STRUCTURE OF GBIF-GERMANY AND DETAILS ON THE ORGANIZATION AND WORK OF THE NODE

1. STRUCTURE OF GBIF-GERMANY AND DETAILS ON THE ORGANIZATION AND WORK OF THE NODE PROKARYA AND VIRUSES

2. To recall: The Global Biodiversity Information Facility had been designed as an ● interoperable, distributed network of scientific biodiversity databases with the goal ● to make the world‘s scientific biodiversity data freely available and easily accessible and the decision ● to initially focus on species- and specimen – level data ● to link into existing molecular, genetic and ecosystem level data

3. Content area responsibilities of GBIF Sequence Data (GenBank, RNA, protein, etc.) Catalog of Names of Known Organisms Biological Specimen Data CHM Geospatial Data Climate Data Search Engines Ecosystems Data Existing responsibilities of other organizations Access/Inter-operability Ecological Data GBIF Content and Connections adapted from GBIF.ORG

4. Heterogeneous Databases Web Services Standardized Structured Data Internet User request/response request/response request/response prerequsite: agreed formats, fields, contents of fields; taxonomic + systematic agreements needed adapted from GBIF.ORG

5. STRUCTURE OF GBIF Governing Board Chair Members: representatives of all participants ● voting, ● associate (countries, economies), ● associate (organizations), ● ex-officio representative Committees ● Budget C‘ttee, ● Executive C‘tee, ● Participant Node Managers C‘ttee, ● Science C‘ttee ● Subc‘ttee Data Access and Data Interoperability ● Subc‘ttee Digitisation of Natural History Collection Data ● Subc‘ttee Electronic Catalogue of Names of Known Organisms ● Subc‘ttee Outreach and Capacity Building Secretariat Director, Deputy Directors, Communications Officer, Liaison Officer, Programme Officers, System Administrators, Secretaries

6. PARTICIPANTS STRUCTURE: NODE REQUIREMENTS AND RECOMMENDATIONS ● the Participants‘ Representative in the GBIF Governing Board should be at the same time the ● NODE‘s Manager with the task of overall node management and the ● Directory Administrator resonsible for updating information at the central GBIF directory ● Nodes can beone or several ● Participants‘ Node (provides the gateway) ● Data Node (provides data) ● in case one central node is established, this serves both purposes ● in case several equivalent nodes are established, all or one of them take over participant node tasks ● contents of the nodes are Data and Metadata describing the service

7. PARTICIPANTS STRUCTURE: NODE REQUIREMENTS AND RECOMMENDATIONS each Node should have ● Node Webmaster who has the task to administer the web design, operation and support, and who coordinates activities with the GBIF Secretariat Webmaster ● Systems Administrator who has the task of host administration and operation, and who may coordinate activities with the GBIF Host Master

8. In Germany we decided for a decentralized GBIF Network Instead of one central node, Germany established a network of nodes, each located and maintained at institutions renowned for their systematic expertise in the field ● coordination of GBIF-D is through the German science and education ministry ● partition of work follows ● systematic structures ● available systematic expertise in Germany ● the expected amount of data Botany +Mycology Vertebrata +Evertebrata I, II, III Prokarya and Viruses

9. Prokarya and Viruses (bacteria, archaea, cyanobacteria, viruses): German Coll. of Microorganisms and Cell Cultures, Braunschweig Botany (vascular plants, mosses, algae, protista): Botanical Garden and Museum, Berlin-Dahlem Vertebrates (fishes, amphibians,reptiles, birds, mammals): Zoological Research Museum König, Bonn Evertebrata III (marine invertebrates, crustaceae, bryozoa, cnidaria, annelida): Senckenberg Research Museum, Frankfurt Evertebrata I (insecta): Natural History Museum, Stuttgart Evertebrata II (mollusca, chelicarata, myriapoda): Zoological Institute, University München Mycology (fungi, lichens): Botanical Institute, University München

