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

Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Yde de Jong 03 Nov '05

03 Nov '05

Dear Donald, Thanks for your e-mail. I agree with Richards reply, the used definition of taxon names and taxon concepts are a bit confusing and not directly matching the zoological point of view. For a zoologist a taxon name is the naked name plus the authorship (author and year). At the species level this includes the epithet and authorship and often a link to the original genus. In the TCS I thought a naked taxon name is called a name-element. For botanists this part of nomenclature is rather implicit and the zoologist's (pre-)occupation on these details quite obscure. When a species-group name (so the epithet/author/year) is linked to a genus-group name we obtain a scientific species name (so the actual binominal), often also called the species concept, but in general we understand as species concept the species name plus the associated subjective synonyms (although the semantics on this point are a bit fuzzy). I think your 'taxon name' is equivalent with the scientific species name. 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. This is caused by the fact that plants are sessile and have to adapt to local circumstances (animals run away from unfavorable environments). Due to local adaptation (phenotypic plasticity) each plant specimen can be considered as a crucial observation to verify a species concept. Another reason is that in contrast to plants asexuality is an exception in most non-sessile animal groups which provides a more randomly cross-breeding population and more morphological homogeneity. For zoologist the issue of taxon concept is more implicit and often merged to the issue of species concept, but of course this much depends on the taxonomic group. The reason why zoologists are more focused on epithets compared to botanist is twofold: (1) Zoologists (particularly entomologists) are not bookkeepers of nomenclatural history in a way botanist are. Especially objective synonymy is (i) not fully catalogued and (ii) solved at the generic level (as synonyms of genus names) if relevant. The historical reason to this practise is highly pragmatic: The -compared to botany- few entomologists have to deal with so many species names, so many parallel descriptive efforts in the past, and commonly incomplete taxonomic treatments that a nomenclatural bookkeeping sensu botany is out of question. Within Fauna Europaea we experienced that many entomologists even don't feel the slightest need to (as they call it) "maintain the trash of history". (2) In zoology we have less homonomy compared to botany, especially when the authorship is taken into account. This could be partly due to the compared to botany extended authorship (also including year) and partly to other constraints (e.g. the fact that the zoological society is more divided and therefore more original in its naming). As a consequence zoologists are less drowning in a sea of homonyms and therefore there is less need to refer to identification anchors like for instance original publications. Thus I think taxon names in zoology are far more suitable for GUIDs compared to botany. ------------------------------ 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. ------------------------------ About TCS, GUIDs and nomenclators. During the TDWG meeting at Christchurch I was happy the TCS did allow the flexibility of building up species and taxon concepts from scratch (so from the name elements). In St Petersburg I discovered that the adapted TCS had been botanized and the starting point moved to the binominal. Due to that zoologists evidently lose some nomenclatural playground and a possibility of 1:1 matching of their names to the schema. However, that's not a major problem because for most mappings zoological databases need to set up views anyway. The root for taxonomic modelling now is the original combination (= basionym) which is persistent, hence OK. My only remaining concern is the implementation of objective synonymy which is fundamentally different in entomology. For practical reasons I think the starting point for assigning GUIDs should be basically nomenclatural. This mean that we should establish nomenclators and leave taxonomy out for the moment. With such nomenclators (plus GUIDs) we have the right tool to backlog scientific names in any database for unambiguous cross-linking. Taxonomy can be kept by the databases themselves and initiatives like the Catalogue of Life. Aside we should distinguish basionyms for unequivocal linking to type specimens and genetic resources. Kind regards, Yde de Jong Zoological Museum Amsterdam >[ Another topic for comments. Please keep the Topic number in responses. ] > >Topic 3: GUIDs for Taxon Names and Taxon Concepts > >Another key area in which TDWG has recognised the need for globally >unique