Difference between revisions of "Publications"

Latest revision as of 21:00, 21 August 2020

• Güntsch, A., Hyam, R., Hagedorn, G., Chagnoux, S., Röpert, D., Casino A., Droege, G., Glöckler, F., Gödderz, K., Groom, Q., Hoffmann, J., Holleman, A., Kempa, M., Koivula, H., Marhold, K., Nicolson, N., Smith, V. S. & Triebel, D. 2017. Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects. – Database, 2017, 1–9. (doi.org/10.1093/database/bax003)

• Hagedorn, G., Plank, A., Link, A., Rambold, G. & Triebel, D. 2016. DiversityDescriptions information model (version 3.0.15, 11 July 2016). – http://www.diversityworkbench.net/Portal/DiversityDescriptionsModel_3.0.15.

• Harjes, J., Link, A., Weibulat, T., Triebel, D. & Rambold, G. 2020. FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results, Database, 2020 (Article ID baaa059), 1–20. (doi.org/10.1093/database/baaa059).

• Harjes, J., Triebel, D., Link, A., Weibulat, T., Glöckner, F. & Rambold, G. 2019. FAIR data in meta-omics research: Using the MOD-CO schema to describe structural and operational elements of workflows from field to publication. Biodiversity Information Science and Standards 3: e37596. https://doi.org/10.3897/biss.3.37596.

• Harjes, J., Triebel, D., Weibulat, T., Link, A. & Rambold, G. 2018. Managing and publishing fungal community barcoding data by use of the process-oriented schema MOD-CO and a GFBio data publication pipeline. – In: Friedrich-Schiller-Universität Jena. https://doi.org/10.22032/dbt.37811.

• Rambold, G., Bensch, K., Kirk, P. M., Yao, Y.-J., Robert, V., Sanz, V. & Triebel, D. 2017. Citation of a taxon name identifier issued by the ICN-recognized registration repositories instead of taxon name author citation. – Taxon 66(5): 1200–1203. (https://doi.org/10.12705/665.12).

• Rambold, G., Bensch, K., Kirk, P. M., Yao, Y.-J., Robert, V. & Triebel, D. 2018. (F-007) Proposal to recommend the use of an identifier as an alternative to the citation of the authors of fungal names. In: Proposals for consideration at IMC11 to modify provisions related solely to fungi in the International Code of Nomenclature for algae, fungi, and plants. – IMA Fungus 9(1): vi–vii. http://www.imafungus.org/Issue/91/MYCONAMES.pdf, see now under https://imafungus.biomedcentral.com/articles/10.1007/BF03449481

• Rambold, G., Yilmaz, P., Harjes, J., Link, A., Glöckner, F.O., Triebel, D. (2018). MOD-CO schema – a conceptual schema for processing sample data in meta’omics research (version 1.0). https://mod-co.net/wiki/MOD-CO_Schema_Reference.

• Rambold, G., Yilmaz, P., Harjes, J., Klaster, S., Sanz, V., Link, A., Glöckner, F. O., Triebel, D. 2019. Meta-omics data and collection objects (MOD-CO): A conceptual schema and data model for processing sample data in meta-omics research. – Database, 2019 (Article ID baz002), 1–13. (doi.org/10.1093/database/baz002). see https://academic.oup.com/database/article/doi/10.1093/database/baz002/5303972

• Triebel, D., Harjes, J., Weibulat, T., Link, A., Weiss, M. & Rambold, G. 2018. 3.2-31: Towards FAIR data: Use case for managing and publishing mycological occurrence and community barcoding data. In: Anonymous (ed.) IMC 11 International Mycological Congress, 16th – 21th July 2018 / San Juan, Puerto Rico. IMC11 Abstract Book: 471-472.

• Triebel, D., Link, A., Hagedorn, G., Plank, A., Weiss, M., Fichtmueller, D., Weibulat, T. & Rambold, G. 2016. Linking external SQL databases and the Semantic Web: A Pipeline for dynamic web publication with stable URI identifiers for database structural information and content schemes. – In Anonymous (ed.) TDWG 2016 Annual Conference. Santa Clara de San Carlos, Costa Rica. 5.–9. December 2016. – Poster Abstract.

• Triebel, D., Peršoh, D., Klaster, S. & Rambold, G. 2014. Omics and meta’omics dataflows in mycology. – In Anonymous (ed.), IMC10 eBook of Abstracts: 219. Bangkok.

