Towards a Research Data Commons in the German National Research Data Infrastructure NFDI: Vision, Governance, Architecture.

Frank Oliver Glöckner Max-Planck-Institut für Marine Mikrobiologie, Bremen, Germany http://www.mpi-bremen.de/Frank_Oliver_Gloeckner.html https://scholar.google.com/citations?user=BmzoT3QAAAAJ Michael Diepenbroek Ivaylo Kostadinov Bernhard Seeger Frank Oliver Glöckner Marius A. Dieckmann Alexander Goesmann Barbara Ebert Sonja Schimmler York Sure-Vetter Towards a Research Data Commons in the German National Research Data Infrastructure NFDI: Vision, Governance, Architecture. 2023 CoRDI https://doi.org/10.52825/cordi.v1i.355 conf/cordi/2023 db/conf/cordi/cordi2023.html#DiepenbroekKSGD23 Barbara Ebert Judith Sophie Engel Ivaylo Kostadinov Anton Güntsch Frank Oliver Glöckner Connecting National and International Data Infrastructures in Biodiversity Research The Case of NFDI4Biodiversity, a German Consortium for Biodiversity, Ecology and Environmental Data. 2023 CoRDI https://doi.org/10.52825/cordi.v1i.346 conf/cordi/2023 db/conf/cordi/cordi2023.html#EbertEKGG23

Gerhard Mayer Wolfgang Müller 0001 Karin Schork Julian Uszkoreit Andreas Weidemann Ulrike Wittig Maja Rey Christian Quast Janine Felden Frank Oliver Glöckner Matthias Lange 0001 Daniel Arend Sebastian Beier Astrid Junker Uwe Scholz Danuta Schüler Hans A. Kestler Daniel Wibberg Alfred Pühler Sven Twardziok Jürgen Eils Roland Eils Steve Hoffmann Martin Eisenacher Michael Turewicz Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. 2021 22 Briefings Bioinform. 5 https://doi.org/10.1093/bib/bbab010 https://www.wikidata.org/entity/Q112806632 db/journals/bib/bib22.html#MayerMSUWWRQFGL21

Robert M. Waterhouse Anne-Françoise Adam-Blondon Donat Agosti Petr Baldrian Bachir Balech Erwan Le Corre Robert P. Davey Henrik Lantz Graziano Pesole Christian Quast Frank Oliver Glöckner Niels Raes Anna Sandionigi Monica Santamaria Wouter Addink Jiri Vohradsky Amandine Nunes-Jorge Nils Peder Willassen Jerry Lanfear Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR. 1238 2021 10 F1000Research https://doi.org/10.12688/f1000research.73825.1 https://www.wikidata.org/entity/Q112650854 db/journals/f1000research/f1000research10.html#WaterhouseAABBCDLPQGRSSAV21

Hendrikje Seifert Marc Weber Frank Oliver Glöckner Ivaylo Kostadinov An open-source GIS-enabled lookup service for Nagoya Protocol party information. 2020 2020 Database J. Biol. Databases Curation https://doi.org/10.1093/database/baaa014 https://www.wikidata.org/entity/Q91866906 db/journals/biodb/biodb2020.html#SeifertWGK20

Rachel Drysdale Charles E. Cook Robert Petryszak Vivienne Baillie Gerritsen Mary Barlow Elisabeth Gasteiger Franziska Gruhl Jürgen Haas Jerry Lanfear Rodrigo Lopez Nicole Redaschi Heinz Stockinger Daniel Teixeira Aravind Venkatesan Alex Bateman Alan J. Bridge Guy Cochrane Robert D. Finn Frank Oliver Glöckner Marc Hanauer Thomas M. Keane Andrew Leach Luana Licata Per Oksvold Sandra E. Orchard Christine A. Orengo Helen E. Parkinson Bengt Persson Pablo Porras Jordi Rambla Ana Rath Charlotte Rodwell Ugis Sarkans Dietmar Schomburg Ian Sillitoe J. Dylan Spalding Mathias Uhlén Sameer Velankar Juan Antonio Vizcaíno Kalle von Feilitzen Christian von Mering Andrew D. Yates Niklas Blomberg Christine Durinx Johanna R. McEntyre The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. 2636-2642 2020 36 Bioinform. 8 https://doi.org/10.1093/bioinformatics/btz959 https://www.wikidata.org/entity/Q95730500 db/journals/bioinformatics/bioinformatics36.html#DrysdaleCPGBGGH20

