Report from the Meeting with the Nomenclatural Code organisations at GBIF Secretariat, January 14, 2005.

1 Summary Report

A meeting with representatives for most of the organisations that publish the Nomenclatural Codes in use in controlling scientific names of organisms in biology was convened at the GBIF Secretariat to discuss topics of relevance to them and to GBIF.

The main topics in discussion were:

Current position and prospects for each Code, regarding registering/indexing of scientific names
Differences and commonalities among Codes – possibilities for harmonizing the terminology
GBIF affiliation or membership for Code organisations

During the meeting a number of actions were agreed which are listed below.

1.1 Registration/indexing of scientific names

The Codes’ representatives discussed how registration or indexing of nomenclatural events can be employed in order to compile authoritative lists of names of species and to which extent such a system is implemented under the different codes.

In microbiology as well as in the virology, inclusion in an official index is essential for a name to enter into official use under their Codes Of Nomenclature – see details below in the minutes.

In Botany, registration has had a trial run but at the moment there is no requirement to register new algal, fungal or plant names/combinations

Zoology has no requirement for registration.

A recent initiative within the fungi has set up a voluntary registration/indexing mechanism that also issues General Unique Identifiers for novel taxonomic concepts.

In general the attendees thought that a requirement for registration/indexing would be a great step forward for those codes that do not already require it. There was agreement that appropriate mechanisms should be put in place, preferably in co-operation with the nomenclator organisations. Web based tools that would enable easy and democratic access to registration may be preferable, although existing systems in microbiology and virology do not currently implement such systems. Linkage to the publishing industry is essential although changes in the Codes that would allow on-line publishing might put publication of new concepts in the public domain. The International Journal of Systematic and Evolutionary Microbiology, which is the official publication for registering/indexing bacterial names is available free of charge on the Internet after 2 years.

Although there was great enthusiasm and agreement, actual proposed action by those Codes, which had not implemented such a system, was scarce. However, everybody agreed to pursue possibilities within their own communities.

1.2 Differences and commonalities among Codes – possibilities for harmonizing the terminology

Among the reasons for wanting to discuss the possible harmonizing or even unification of the nomenclatural codes were mentioned

a) the general impression of the codes “getting their act together” would improve their impact and credibility towards other branches of biology and the world in general

b) there is a need for the reduction of the number of terms or at least a mechanism for cross mapping between them - or a controlled vocabulary – when wishing to build advanced database integration projects (like GBIF)

c) the increasing problems of treating ambiregnal organism groups coherently

d) facilitating the teaching of nomenclature in taxonomic courses

During the course of contacting various scientists to attend the meeting, as well as during the course of the meeting it was noticed that several members present had already been involved in “inter Code” discussions and were members of the International Commission on Bionomenclature (ICB) – a joint IUBS/IUMS body. This greatly assisted the discussions, as well as indicating that much background work had already been done, even if this was not always generally known. Discussion centered around the BioCode initiative and what was to be it’s fate – whether to try to revitalize it or rather try to propose advanced mechanisms (ontologies seem to be the word) for cross walking between codes. A number of action items were proposed. The question would be a good topic for a small white paper contract if funds could be identified.

There was general agreement to involve the international bodies that govern the nomenclatural codes – i.e. IUBS and IUMS, as well as to draw on past experience from the ICB initiative.

1.3 GBIF affiliation or membership for Code organisations

There was in general an interest for the code organisations to seek closer affiliated with GBIF. Based on the fact that both the codes and GBIF have a common interest in nomenclature, they would profit from getting involved as it would highlight to the biodiversity community that efforts were being taken to integrate the process of building a coherent nomenclatural (and eventually taxonomic) view on the world’s organisms.

Jim Edwards discussed the possibilities for the codes to become Associate Participants (see minutes) of GBIF and the representatives agreed to pursue the possibilities.

Specifically it was mentioned that it would be advantageous for GBIF to draw on the expertise of those scientists who were closely associated with, and understood the workings of the codes to validate and clarify the way that the GBIF data portal uses nomenclature. This could be done through small common projects or contracts.

