STRUCTURE OF GBIF-GERMANY

AND DETAILS ON THE ORGANIZATION AND WORK

OF THE NODE

PROKARYA AND VIRUSES

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

GBIF Content and Connections

Existing responsibilities

of other organizations

Climate Data

Climate Data

CHMCHM

Sequence Data (GenBank, RNA, protein,

etc.)

Sequence Data (GenBank, RNA, protein,

etc.)

Ecosystems Data

Ecosystems Data

Geospatial Data

Geospatial Data

Ecological Data

Ecological Data

Content area responsibilities of GBIF

Catalog of Names of

Known Organisms

Catalog of Names of

Known Organisms

Search Engines

Biological Specimen

Data

Access/Inter-

operability

adapted from GBIF.ORG

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

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

STRUCTURE OF GBIF

PARTICIPANTS STRUCTURE: NODE REQUIREMENTS AND RECOMMENDATIONS

● the Participants‘ Representative in the GBIF Governing Boardshould 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 be one 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 areData andMetadata describing the service

each Node should have

● Node Webmasterwho 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

PARTICIPANTS STRUCTURE: NODE REQUIREMENTS AND RECOMMENDATIONS

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

In Germany we decided for a decentralized GBIF Network

Botany (vascular plants, mosses, algae, protista): Botanical Garden and Museum, Berlin-Dahlem

Prokarya and Viruses (bacteria, archaea, cyanobacteria, viruses): German Coll. of Microorganisms and Cell Cultures, Braunschweig

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

Evertebr. I

Evertebr. III

Evertebr. II‘marine‘

Room has been Given for Systematic Overlap Between Nodes for e.g. Technical or Ecological Reasons

Prokarya+Viruses

Mycology‘filamentous‘

Botany

‘cellular level‘

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Overarching Coordination Structure of GBIF-Germany

status seminars, regular meetings

E.g. Cooperating Partners Prokarya and Viruses

E.g. Cooperating Partners Botany

Each Node Established its Own Cooperative Network

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

(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

Some Characteristics of Microbiological Collections

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

REORGANIZATION OF BACTERIAL TAXONOMY 1980

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

CONCEPT OF SPECIES VALIDATION

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

CONCEPT OF SPECIES VALIDATION

original publication or validation list

Regularly Updated Information Combining Approved Lists and All Validation Lists

Expertise of WFCC, ECCO, CABRI etc. is feeding into GBIF

INTERNATIONAL LEVEL

REGIONAL LEVEL

NATIONAL LEVEL

DSMZINDIVIDUAL NAT. INSTITUTIONS

GBIF WFCC/WDCM

ENBI

EBRCN/CABRI/ ECCO

GBIF-D GBIF-Y

OECD-BRCOECD-BRC

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

Institute No. of Strains

Data digitized non-digitized

public release

MTA1 Interested in

Cooperat. Myxobakterien, GBF, Braunschweig

8.000 - + + + +

Inst. Meereskunde, Kiel, WGL

4.000 few + + + +

TU München 3.500 few + + + + Phytopathogene Bakt. Göttingen, Univ.

3.100 most + + + +

Hohenheim, Univ. 3.000 few + + + + Tübingen, Univ. 3.000 most + + + + Konstanz, Univ. 2.000 most + + + + Mainz, Univ. 1.900 few + n.a. n.a. + Regensburg, Univ. 1.500 - + + + + Rostock, Univ. 1.000 most + + + + Hannover, Univ. 900 few + + - + Würzburg, Univ. 500 few + n.a. - + Oldenburg, Univ. 500 few + + + + Ernährungsforschung Potsdam, WGL

160 most + + - +

GH Essen, Univ. 100 most + + + + Leipzig, Univ. 50 few + + - + Marine Mikrobiologie, MPI, Bremen

15 few + + + +

1 MTA, Material Transfer Agreement (supply to third parties only under non-commercial use; part. = partially; n.a. = no answer

