[Zoobank-list] RE: ZooBank Data Objects

Tue Mar 6 21:08:34 GMT 2007

Hi Rich et alia-

I hope you all don't mind too much if a botanist chimes in here.  As many of you know, I am working with Chris on the INOTAXA project which includes a standard format (taXMLit) to mark up works of taxonomic literature (from journal articles to multivolume works and from Linnaeus to today).  

Chris & I have just been discussing how to generate GUIDs in our context of individual works being marked up (which seems to parallel Rich's usage instances--though I would appreciate it if Rich could verify).  It is clearly important that we are able to generate a GUID for each taxon treated in a work.  In addition, we favor generating a GUID for each synonym (whether defined as a botanist or a zoologist--i.e., taxonomic/heterotypic, nomenclatural/homotypic, junior or senior synonyms (I confess I always get confused about the meaning of junior/senior, sorry) misspellings, misusage, etc.  Whatever is listed.  In addition, other names may be used in discussion, or even in keys (I'm looking at a weevil treatment at this moment where this is the case) which are also some sort of synonym, which also should have a GUID.

While I agree, that only the treated name should be a top priority for Zoobank, as long as we are marking the text up and generating information with GUIDs, I would certainly hope that Zoobank would want all (and take now as opposed to coming back to us for later after the priority is 'finished') of these names along with the information that we may generate about what kind of synonym, even though they are mostly 'non-Code-governed' uses.

Further, there are other names that are cited in this work (e.g., host plants, vernacular names, parasites, etc.).  I think that those too should have GUIDs from our work, but whether or not Zoobank (or IPNI--currently an informal botanical registry) wants them, GBIF and uBio should!  Again, I would be interested in whether these fit into Rich's definition of 'usage instance'--though there may not be a formal taxonomic concept involved.

[Off topic, but in case anyone is interested, these name-related GUIDs are not the only GUIDs we will generate by any means, however, they are the ones that are of interest here.]

Cheers,
Anna

Anna L. Weitzman, PhD
Informatics Branch Chief, ITO
Informatics, Botany and Biodiversity Research
National Museum of Natural History
Smithsonian Institution

202.633.0846
weitzman at si.edu

________________________________

From: zoobank-list-bounces at afriherp.org on behalf of Richard Pyle
Sent: Tue 06-Mar-07 3:39 PM
To: 'Zoobank Discussion List (ICZN)'
Subject: RE: [Zoobank-list] RE: ZooBank Data Objects

I think we're discussing two separate issues here.  The first concerns the scope of ZooBank's "realm" -- e.g., whether or not certain unavailbale names are of importance to users of ZooBank (I wholeheartedly agree with Chris that they are).  The second concerns issues of prioirty of content and authority of content.  That is, what are the most urgently needed services we wish ZooBank to provide, and how should we prioritize the building of ZooBank's content.  On this, I find myself agreeing with Wolfgang's semtiments. But these are not mutually exclusive, nor even competitive issues.  We can scope the role of ZooBank broadly, but focus more narrowly on initial content generation (while certainly not preventing the accumulation of content that falls outside the identified priority areas).

Regarding the question of who best should manage certain parts of the global universe of biodiversity data (e.g., ZooBank vs. GBIF vs. uBio etc.), I think there are alternate views about this, and from my perspective, these are not yet close to being resolved. I am increasingly of the belief that the core unit of data exchange for nomenclature should be what I have been calling "usage instances" (I would be more than happy to abandon this moniker in favor of a better one, if someone could propose such).  That is, I find very little merit in establishing the notion of a "name" as something that exists outside the context of usage instances, and so I think that the GUIDs should be assigned to the usage instances, not the names.

>From the ZooBank perspective, then, certain usage instances fall under the governance of the ICZN Code -- these include original descriptions of new names, typifications, emmendations, first reviser, etc.  But just because a particular usage instance doesn't fall under governance of the ICZN Code per se, doesn't mean it is of no interest to ZooBank.  Non-code-governed usage instances are also important from a nomenclatural perspective, because they form the basis of notions such as "prevailing use" (for example).

So, I envision a global pool of usage instances of *all* organism names (all Codes, plus vernacular and other non-goverened names) -- something on the scale of what uBio is focused on.  Then certain subsets of these usage instances are recognized as having special meaning to certain organizations.  For example, the aforementioned usage instances that involve nomenclatural acts relevant to ICZN would be of special interest to ZooBank.  Other usage intances of nomenclatural relevance to the ICBN would be of particular interest to IPNI or IF; and of course the bacteriological registry would concern itself with usage instances associated with bacteria names.

The exact role of ZooBank in the broader picture will need to be clarified, but certainly elements of data quality would be a large part of those services, as well as obvious roles such as identifying which name-usage instances have nomenclatural standing under the ICZN, and how the rules of the Code apply to them.

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 at bishopmuseum.org
http://hbs.bishopmuseum.org/staff/pylerichard.html

________________________________

	From: zoobank-list-bounces at afriherp.org [mailto:zoobank-list-bounces at afriherp.org] On Behalf Of Chris Lyal
	Sent: Tuesday, March 06, 2007 12:13 AM
	To: Zoobank Discussion List (ICZN)
	Subject: RE: [Zoobank-list] RE: ZooBank Data Objects

	I would suggest that although the register must be of Available names, it also has to cover those names which are not available.  One of the problems we face is the number of unavailable names in the literature that need to be researched each time cataloguing work is done.  These need to be 'nailed' just as much as the available ones.  In fact, as we are thinking about developing registration systems for published names, the reasons why a name might be unavailable are captured by default.  I recognize that the list of unavailable names is possibly infinite, but there are many such names that do fall within the realm of usual taxonomic practice - published (or manuscript) names that fail to satisfy one or more articles of the Code.  The ICZN already maintains a list of rejected names - this is the logical extension.

	Chris

	Christopher H. C. Lyal, 

	Department of Entomology

	The Natural History Museum

	Cromwell Road

	London SW 7 5BD

	UK

	tel: +44 (0)207 942 5113

________________________________

	From: zoobank-list-bounces at afriherp.org [mailto:zoobank-list-bounces at afriherp.org] On Behalf Of Faunaplan at aol.com
	Sent: 06 March 2007 09:56
	To: zoobank-list at afriherp.org
	Subject: [Zoobank-list] RE: ZooBank Data Objects

	Thanks for all those detailed new info! 
	>From explanations and examples given it seems clear that a GUID supported naming scheme needs to be more inclusive, not being restricted to nomenclatural acts as traditionally governed by the Code. 
	So why not divide the issue in two chapters:

	- one related to ZooBank's "realm", - i.e., Code-compliant, available zoological names. 
	- another one comprising all those "name instances" (incl. misspellings, misidentified names, in litteris names) as they occur in off- and online publications, on specimen labels, etc.
	The latter "realm" may be better governed by other initiatives like uBio? (or GBIF's "Electronic Catalogue of Names"?) that are already collecting ALL names, including names of bacteria, plants, etc. and even including vernacular names?
	I'd like to give urgent priority to the first chapter, the second chapter could be written as a long-term step-by-step process which may even lead to a better co-ordination of the realms of botany, zoology, bacteriology...

	In my opinion, one of the functions of ZooBank that is most urgently needed is to serve as a reliable register of all AVAILABLE names in zoology. As you know, currently we even don't have a reliable list that tells us which genus- or family-group names are already pre-occupied! Nomenclator Zoologicus and Zoological Record are excellent springboards for a search but they are incomplete and do not provide information about availability of names etc. 

	Best wishes,
	Wolfgang
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