Agnes Kirchhoff

Project Support Office

Research Assistant, Biodiversity Informatics Projects

phone

+49 30 838 50167

fax

+49 30 838-4 50167

a.kirchhoff@bgbm.org

Botanischer Garten und Botanisches Museum Berlin-Dahlem

Freie Universität Berlin

Königin-Luise-Straße 6-8

14195

Berlin

Deutschland

Tasks

StanDAP-Herb Projekt

Research interests

Biodiversity Informatics

Research projects

StanDAP-Herb - a standardised and optimised process for data acquisition from digital images of herbarium specimens
On herbarium sheets, data like plant name, collection site, collector, barcode, accession number, etc. are found mostly on labels glued on the sheet. The data is thus visible on images taken of the specimen. Currently, they are mostly entered manually into collection databases. The StanDAP-Herb Project funded by the DFG (German Research Foundation) develops a standard process for (semi-) automatic detection of meta-data on Herbarium specimens to replace the time consuming manual data input as much as possible. Image processing software detects objects such as labels or barcodes on the digitized record and classifies them. Text objects are transformed into structured information using text mining algorithms. For handwriting, author identification is attempted. The project evaluates and enhances existing software to comply with standard interfaces and integrate them into an open software architecture based on established IT standards. The software modules thus become available for work flow processing, in order to verify data quality, facilitate data discovery and enhance the application of collection data in research. The project addresses a large proportion of scientific collections: approximately 22 million herbarium specimens exist as botanical reference objects in Germany, about 500 million worldwide.
reBiND – Biodiversity Needs Data
EDIT – European Distributed Institute of Taxonomy
MoPuK Excellenzcluster
GBIF-D Botanik – Global Biodiversity Information Facility - Germany, Botanical Node
BIOLOG-BoGART – Datenbank der Lebendsammlung des Botanischen Gartens

Publications

Papers in peer reviewed journals (published and in press)

Güntsch, A., Fichtmüller, D., Kirchhoff, A. & Berendsohn, W.G. 2012: Efficient rescue of threatened biodiversity data using reBiND-workflows. Plant Biosystems, 146(4): 752-755. DOI:10.1080/11263504.2012.740086

Hahn, A., Kirchhoff, A. & Berendsohn, W.G. 2004: The Global Biodiversity Information Facility (GBIF) and the German response. Scripta Bot. Belg. 29: 71-77.

Journals, not peer reviewed

Kirchhoff, A., Güntsch, A., Hoffmann, N., Kohlbecker, A., Müller, A., Revilla, F. & Berendsohn, W.G. 2011: A versatile toolkit for taxonomists: The EDIT Platform for Cybertaxonomy. P. 190 in: Borsch, T.; Giere, P.; Hoffmann,J.; Jahn, R.; Löhne, C.; Nordt, B.; Ohl, M. (ed.) Biosystematics 2011, Berlin, ISBN 978-3-921800-68-3

Güntsch, A., Hoffmann, N., Kohlbecker, A., Müller, A., Kirchhoff, A. & Berendsohn, W.G. 2011: The EDIT Platform for Cybertaxonomy – an open architecture for taxonomic data processing. Pp. 149-150 in: Borsch, T., Giere, P., Hoffmann, J., Jahn, R., Löhne, C., Nordt, B., Ohl, M. (ed.) Biosystematics 2011, Berlin, ISBN 978-3-921800-68-3

Kohlbecker, A., Güntsch, A., Kirchhoff, A., Müller, A., Hoffmann, N., Revilla, F. & Berendsohn W.G. 2011: Biulding rich biodiversity data portals using the EDIT platform for Cybertaxonomy. Pp. 199-200 in: Borsch, T., Giere, P., Hoffmann, J., Jahn, R., Löhne, C., Nordt, B., Ohl, M. (ed.) Biosystematics 2011, Berlin, ISBN 978-3-921800-68-3

