The DNA Bank Network Gabriele Droege Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität Berlin.

Slides:

Advertisements

Similar presentations

Current Trends in Biodiversity Collection Description Neil Thomson The Natural History Museum.

Advertisements

The DNA Bank Network Use Cases Gabriele Droege Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität Berlin.

TF Data Standards & Data Access GGBN 2012 Meeting Plenary Gabi Droege (Chair), Jonathan Coddington, Paul Flemons, Adrian Hine, Éamonn Ó Tuama.

The SYNTHESYS Specimen and Observation Portal Kelbert, P., Holetschek, J., Güntsch, A., Kusber, W.-H., Zippel, E. & Berendsohn, W.G. Freie Universität.

Beispielbild The EDIT Platform for Cybertaxonomy Anton Güntsch Freie Universität Berlin Botanic Garden and Botanical Museum Berlin-Dahlem.

OpenUp! Technology Developments Anton Güntsch (FUB-BGBM) Gavin Malarky (NHM) & Gerda Koch (AIT) Heimo Rainer (NHMW) Freie Universität Berlin Botanic Garden.

OpenUp! General Overview. OpenUp! – What it aims at: Because access to multimedia resources from natural history collections in Europe.

OpenUp! General Overview. OpenUp! – What it aims at: Because access to multimedia resources from natural history collections in Europe.

Beth GambleSenior Systems Analyst Jamie WhitacreScience Technology Systems Analyst and Liaison National Museum of Natural.

Beispielbild CETAF summary of state of play Anton Güntsch Freie Universität Berlin Botanic Garden & Botanical Museum Berlin-Dahlem Dept. of Research and.

NYBG + KE EMu The New York Botanical Garden + KE EMu Melissa Tulig Botanical Information Management.

Integrating Biodiversity Data

BIS TDWG Conference, New Orleans, 2011 GBIF: Issues in providing federated access to digital information related to biological specimens David Remsen Senior.

Entomological Collections Network Meeting, Indianapolis, IN 13 December 2009 Darwin Core Ratified in the Year of Darwin Gail E. Kampmeier Illinois Natural.

OpenUp! A New Project on Opening up the European Natural History Heritage for EUROPEANA W. G. Berendsohn, A. K. Michel, A. Güntsch, W.-H. Kusber (2011)

SpeciesLink A System for integrating distributed primary biodiversity data Vanderlei Perez Canhos Centro de Referência em Informação Ambiental, CrIA.

Global Biodiversity Information Facility GLOBAL BIODIVERSITY INFORMATION FACILITY Hannu Saarenmaa, Donald Hobern, Larry Speers, Per Bjørn & Giorgos Ksouris.

Data Sources & Using VIVO Data Visualizing Scholarship VIVO provides network analysis and visualization tools to maximize the benefits afforded by the.

Beispielbild Cooking Class: Boiling Down ABCD to DarwinCore Archives Jörg Holetschek Botanic Garden & Botanical Museum Berlin-Dahlem Dept. of Biodiversity.

Sources of Funding for Digitization and Georeferencing Natural History Collections Presentation and Discussion.

The EDIT Platform for Cybertaxonomy as an information broker in name infrastructures Andreas Kohlbecker 1, Yde de Jong 2, Cherian Mathew 1, Lorna Morris.

Botanic Garden and Botanical Museum - Berlin-Dahlem - FU Berlin.

Please notice, the use of this compilation of charts is only allowed for presentations by GBIF-D Node Members ( ). If you have any questions please.

II Course on GBIF Node Management Arusha, Tanzania 31 st October and 1 st November 2008 Tim ROBERTSON Systems Architect GBIF Secretariat Data Publishing.

Beispielbild SYNTHESYS II: Updating the BioCASe Technology Suite Jörg Holetschek Botanic Garden & Botanical Museum Berlin-Dahlem Dept. of Biodiversity.

GGBN Working Group for DNA/Tissue Classes TDWG 2012 Conference Working Group: Katie Barker, John Deck, Gabi Droege, Paul Flemons, Anton Guentsch, Éamonn.

GLOBAL BIODIVERSITY INFORMATION FACILITY The Global Biodiversity Information Facility (GBIF ): The distributed architecture Samy Gaiji Head of Informatics.

Sustaining a biodiversity data infrastructure: OpenUp!, BioCASe and GBIF Walter Berendsohn Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität.

