Module 2B - Building GBIF Nodes III: strategically positioning your Node
STRUCTURE OF GBIF-GERMANY AND DETAILS ON THE ORGANIZATION AND WORK OF THE NODE
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Transcript of STRUCTURE OF GBIF-GERMANY AND DETAILS ON THE ORGANIZATION AND WORK OF THE NODE
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 ([email protected])
SysTax, Universität Ulm
341.552
SysTax ist Provider von Evertebrata I, II, Vertebrata: Jürgen Hoppe ([email protected])
FH Weihenstephan 263.572
GBIF-D Botanik "Süddeutsche Bergwälder": Anbieter: Prof. Dr. Jörg Ewald, Kontakt: Agnes Kirchhoff ([email protected])
FIS Forschungsinstitut Senckenberg, Frankfurt a. M.
256.514
GBIF-D Evertebrata III: verschiedene Daten einschließlich am FIS gehosteter Datenbanken Kontakt: Dr. Michael Türkay ([email protected])
IPK Gatersleben 109.711
GBIF-D Botanik, Teilprojekt 4 - Alliaceae, Lamiaceae, DB Genebank Akzessions: Anbieter: Dr. Helmut Knüpfer, Kontakt: Agnes Kirchhoff ([email protected])
BGBM Botanischer Garten und Botanisches Museum Berlin-Dahlem
81.279
GBIF-D Botanik: verschiedene Daten einschließlich am BGBM gehosteter Datenbanken ; Kontakt: Agnes Kirchhoff ([email protected])
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 (Dipteren-Sammlung)
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])
DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig
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
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 !