Vignes-Lebbe, R., Causse, F., Fradin, H., Güntsch, A., Hoffmann, N., Kirchhoff, A., Kohlbecker, A., Kutzelmann, K., Maiocco, O., Müller, M., Ung, V., Venin, M. & Berendsohn, W.G. 2011: Editing and publishing descriptive data with the EDIT Platform. Pp. 373-274 in: Borsch, T., Giere, P., Hoffmann, J., Jahn, R., Löhne, C., Nordt, B., Ohl, M. (ed.) Biosystematics 2011, Berlin, ISBN 978-3-921800-68-3

Kirchhoff, A., Müller, A., Berendsohn, W. G., Janssen, T., Roos, M. C., Sierra, S.E.C. 2011: Using the EDIT Platform for Cybertaxonomy to elaborate and disseminate complex floristic information. EDIT newsletter 25: 26-28. ISSN 1958-5152

Sierra, S. E. C., Roos, M. C., Hamann, T., Berendsohn, W. G., Güntsch, A., Kirchhoff, A., Kirkup, D. & Janssen, T. 2011: Toward an Open Access repository and data services for plant biodiversity research. EDIT newsletter 25:4-7. ISSN 1958-5152

Kirchhoff, A., Berendsohn, W. 2010: Die EDIT 'Platform for Cybertaxonomy.

GfBS news 23: 38-42. ISSN 1867-6766 (Printausgabe), ISSN 1867-6774 (Internetausgabe)

Kirchhoff, A. 2010: The EDIT Platform for Cybertaxonomy, SPNHC newsletter 24:1-2, 19. ISSN 1071-2887

Kirchhoff, A., Kohlbecker, A., Hoffmann, N., Güntsch, A.2010: CDM setups site, How to install the software modules of the EDIT Platform for Cybertaxonomy, EDIT newsletter 21: 6-7. ISSN 1962-3402

Hoffmann, N., Kohlbecker, A., Müller, A., Revilla F., Kirchhoff, A., Güntsch, A., Berendsohn, W. 2010: Generating printed publications with the EDIT common data model (CDM), EDIT newsletter 23: 11-12. ISSN 19623402

Venin, M., Kirchhoff, A., Fradin, H., Güntsch, A., Hoffmann, N., Kohlbecker, A., Kuntzelman, E., Maiocco, Ô., Müller, A., Vignes Lebbe, R., Berendsohn, W. G.2010: Descriptive Data in the Platform for Cybertaxonomy, In: Nimis, P.L., Vignes Lebbe, R., (eds.) Tools for Identifying Biodiversity: Progress and Problems – pp. 7-11, Proceedings of the International Congress, Paris, September 20-22, 2010. ISBN 978-88-8303-295-0. EUT, 2010.

Kirchhoff, A., Paar, P., Mülder, J. 2009: Die virtuelle Rekonstruktion von Herodes’ drittem Winterpalast und der Oase von Jericho, HASB Bern 21: 151-161.

Kirchhoff, A., Hahn, A., Holetschek, J., Kelbert, P., Jahn, R. & Berendsohn, W. G. 2007: Open Access to Biodiversity Collection Data – GBIF Germany and the Botanical Node in: Kusber, W.-H. & Jahn, R. (ed.): Proceedings of the 1st Central European Diatom Meeting 2007: 79-82. Berlin. doi:10.3372/cediatom.116

Kirchhoff, A. 2007: Florenkartierung und Global Biodiversity Information Facility (GBIF), Floristische Rundbriefe, Beiheft 8: 93-98.

Kirchhoff, A., Hahn, A., Berendsohn, W.G. 2005: A Portal for Botanical Collections and Databases in Germany - The Botanical Node within GBIF-D, Verhandlungen der Gesellschaft für Ökologie, Proceedings of the GFÖ, Vol. 35 ( landscapes, ecosystems and populations - dynamics, functions and conservation): 489, Laufen/Salzach

Kirchhoff, A. 1998: Sequoiadendron giganteum in Schweizer Gärten. Schweizerische Gesellschaft für Gartenkultur, Mitteilungen 2: 51-57.