Gerhard Mayer Christian Quast Janine Felden Matthias Lange 0001 Manuel Prinz Alfred Pühler Chris Lawerenz Uwe Scholz Frank Oliver Glöckner Wolfgang Müller 0001 Katrin Marcus Martin Eisenacher A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects. 1215-1221 2019 20 Briefings Bioinform. 4 https://doi.org/10.1093/bib/bbx140 https://www.wikidata.org/entity/Q47676185 db/journals/bib/bib20.html#MayerQFLPPLSGMM19

Gerhard Rambold Pelin Yilmaz Janno Harjes Sabrina Klaster Veronica Sanz Anton Link Frank Oliver Glöckner Dagmar Triebel Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research. baz002 2019 2019 Database J. Biol. Databases Curation https://doi.org/10.1093/database/baz002 https://www.wikidata.org/entity/Q61804943 db/journals/biodb/biodb2019.html#RamboldYHKSLGT19

Emiliano Pereira-Flores Frank Oliver Glöckner Antonio Fernandez-Guerra Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data. 453:1-453:13 2019 20 BMC Bioinform. 1 https://doi.org/10.1186/s12859-019-3031-y https://www.wikidata.org/entity/Q93128554 db/journals/bmcbi/bmcbi20.html#Pereira-FloresG19

R. Henrik Nilsson Karl-Henrik Larsson Andy F. S. Taylor Johan Bengtsson-Palme Thomas S. Jeppesen Dmitry Schigel Peter Kennedy Kathryn Picard Frank Oliver Glöckner Leho Tedersoo Irja Saar Urmas Kõljalg Kessy Abarenkov The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. D259-D264 2019 47 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gky1022 https://www.wikidata.org/entity/Q58106124 db/journals/nar/nar47.html#NilssonLTBJSKPG19

Daniel Wibberg Bérénice Batut Peter Belmann Jochen Blom Frank Oliver Glöckner Björn A. Grüning Nils Hoffmann Nils Kleinbölting René Rahn Maja Rey Uwe Scholz Malvika Sharan Andreas Tauch Ulrike Trojahn Björn Usadel Oliver Kohlbacher The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. 1877 2019 8 F1000Research https://doi.org/10.12688/f1000research.20244.1 https://www.wikidata.org/entity/Q101457504 db/journals/f1000research/f1000research8.html#WibbergBBBGGHKRRSSTTUK19

Alan Beccati Jan Gerken 0001 Christian Quast Pelin Yilmaz Frank Oliver Glöckner SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees. 433:1-433:4 2017 18 BMC Bioinform. 1 https://doi.org/10.1186/s12859-017-1841-3 https://www.wikidata.org/entity/Q42368041 db/journals/bmcbi/bmcbi18.html#BeccatiGQYG17

Michael Richter Ramon Rosselló-Mora Frank Oliver Glöckner Jörg Peplies JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. 929-931 2016 32 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btv681 https://www.wikidata.org/entity/Q40312977 db/journals/bioinformatics/bioinformatics32.html#RichterRGP16

Pelin Yilmaz Laura Wegener Parfrey Pablo Yarza Jan Gerken 0001 Elmar Pruesse Christian Quast Timmy Schweer Jörg Peplies Wolfgang Ludwig Frank Oliver Glöckner The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. 643-648 2014 42 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkt1209 https://www.wikidata.org/entity/Q34389055 db/journals/nar/nar42.html#YilmazPYGPQSPLG14

Michael Diepenbroek Frank Oliver Glöckner Peter Grobe Anton Güntsch Robert Huber Birgitta König-Ries Ivaylo Kostadinov Jens Nieschulze Bernhard Seeger Robert Tolksdorf Dagmar Triebel Towards an Integrated Biodiversity and Ecological Research Data Management and Archiving Platform: The German Federation for the Curation of Biological Data (GFBio). 1711-1721 2014 GI-Jahrestagung conf/gi/2014 db/conf/gi/gi2014.html#DiepenbroekGGGHKKNSTT14 https://dl.gi.de/handle/20.500.12116/2782

Christian Quast Elmar Pruesse Pelin Yilmaz Jan Gerken 0001 Timmy Schweer Pablo Yarza Jörg Peplies Frank Oliver Glöckner The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. 590-596 2013 41 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gks1219 https://www.wikidata.org/entity/Q29547623 db/journals/nar/nar41.html#QuastPYGSYPG13

Heiner Klingenberg Robin Martinjak Frank Oliver Glöckner Rolf Daniel Thomas Lingner Peter Meinicke Dinucleotide distance histograms for fast detection of rRNA in metatranscriptomic sequences. 80-89 2013 GCB https://doi.org/10.4230/OASIcs.GCB.2013.80 conf/gcb/2013 db/conf/gcb/gcb2013.html#KlingenbergMGDLM13

