up, I could create functional ones if it woulod help the discussion]. The "dc" and "dcterms" are from the Dublin Core namespace (http://dublincore.org). This illustrates a point I've made elsewhere, but one of my biggest gripes about current XML efforts in taxonomy is the use of XML schema and custom namespaces for everything, whereas I think RDF is much leaner and we can employ existing namespaces for most (but not all) of what we need. Plus we can embed our efforts in a much larger community of projects. Again, I recommend keeping things simple and using existing standards wherever possible. 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: Summary of Nomenclature and GUIDs
by Yde de Jong 10 Nov '05

10 Nov '05

Dear Roger, Thanks for your nice summary. >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. Nevertheless we should try to guide ZooBank, IPNI, and other nomenclator initiatives in the best possible way to support the GBIF objectives. Especially ZooBank is starting from scratch, which seems to be an ideal situation to develop a congruent system. >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. I think nomenclators could play an important stabilizing role particularly on the standardization and caching of variant spellings (orthographs, diacritics within author names, gender endings). I mean that if a nomenclator can keep all relevant spelling variants for a certain TaxonName (linked to one GUID), this will much facilitate and accurate the search functions of the GBIF portal. Indeed -analogous to GeneBank- nomenclators should have a routine to issue a GUID after the submission of a taxon name or taxon concept when certain criteria have been approved. In this respect, like for instance 'MorphoBanks', I expect nomenclators will play an important role in future 'cybertaxonomy' advances (on-line publishing, etc.). >So debates about what the nomenclators issue GUIDs for can spin out >to the relevant nomenclator lists (does ZooBank have one yet?). Please look at the ZooBank article in <http://www.nature.com/nature/journal/v437/n7058/full/437477a.html>Nature and at <http://www.iczn.org/new%20ZooBank.htm>ICZN. If I am right, as a start ZooBank would like to upload data from BIOSIS, ITIS, Species2000, ECAT, Fauna Europaea, etc. >There is a great deal to flesh out on this but is it something we >could agree on as a basic plan? A detail I would like to discuss within this context in the near future is the best possible way to link species names to genetic resources (e.g. DNA barcodes). Kind regards, Yde

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