Other publications

Haston, E., Albenga, L., Chagnoux, S., Drinkwater, R., Durrant, J., Gilbert, E., Glöckler, F., Green, L., Harris, D., Holetschek, J., Hudson, L., Kahle, P., King, S., Kirchhoff, A.,Kroupa, A., Kvacek, J., Le Bras, G., Livermore, L., Mühlenberger, G., Paul, D., Phillips, S., Smirnova, L., Vacek, F., Walker, S. 2015: Automating Data Capture from Natural History Specimens. (Synthesys 3, Work Package 4, Task 1.2., Deliverable 4.2, http://www.synthesys.info/joint-research-activities/jra-1-synthesys-3/)

Rücknagel, J., Vierkant, P., Ulrich, R., Kloska, G., Schnepf, E., Fichtmüller, D., Reuter, E., Semrau, A., Kindling, M., Pampel, H., Witt, M., Fritze, F., van de Sandt, S., Klump, J., Goebelbecker, H.-J., Skarupianski, M., Bertelmann, R., Schirmbacher, P., Scholze, F., Kramer, C., Fuchs, C., Spier, S., Kirchhoff, A. : Metadata Schema for the Description of Research Data Repositories: version 3.0, 29 p., DOI: http://doi.org/10.2312/re3.008

Kirchhoff, A.; Berendsohn, W.G.; Bügel, U.; Chaves, F.; Guan, C.; Lindhorst, M.; Röpert, D.; Santamaria, E. Steinke, K.-H.; Zheng, H. (2014): StanDAP-Herb develops a standard process for extracting metadata from digitised herbarium specimens, TDWG Annual Conference 2014, Jönköping, Schweden. https://mbgserv18.mobot.org/ocs/index.php/tdwg/2014/paper/view/584

Berendsohn, W.G.; Chaves, F.; Kirchhoff, A.; Röpert, D.; Steinke, K.-H.; Usländer, T. (2014): Metadata extraction from digital specimen: a standardized software driven approach. Digital Specimen Conference 2014, Berlin, Deutschland. http://www.naturkundemuseum-berlin.de/forschung/tagungen/digitalspecimen-berlin-2014/home/abstracts-of-presentations/#c31140

Vierkant, P., Spier, S., Rücknagel, J., Gundlach, J., Fichtmüller, D., Pampel, H., Kindling, M., Agnes Kirchhoff, Göbelbecker, H.-J., Klump, J., Bertelmann, R., Schirmbacher, P., Scholze, F. 2012: Vocabulary for the Registration and Description of Research Data Repositories. Version 2.0. December 2012. DOI:10.2312/re3.002, http://www.re3data.org.

Luther, K., Kirchhoff, A., Fichtmüller, D. 2011: reBiND: saving endangered data, TDWG annual conference 2011, New Orleans, USA

Kirchhoff, A., Güntsch, A. 2011: Biodiversity archives: saving endangered data, 18.-23. 09.2011, Botanikertagung, Berlin, Germany, conference book: 113

Hahn, A., Kirchhoff, A., Berendsohn, W.G. 2005: Remote annotation in a distributed access system - How to provide feedback? - Annual meeting of the Taxonomic Databases Working Group 2005, St. Petersburg,

Hahn, A., Kirchhoff, A., Berendsohn, W.G. 2004: Virtual Herbarium, portal and organisation of the Botanical node within GBIF-D, GBIF-Deutschland, German Participation in the Global Biodiversity Information Facility, Status Report 2004: 48-49, DLR Bonn

Hahn, A., Kirchhoff A., Berendsohn., W. G. 2004: Networking biodiversity data - online access to distributed data sources in GBIF-D, Ocean Biodiversity Informatics; International Conference on Marine Biodiversity Data Management, 29-30 Nov 2004, Hamburg.

Hahn, A., Kirchhoff A. , Berendsohn W.G. 2003: Virtual Herbarium, portal and organisation of the botanical node within GBIF-D. - In: Sustainable use and conservation of biological diversity - a challenge for society, Symposium Report Part A: 259-260. Bonn.