Hanno Teeling Frank Oliver Glöckner Current opportunities and challenges in microbial metagenome analysis - a bioinformatic perspective. 728-742 2012 13 Briefings Bioinform. 6 https://doi.org/10.1093/bib/bbs039 https://www.wikidata.org/entity/Q34410918 db/journals/bib/bib13.html#TeelingG12

Elmar Pruesse Jörg Peplies Frank Oliver Glöckner SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes. 1823-1829 2012 28 Bioinform. 14 https://doi.org/10.1093/bioinformatics/bts252 https://www.wikidata.org/entity/Q42160739 db/journals/bioinformatics/bioinformatics28.html#PruessePG12

Marcin Radom Agnieszka Rybarczyk Renzo Kottmann Piotr Formanowicz Marta Szachniuk Frank Oliver Glöckner Dietrich Rebholz-Schuhmann Jacek Blazewicz Poseidon: An information retrieval and extraction system for metagenomic marine science. 10-15 2012 12 Ecol. Informatics https://doi.org/10.1016/j.ecoinf.2012.07.003 https://www.wikidata.org/entity/Q57387726 db/journals/ecoi/ecoi12.html#RadomRKFSGRB12

Wolfgang Hankeln Pier Luigi Buttigieg Dennis Fink Renzo Kottmann Pelin Yilmaz Frank Oliver Glöckner MetaBar - a tool for consistent contextual data acquisition and standards compliant submission. 358 2010 11 BMC Bioinform. https://doi.org/10.1186/1471-2105-11-358 https://www.wikidata.org/entity/Q33621959 db/journals/bmcbi/bmcbi11.html#HankelnBFKYG10

Renzo Kottmann Ivaylo Kostadinov Melissa Beth Duhaime Pier Luigi Buttigieg Pelin Yilmaz Wolfgang Hankeln Jost Waldmann Frank Oliver Glöckner Megx.net: integrated database resource for marine ecological genomics. 391-395 2010 38 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkp918 https://www.wikidata.org/entity/Q33600690 db/journals/nar/nar38.html#KottmannKDBYHWG10

Wolfgang Hankeln Pier Luigi Buttigieg Ivaylo Kostadinov Renzo Kottmann Pelin Yilmaz Melissa Beth Duhaime Frank Oliver Glöckner Applying graph theoretic approaches to microbial metagenomes: ecological perspectives on function. 478-480 2010 BCB https://doi.org/10.1145/1854776.1854863 https://www.wikidata.org/entity/Q57003226 conf/bcb/2010 db/conf/bcb/bcb2010.html#HankelnBKKYDG10

Uta Bohnebeck Thierry Lombardot Renzo Kottmann Frank Oliver Glöckner MetaMine - A tool to detect and analyse gene patterns in their environmental context. 2008 9 BMC Bioinform. https://doi.org/10.1186/1471-2105-9-459 https://www.wikidata.org/entity/Q28755833 db/journals/bmcbi/bmcbi9.html#BohnebeckLKG08

Michael Richter Thierry Lombardot Ivaylo Kostadinov Renzo Kottmann Melissa Beth Duhaime Jörg Peplies Frank Oliver Glöckner JCoast - A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. 2008 9 BMC Bioinform. https://doi.org/10.1186/1471-2105-9-177 https://www.wikidata.org/entity/Q31151212 db/journals/bmcbi/bmcbi9.html#RichterLKKDPG08

Thierry Lombardot Renzo Kottmann Gregory Giuliani Andrea de Bono Nans Addor Frank Oliver Glöckner MetaLook: a 3D visualisation software for marine ecological genomics. 2007 8 BMC Bioinform. https://doi.org/10.1186/1471-2105-8-406 https://www.wikidata.org/entity/Q33303483 db/journals/bmcbi/bmcbi8.html#LombardotKGBAG07

Hanno Teeling Frank Oliver Glöckner RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. 66 2006 7 BMC Bioinform. https://doi.org/10.1186/1471-2105-7-66 https://www.wikidata.org/entity/Q33233833 db/journals/bmcbi/bmcbi7.html#TeelingG06

Thierry Lombardot Renzo Kottmann Hauke Pfeffer Michael Richter Hanno Teeling Christian Quast Frank Oliver Glöckner Megx.net - database resources for marine ecological genomics. 390-393 2006 34 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkj070 https://www.wikidata.org/entity/Q25257920 db/journals/nar/nar34.html#LombardotKPRTQG06

Yadhu Kumar Ralf Westram Sebastian Behrens Bernhard Fuchs Frank Oliver Glöckner Rudolf Amann Harald Meier Wolfgang Ludwig Graphical representation of ribosomal RNA probe accessibility data using ARB software package. 61 2005 6 BMC Bioinform. https://doi.org/10.1186/1471-2105-6-61 https://www.wikidata.org/entity/Q24811507 db/journals/bmcbi/bmcbi6.html#KumarWBFGAML05

