June 2010 - tdwg-content - lists.tdwg.org

[tdwg-phylo] Birds-of-a-Feather gatherings for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 14 Jun '10

14 Jun '10

In anticipation of the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), we solicit all attendees to propose and discuss Birds-of-a-Feather gatherings. See below for details. Birds-of-a-Feather gatherings (BoFs) are informal, ad-hoc, focused face-to-face discussion groups that form around a shared interest. BoFs have a leader (usually, but not necessarily, the proposer) who initiates or moderates the discussion, but typically not a preset agenda. The topics of BoFs can range widely, including general cultural or computational infrastructure issues, or narrower questions such as how to make the best use of a particular software tool or how to solve a particular computational challenge. Anyone willing to lead such a group can propose a BoF. iEvoBio will provide space that can accommodate up to 8-10 BoFs. Sign-up sheets will be provided on-site on the first day of the conference where attendees can propose a BoF or sign up for one proposed by someone else. BoFs will be about 1 hr in duration and take place in the afternoon of the second day of the conference. In line with their informal nature, there is no official prior call for or submission of BoFs. However, we encourage those intending to propose one to sound out or rally potential attendees ahead of time. We suggest to employ Twitter (http://twitter.com) for this, using the #ievobioBof tag to mark BoF proposals and comments. Birds-of-a-Feather gatherings are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks (waiting list only), 3) Challenge entries, and 4) Software Bazaar entries. The Calls for Challenge entries (http://ievobio.org/challenge.html) and Software Bazaar entries (http://ievobio.org/ocs/index.php/ievobio/2010/) remain open. More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona)

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Re: [tdwg-content] Name is species concept thinking
by Richard Pyle 14 Jun '10

14 Jun '10

Warning to Tim: Go get your cup of tea before reading.... Hi Jerry, I believe what you describe: > I think we do need an agreed way for identifying a 'set of > name/article pointers' that define a useful grouping (which I > would hesitate to call a concept). I don't think an > open-ended linked data chain does provide that defined grouping. ...is already built into the GNUB data model. Starting with a particular TaxonNameUsageID instance, we can directly get a set of Protonyms that are asserted in the Usage to be included within the taxon. From these Protonyms, we can explode out as far as you want to go. The limitation, however, is that GNUB only includes the explict facts, not the interpreted meanings. In other words, we may know that Smith 1955 regarded Aus cus, Aus dus, and Aus eus as synonyms of Aus bus; but if he never mentioned Aus xus (either as another synonym, or as a distinct species) we can't know whether his circumscription of Aus bus would have included the type and implied other members of Aus xus. So, the facts alone don't cut it. So if Smith treated Aus bus as follows (synonym indended below asserted valid name): Aus bus L. - Aus bus L. - Aus cus Jones - Aus dus Brown - Aus eus Lamarck And Pyle treated Aus bus as Aus bus L. - Aus bus L. - Aus cus Jones - Aus dus Brown - Aus eus Lamarck - Aus xus Cooper [without any mention of Smith's treatment of Aus bus] ...then we need a third party to assert whether or not "Aus bus sec. Smith" and "Aus bus sec. Pyle" are congruent. With our new GNUB data model, we *could* represent these third-party assertions; but my gut feeling is that the third-party assertions should be external to the core GNUB model. But this is, of course, open for discussion. > Pete's point about the two different name/article > intersections referring to the same 'concept' is resolved by > the fact they are based on the same type, and that issue I > prefer to see resolved at the nomenclatural level by > protologue & type-collection pointers (as in the GNUB model). Types don't do it for us. Using my example above, suppose we have DeVries' treatment of the Aus bus complex as follows. Aus bus L. - Aus bus L. - Aus cus Jones - Aus dus Brown Aus eus Lamarck - Aus xus Cooper That is, he treated Aus bus and Aus eus as valid species, and included Aus xus as a synonym of the latter. In all three treatements of Aus bus (Smith, Pyle, DeVries), the name "Aus bus" shares the same type -- but that doesn't mean that all three had the same taxon concept (circumscription). So, in my mind, the real question is: Do we need a separate "taxonConceptID" (as in the TDWG version of DwC) that we can use to brand the abstract Concept? Or are we able to assemble the same results from individual usage-instance mappings? So, let's say that we are confident that Smith and Pyle both had the same idea for the taxon concept/circumscription of Aus bus (it's just that Smith forgot to list Aus xus in his synonymy). Do we need a single taxonConceptID to express the fact that they are the same taxon concept? Or can we derive that easily enough from a third-party assertion of the congruency of the concepts represented by the two usage-instances? Presumably we would also have separate taxonConceptID's for "Aus bus sec. DeVries", and for "Aus eus sec. DeVries". > I think it would help if we took a step back from using the > term 'taxon concept' and agreed on what we are trying to > achieve by linking/grouping the various constructs, and then > arrive at a more precisely defined vocabulary for > name/article intersections, and the open-ended universe of > related stuff. AGREED!!! > I suspect we will find that different end-user groups (e.g. > hard core nomenclaturalists, nomenclaturally savvy > taxonomists, most taxonomists, and the most important group > ... non taxonomic savvy end-users of taxonomic services) all > have differing and overlapping requirements, and a different > understanding of the words being used. NO DOUBT! > Despite my peripheral involvement in taxon concept space for > many years I suspect the above comments reflect a deep seated > blinkered view that stops me seeing how it should work given > the existing vocabulary! ME TOO! :-) Rich

