Transcript Folie 1

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
Content area responsibilities of GBIF
Biological
Specimen
Data
Catalog of
Names of
Known
Organisms
Sequence Data
(GenBank, RNA, protein,
etc.)
CHM
Geospatia
l Data
Climate
Data
Search
Engines
Access/Inter
-operability
Ecosystems
Data
Ecological
Data
adapted from GBIF.ORG
Existing
responsibilities
of other
organizations
Heterogeneous
Databases
Web
Services
Standardized
Structured Data
Internet
User
request/response
prerequsite: agreed formats, fields, contents of fields;
taxonomic + systematic agreements needed
adapted from GBIF.ORG
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
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 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 are
Data and
Metadata describing the service
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
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
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
Botany (vascular plants, mosses,
algae, protista): Botanical Garden
and Museum, Berlin-Dahlem
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
Room has been Given for Systematic Overlap Between
Nodes for e.g. Technical or Ecological Reasons
Evertebr. I
Evertebr. III
‘filamentous‘
Mycology
Prokarya
+Viruses
Botany
‘marine‘
‘cellular level‘
Evertebr. II
Overarching Coordination Structure of
GBIF-Germany
status seminars, regular meetings
Each Node Established its Own Cooperative Network
E.g. Cooperating Partners
Prokarya and Viruses
E.g. Cooperating
Partners Botany
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
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
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
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
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
OECD-BRC
GBIF
ENBI
REGIONAL
LEVEL
EBRCN/
CABRI/
ECCO
GBIF-D
GBIF-Y
DSMZ
INDIVIDUAL NAT.
INSTITUTIONS
NATIONAL
LEVEL
WFCC/WDCM
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
EXCERPT FROM EVALUATION OF QUESTIONNAIRE
Institute
No. of
Strains
Data
digitized
non-digitized
public
release
MTA1 Interested
in
Cooperat.
+
+
Myxobakterien, GBF,
8.000
+
+
Braunschweig
Inst. Meereskunde,
4.000
few
+
+
+
+
Kiel, WGL
TU München
3.500
few
+
+
+
+
Phytopathogene Bakt.
3.100
most
+
+
+
+
Göttingen, Univ.
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
160
most
+
+
+
Potsdam, WGL
GH Essen, Univ.
100
most
+
+
+
+
Leipzig, Univ.
50
few
+
+
+
Marine Mikrobiologie,
15
few
+
+
+
+
MPI, Bremen
1
MTA, Material Transfer Agreement (supply to third parties only under non-commercial use;
part. = partially; n.a. = no answer
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
user
Defining kind, amount and distribution of work
user
GBIF international
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
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
BfN - Bundesamt für
Naturschutz,
Zentralstelle für
Phytodiversität, Bonn
GBIF-D Botanik, Teilprojekt
Floraweb: Anbieter: Dr. Rudolf
4.191.371
May, Kontakt: Agnes Kirchhoff
([email protected])
SysTax, Universität
Ulm
FH Weihenstephan
FIS Forschungsinstitut
Senckenberg,
Frankfurt a. M.
IPK Gatersleben
BGBM Botanischer
Garten und
Botanisches Museum
Berlin-Dahlem
Contact
341.552
SysTax ist Provider von
Evertebrata I, II, Vertebrata: Jürgen
Hoppe
([email protected])
263.572
GBIF-D Botanik "Süddeutsche
Bergwälder": Anbieter: Prof. Dr.
Jörg Ewald, Kontakt: Agnes
Kirchhoff ([email protected])
256.514
GBIF-D Evertebrata III:
verschiedene Daten einschließlich
am FIS gehosteter Datenbanken
Kontakt: Dr. Michael Türkay
([email protected])
109.711
GBIF-D Botanik, Teilprojekt 4 Alliaceae, Lamiaceae, DB
Genebank Akzessions: Anbieter:
Dr. Helmut Knüpfer, Kontakt:
Agnes Kirchhoff
([email protected])
81.279
GBIF-D Botanik: verschiedene
Daten einschließlich am BGBM
gehosteter Datenbanken ; Kontakt:
Agnes Kirchhoff
([email protected])
Collection Data of GBIF Germany Online as of 29 June 2006
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 ([email protected])
Herbarium Hamburg
34.951
Herbarium Hamburg; Kontakt:
Agnes Kirchhoff
([email protected])
ZFMK- Zoologisches
Forschungsinstitut und
Museum A. Koenig,
Bonn (DipterenSammlung)
18.587
GBIF-D Evertebrata I:
verschiedene Daten einschließlich
am SMNS gehosteter
Datenbanken; Kontakt: Dr.
Christoph Häuser
([email protected])
Bodensee Naturkundemuseum
Konstanz
15.827
(Bodensee-Naturkundemuseum
Konstanz)
HU - Humboldt
Universität Berlin
15.326
Tierstimmenarchiv im Institut für
Biologie; Kontakt: Dr. Karl-Heinz
Frommolt ([email protected])
10.961
GBIF-D Prokaryonten: Prof. Dr.
Erko Stackebrandt
([email protected]), Dr. Dagmar
Fritze ([email protected])
BSM - Botanische
Staatssammlung
München
7.867
GBIF-D Mykologie: verschiedene
Daten einschließlich am BSM
gehosteter Datenbanken; Kontakt:
Dr. Dagmar Triebel
([email protected])
HU - Humboldt
Universität Berlin
2.892
Museum für Naturkunde Berlin
Summe
5.361.467
DSMZ - Deutsche
Sammlung von
Mikroorganismen und
Zellkulturen,
Braunschweig
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
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 nonclassified isolates
THANK YOU !