Stevens, A.-D., Kirchhoff, A., Hahn A., Berendsohn, W.G. 2003: German Botany within the Global Biodiversity Information Facility (GBIF) – In: J. Rammeloo & A. Bogaerts (eds.). EuroGard III Congress and BEDUCO II Congress Abstracts, Scripta Botanica Belgica 27: 49.

Hahn, A., Kirchhoff, A., Matthäs, U., Surma A., Berendsohn W. G. 2001: BoGART - the Information System of the Berlin Botanic Garden, BIOLOG - German Programme on Biodiversity and Global Change, Status Report 2001: 228-229, Bonn.

Hahn, A., Kirchhoff A., Matthäs, U., Surma A., Berendsohn W. G. 2002: BoGART - Information management for the Berlin Botanic Garden. - 18th annual meeting of the Taxonomic Databases Working Group 2002, Indaiatuba, Brasil

Kirchhoff, A. 2002: (XSLT) Stylesheets für die XML-Ausgabe einer Datenbank. FH Potsdam, Institut für Information und Dokumentation (http://ww2.bgbm.org/bogartdb/BogartPublic.asp)

Talks

Kirchhoff, A., Berendsohn, W.G., Bügel, U., Chaves, F., Guan, C. , Lindhorst, M., Röpert, D., Santamaria, E., Steinke, K.-H., Zheng, H. 2014: StanDAP-Herb develops a standard process for extracting metadata from digitized herbarium specimens. TDWG annual conference: Biodiversity Information Standards, 26.-31.10.2014, Jönköping, Sweden. http://www.tdwg.org/fileadmin/2014conference/slides/Kirchhoff_StanDAPHer...

Berendsohn, W.G., Chaves, F., Kirchhoff, A., Röpert, D., Steinke, K.-H., Usländer, T. 2014: Metadataextraction from digital specimens: a standardised software driven approach. Digital Specimen Conference, Museum für Naturkunde, 8.-12.09. 2014, Berlin, Germany.

Kirchhoff, A.; Berendsohn, W.G.; Bügel, U.; Chaves, F.; Guan, C.; Lindhorst, M.; Röpert, D.; Santamaria, E.; Steinke, K.-H; Zheng,H. (2014): StanDAP-Herb develops a standard process for extracting metadata from digitised herbarium specimens, TDWG Annual Conference 2014, Jönköping, Schweden.

Kirchhoff, A. 2012: Field experiences in ATBI+M Gemer, EDIT Conservation Stakeholder Workshop 'Taxonomy meets nature conservation', Berlin, 16.-17. June 2010,

Häuser, C., Monje, C., Kirchhoff, A., Hoffmann, A., Kroupa, A. 2010: ATBIs best practices and tools, expertise and information management, Scoping Workshop Pondoland Center of Endemism: All Taxa Biodiversity Inventory, 30.08- 03.09.2010, Port Edward, South Africa

Kirchhoff, A. 2006: GBIF-D Botanikknoten, GBIF-D Botanikworkshop, 22.6.2006, BGBM Berlin-Dahlem

Kirchhoff A. 2005: Erfahrungen mit Bilddigitalisierung am Botanischen Museum in Berlin, Vavilov-Seminar 26.10.2005, Institute of Plant Genetics and Crop Plant Research, Gatersleben

Kirchhoff, A. Hahn, A. Berendsohn W.G.2005: A Portal for Botanical Collections and Databases in Germany - The Botanical Node within GBIF-D', 35th Annual Conference of the Ecological Society of Germany, Switzerland and Austria (GfÖ) 19.-23. Sept. 2005, Regensburg

Kirchhoff A., 2005:The organisational structure of GBIF Germany, 2nd ENBI Workshop, 10.-12.05.2005, Universitat de les Illes Balears, Palma de Mallorca

Kirchhoff, A., Hahn A., Berendsohn W.G. 2005: Alte Daten in neue Systeme? Rückwirkende Georeferenzierung, ein Überblick, 4. Workshop 'Vegetationsdatenbanken', 16.-18.03.2005, Institut für Geobotanik, Universität Halle

Jahn, R., Kirchhoff A., Hahn, A. 2003:Virtuelle versus Physische Sammlungen - Probleme und Lösungsansätze. - 16.9.2003 Tagung der Gesellschaft für biologische Systematik (GfbS), Dresden.