Australian Partnership for Sustainable Repositories University of Sydney practices and test-bed projects, sustainability in a distributed.

Sabine von Mering & Walter G. Berendsohn Botanischer Garten und Botanisches Museum Berlin-Dahlem Freie Universität Berlin GBIF Germany – an overview –

Resource Identification for a Biological Collection Information Service in Europe An introduction to the BioCISE project Walter G. Berendsohn Botanical.

1 DanBIF Danish Biodiversity Information Facility Arbejdsseminar om GBIF i Norge Norges Forskningsråd, Oslo 25. September 2003 Isabel Calabuig.

Franck Theeten 1, Patricia Mergen 1, Olivier Bakasanda 2, Jörg Holetschek 3, Patricia Kelbert 3, Motonobu Kasajima 2, Garin Cael 1, Charles Kahindo 4 1.

From the World Directory of Collections of Cultures of Microorganisms towards Mash-up of Biodiversity and Sequence Databases Director, WFCC-MIRCEN World.

OpenUp! – accessing pictures on Europeana Zágoršek, Kamil & Berendsohn, Walter National museum Prague & Botanical Museum and Botanical Garden, Freie Universität.

Digitization of Natural History Collections (DIGIT) Larry Speers Program Officer Digitization of Natural History Collections Data TDWG Annual Meeting Oct.

TDWG 2006, Missouri, U.S.A. Exchange of germplasm datasets with PyWrapper/BioCASE October 16, 2006 TDWG annual Meeting 2006 Missouri Botanical Garden St.

ISTC-CMSA workshop Brief description of collections (~ 37milj objects ~ type specimens)  Recent zoological collections  Section Invertebrates 

ISpheresImage iSpheresImage Feature Overview and Progress Summary.

CBoL Taipei, september 2007 BARCODE DATA, MUSEUM CATALOGS AND GBIF Simon Tillier.

BioCASE – A Biological Collection Access Service for Europe BioCASE programme – metadata and computing methods The Irish National Node Workshop: October.

Global Biodiversity Information Facility GLOBAL BIODIVERSITY INFORMATION FACILITY DNA Barcoding in Southern Africa Cape Town 7 April

LifeWatch E-Science and Observatory Infrastructure for Biodiversity & Ecosystem Science Olaf Bánki.

Global Biodiversity Information Facility GLOBAL BIODIVERSITY INFORMATION FACILITY Meredith A. Lane CODATA/ERPANET Workshop: Scientific Data Selection &

BGBM IT infrastructure and collection management Anton Güntsch.

GBIF Data Access and Database Interoperability 2003 Work Programme Overview Donald Hobern, GBIF Programme Officer for Data Access and Database Interoperability.

An introduction to data exchange protocols in TDWG Renato De Giovanni TDWG 2008.

Canadensys update. Canadensys: what is it? A Canadian network of 11 universities, 5 botanical gardens and 2 museums. Over 25 biological collections and.

Beispielbild OpenUp! BioCASe Workshop Jörg Holetschek, Gabriele Dröge Botanic Garden & Botanical Museum Berlin-Dahlem Dept. of Biodiversity Informatics.

Beispielbild BioCASe, ABCD and its extensions Jörg Holetschek Botanic Garden & Botanical Museum Berlin-Dahlem Dept. of Biodiversity Informatics and Laboratories.

Context: The Strategic Plan for Establishing the Network Integrated Biocollections Alliance Judith E. Skog, Office of the Assistant Director, Biological.

CEPDEC-TZ Training course: Digitisation of Biodiversity Information 13th – 17th July 2009 Dar es Salaam, Tanzania GLOBAL BIODIVERSITY INFORMATION FACILITY.

Taxonomic Workflow in the EDIT Platform for Cybertaxonomy Andreas Kohlbecker, Pepe Ciardelli, Niels Hoffmann, Katja Luther, Andreas Müller Botanic Garden.

Networking Biodiversity Data – Online Access to Distributed Data Sources in GBIF-D Andrea Hahn, A. Kirchhoff & W.G. Berendsohn Botanic Garden and Botanical.

Fire Emissions Network Sept. 4, 2002 A white paper for the development of a NSF Digital Government Program proposal Stefan Falke Washington University.

The New GBIF Data Portal Web Services and Tools Donald Hobern GBIF Deputy Director for Informatics October 2006.

