wiki-archive/twiki/data/Executive/CybertaxonomyExemplar.txt

%META:TOPICINFO{author="RichardPyle" date="1192578967" format="1.1" version="1.1"}%
%META:TOPICPARENT{name="Outreach2007And2008"}%
---++The Next 250 Years: Demonstrating Cybertaxonomy - Richard Pyle

In April of this year, the BBC sponsored an expedition across the Caroline Islands to film a documentary about our team discovering new species of fishes on deep coral reefs. Among the many new species we found, the most conspicuous (and unambiguously new) were several species in the damselfish genus Chromis. The most spectacular of these is intensely blue, and lives at 120m and deeper. The BBC documentary is to be called “Pacific Abyss”, and a shortened/Americanized version of it was broadcast in the U.S. on the Discovery Channel on October 14th (rebreoadcast again on October 21st). The BBC plans to fly me out to London when the 3-part documentary premieres sometime later this year (or early next year) on BBC-1, so I can be interviewed by various media outlets.  They plan to generate a lot of high-profile publicity for this documentary program.

In our deep-diving world, we already get too much publicity, so I started thinking of ways that we could re-direct some of that exposure over to the biodiversity informatics realm, such as ZooBank (the prototype of which I am tasked, as an [[http://www.iczn.org/][ICZN]] Commissioner, of developing). For more information about ZooBank, see the commentary published in [[http://www.iczn.org/Nature_Commentary.pdf][Nature]], and a [[http://www.iczn.org/ZooBank_Paper.htm][technical paper]] published in the Bulletin of Zoological Nomenclature. ZooBank is effectively ready to start assigning “Official” and permanent registration identifications to “Nomenclatural Acts”, such as new species. The LSID resolver and TAPIR service are operational, and the user-friendly front-end will be developed and ready for user submissions before the end of this year.

The thought occurred to me that if one of the new species discovered during the BBC expedition was accepted as the very first "official" proactively registered ZooBank entry, it would represent an exciting scientific “hook” that would generate media interest.  Before leaving to attend the [[http://www.tdwg.org/conference2007/][TDWG meeting in Bratislava]] in mid-September, I suggested this idea to both Andrew Polaszek (executive secretary of ICZN) and the BBC producer, and both responded very favorably to the idea.

When I arrived at the TDWG meeting in Bratislava and heard many of the presentations about emerging standards, I realized that ZooBank registration could be just the start of it.  I thought that perhaps this publication with the several new Chromis spp. descriptions could serve as an “exemplar” document to show how the future of “cybertaxonomy” could be.  For example:
   1. We would describe several new species of Chromis in a single paper, to be published on 1 January 2008 – 250 years to the day after the ICZN-fixed date for the 10th Edition of Linnaeus’ [[http://www.iczn.org/iczn/index.jsp?article=3&nfv=#1][Systema Naturae]], which represents the official start of modern zoological nomenclature. We have already discussed this with Zhi-Qiang Zhang and other representatives of the Journal [[http://www.mapress.com/zootaxa/][Zootaxa]], and the timeline (and planned format) seems feasible (so far, anyway…assuming we can have the paper version of the MS ready for submission within the next week).
   1. All taxon names mentioned in the document – including (but not limited to) all new species – will be registered in ZooBank. LSIDs (the standard type of Globally Unique Identifiers, or [[http://www.tdwg.org/activities/guid/][GUIDs]] as adopted by [[http://www.tdwg.org/][TDWG]] and [[http://www.gbif.org/][GBIF]]) for all registered ZooBank names, and the LSIDs will be represented in the published PDF version of the Zootaxa article as embedded links to the ZooBank website for each respective registration record.
   1. All descriptive data related to all specimens of the new species, as well as comparative data for other species, will be marked up with [[http://www.tdwg.org/activities/sdd/][SDD]] (TDWG standard for descriptive data such as characters, etc.), so that the raw data can be downloaded directly as XML and/or other formats.
   1. The descriptions themselves will be marked up with both [[http://research.amnh.org/informatics/taxlit/schemas][TaxonX]] and [[http://www.sil.si.edu/digitalcollections/bca/documentation/taXMLitv1-3Intro.pdf][taXMLit]] (emerging standards for marking up taxonomic publications with XML tags), or a merged version of these two standards.
   1. All holotype specimens of new species for which we have tissue samples (most species) will get a DNA "Barcode", appropriately registered with the fish Barcode of Life ([[http://www.fishbol.org/][FishBOL]]).
   1. All images (both published in the article itself, and others not included in the article – including radiographs) will be deposited in [[http://www.morphbank.net/][Morphbank]], with embedded links in the PDF file itself to the Morphbank images or image collections.
   1. All cited specimens will have embedded links to their respective Museum online databases (when available) and/or via the [[http://data.gbif.org/welcome.htm][GBIF portal]].
   1. All bibliographic citations (which will include citations for all original descriptions of all mentioned taxon names) will be linked to the [[http://www.biodiversitylibrary.org/][Biodiversity Heritage Library (BHL)]]. As many as possible will be directly available as scanned page images.
   1. All citations of taxon names will be represented in the form of taxon concepts, with associated [[http://www.tdwg.org/activities/tnc/][TNC/TCS]] XML.
   1. Many video clips of these new species will be accessible via embedded links within the PDF version of the document (a first???). See an [[http://video.google.com/videoplay?docid=153611051098248174][example clip] (the original clip is MUCH better resolution). Perhaps this could be coordinated with [[http://www.arkive.org/][ARKive]].
   1. All taxon names will be cross-linked to GBIF data records for associated species.
   1. Following discussions with Graham Higley and Jim Edwards, these species may be spotlighted in the public launch of the [[http://www.eol.org/][Encyclopedia of Life (EoL)]].
   1. Pending discussions with Bill Eschmeyer, all new species names will be included within the [[http://www.calacademy.org/research/ichthyology/catalog/fishcatsearch.html][Catalog of Fishes]] (although this technically has to happen after the document is published).
   1. Pending discussions with Rainer Froese, all species will be included within [[http://www.fishbase.org/][FishBase]] (and hence, [[http://www.sp2000.org/][Species2000]], the [[http://www.coml.org/][Census of Marine Life (CoML)]], and the [[http://www.catalogueoflife.org/][Catalog of Life]]).
   1. Pending discussions with Tom Orrell, all names will be included in [[http://www.itis.gov/][ITIS]] (and hence, the Catalog of Life).
   1. Pending discussions with Nigel Robinson of Thomson Scientific, all new names will be included within the [[http://scientific.thomson.com/products/zr/][Zoological Record]].