• Triebel, D., Reichert, W., Bosert, S., Feulner, M., Osieko Okach, D., Slimani, A. & Rambold, G. 2018. A generic workflow for effective sampling of environmental vouchers with UUID assignment and image processing. – Database, 2018 (Article ID bax096), 1–10. (doi.org/10.1093/database/bax096), see https://academic.oup.com/database/article-abstract/doi/10.1093/database/bax096/4797113.

• Yilmaz, P., Klaster, S., Link, A., Weibulat, T., Glöckner, F. O., Triebel, D. & Rambold, G. 2016. Towards an integrative and comprehensive standard for meta-omics data of collection objects (MOD-CO). – In Anonymous (ed.) 17th Annual Meeting of the Gesellschaft für Biologische Systematik. 21.–24. February 2016. Abstracts. – Zitteliana 88: 55. München.

• Yilmaz, P., Link, A., Weibulat, T., Glöckner, F.O., Triebel, D. & Rambold, G. 2016. Management and publication of an integrative and comprehensive scheme for meta-omics data of collection objects (MOD-CO). – In Anonymous (ed.) TDWG 2016 Annual Conference. Santa Clara de San Carlos, Costa Rica. 5.–9. December 2016. – Poster Abstract.

• Mehr Verständnis durch Struktur – Umweltproben an naturhistorischen Sammlungen analysieren. Interview in Journal Laborpraxis 10, October 2014

• New Knowledge from Old Collections: DFG Supports Indexing and Digitisation of Research-Relevant Objects. DFG Press Release No. 5, March 11th, 2014.

• Umweltproben an naturhistorischen Sammlungen – ein neues Forschungsprojekt entwickelt Standards zur Erschließung forschungsrelevanter Information. SNSB Press Release, June 3rd, 2014.

Relevant Publications until project start in 2014

• Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA (2009) Topographical and Temporal Diversity of the Human Skin Microbiome. Science 324: 1190–1192

• Hagedorn G, Plank A, Link A, Rambold G & Triebel D (2014) DiversityDescriptions information model (version 3.00.09, 13 March 2014). – http://www.diversityworkbench.net/Portal/DescriptionsModel_v3.00.09.

• Hagedorn G, Thiele K, Morris R, Heidorn PB (2006) The Structured Descriptive Data (SDD) w3c-xml-schema, version 1.1. – http://rs.tdwg.org/UBIF/2006/rddl.html.

• Kottmann R, Kostadinov I, Duhaime MB, Buttigieg PL, Yilmaz P, Hankeln W, Waldmann J, Glöckner FO (2010) Megx.net: integrated database resource for marine ecological genomics. Nucleic Acid Res. 38: D391–D395.

• Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale. Appl. Environ. Microbiol. 75: 5111–5120

• Peršoh D (2013) Factors shaping community structure of endophytic fungi – evidence from the Pinus-Viscum-system. Fungal Diversity (accepted). (doi: 10.1007/s13225-013-0225-x).

• Peršoh D, Theuerl S, Buscot F, Rambold G (2008) Towards a universally adaptable method for quantitative extraction of high-purity nucleic acids from soil. J. Microbiol. Methods 75: 19–24.

• Peršoh D, Rambold G (2009) New protocols for the extraction of nucleic acids from soil. J. Appl. Microbiol. 107: 2118.s.

• Peršoh D, Weig A, Rambold G (2012) A transcriptome-targeting EcoChip for assessing functional mycodiversity. Microarrays 1: 25–41.

• Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acid Res. 41: D590–D596.

• Richter M, Lombardot T, Kostadinov I, Kottmann R, Duhaime MB, Peplies J, Glöckner FO (2008) JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta) genomes. BMC Bioinformatics 9: 177.

• Teeling H, Glöckner FO (2012) Current opportunities and challenges in microbial metagenome analysis - a bioinformatic perspective. Brief. Bioinform. 13: 728–742.

• Triebel D, Hagedorn G, Jablonski S & Rambold G (eds.) (1999) onwards. Diversity Workbench – A virtual research environment for building and accessing biodiversity and environmental data. – http://www.diversityworkbench.net.

• Weig A, Peršoh D, Werner S, Betzlbacher A, Rambold G (2013) Diagnostic assessment of mycodiversity in environmental samples by fungal ITS1 rDNA length polymorphism., Mycol. Progress. (doi: 10.1007%2Fs11557-012-0883-1).

• Yilmaz P et al. (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotechnol. 29: 415–420.