10. Room has been Given for Systematic Overlap Between Nodes for e.g. Technical or Ecological Reasons Evertebr. I Evertebr. III } } } Evertebr. II ‘marine‘ ‘filamentous‘ Mycology } Prokarya+Viruses ‘cellular level‘ Botany

11. Overarching Coordination Structure of GBIF-Germany status seminars, regular meetings

12. Each Node Established its Own Cooperative Network E.g. Cooperating Partners Prokarya and Viruses E.g. Cooperating Partners Botany

13. Structure and Work of the German Node Prokarya and Viruses Coordinator DSMZ Organisms covered: Bacteria, Archaea, Plant Viruses General Aims: ● Creation of a common internet portal for the prokaryotic collection data bases of Germany and connection to GBIF international ● Furthering of the digitisation of available data ● Harmonization of raising of data in German collections of prokaryotes and viruses ● Creation of virtual microbial collections across fields of work ● Close cooperation with the other national nodes, with GBIF international and other national and international organisations

14. Some Characteristics of Microbiological Collections (1) earlier than all other collections of biological material we have provided information on that material via hard copy and electronic catalogues, not only individually but also as cooperation initiatives (2) examples for digitization efforts and electronic catalogues are WDCM (since the early 70ies, www.wdcm.org), MINE (‘86-‘93) and CABRI (’96-’99, www.cabri.org) (3) 1980 reorganization of bacterial taxonomy and nomenclature (4) we collect and hold living biological material

15. REORGANIZATION OF BACTERIAL TAXONOMY 1980 CONCEPT OF SPECIES VALIDATION Approved Lists >> date for recognition of priority of new names APPROVED LISTS (1980) >40.000 species reduced to ~ 4.000 Criteria:  adequately described;  cultivable;  type -, neotype - or reference strain available  Only those names listed need to be taken into consideration when describing a new species

16. CONCEPT OF SPECIES VALIDATION LAYS DOWN RULES FOR THE DESCRIPTION OF A BACTERIAL SPECIES e.g. ● publication of new name in IJSB/ IJSEM ●or in its Validation List ●deposit of type strain Rule 30: A viable culture of the type strain of a given species must be deposited with two public service culture collections, located in two different countries [preferably in two different regions in the world], from which subcultures would be readily available

17. CONCEPT OF SPECIES VALIDATION original publication or validation list

18. Regularly Updated Information Combining Approved Lists and All Validation Lists

19. Expertise of WFCC, ECCO, CABRI etc. is feeding into GBIF OECD-BRC GBIF WFCC/WDCM INTERNATIONAL LEVEL ENBI REGIONAL LEVEL EBRCN/CABRI/ ECCO GBIF-D GBIF-Y NATIONAL LEVEL INDIVIDUAL NAT. INSTITUTIONS DSMZ

21. Structure and Work of the German Node Prokarya and Viruses First Steps: Document national prokaryotic collections in universities and other research institutions and to ●evaluate their contents with respect to amount of digitized and non-digitized data ●availability of biological material ● and quality of data and material Questionnaire main content: ● kind of material collected, ● size of collection, ● kind of data available, ● level of digitization of data, ●general willingness of curators to provide access to data and biological material prerequisite for participation (1) availability of biological material (2) quality of data Ad (2): level of minimum data required; based on CABRI

22. EXCERPT FROM EVALUATION OF QUESTIONNAIRE

23. Structure and Work of the German Node Prokarya and Viruses Selection criteria for Partners Priority was given to ● specialized collections of agricultural, environmental or medical relevance ● which may be physiologically, phylogenetically or ecologically defined ● complementing the holdings of DSMZ