I've spoken with the key players for most of these respective technologies/initiatives and have received universal enthusiasm in response – everyone is willing to chip in their time to make it happen. Key people at GBIF and TDWG love the idea, and we can probably get some financial support for it, if needed. There is also interest in developing a short (2-minute) video using this example to illustrate the process of discovering and describing new species.

Most of my involvement (besides as an author of the new Chromis MS) will be coordinating all the pieces, and serving or mirroring most of the data content through the web portals currently being developed at [[http://www.bishopmuseum.org/][Bishop Museum (BPBM)]], in partnership with the [[http://pbin.nbii.gov/][Pacific Basin Information Node (PBIN)]] of the [[http://www.nbii.gov/][U.S. National Biological Information Infrastructure (NBII)]], and the [[http://www.pbif.org/][Pacific Biodiveristy Information Forum (PBIF)]] member to GBIF. If done successfully, we will have a document to show how the future of taxonomy “could be” in this brave new world of the internet, where supplemental information concerning taxa are available with just a few mouse clicks (rather than long hours in libraries and individual requests to data content holders for access to more information) – using and cross-linking all of the various biodiversity informatics standards and repositories.  As per standard practice with the journal Zootaxa, the paper-printed version will be the Code-compliant nomenclatural act of establishing the availability of the new names.  However, the PDF version of the document will have many links embedded within it, such that full details of names, images, videos, publications, etc. are just a mouse-click away. 

Although this first document would need to be created manually, it would not take much effort to generate templates and software to automate the annotations in the future, so that it would cost very little to implement more broadly.

Indeed, we are already planning a second article to be published concurrently or soon after that describes the “making of” this new-species document, describing in detail all of the standards and technologies used/followed, how they were implemented for this article, and what would be needed in terms of software and other tools to make the generation of such documents much simpler and more straightforward for other taxonomists in the future.

The main publicity thrust will coincide with the premiere of the BBC documentary, the date for which has not yet been set (possibly as early as November, but I suspect more likely in December or even later).  Ideally, this publicity blitz will follow not long after the 1 January 2008, which for historical purposes I think should be the target publication date for the “exemplar” cybertaxonomy article in Zootaxa. The idea would be to coordinate with the BBC and other media-aware initiatives associated with this document towards orchestrating a larger/coordinated publicity blitz coming from various directions all at once (e.g., ICZN press release, BBC press release, GBIF Press Release, TDWG Press release, and perhaps others as well, such as BHL and EoL).

All feedback, comments, and questions welcome.
 
-- Main.RichardPyle - 16 Oct 2007