[Zoobank-list] zoobank prototype

[Jim Mallet]

Well said!  I wrote privately to Andrew about exactly this, and maybe there 
are a lot of other people who did as well.  Jim

At 16:07 12/09/2006, you wrote:
>Wolfgang’s recent posting is constructive, helpful, and interesting.  We 
>now see the emergence of two different agendas.  One deals with what is 
>now on display ­ let’s call it ZooBank 1 ­ and this is what Wolfgang 
>addresses.  The other agenda is what we want ZooBank to become - a 
>code-compliant names registry.  This is ZooBank 2 ­ and this is what Frank 
>and Andrew have focused on.
>
>I absolutely applaud the emergence of ZooBank ­ both 1 and 2. We all owe a 
>considerable debt to Andrew who has worked extremely hard to bring the 
>operations of the Commission forward.
>
>That said, the criticisms of ZooBank 1, such as through the Taxacom list 
>serve, are fully justified.  The community out there has certain 
>expectations of the Commission.  ZooBank 1 has not met those 
>expectations.  We can point to our expectations of ZooBank 2, but a poor 
>quality product does not serve us well and could push ZooBank 2 
>backwards.  We need to bring the community back on side, and I think 
>Wolfgang’s posting helps us to chart out a path.
>
>ZooBank 1 delivers a repackaging of Thomson’s products, so the problems 
>derives from Thomson.  In April, I wrote to the then commissioners with my 
>concerns about the association of ZooBank with a single commercial player, 
>and all commissioners who responded to me agreed.  I attach my letter.
>
>As one of the founders of the uBio project, many of the criticisms of 
>ZooBank 1 are not unfamiliar.  uBio has received similar comments.  uBio 
>has a different agenda to ZooBank 2.  I am not entirely sure what the 
>agenda of ZooBank 1 is.  I am hoping that inter alia it will become the 
>nomenclator of code-compliant names created previously, whereas ZooBank 2 
>becomes the nomenclator of code-compliant names of the future.  uBio’s 
>objective has been to use names and hierarchies as informatics tools.
>
>In building up NameBank, uBio’s activities overlap considerably with those 
>of ZooBank 1 and 2 (and with Species 2000, ITIS, and many other 
>players).  Those of us who seek to deliver known names, for whatever 
>reason, face the same problems (such as importing mis-spellings, errors in 
>authorship, chresonyms treated as name and authority combinations, 
>undisambiguated homonyms, shifts in generic vehicles not identified as 
>such, and so on).
>
>Now I limit myself to the problems with ZooBank 1, although it should be 
>clear that much of this is also relevant to NameBank 2.   If more than one 
>initiative share the same problems, then it is prudent to work together to 
>fix them.  Names are an objective layer of information (and, in the uBio 
>view, metadata) upon which we all depend.  They are a communal resource 
>for which we can have communal responsibility.
>
>uBio has a very robust and flexible data model which has been developed on 
>the basis that names need to be shared and that there will be problems to 
>be addressed.  Many of the names problems identified by the Taxacom 
>readership can be addressed within what we refer to as ‘reconciliation’ 
>groups.  These groups link together alternative names for the same 
>taxon.  So, for example, Paramecium acudatum (a mis-spelling served by 
>Thomson as a species) is assigned to the reconciliation group for 
>Paramecium caudatum.  Similarly, the ‘species’ 'Paramecium cilia’ can be 
>assigned to the reconciliation group ‘Paramecium’.  Reconciliation groups 
>can convert a query initiated with one name into an action that involves 
>all names ­ such that a query on Paramecium caudatum will find the content 
>labeled with the name Paramecium acudatum.
>
>Within reconciliation groups, the status of each name can be 
>identified.  Reconciliation groups not only fix problems but serve other 
>needs of ZooBank by providing a means to indicate the nomenclatural status 
>of names.
>
>The creation of reconciliation groups requires experts to be involved.  An 
>appropriate workbench, going beyond those offered through Platypus or 
>ITIS, can allow experts to map names against one another (i.e. to create 
>reconciliation groups), annotate names (to indicate their nomenclatural 
>status etc.), and reshape hierarchical arrangements.  If we seek to be 
>inclusive, we are obligated to adopt an approach that is able to deal with 
>all names of all organisms, within a unified, authoritative, current 
>hierarchy that can depict all subjective views.  This is referred to as a 
>Union approach.
>
>So extending Wolfgang’s suggestions, I believe ZooBank 1 can be used to 
>lead the development of a names-management co-operative that charts a path 
>to serve the needs of many players.  This group should not only be 
>concerned with animal names.  uBio obviously has tools and services to 
>contribute.  There are numerous aggregators and hundreds of expert players 
>out there who have expertise and concept.  ICZN has a clientele and a 
>vision.  Thomson provides links into literature.  As the Biodiversity 
>Heritage Library comes on line, so much more literature will become available.
>
>Co-operation can be efficient.  A federated and communal environment that 
>is held together through network services can extend benefits to all 
>users.  This does not require a loss of ownership.  Editing environments 
>can give the impression that names are being added to or corrected within 
>one location (e.g. ZooBank) but in reality are happening at a deeper layer 
>so that they can re-emerge to benefit any other users of names of 
>animals.  Similarly, changes made to names elsewhere can flow to ZooBank.
>
>Dealing with Thomson content was never identified as a priority for 
>ZooBank ­ which was sold on the vision of ZooBank 2.  But the box has been 
>opened and we need to do something about what has been released. 
>Wolfgang’s suggestions of dealing separately with species, genera, and 
>families makes sense as it will break up the challenge of dealing with the 
>inherited problems into reasonably sized tasks.  A web based workbench 
>will allow many tasks to be addressed simultaneously - one group can be 
>creating a consensus list of carabid genera, while others correct the 
>plethora of errors among ciliate species names.
>
>Moving focus a little, some other services that serve the needs of the 
>commission can be delivered very quickly. uBio can deliver a list of all 
>generic names known to us (whether viral, plant, animal, prokaryotic, 