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Re: [tdwg-content] Name is species concept thinking
by Mark Wilden 10 Jun '10

10 Jun '10

On Thu, Jun 10, 2010 at 2:55 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: > > Hmm...not sure I agree. At the moment that spcific atom is part of the ant, > then it seems to me that it is also part of Formicidae. It gets weird, > though, because atoms enter and leave the circumscribed individual ant over > time, whereas the abstract notion of "the ant" stays the same from its birth > to its death. But then again, if Formicidae is circumscribed by its member > individual ants, then these individual ants then enter and leave the > circumscription (when they are born or conceived, and when they die). I don't think it's enough to say "is circumscribed by its member individual ants." You have to also state the basis of that circumscription, as it obviously can't just be by enumeration. For example, I think it would be fair to say that in order to be a member of Formicidae, an entity must be an ant (there may be other, better criteria, but you get the idea). That's why I say that a specimen is the ultimate circumscription, at least of the taxonomic kind. An atom isn't a kind of ant, but an ant has an atom. Inheritance vs. composition. ///ark

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FW: Name is species concept thinking
by Kevin Richards 10 Jun '10

10 Jun '10

Forwarded for Jerry, as his email was bounced... -----Original Message----- From: Jerry Cooper Sent: Friday, 11 June 2010 9:43 a.m. To: Richard Pyle; Kevin Richards; 'Peter DeVries' Cc: tdwg-content(a)lists.tdwg.org Subject: RE: [tdwg-content] Name is species concept thinking I hesitate to contribute to this debate, but it is useful. Kevin articulated an issue that has bugged me forever. I think we do need an agreed way for identifying a 'set of name/article pointers' that define a useful grouping (which I would hesitate to call a concept). I don't think an open-ended linked data chain does provide that defined grouping. Pete's point about the two different name/article intersections referring to the same 'concept' is resolved by the fact they are based on the same type, and that issue I prefer to see resolved at the nomenclatural level by protologue & type-collection pointers (as in the GNUB model). I think it would help if we took a step back from using the term 'taxon concept' and agreed on what we are trying to achieve by linking/grouping the various constructs, and then arrive at a more precisely defined vocabulary for name/article intersections, and the open-ended universe of related stuff. I suspect we will find that different end-user groups (e.g. hard core nomenclaturalists, nomenclaturally savvy taxonomists, most taxonomists, and the most important group ... non taxonomic savvy end-users of taxonomic services) all have differing and overlapping requirements, and a different understanding of the words being used. Despite my peripheral involvement in taxon concept space for many years I suspect the above comments reflect a deep seated blinkered view that stops me seeing how it should work given the existing vocabulary! Jerry -----Original Message----- From: Richard Pyle [mailto:deepreef@bishopmuseum.org] Sent: Friday, 11 June 2010 9:03 a.m. To: Kevin Richards; 'Peter DeVries' Cc: tdwg-content(a)lists.tdwg.org; Jerry Cooper Subject: RE: [tdwg-content] Name is species concept thinking > This is something that has been slightly confused over the years, ie there seems to be 2 ways of defining a "taxon concept": > 1. A Taxon Name (nomenclatural data) + Literature Reference - ie Name X as defined in article Y > 2. As you have said a grouping of data that define a taxon concept (Name + Reference + Synonyms + Type Specimen + Protologue, .) I don't think of these as two different ways of defining a concept. I see #1 as a way of *pointing to* a taxon concept definition, and #2 as the concept definition itself. Basically, #1 (usage instance) is effectively a container or an identifier for the taxon concept definition. However, there is somewhat of a dichotmy in the way that taxon concepts are defined - one is by included members (i.e., specimens, presumably including at least one name-bearing type specimen, from which a name-label is derived), the other is by properties (i.e. characters -- morphologic, genetic, or otherwise). In practice, most concept definitions include both. But I think the "definition" of the concept (i.e., the circumscription boundaries) is the same for both -- it's just that those boundaries can be articulated in different ways (i.e., by examplar members, and by purported properties). > 1 has been covered quite well with the various schemas we have come up > with over the years, but I think these schemas have failed to capture > 2 very well (the data fields are there, but the encompassing ID is not), ie Agreed -- sort of. I think the schemas are there, but have not been organized appropriately (yet). See below. > TaxonName ID = N1, FullName = "Aus bus" > Reference ID = R1, Citation = "Richards, how to define a taxon concept" > TaxonConcept ID = C1, NameID = N1, ReferenceID = R1 > BUT, the taxon concept C1 does not encompass all related data that defines that concept (synonyms etc) No, but it could, through a network of linkages, as I tried to describe in one of my recent posts. > To do that we need more Concept Ids and relationships between these concepts, eg Exactly! And we need a schema-based process to capture the relevant information (diagnoses, etc.), anchored to the Concept Ids. At a basic level, Plazi/TaxonX does this. However, it usually only goes as far as the text-blob. To parse the text blob, we need to either look towards SDD (for character-based concept definition stuff) or DwC/Occurrence (for specimen-based concept definition stuff). > ConceptRelationship ID=CR1 ConceptFromID=C2, ConceptToID =C1, RelationshipType='has preferred name' Yes, I agree we need this as well! But again, I see this as a way of networking pointers to taxon concept defintions, not describing the definitions themselves. Man, these conversations really hurt my brain.... :-) Aloha, Rich Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