24. Level of Availability of Data and Necessary Work Expl. Myxobact., 8000 strains, non-digitized data, direct transfer into DSMZ format Expl. Göttingen, 3000 strains, basic data digitized, excel tables Expl. Lab.1, No of strains <1000, basic data partially digitized, data base exists, format partially compatible Expl. Lab.2, No of strains <1000, basic data partially digitized, word processor lists+tables Expl. Lab.3, No of strains <1000, non-digitized data connection to GBIF digitiz. of data construc./adapt. of DB scient. eval. of data implement. of QC

25. SELECTED SUBPROJECTS WITHIN NODE PROKARYOTES AND VIRUSES • Antagonistic bacteria against phytopathogenic fungi, University of Rostock • (2) Collection of phytopathogenic bacteria, University of Göttingen • (3) Collection of myxobacteria 'Reichenbach‘, GBF Braunschweig • (4) Collection of Gram positive and Gram negative pathogens, University of Würzburg • (5) own DSMZ Data bases • (5a) bacteria and archaea • (5b) plant viruses • additionally, not included in project • (5c) fungi • (5d) plant cell cultures

26. adaptation of DB digitization of data by coop. partner CABRI standard in coop. with DSMZ DB on partner server curating and updating at partner site construction of DB digitization of data by coop. partner CABRI standard in coop. with DSMZ DB to be hosted on DSMZ server curating and updating by partner digitization at DSMZ CABRI standard at DSMZ data included into DSMZ DB curating and updating at DSMZ biol. mat. transferred to DSMZ Defining kind, amount and distribution of work user GBIF international user user GBIF national user DSMZ SERVER ●queries in data bases held DBs of DSMZ DBs of coop. partners ●links to external DBs own DB: transformation into dynamic web pages, while maintaining static ones registration of DBs

27. A FEW GENERAL REMARKS • ●GBIF does not yet fully serve the requirements of microbial diversity • ●GBIF needs more microbiologically driven input (not least with a view to emerging discussion on GUIDS) • ●ABCD Format is closer to our needs than DarwinCode and is developing • ●When designing the databases for our partner collections their particular needs and wishes were widely followed; this resulted in more detailed work as originally necessary for GBIF and in more data than presently acceptable by GBIF • The rationale behind was • ●microbiology can not wait until the zoological and botanical taxonomists have done their ‘home work‘ • ●maintain attractiveness of these databases after cessation of GBIF funding • ● provide prototypes for detailed-data databases with a view to potential future expansion of the GBIF network

28. Expl. 1: User-surface; retrieval of data reports for antagonists, plant pathogens (drop-down menue opened), antagonistic metabolites or enzymes

29. Bacterial Strains Exerting Antagonistic Activity Against Plant Pathogen Rhizoctonia solani (Top of Data Report)

30. Antagonistic Bacterial Strains Producing Pectinases (Top of Data Report)

31. Expl. 2: Data Input; E.g. Data of Biosafety/Biosecurity Relevance

32. Expl. 3: Data Entry; Synonyms of Bacterial Species. ‘Correct Name‘ is that one, which, According to the International Code of Nomenclature of Bacteria (1990 Revision) should preferably be used

33. Data entry: Detailed Information on Names of Bacterial Species

34. Data Entry: Taxonomic Literature Data Entry: E.g. Collection Numbers of Type Strains

35. Collection Data of GBIF Germany Online as of 29 June 2006

36. Collection Data of GBIF Germany Online as of 29 June 2006

37. Facts that need to be considered by collections that hold living biological material wishing to contribute to GBIF: • ● when data of holdings are made available, interest rises in the biological material, thus more requests will come in • ● when supplying the living biological material, the stock may be used up • ● which would make recultivation, reconservation, reidentification etc. necessary • ● transport of living biological material underlies stringent requirements, laws and regulations • ● it is clear that infrastructure at collections needs to match the demands • ● expert staff in laboratory and office • ● technical equipment

38. Outlook/Remaining Work The task is enormous in the microbial world ●estimation that only 0.1% of existing microbial species have been described to data ●a manifold (x100?) of this figure are additional strains and non- classified isolates

39. THANK YOU !