2 Action items

2.1 ECAT Science Sub Committee membership

Ensure that we have representation on ECAT of all groups and discuss formats and spot introduced errors (Per + Chris)

2.2 Affiliation of Codes and GBIF

Virus and prokaryote meeting (Microbiological Congress) in San Francisco later this year – Per to attend and discuss further developments of association between GBIF and Microbiology and Virus Codes. BT will report back to the ICSP at that meeting
JM and DH will talk to Tod Stuessy about the IAPT becoming an Associate Participant
MM will present positive report to his committees and propose joint fundraising activities.
AP will propose that ICZN become an Associate Participant.

2.3 GBIF portal interface display improvement

Virus GBIF names are not italicised entirely correctly - rules needed and application of these; find where the orthography originates – PB in communication with MM
Prokaryotes: we need to confirm that the field structure we use is representing the different formal and non-formal names appropriately, and we are not using rules that misrepresent them. PB + BT
If name is in “quotation marks” it is not validly published according to the Code (but maybe in a synonym list for historical reasons). Action point – these are not used in the GBIF mediated data (but data provider does not either). Needs to be corrected in some way – PB, Donald Hobern + BT to discuss
Need to let GBIF know of problems in GBIF.net (BT raised need Jim Edwards agrees)
Need for GBIF to indicate whether names are validly published/available [BT]

2.4 Harmonisation of codes

Training/best practices – differences between codes and the appropriate way of entering and using data – how to provide this? – contracted work for GBIF?
As we develop toolkit and best practices for ECAT data providers we need to use controlled vocabulary. Might use unified terms as adopted and recommended by IUBS. Will involve codes – action CL+PB
Controlled vocabulary – IUBS/IUMS and The International Committee on Bionomenclature have had discussions on harmonisation and proposed harmonisations in 1994 – meeting to address issues of harmonization.
Could GBIF identify terminology it wishes to use and publicise this? [DH has an extensively updated draft of the 1994 pink book]
DH will try to get the ICB reactivated and work with IUBS, IUMS to organise a meeting and/or an across-the-codes training workshop.

2.5 Sharing data

AP – thinking of project to digitise Official Lists – to talk about in near future. – perhaps further discussion in Paris meeting, including discussions with IUBS.
BT will investigate possibility of moving static website to a database – this would have to involved the LBSN project.
NT will talk with McGill and Crosby about the Index of Mosses, and with the Flora projects about their names lists

2.6 Miscellaneous

GBIF should add links to the Code sites on our links page. PB - Done

Should we plan another get-together of Code reps with GBIF? If all become Associate Participants, then our GB meeting would provide that.

3 Agenda,

Workshop of representatives of the taxonomic code organisations

GBIF Secretariat, Copenhagen, January 14^th 2005

Welcome and presentations

Discussion on the scope of the workshop (adoption of Agenda)

Introduction to GBIF [PB]

ECAT: general overview;

The ECAT SSC [CL]

Mutual benefits of GBIF – Code partnerships

Progress in the work with the Nomenclators;

GUIDS (Global Unique Identifiers) and taxonomic names;

How electronic registration of nomenclatural actions (new species, new combinations) would help GBIF.

Presentations of the individual coding organisations [person from each code]

Current position and prospects for each Code regarding registration of names / GUIDs

Examples of current registration mechanisms [BT (prokaryotes), MM (Viruses)]

Discussion and planning of actions

Differences and commonalities among Codes

What problems for GBIF’s goals are caused by the differences between Codes – can they be solved?

What procedures are needed for each Code to solve these problems?

Discussion and planning of actions (how can GBIF help?)

GBIF affiliation/membership for Code organisations – pros and cons [JE]

Discussion and planning of actions

4 Minutes, Workshop of representatives of the taxonomic code organisations

GBIF Secretariat, Copenhagen, January 14^th 2005

4.1 Present

Per de Place Bjørn (GBIF ECAT) – PB

Chris Lyal (Chair, ECAT SSC) - CL

Nick Turland (botany) - NT

David Hawksworth (IUBS/IUMS Committee on Bionomenclature, and fungi) - DH

John McNeill (botany, cultivated) - JM

Andrew Polaszek (zoology) - AP

Mike Mayo (viruses) - MM

Brian Tindall (prokaryotes) - BT

Claus Nielsen (zoology) – CN

Meredith Lane (GBIF) - ML

Jim Edwards (GBIF) - JE

4.2 Introduction

Per de Place Bjørn opened the workshop with a brief introduction to GBIF, ECAT and the GBIF Names Service. See PowerPoint presentation

Chris Lyal followed on to describe the ECAT SSC and its advisory function relative to GBIF activities.