identifiers is in connection with taxon names and the various >concepts associated with them. This issue actually also intersects >with that of identifiers for taxonomic publications. > >Definitions > >In the following discussion, a "taxon name" is a scientific name >string which simply identifies a name assigned in the taxonomic >literature. In many cases such a name may have been applied in >different ways by the original author and subsequent taxonomists. >Each such application of a taxon name by a taxonomist to a set of >organisms is here referred to as a "taxon concept". An >understanding of the taxon concept adopted by a researcher is >frequently essential if data are to be interpreted correctly. In >its most basic form a "taxon concept" can be considered to be the >use of a given "taxon name" in a given "taxonomic publication", in >other words something that could be represented as, "Agenus aspecies >Author1 Year1 sec. Author2 Year2". One possible approach to >assigning identifiers to taxon concepts would therefore be to assign >identifiers to taxon names and to taxonomic publications and to use >a combination these identifiers to identify each taxon concept. > >Note that a taxon concept may be defined at least in part by a set >of assertions about the relationship between the present concept and >the concepts adopted by earlier taxonomists. In addition it is >possible for other researchers to make their own assertions about >the relationships between the concepts published by different >taxonomists. Much of the interest and value to be gained from >modeling taxonomy relates to the interpretation of these asserted >relationships. > >Although the distinction between taxon names and taxon concepts may >seem (over-)subtle, it is important that we should know whether we >are referring simply to a nomenclaturally valid name, quite >independently of any set of organisms to which it may be applied, or >to a taxon concept which somehow applies such a name to such a set >of organisms. Without this distinction, we will be restricted in >our ability to develop biodiversity informatics, although of course >there will be many cases in which all we can say is that a data set >refers to some unspecified taxon concept associated with a given >taxon name. > >Identifiers > >Clearly there are many situations in which a taxon name can itself >be treated as a unique identifier without any apparent ambiguity >about which name is being referenced (e.g. Turdus merula; Poa >annua), but the existence of homonyms prevents this from being >generally true. Even when taxon names include citations of the >original publications (e.g. Turdus merula Linnaeus, 1758; Poa annua >L.), they can be very difficult to compare since the form of the >citations may vary greatly. Even where there is no ambiguity about >which name is being referenced, such a name does not by itself serve >to identify which associated concept is being referenced. > >There are many different systems in place for associating other >identifiers with either taxon names or taxon concepts. ITIS >(<http://www.itis.usda.gov/>http://www.itis.usda.gov/, ><http://www.cbif.gc.ca/pls/itisca>http://www.cbif.gc.ca/pls/itisca, ><http://siit.conabio.gob.mx/>http://siit.conabio.gob.mx/) assigns >Taxonomic Serial Numbers (TSNs) to each name in its system. Other >species databases have their own identifiers for taxon concepts. >Recording schemes often have their own identifiers for taxa (e.g. >Bradley and Fletcher numbers for Lepidoptera in the UK, various >systems of four-letter codes for North American bird species). >These are often used to provide some stability and clarity in the >taxonomy used by a given project. > >Questions > >I would like therefore to ask the following questions of any of you >who use scientific names in your databases (either taxonomic >databases recording a list of taxa, or databases recording >information about taxa, specimens, observations, etc.): > > >1. Is your data organised using taxon names or to taxon concepts? >2. Do you assign any reusable identifiers to taxon names or >concepts (i.e. identifiers used in more than one database)? >3. If so, what is the process in assigning new identifiers for >additional taxa and for accommodating taxonomic change? >4. Where are these identifiers used (other organizations, >databases, data exchange, recording forms, etc.)? >5. Do you use identifiers from any external classification >within your database? >6. Would there be any social or technical roadblocks to >replacing these identifiers with a single identifier that was >guaranteed to be unique? > > >As before I am looking for information on existing practices and any >requirements that would need to be accommodated within any general >system of identifiers. > >Thanks, > >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 >--------------------------------------------------------------- >