>fungal or protist) ­ and can indicate who holds those names (so we can try 
>to trace errors to their source).  A list of all genera will assist 
>taxonomists in dealing with homonyms now.  A list of all genera will ease 
>the informatics challenges of the future if it entices us to avoid 
>voluntarily homonyms with any generic name whether of an animal or not.
>
>None of this will be achieved without funding.  The cost of modifying the 
>names-based infrastructure that we have been developing at the MBL to 
>create the expert interface and the union editing environment is not 
>great.  I believe that the system could be in place within 18 months 
>assuming a single coder.  In respect of funding, any developments of 
>ZooBank 1 and of ZooBank 2 will improve the services (market position and 
>profitability) of the commercial agency (Thomson).  I would expect them to 
>provide support to help bring the vision to fruition. Perhaps GBIF also 
>may be able to assist in making progress.
>
>Although funding is needed for tools, the critical determinant to success 
>with ZooBank 1 is how well we engage the taxonomic community and the 
>numerous other initiatives.  Our performance there may determine the 
>acceptance of the real ZooBank with the interested community.  Our 
>workbench must impose a negligible extra load on the shoulders of the 
>experts, and should return to them considerably more than they 
>invest.  This is where the informatics prowess of uBio would serve the 
>needs of Zoobank very well.  Contributors should have free access to tools 
>and services that accelerate and enhance their own operations.  A simple 
>example of a benefit would be a taxonomically informed alert system that 
>delivers to users a customised weekly email to let them know of new names 
>and combinations in their area of taxonomic interest, recent publications 
>or additions to web sites, additions to the Biodiversity Heritage Library, 
>GBIF or other on-line data providers changes and input into the underlying 
>nomenclatural systems, etc.
>
>We are no longer in the world of wishful thinking.  All of these things 
>can happen with a relatively small investment.  The next step?  A meeting 
>with 10-20 interested players?
>
>David Patterson
>12th September 2006
>
>
>My April letter to the commissioners follows:
>
>Fellow commissioners
>
>The ‘30’ email from Andrew contained a paragraph about ZooBank. You will 
>probably know that I am a very strong advocate of moving nomenclatural 
>activities forward, and believe that ZooBank is a great development. 
>However, I am increasingly concerned about the potential of problems 
>should ZooBank develop an exclusive relationship with a single commercial 
>agency (Thomson). The large scientific publishers have, over the last 
>decade, shown to us that their economic performance takes priority over 
>the provision of service, and some have become excessively 
>exploitational.  Some taxonomists refer to publishers as a new ‘taxonomic 
>impediment’.  There are now significant political counter-moves to promote 
>open access to publicly funded and other scientific content.
>
>When we submitted our thoughts to Nature, we conceived of ZooBank as 
>embedded within a community of complementary initiatives (and we specified 
>a number of these, such as uBio, Species2000, ITIS and GBIF). By the time 
>the technical paper was written this array had narrowed rather than 
>expanded.  This reveals a shift in the wrong direction.
>
>Thomson and Zoological Record do add considerable value to ZooBank, but it 
>is not the only agency capable of enriching the initiative.  uBio (the 
>project that I am associated with) offers a different but still 
>complementary array of valuable assets.  It holds the contents of 
>Nomenclator Zoologicus.  Having now passed through the 7.5 million record 
>mark (making Thomson’s claim that ION with 1.7 million names is the most 
>comprehensive organism names database rather inaccurate) we can access 
>most of the homonyms that were created under other codes.  Significantly, 
>we embed the names of organisms within a growing array of freely-available 
>taxonomically intelligent services that not only help taxonomists do their 
>work, but display the significance of nomenclature to a wider 
>public.  GBIF too has many valuable dimensions, not the least of which is 
>the growing coverage of specimens which form key connections between names 
>and concepts. ITIS and Species2000 offer environments where we obtain 
>taxonomic value that has been added around names.  New initiatives such as 
>the Biodiversity Heritage Library will release vast amounts of 
>taxonomically relevant literature and the names that are contained within 
>this.  ZooBank should aim to be connected to all of these.
>
>Given that the objective of publishers is to make money, we need to 
>protect ZooBank from situations where the publisher exercises control over 
>our capacity to submit names into ZooBank, or try to control ­ through 
>financial charges ­ our access to names, or to the taxonomic descriptions 
>or associated bibliographic information. Publishers have already done this 
>with the general scientific literature.  The financially weak position of 
>the Trust does not make us equal players. It behooves ZooBank to protect 
>itself against any complications that might emerge from an exclusive 
>relationship with a commercial enterprise. Andrew can, of course, ask for 
>contracts that guarantee free and open access to names and the key 
>literature in which the names are embedded in perpetuity (maybe such 
>contracts already exist, I am not privy to the dialog with 
>Thomson).  However, I do not believe that such documents are 
>sufficient.  Rather, I suggest we aim to mirror ZooBank operations at more 
>than one location to break any threat of a monopoly.  Any resistance to 
>this or to the movement of content would help us to identify those players 
>who are in the game for the right reason.  I do not believe ZooBank would 
>have any difficulty in attracting additional partners, or in getting GBIF 
>to agree to occupying an overarching role in which they establish a 
>taxonomic engine coupled with universal and unique persistent identifiers 
>that will unify all names-based initiatives.  Each additional partner can 
>be selected on the basis of the value that they add to ZooBank.
>
>
>
>
>
>
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James Mallet
http://www.ucl.ac.uk/taxome/jim/


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