Discussion of the mutual benefits of GBIF – Codes partnerships

GBIF can provide: infrastructure (standards, technical); enhance recognition of biodiversity informatics (support, IPR); seed money awards; partnering

GBIF needs nomenclatural validation and partnerships

Liaison with Nomenclators: Zoological Record, IPNI, Index Fungorum, ICTVdB, LBSN

GUIDs and taxonomic names – taxonomic concepts need to be identified uniquely

Indexing of nomenclatural events: A GUID could be issued immediately on creation of new names would result in a list of “accepted” names

Problems for GBIF: Differences between the codes … to fix: controlled vocabularies and ontologies to translate

There followed a discussion of the problematic issues that are brought up by lack of vouchers, or the lack of means to link taxonomic concepts to vouchers, developments of multiple classifications, microbiological samples as opposed to isolates, degree of scrutiny given to usage of names, technological possibilities for solutions versus sociological issues (lack of taxonomic understanding by sequence contributors), annotations, spurious names coming into the system via the specimen databases rather than names databases, identical names in different kingdoms

Brian Tindall: issues with names going into sequence databases – often ‘incorrect’ names, which are not updated. Do have a problem in prokaryotes and sequence data and tracking concepts.
NCBI–view is that the name associated with an entry is the ‘property’ of the provider and should not be changed by someone else. – [Could be annotated though].
Chris Lyal: the Napier schema is being developed so that we can track taxonomic concepts across a distributed network, this needs Globally Unique Identifiers (GUIDs) to make a workable system
Discussion on need for concepts/names/voucher specimen data mapping through GBIF.
GBIF link to GenBank to be strengthened through Barcode meeting.

4.3 Presentations of the individual coding organizations

Botany (John McNeill):

The ICBN is a legal framework to determine what name is the right one to use within a particular taxonomy just like in zoology.
Not a single commission; dispersed system; around international botanical congress (every 6 years) – Nomenclature Section meets before Congress (next one is this year in Vienna); debates previously published proposals for changes in Code Congress; formally approves actions of the Nomenclature Section
Proposals for changes in the Code and to override the effects of the rules in particular cases (“conservation” and “rejection” of names) published in Taxon by IAPT
People submit to Taxon any changes they want to see in the Code (closing date a year before the Congress). Comments will appear in February issue of Taxon.
Votes from Institutions (transferable) and those individuals attending the [Nomenclature Section of] the Congress, with 60% majority required for changes.
Specific proposals on conservation or suppression (“rejection”) of names dealt with between congresses through taxon-focussed committees (e.g. Fungi, Algae etc.). These are then considered by the “General Committee” (the IUBS Commission on Botanical Nomenclature) and, if endorsed, signed off by Congresses.
There is a separation between taxonomy and nomenclature, and the ICBN seeks to remain completely neutral regarding taxonomy. There is a Bureau of Nomenclature responsible for the running of the Nomenclature Section (NT and JM are both on this).
The governance structure of the Code is quite complex – which means that a lot of people would have to be brought on board by GBIF if any changes in the Code would be proposed. It is also important to remember that while lists such as IPNI (http://www.ipni.org/index.html), covering vascular plants, and many of those for other groups have managed to weed out many of the “names” that are nomina nuda or otherwise not validly published, there are no lists distinguishing the names actually being used from the very many validly published synonyms, some of which have not been used for decades and are unlikely ever to be. The Names in Current Use (NCU) initiative was designed to do this (and then to “protect” these names), but this important initiative did not quite gain the necessary 60% majority in Tokyo (1993) and was also not acceptable in St. Louis (1999).
1st draft NCU list of genera had many errors and this counted against concept. Any move to ‘enshrine’ such lists would come only after production of the lists.
In this context, JM made a case for the work being done at Kew by Govaerts.