TDWG – Looking Backward and Forward Donald Hobern, Director, Atlas of Living Australia 20 October 2008.

IABIN Species and Specimens Thematic Network (SSTN) IABIN Executive Committee/Coordinating Institution Meeting. Tierras Enamoradas, Costa Rica. February.

The Global Genome Biodiversity Network (GGBN) Data Portal & ABCDDNA Gabriele Droege Botanic Garden and Botanical Museum Berlin-Dahlem.

Applications in the EDIT Platform for Cybertaxonomy Andreas Müller 1, Andreas Kohlbecker 1, Cherian Mathew 1, Alexander Oppermann 1, Patrick Plitzner 1,

IABIN Standards & Protocols Presented by: Mike Frame, USGS NBII Developed by Darrell McClarty IABIN Regional Coordinator.

The OpenUp Data Quality Toolkit TDWG 2013 Anton Güntsch Freie Universität Berlin Botanic Garden and Botanical Museum Berlin-Dahlem.

IPT + Darwin Core OBIS XML Schema OBIS Database Schema Explained Mike Flavell OBIS Data Manager OBIS Nodes Training Course, Oostende, Belgium, 6 May 2014.

ISC321 Database Systems I Chapter 2: Overview of Database Languages and Architectures Fall 2015 Dr. Abdullah Almutairi.

Botanic Garden and Botanical Museum Berlin-Dahlem Collections and Research on the Biodiversity and Evolution of Plants.

Funded by the Connecting Europe Facility OpenUp! The Natural History aggregator for Europeana, Europe’s digital library Jörg Holetschek.

Database System Concepts and Architecture

Flanders Marine Institute (VLIZ)

GLOBAL BIODIVERSITY INFORMATION FACILITY

INHS Insect collection digitization workflow

Presentation transcript:

The DNA Bank Network Gabriele Droege Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität Berlin

Existing components Source material / specimens

GBIF – Data Architecture

DiGIR = Digital Generic Information Retrieval BioCASe = Biological Collection Access Service ABCD = Access to Biological Collection Data Wrappers Transformation of individual database structures into a standard xml schema Enable „live“ connection to original data provider DarwinCoreABCD

DNA Bank Network The Data Architecture

Provider xy Different voucher data sources DiGIR/BioCASe DarwinCore/ABCD Specimen databases Data Architecture

Data architecture – DNA data DNA Module –MySQL and PHP –Local use or with external server (web-based) –Several tools for entry and management of DNA data and customer requests –Reference to specimen data via wrappers –Specimen Tool for specimen data not available via GBIF

Provider xy DNA Module DNA Different voucher data sources DiGIR/BioCASe DarwinCore/ABCD Specimen databases Data Architecture

Provider xy BioCASe ABCDDNA DNA Module DNA Different voucher data sources DiGIR/BioCASe DarwinCore/ABCD Specimen databases Data Architecture Web index/ Web portal

-Dynamically generated during web query aggregating data from multiple sources -April 2012: > DNA and tissue samples available -Customers have to sign MTA -Partners work independent

DNA Bank Network The Future

GBIF records worldwide 311,209,813 georeferenced data

GBIF records of current GGBN partners 9,299,217 georeferenced data

Sustainability Use of existing systems (e.g. GBIF, GenBank, BOLD, CoL) BGBM: two new permanent positions (from July 2012) –BioCASe & ABCD - Jörg Holetschek –DNA Bank Network - Gabi Dröge  technical support for future GGBN data portal possible DFG proposal (deadline 31. July 2012); DFG = Deutsche Forschungsgemeinschaft (German Research Foundation)

DFG proposal DFG = Deutsche Forschungsgemeinschaft (German Research Foundation) Programme: Knowledge Transfer Projects –Deadline: 31. July 2012 –Transfer projects are based on results generated by DFG-funded research projects –Core of the project is a joint work programme, focusing on intensive mutual exchange of scientific knowledge –Funds for German partner only –Appropriate input by the application partner expected –Should be not more than one application partner Discussion with GGBN-ISC and TF Data Standards

DFG proposal Working title: “Building the technical node of the Global Genome Biodiversity Network (GGBN)” SI represents GGBN within the project BGBM leads the technical node of GGBN All GGBN partners could benefit: –Best practices and data workflows can be adopted by all GGBN partners GGBN works independent and does not depend on the grant and vice versa