EXCERPT FROM EVALUATION OF QUESTIONNAIRE

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

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

digitiz. of data

scient. eval. of data

connection to GBIF

implement. of QC construc./adapt. of DB

SELECTED SUBPROJECTS WITHIN NODE PROKARYOTES AND VIRUSES

(1) 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

Defining kind, amount and distribution of work

DSMZ SERVER

● queries in data bases held DBs of DSMZ DBs of coop. partners

● links to external DBs

GBIF international

GBIF national

user

user

user

user

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

adaptation of DBdigitization of data by coop. partnerCABRI standard in coop. with DSMZDB on partner servercurating and updating at partner site

registration of DBs

digitization at DSMZ

CABRI standard at DSMZ

data included into DSMZ DB

curating and updating at DSMZ

biol. mat. transferred to DSMZ

own DB: transformation into dynamic web pages, while maintaining static ones

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

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

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

Antagonistic Bacterial Strains Producing Pectinases (Top of Data Report)

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

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

Data entry: Detailed Information on Names of Bacterial Species

Data Entry: Taxonomic Literature

Data Entry: E.g. Collection Numbers of Type Strains

Collection Data of GBIF Germany Online as of 29 June 2006

Data Provider Online Data

Contact

BfN - Bundesamt für Naturschutz, Zentralstelle für Phytodiversität, Bonn

4.191.371

GBIF-D Botanik, Teilprojekt Floraweb: Anbieter: Dr. Rudolf May, Kontakt: Agnes Kirchhoff (a.kirchhoff@bgbm.org)

SysTax, Universität Ulm

341.552

SysTax ist Provider von Evertebrata I, II, Vertebrata: Jürgen Hoppe (juergen.hoppe@biologie.uni-ulm.de)

FH Weihenstephan 263.572

GBIF-D Botanik "Süddeutsche Bergwälder": Anbieter: Prof. Dr. Jörg Ewald, Kontakt: Agnes Kirchhoff (a.kirchhoff@bgbm.org)

FIS Forschungsinstitut Senckenberg, Frankfurt a. M.

256.514

GBIF-D Evertebrata III: verschiedene Daten einschließlich am FIS gehosteter Datenbanken Kontakt: Dr. Michael Türkay (michael.tuerkay@senckenberg.de)

IPK Gatersleben 109.711

GBIF-D Botanik, Teilprojekt 4 - Alliaceae, Lamiaceae, DB Genebank Akzessions: Anbieter: Dr. Helmut Knüpfer, Kontakt: Agnes Kirchhoff (a.kirchhoff@bgbm.org)

BGBM Botanischer Garten und Botanisches Museum Berlin-Dahlem

81.279

GBIF-D Botanik: verschiedene Daten einschließlich am BGBM gehosteter Datenbanken ; Kontakt: Agnes Kirchhoff (a.kirchhoff@bgbm.org)

Gesellschaft wissenschaftlicher Datenverarbeitung mbh, Göttingen

45.102

GBIF-D Botanik, Teilprojekt 6 - Moostypen und neotropische Moose Göttingen: Anbieter: Prof. Dr. S.R. Gradstein, Kontakt: Agnes Kirchhoff (a.kirchhoff@bgbm.org)

Herbarium Hamburg 34.951 Herbarium Hamburg; Kontakt: Agnes Kirchhoff (a.kirchhoff@bgbm.org)

ZFMK- Zoologisches Forschungsinstitut und Museum A. Koenig, Bonn (Dipteren-Sammlung)

18.587

GBIF-D Evertebrata I: verschiedene Daten einschließlich am SMNS gehosteter Datenbanken; Kontakt: Dr. Christoph Häuser (chaeuser@gmx.de)

Bodensee -Naturkundemuseum Konstanz

15.827 (Bodensee-Naturkundemuseum Konstanz)

HU - Humboldt Universität Berlin

15.326 Tierstimmenarchiv im Institut für Biologie; Kontakt: Dr. Karl-Heinz Frommolt (tsa@rz.hu-berlin.de)

DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig

10.961

GBIF-D Prokaryonten: Prof. Dr. Erko Stackebrandt (erko@dsmz.de), Dr. Dagmar Fritze (dfr@dsmz.de)

BSM - Botanische Staatssammlung München

7.867

GBIF-D Mykologie: verschiedene Daten einschließlich am BSM gehosteter Datenbanken; Kontakt: Dr. Dagmar Triebel (triebel@bsm.mwn.de)

HU - Humboldt Universität Berlin

2.892 Museum für Naturkunde Berlin

Summe 5.361.467

Collection Data of GBIF Germany Online as of 29 June 2006

● 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

Facts that need to be considered by collections that hold living biological material wishing to contribute to GBIF:

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

THANK YOU !