(Nick Turland):

The ICBN can only be used to identify names that are validly and effectively published and therefore potentially useable. A non-taxonomist can do this part, but when it comes to identifying the accepted name, a taxonomist is required.
Registration had been approved as a concept in previous congress (Tokyo) but rejected by St Louis.

Approval was subject to a workable system being presented to St Louis.
Trial period for several years, coordinated by IAPT; some journals printed that they were accredited. Gerry Moore secretary of a Committee still working on it.
Not enough people at St Louis liked the system.
Valid publication depended on the registration, and this counted against it. Need incentive, but used stick rather than carrot.
Developing countries with limited internet access did not like the process (including China). Bandwidth and political blocking are both issues.
If published in a journal that did not have registration authority could send reprints through the post - however, if postal service bad you might never know if the name is registered or not.
Needs funding – this is more difficult now than it was, perhaps. IAPT might be coordinating body
MycoBank – setting it up anyway and will provide a model.

JM was chair of IOPI – a project that had initially attempted to merge existing databases (quick and dirty) – insufficient funds at the time. Although being weeded out, noted existence still in IPNI of “names” that were based on someone’s circumscription (“misidentifications”) and were not typifiable names.
2 proposals on electronic publication up for next congress:

e-journal which is ‘deposited’ in ‘several’ botanical libraries; pdf on website;
cd-rom, to be deposited in a number of libraries
Both are likely to fail.

May be progress on harmonisation of terms (some specific proposals) – need to have agreement in principle with other codes – will probably go though a system of multiple synonym terms being used.
Generic names must not end in ‘-virus’, ‘-viridae’ etc to avoid confusion with viruses

Zoology (Andrew Polaszek):

ICZN, founded 1895, 25 commissioners from 20 countries (Neal Evenhuis, President).
Supported by the International Trust for Zoological Nomenclature. Currently no direct government funding
Mandates: CBD, IUBS, ICSU.
Commission decides on nomenclatural questions that are published in the Bulletin of Zool. Nom.; Acceptance – Rejection of names, etc.
ICZN needs to catch up with new technologies.
In future wants to

move toward web-based taxonomy,
provide an annotated, user-friendly ICZN on the web
produce an electronic version of the Bulletin,
collaborate in the production of authoritative lists of genus and species names,
win support from the user community to act as registrar for the validation of new animal names, re-examine the feasibility of a unified code for naming all organisms (biocode).
find technical solution to several nomenclatural difficulties (e.g. gender agreement).

Changes in the code are needed to promote rapid naming of remaining biodiversity: A list of authoritative (available) animal names. Automatic catching of junior homonyms, automatic orthographic correction, etc. etc.
Note CBD endorsement from IV/1.D (for all codes)

Virus (Mike Mayo):

Regulated nomenclature only since 1966.
Includes both taxonomy and nomenclature!
The main need was for taxonomic order; only recently has nomenclature come to the fore.
Just within the last 5 or 6 years have species been recognized; taxonomic recognition of species is still wobbly.
Genus name follows the species name!
Genus names will end in ‘-virus’ if they are brought into use
If a name is written in italics it refers to the species, if not in italics it refers to a member of the species
Vernacular name of virus is same as species name
Not all viruses are in families
Many viruses of insects are given the Latin name of the insect followed by ‘virus’
No rule of priority; the ICTV votes on whether a name is valid or not.
There are only 2000 species recognized. 5000+ ‘isolates’ in database, each with identification number (=GUID)
What is a species? Much debate; is decided upon by groups of experts.
Building the ICTVdB; it is sharing information with ITIS and Species 2000.
Conservation of the common name within the scientific name.
GBIF names are not italicised entirely correctly

Botanical practice is to italicise names above genus; we should look at database representation

Bacteria / Prokaryotes (Brian Tindall):

Please see additional details about the Role of the ICSP in the Nomenclature and Taxonomy of Prokaryotes in the appendix at the end of this document.