Hanno Teeling Jost Waldmann Thierry Lombardot Margarete Bauer Frank Oliver Glöckner TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. 163 2004 5 BMC Bioinform. https://doi.org/10.1186/1471-2105-5-163 https://www.wikidata.org/entity/Q24796998 db/journals/bmcbi/bmcbi5.html#TeelingWLBG04

Kessy Abarenkov Anne-Françoise Adam-Blondon Wouter Addink Nans Addor Donat Agosti Rudolf Amann Daniel Arend Jordi Rambla De ArgilaJordi Rambla Petr Baldrian Bachir Balech Mary Barlow Alex Bateman Bérénice Batut Margarete Bauer Alan Beccati Sebastian Behrens Sebastian Beier Peter Belmann Johan Bengtsson-Palme Jacek Blazewicz Jochen Blom Niklas Blomberg Uta Bohnebeck Andrea de Bono Alan J. Bridge Pier Luigi Buttigieg Guy Cochrane Charles E. Cook Erwan Le Corre Rolf Daniel Robert P. Davey Marius A. Dieckmann Michael Diepenbroek Rachel Drysdale Melissa Beth Duhaime Christine Durinx Barbara Ebert Jurgen EilsJürgen Eils Roland Eils Martin Eisenacher Judith Sophie Engel Kalle von Feilitzen Janine Felden Antonio Fernandez-Guerra Dennis Fink Robert D. Finn Piotr Formanowicz Bernhard Fuchs Elisabeth Gasteiger Jan Gerken 0001 Vivienne Baillie Gerritsen Gregory Giuliani Alexander Goesmann Peter Grobe Franziska Gruhl Björn A. Grüning Anton Güntsch Jürgen Haas Marc Hanauer Wolfgang Hankeln Janno Harjes Nils Hoffmann Steve Hoffmann Robert Huber Thomas S. Jeppesen Astrid Junker Thomas M. Keane Peter Kennedy Hans A. Kestler Sabrina Klaster Nils Kleinbölting Heiner Klingenberg Oliver Kohlbacher Urmas Kõljalg Birgitta König-Ries Ivaylo Kostadinov Renzo Kottmann Yadhu Kumar Jerry Lanfear Matthias Lange 0001 Henrik Lantz Karl-Henrik Larsson Chris Lawerenz Andrew Leach Luana Licata Thomas Lingner Anton Link Thierry Lombardot Rodrigo Lopez Wolfgang Ludwig Katrin Marcus Robin Martinjak Gerhard Mayer Johanna R. McEntyre Harald Meier Peter Meinicke Christian von Mering Wolfgang Müller 0001 Jens Nieschulze R. Henrik Nilsson Amandine Nunes-Jorge Per Oksvold Sandra E. Orchard Christine A. Orengo Laura Wegener Parfrey Helen E. Parkinson Jörg Peplies Emiliano Pereira-Flores Bengt Persson Graziano Pesole Robert Petryszak Hauke Pfeffer Kathryn Picard Pablo Porras Manuel Prinz Elmar Pruesse Alfred Pühler Christian Quast Marcin Radom Niels Raes René Rahn Gerhard Rambold Ana Rath Dietrich Rebholz-Schuhmann Nicole Redaschi Maja Rey Michael Richter Charlotte Rodwell Ramon Rosselló-Mora Agnieszka Rybarczyk Irja Saar Anna Sandionigi Monica Santamaria Veronica Sanz Ugis Sarkans Dmitry Schigel Sonja Schimmler Uwe Scholz Dietmar Schomburg Karin Schork Danuta Schüler Timmy Schweer Bernhard Seeger Hendrikje Seifert Malvika Sharan Ian Sillitoe J. Dylan Spalding Heinz Stockinger York Sure-Vetter Marta Szachniuk Andreas Tauch Andy F. S. Taylor Leho Tedersoo Hanno Teeling Daniel Teixeira Robert Tolksdorf Dagmar Triebel Ulrike Trojahn Michael Turewicz Sven Twardziok Mathias UhlenMathias Uhlén Björn Usadel Julian Uszkoreit Sameer Velankar Aravind Venkatesan Juan Antonio Vizcaíno Jiri Vohradsky Jost Waldmann Robert M. Waterhouse Marc Weber Andreas Weidemann Ralf Westram Daniel Wibberg Nils Peder Willassen Ulrike Wittig Pablo Yarza Andy YatesAndrew D. Yates Pelin Yilmaz