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Richard Pyle 03 Nov '05

03 Nov '05

Hi Kevin, > I am trying to understand how you imagine a name guid > system will work. When you say "what gets a name guid?", > what data/database do you think will get the guid - a > central name repository? Are you thinking that all > records in various databases around the world that are > referring to the "same" name will have the same "Name Guid"? > For resolvable GUIDs this will mean the name will always > resolve to the central repository data. I think that would be WONDERFUL -- and might even be feasible for zoological names once ZooBank is up and running. But that's tangential to my main point -- which is that TDWG Standards should establish a clear definition for what a "Name" is. At the very basic level, we need to be able to understand the difference between, say, a Specimen GUID vs. a Publication GUID vs. a Taxon Name GUID. Granted, the resolution service should take care of this distinction (a GUID is, after all, a *G*UID), in which case we would't really need to distinguish between these domains. We really need only one GUID system for all object domains (specimens, publications, names, concepts, etc.). But Donald's question of 29 October and the TDWG GUID Wiki, imply that there are different issues to consider for different GUID domains (e.g., "GUIDsForCollectionsAndSpecimens" vs. "GUIDsForTaxonNamesAndTaxonConcepts"). So, *IF* we are partitioning GUID domains (rather than letting the resolution service determine the difference between a specimen and, say, a publication), and *IF* we are thinking about "GUIDsForTaxonNamesAndTaxonConcepts", then I believe it is critical to come up with clear definitions for what the scope of a "Name" is. If TDWG does not impose some standards of this sort, then cross-walking different datasets will be every bit as much a nightmare as it currently is. I would see that as a most unfortunate outcome for the broader goal of global biological data exchange. Maybe I misunderstood your question? Aloha, Rich

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Re: [tdwg-tapir] Tapir > Capabilities > Schemas > Concepts
by "Döring, Markus" 03 Nov '05

03 Nov '05

Roger, you are right in your core thoughts. If we do not allow dynamic views we dont need to expose the mapped conceptual schema "concepts". But thats only the case if we treat the static views as the source of our concepts. So yuo would have to use only those static view concepts (may I call them "local" concepts as defined in the local/inline view) in your request for filters. You couldnt request a darwincore record and specify a filter from abcd for example. One more thing about the concepts: their id or "path" attribute looks like an xpath, but it is not! It is treated as a unique string and nothing more. So there is no implied parent/child relationship between any concepts - they are just a list of independent ids. If a concept is searchable (default=true), then you can use it in a filter. If its not searchable, you can still use it in the response structure! Theres another attribute called mandatory which a provider can set to indicate that this concept is required to be rpesent in a response structure. Useful to force people to include some IPR for example. Markus -----Ursprüngliche Nachricht----- Von: tdwg-tapir-bounces(a)lists.tdwg.org [mailto:tdwg-tapir-bounces@lists.tdwg.org] Im Auftrag von Roger Hyam Gesendet: Donnerstag, 3. November 2005 14:17 An: tdwg-tapir(a)lists.tdwg.org Betreff: [tdwg-tapir] Tapir > Capabilities > Schemas > Concepts I am a little confused as to what is included in the capabilities response under capabilities/schemas/schema. The annotation says: "Each known and mapped concept of a schema listed with a boolean flag indicating if its searchable (default = true)." I have a genus field in my database and I map it to the following concept: <concept path="/DataSet/TaxonNames/TaxonName/CanonicalName/Genus" searchable="true" /> Should I also include the parent concepts: <concept path="/DataSet/TaxonNames/TaxonName/CanonicalName" searchable="false" /> <concept path="/DataSet/TaxonNames/TaxonName" searchable="false" /> <concept path="/DataSet/TaxonNames" searchable="false" /> <concept path="/DataSet" searchable="false" /> or are they implied? I presume if they are included then they aren't searchable as they can't be used to build filters. Does this: <concept path="/DataSet/TaxonNames/TaxonName/CanonicalName/Genus" searchable="true" /> mean: * This concept has been mapped to data and can be used in arbitrary response structures and filters in combination with concepts from any of the other conceptual schemas listed in here. If so is the entire schemas section of capabilities response optional if arbitrary views are not supported? Both the schemas and concepts are given in views anyhow - so do we need to list them here? Your thoughts most appreciated - I may just have the wrong end of the stick. Roger -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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[tdwg-tapir] Tapir > Capabilities > Schemas > Concepts
by Roger Hyam 03 Nov '05