ICNB originated in a split off from botany, and is changing its name to an ICN of Prokaryotes.
Like all codes: it regulates nomenclature, requires designation of types, and a formal circumscription.
First pure cultures established in about 1880; anaerobes from about 1930. The concept of a type strain dates from about 1920 – 1930.
Had to break with the past and selected a new starting date: 1 Jan 1980.
The first step was to create the Approved Lists of Bacterial Names and “protect” them. Some names maintained, with a reference back in time (and refer back to the original description).
The Approved Lists contains all names considered to have standing in nomenclature at 1.1.80; no names may be added or deleted from this list
Older names not in the Approved lists may be reused, but their authors and dates are those determined at the time of publication. (but may still refer to the original description)
Names considered to be validly published only if published in Int J. Syst Bact [=Int.J.Syst.Ev.Mic.] (- a form of compulsory registration / indexing) – may be repeated from other journal, but date of publication is the IJSEM
Taxonomic synonyms highly complicated because of differing and rapidly changing concepts.
Are tracking taxonomic concept (circumscription) in synonymies, even though these are not covered by code – is a practice not a requirement – yet voluntary form of tracking changing concepts has been introduced.
Some known (homotypic) synonyms are on the Approved Lists (because of taxonomic uncertainties at that time)
Others are not (e.g. Bacillus pestis is not to be found because only Yersinia pestis is there – and reflected the consensus of taxonomic opinion at the time)
Code is no longer independent of botanical and zoological codes, although past codes did accept homonyms of zoological and botanical names which were NOT fungal, algal, or protozoan names
Problem to locate these homonyms and determine whether there are dangers of misunderstandings with botanical and zoological names
Users include regulatory authorities – Risk groups 1-4 and transport regulations (A/B) – medical and food microbiology community, laboratory safety, national/EU regulations – therefore v. important to portray synonyms in correct fashion and get names right.
Also important to get subspecies and serovar correct
If name is in “quotation marks” it is not validly published according to the Code (may be in synonym list for historical reasons).
Serotypes (serovars) may be placed in genera - but they are not species (there may be many hundreds within a species).

4.4 Discussion of indexing and listing – Registration/indexing

viruses and bacteria have means in place; zoology has a desire to move in this direction. Botany had it but has dropped it. All following action points have already been implemented in microbiology and virology.
It seems that the potential for adoption of registration/indexing is not too far in the future.
Worry about the amateur taxonomic community.
“Gentle registration/indexing” needed, good and easy to use product.
Start with such lists as exist of validly published / available names. Now build lists of names in common use.
Botanists less concerned with developing list of validly published names than are zoologists, but problems in compiling such a list are fewer
Consensus that “quick and dirty” lists should be made available (with caveats) with plea for community input to the corrections.

4.5 Harmonisation of Codes

Revive discussion of the Codes, particularly harmonisation of the terms as a start (Hawksworth).
Make GBIF – Code agreements to have GBIFs display of lists checked by Code experts so that the form of names in our lists is correct (short term).
In longer term, GBIF could work with the Codes toward lists of Names in Current Use and harmonisation of terms (Jim Edwards).
There appears to be need for an in depth discussion about the different way certain concepts are implemented – dichotomy between zoology vs botany-bacteriology apparent.

4.6 GBIF affiliation/membership for Code organisations – pros and cons

(Jim Edwards)

GBIF needs to be able to capture names correctly and appropriately – we need agreement with each of codes separately to vet current lists and clean up the contents
The Three Year Review of GBIF points out that GBIF does not have enough funding, and needs to restructure and rethink in order to conduct proposed mission; it is now the time to think how to work with codes in Phase II, beginning January 2007.
GBIF cannot provide day-to day support for Codes and their secretariats
Can identify project oriented activities, e.g. format and display of names (Could develop projects this year on this.) Development of tools to develop Codes and taxonomists in their day-to-day work. [BBSRC has called for proposals due on Wednesday to implement Godfray’s ideas –check it out! – proposed mechanism needs to work with GBIF]. MoC cf that with Catalogue of Life Partnership, where funds are being provided to increase the rate of data provision.
If Codes are associate participant, they could provide info such as web sites with codes, terms and glossaries and equivalent terms
Joint projects to put before foundations or other funding organisations.
(right now working with TDWG on this basis to put it on a better footing)
Associate Participants provide data (of some sort); get to be at the table and make views known and get a seat on NODES. Have to find funds to get delegations to GB meetings.