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Name is species concept thinking
by Peter DeVries 10 Jun '10

10 Jun '10

I was looking through the latest DarwinCore and comments related to the TaxonConceptID. Since the name serves as both a unique identifier and a phylogenetic hypothesis, you are effectively saying that observations labeled *Aedes triseriatus* and *Ochlerotatus triseriatus* Are separate species concepts, and should therefore be treated as separate things. i.e. The name is the concept. Also since there are several name variants for each "species", how do you distinguish which of these nameID's are the same species and which are different? - Pete ---------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 GeoSpecies Knowledge Base About the GeoSpecies Knowledge Base ------------------------------------------------------------

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Re: [tdwg-content] Name is species concept thinking
by Richard Pyle 10 Jun '10

10 Jun '10

I know the Parent Taxon is itself a circumscription of its included children. But my question was whether the parent taxon is an intrinsic property of each child? Basically, assuming that "Aedes triseriatus" and "Ochlerotatus triseriatus" refer to precisely the same set of individual organisms, should they be regarded as separate "taxon concepts", because the same species epithet in each case is the child of a different parent? If "Parent Taxon" is an intrinsic property of a "taxon concept", then they are different. But if taxon concept effectively equals circumscription, then these two name-combinations are different labels for the *same* taxon concept. Rich P.S. As far as we know, the ultimate circumscription is a subatomic particle, with layers of atoms, molecules, organelles, cells, and organs below the specimen-level circumsctiption... :-) > -----Original Message----- > From: Mark Wilden [mailto:mark@mwilden.com] > Sent: Thursday, June 10, 2010 10:10 AM > To: Richard Pyle > Cc: Peter DeVries; tdwg-content(a)lists.tdwg.org > Subject: Re: [tdwg-content] Name is species concept thinking > > On Thu, Jun 10, 2010 at 1:00 PM, Richard Pyle > <deepreef(a)bishopmuseum.org> wrote: > > > > I guess a key question that I'd like to get feedback from > others on > >is whether "Parent Taxon" and "circumscribed organisms" are > > *both* intrinsic properties of "taxon concept", or if > "taxon concept" > >is effectively equivalent to "circumscription", relegating "parent > >taxon" as a property of Classification, separate from > "Taxon Concept". > > But "Parent Taxon" is a circumscription itself. Its children are > circumscriptions of circumscriptions. A specimen is the ultimate > circumscription. > > ///ark >

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[tdwg-phylo] Deadline for Call for Challenge entries for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 08 Jun '10

08 Jun '10

This is a reminder that the Call for Challenge entries for the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) closes in two weeks on June 21, 2010. The theme of the 2010 iEvoBio conference challenge is "New visualization methods for evolutionary data". Visualizing evolution is a key part of our discipline and presents opportunities as much as it does obstacles. The iEvoBio Challenge is deliberately wide ranging: entries could range from geophylogenies to visualizing extremely large phylogenetic trees, to mashups showing relationships between lineages and other types of data (e.g. conservation status). Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website at http://ievobio.org/challenge.html . Selected candidates will make short oral presentations to demonstrate their visualization in a "Challenge session" at the conference, and will automatically be entered into the Software Bazaar if suitable. The winners of the Challenge will be judged collectively by the iEvoBio participants. There will be cash prizes for the first place ($1,000) and runner up entries. Challenge entries are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks, 3) Software Bazaar entries, and 4) Birds-of-a-Feather gatherings. The Calls for Lightning Talks and Software Bazaar entries remain open (see http://ievobio.org/ocs/index.php/ievobio/2010/), and information on the Birds-of-a-Feather session is forthcoming. More details about the program and guidelines for contributing content are available at http://ievobio.org. Continuous updates can also be found on the conference's Twitter feed at http://twitter.com/iEvoBio. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona)

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