03 Nov '05

I am a little confused as to what is included in the capabilities response under capabilities/schemas/schema. The annotation says: "Each known and mapped concept of a schema listed with a boolean flag indicating if its searchable (default = true)." I have a genus field in my database and I map it to the following concept: <concept path="/DataSet/TaxonNames/TaxonName/CanonicalName/Genus" searchable="true" /> Should I also include the parent concepts: <concept path="/DataSet/TaxonNames/TaxonName/CanonicalName" searchable="false" /> <concept path="/DataSet/TaxonNames/TaxonName" searchable="false" /> <concept path="/DataSet/TaxonNames" searchable="false" /> <concept path="/DataSet" searchable="false" /> or are they implied? I presume if they are included then they aren't searchable as they can't be used to build filters. Does this: <concept path="/DataSet/TaxonNames/TaxonName/CanonicalName/Genus" searchable="true" /> mean: * This concept has been mapped to data and can be used in arbitrary response structures and filters in combination with concepts from any of the other conceptual schemas listed in here. If so is the entire schemas section of capabilities response optional if arbitrary views are not supported? Both the schemas and concepts are given in views anyhow - so do we need to list them here? Your thoughts most appreciated - I may just have the wrong end of the stick. 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: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Richard Pyle 03 Nov '05

03 Nov '05

Hi Yde, Great post! 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). > - 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)? > 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. > Aside we should distinguish basionyms for unequivocal linking > to type specimens and genetic resources. I completely agree! Aloha, Rich Richard L. Pyle, PhD Database Coordinator for Natural Sciences and Associate Zoologist in Ichthyology 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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I3C folds
by Roderic Page 02 Nov '05

02 Nov '05

A colleague spotted this news item in Bio-IT World (http://www.bio-itworld.com/newsitems/2005/oct2005/10-27-05-news-i3c? page=1) about I3C (the Interoperable Informatics Infrastructure Consortium) folding. I3C were instrumental in getting LSIDs of the ground. This might seem to bode poorly for LSIDs, but I think it's clear that the future of LSIDs is distinct from that of I3C -- the source code is available, and LSIDs are being used. For me the interesting point made by the article is that the goals of I3C overlap with the Semantic Web community, and hence the pressing need for I3C began to fade. My sense is that much of what we want to achieve can be done on the back of work being done by the Semantic Web community -- indeed my own work on taxonomic and phylogenetic databases is heavily influenced by these ideas. As the Bio-IT World article points out, a key step towards using Semantic Web technologies is the use of globally unique identifiers, i.e., LSIDs. 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/

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Nico Franz 01 Nov '05

01 Nov '05

Hi all: I am a member of the SEEK Taxon group. Donald has given a useful overview of the names vs. concepts issue. I want to add that the "performance" of taxonomic names over time in terms of reliably and precisely identifying the same set of organisms can be quantified using the concept approach. Geoffroy and Berendsohn (2003) have pioneered this kind of analysis for the German moss data. Now Alan Weakley (UNC herbarium) has a dataset with more than 44,000 concept relationships that can be analyzed this way. Several smaller data sets on weevils, birds, plants, and possibly bats, fishes, and rodents are being prepared at the moment for a synthesis manuscript. We hope that such a broad-scale empirical analysis of the reliability of names through time will motivate more database providers to try out the concept approach. At the same time we're working on a tutorial-type paper that explains how to establish third-party concept relationships given two preselected classifications. Best, Nico Nico M. Franz, Ph.D. National Center for Ecological Analysis and Synthesis MSB, Room # 3411, University of California Santa Barbara, CA 93106-6150 Phone: (805) 893-5934; Fax: (805) 893-8062; E-mail: franz(a)nceas.ucsb.edu Website: http://www.nceas.ucsb.edu/~franz/ On Sun, 30 Oct 2005 09:31:54 +0100, Donald Hobern <dhobern(a)GBIF.ORG> wrote: >[ Another topic for comments. Please keep the Topic number in responses. ] > >Topic 3: GUIDs for Taxon Names and Taxon Concepts > .... >Questions > >I would like therefore to ask the following questions of any of you who use >scientific names in your databases (either taxonomic databases recording a >list of taxa, or databases recording information about taxa, specimens, >observations, etc.): > >1. Is your data organised using taxon names or to taxon concepts? >2. Do you assign any reusable identifiers to taxon names or concepts >(i.e. identifiers used in more than one database)? >3. If so, what is the process in assigning new identifiers for >additional taxa and for accommodating taxonomic change? >4. Where are these identifiers used (other organizations, databases, >data exchange, recording forms, etc.)? >5. Do you use identifiers from any external classification within your >database? >6. Would there be any social or technical roadblocks to replacing these >identifiers with a single identifier that was guaranteed to be unique? > >Thanks, > >Donald

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