Positive responses from around the table – with exception of a general agreement that the work associated with Codes was not fully appreciated and that such work also needs sound, long term funding, on which various ongoing databases, such as NCBI can continue to draw. General discussion followed.

Appendix

The Role of the ICSP (International Committee on Systematics of Prokaryotes) in the Nomenclature and Taxonomy of Prokaryotes.

The ICSP is an international committee within the International Union of Microbiological Societies (IUMS) which is responsible for matters relating to prokaryote nomenclature and taxonomy.

The ICSP consists of an executive board, the members of the Judicial Commission, and members elected from member societies of the IUMS. In addition the ICSP also has a number of subcommittees which deal with matters relating to the nomenclature and taxonomy of specific groups of prokaryotes. The ICSP is also responsible for overseeing the publication of the Internationl Code of Nomenclature of Bacteria (the Bacteriological Code) and the International Journal of Systematic and Evolutionary Microbiology (formerly the International Journal of Systematic Bacteriology). IUMS has now agreed to transfer copyright of future versions of the Internatioanl Code of Nomencalture of Bacteria (to be renamed the International Code of Nomenclature of Prokaryotes) to the ICSP.

During the 1960's the Judicial Commission recognised the need to deal with a problem which continues to affect other Codes of Nomenclature, the problem of knowing how to apply all published names of taxa. The solution which was sought involved the review of as many published names as possible, with respect to forgotten (old) and useless names. Although botany and zoology have examined ways of solving this problem by the use of "Names in Current Usage" (botany) or introducing a rule by which names not used for 50 years need no longer be taken into consideration (zoology), none of these solutions have been totally satisfactory (or abandonded). The solution in prokaryote nomenclature was to introduce a list of protected names (the Approved Lists of Bacterial Names) together with an official system of registration/indexing of new names and combinations. The Bacteriological Code was altered in order to conform to this new way of working. The publication of the Approved Lists in January 1980 included those names which had been identified by appropriate types and circumscriptions. Names which were not included on this list were considered to no longer have standing in nomenclature. In addition, only names which were published in accordance with the Bacteriological Code (officially registered/indexed) could be considered to have standing in bacterial nomenclature. Technically, such names are "validly published", but there may be confusion with the same term under the ICBN, where it does not (currently) involve compulsory registration/indexing.

In order for the current system to work all new names and combinations validly published appear in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). This journal is the official journal of the ICSP and ensures that the system of valid publication of a name or a new combination is also overseen by the ICSP. Valid publication of a new name or a new combination may be either via an original publication in the IJSEM or by notification of the fact that effective publication of the name or new combination has appeared in another journal, via the "Notification Lists". In continuing it's policy of innovation members of the ICSP have seen the need to also provide a central list of changes of taxonomic opinion which have not resulted in the creation of new names or new combinations. Both these lists and the "Notification Lists".are the responsibility of the "Lists Editor", who is currently Dr. Jean P. Euzéby.

Within the ICSP, the Judicial Commission is responsible for ruling on any problems which arise in the nomenclature of prokaryotes, and the editorial board of the Bacteriological Code is responsible for overseeing and publishing changes to the published version of the Code.

The ICSP (including the Judicial Commission and the Lists Editor) is responsible for the working of the current Bacteriological Code and it's system of registering/indexing names. Consequently, this body is the sole "authority" for governing on the implementation of the Bacteriological Code and determining which names are validly published (or may be validly published). Some confusion has arisen in the past (and continues to be perpetuated at present) by drawing up lists of names which either have not taken the Bacteriological Code into consideration, or have resulted from incorrect interpretation of the Code. It is important that any future work involving the drawing on of lists of names of prokaryotes involves those people who are familiar with those lists and their contents, together with the workings of the Bacteriological Code. This should avoid misunderstandings, or misinterpretations relating to the content and purpose of lists of validly published prokaryotic names, as well as using them as a basis for lists which may be developed, based on the application of the taxonomic opinion of appropriate authorities in this field.

Hans G. Trüper

Chaiman of the Judicial Commission of the ICSP

Brian J. Tindall

Vice chairman of the Judicial Commission of the ICSP

Braunschweig 1st. June, 2005