- Bergey’s Manual
uBio – Universal Biological Indexer and OrganizeruBio develops the Taxonomic Names Server, a catalogue of names and classifications that enable enhanced searches in literature resources by linking names together, relation. The system is originally developed for the Library community but has great potential in scientific use.Names are stored in a layered model, where classifications/opinions/taxonomy (in ClassificationBank) is abstracted from the factual names occurrences together with objective synonyms (in NameBank). The layers are held together by a Management System.Numerous application tools for retrieving and storing information in the system are developed. Special emphasis on tools to match lists of names coming from users with the names already occurring in the system.The Online Computer Library Center’s (OCLC) WorldCat reference catalogue’s (http://www.oclc.org/worldcat) validation procedures were demonstrated as a possible solution for rapidly getting the system populated with names which then subsequently could become peer evaluated.uBio would like to collaborate with GBIF on developing the NameBank and share this resource among the organisations.
CoLp – The Catalogue of Life PartnershipThe CoLp operate a network of Global Species Databases and also some nomenclators are integrated with the system.CoLp has a MoC with GBIF, allowing GBIF to use their data in the GBIF Data Portal, provided that proper source recognition is transmitted with the data.
ICTVdB – The Universal Virus Database International Committee on Taxonomy of Viruses The ICTVdB is the de facto authority on both nomenclature and taxonomy of vira and stores a list of approved virus names.Virus taxonomy has no kingdom or phyla but handles strains and isolates. The ICTVdB, however, handles names only at the species level and above.The data is considered not complete, missing the rejected names.The names are stored in a DELTA based system which is scheduled to move into XML.Names are freely available through websiteICTVdB is already incorporated in the CoL and will want to collaborate with GBIF on bringing the Virus names into the system. Resources are needed to bring names from the present system and into a web-service.
IPNI – The International Plant Names IndexIPNI is a collaboration between The Royal Botanic Gardens, Kew, The Harvard University Herbaria, and the Australian National Herbarium. It contains a significant amount of all published plant names, but cleaning up the data, coming from three widely overlapping sources, is still an overwhelming task.The data sits in a highly integrated database system which provides a contributing mechanism and is machine reachable in a number of formats. The system can deliver query results as XML – there is a 5000 names limit per request.A condition for utilizing the data is that corrections are provided back into the system.APNI has a larger amount of data associated with the names than the other sources.IPNI has at present limited programming hours and need funding for additional work. However, great interest in collaboration is expressed.
Bergey’s Manual TrustBergey’s Manual can be seen as a Global Species Database (GSD) of all bacteria, containing 6466 prokaryote species and an authored taxonomy. The Manual is a commercial product, published by Springer-Verlag, the content forming base for income for the Trust.The data is – however – available free of charge in the form of pdf-files. The bacterial genera can be downloaded form the Trust’s homepage, the species can be acquired by contacting the Trust.Data is stored in a highly advanced system, stream-lined for publishing. The format is a specialized SGML.The taxonomy has links to GenBankIn order to establish machine access to the system, a mutual benefit statement will have to be developed.
ICSP – International Committee on Systematics of ProkaryotesModern prokaryote nomenclature has its starting point at January 1. 1980. The ICSP (then the International Committee on Systematics of Bacteria – ICSB) was involved in publishing the Approved Lists of Bacterial Names (ALBN) containing the bacterial names and combinations considered to have standing in nomenclature as of that date. Names in use previously, but not appearing on that list lost standing in nomenclature.The International Journal of Systematic and Evolutionary Microbiology (IJSEM) (formerly International Journal of Systematic Bacteriology) is the official organ of the ICSP, and is published for IUMS by the Society for General Microbiology (UK)– the journal in which a new prokaryote name or new combination must appear in order to be validly published.Hereby the name is also registered/indexed, which means that the ICSP officially publishes a complete nomenclatoral resource of prokaryotes. This comprises original publications in the IJSEM as well as the “Validation Lists”, in which new names or new combinations published outside of the IJSEM may be validly published (and registered/indexed). In addition, the “Notification Lists” in the IJSEM summarises formal nomenclatural changes which have appeared in articles in the IJSEM. Both the Validation Lists and the Notifications Lists are edited by the “List Editor” of the IJSEM, Jean P. Euzéby.The List of Bacterial Names with Standing in Nomenclature (LBSN) – a combination of the ALBN and the names appearing in the IJSB/IJSEM, is, compiled by J.P. Euzéby. The LBSN can be accessed at the LBSN website in HTML format.
IF – Index FungorumIF is the nomenclator of Fungi. Fungal names are available on-line through the IF web-site and as a web-service. For IPR reasons, detailed data concerning newly added names are not served.The IF web-service could relatively easily be integrated with GBIF. Data from the last five years will be provided with limited record contents.
ION – Index to Organism NamesThe animal names appearing in Zoological Record are being integrated into the ION which is searchable on the web. The issues dating back to 1970 have been scanned and incorporated. A CGI interface is available, possibilities for a Web-serviceThrough the 2003 Seed Money award to BIOSIS it is already established that GBIF will receive a package of all names appearing in ZR from 1970 to present. The access to earlier data will be topic of negotiation.
INA – Index Nominum AlgarumThe INA stores image files of a card file for all published algal names. The card files are in the process of being digitized into a database. The data include the basionym along with type information, locality and to some extend new combinations. INA’s web-site gives access to all images and all digitized names. No machine reachable data available.INA is in principle interested in providing data to GBIF, but infrastructure and resources will have to be worked out in order to make it happen.