Kirchhoff, A., Hahn, A., Stevens A.-D., Berendsohn W.G. 2003: The Global Biodiversity Information Facility (GBIF) and the German Response. 22.7.2003 EuroGard III Congress, Meise, Belgium.

Poster

Kirchhoff, A., Röpert, D., Güntsch, A., Berendsohn, W.G., Steinke, K.-H., Guan, C., Zheng, H., Chaves, F., Bügel, U., Santamaria, E. (2016): Information-Extraction from Herbarium Specimens: The StanDAP-Herb Project. SPNC Annual Meeting 20.-25.06.2016, Berlin, Germany.

Kirchhoff, A., Röpert, D., Güntsch, A., Steinke, K.-H., Lindhorst, M., Guan, C., Zheng, H., F. Chaves, F., Bügel, U., Santamaria, E., Saliu, G., Papantonis,I. 2016: Informationsextraktion aus Herbarbelegen: Das StanDAP-Herb Projekt. DFG Workshop: Forschungsrelevante Sammlungen wissenschaftlicher Objekte. 28.-29.01. 2016, Bonn, Germany.

Kirchhoff, A. Fichtmüller, D., Güntsch, A. 2012: Saving endangered data – the reBiND project. BHL final events, 4 June 2012, Berlin.

Fichtmüller, D., Kirchhoff, A. Güntsch, A. 2012: Biodiversity needs data - the reBiND Project provides workflows and software for archiving biodiversity data, GBIF Nodes Meeting, Mar 2012 Berlin-Dahlem

Luther, K., Kirchhoff, A., Fichtmüller, D., Güntsch, A. 2011: reBiND saving endangered data. TDWG annual conference, Oct 2011, New Orleans, USA.

Kirchhoff, A., Güntsch, A. 2011: Biodiversity archives saving endangered data. Botanikertagung, 21. Sept. 2011, Berlin.

Kirchhoff, A., Holetschek, H., Hahn, A., Kelbert, P., Jahn, R., Berendsohn W.G.2007: GBIF-Germany and the Botanical Node, 1st central European diatom meeting, 23.-25. Mar 2007 Berlin-Dahlem.

Agnes Kirchhoff, Anton Güntsch, Walter G. Berendsohn 2007: EDIT – Taxonomy for Biodiversity Research and Conservation, 6th meeting on vegetation databases to be held in conjunction with the floristic survey, Surveys of vegetation and floras - new prospects, joint ways, 28 Feb-02 Mar 2007, Bonn.

Kirchhoff, A., Hahn, A., Berendsohn W.G. 2005: The Botanical Node within the German GBIF Network, 17.-23.07.2005, XVII. International Botanical Congress, Vienna.

Kirchhoff, A., Hahn, A. , Berendsohn, W.G. 2004: The Botanical Node in GBIF-D – status and perspectives, GBIF-D Statusseminar ", 6.-7.12.2004, Bonn.

Kirchhoff, A., Hahn, A., Jahn R., Berendsohn W.G. 2004: Biodiversity in past, present, and future - joint access to botanical data with GBIF, 7. Jahrestagung der GfBS Stuttgart, 14. September 2004, Staatliches Museum für Naturkunde Stuttgart.

Kirchhoff, A., Hahn, A., Berendsohn W.G. 2004: Living Collections and the GBIF-D Botanical Node, International Symposium: 'Botanic Gardens: Awareness of Biodiversity' 4.-6. June 2004 , BGBM, Berlin.

Kirchhoff, A., Hahn A., Berendsohn W.G. 2004: Botanische Beleg- und Beobachtungsdaten vernetzt -Der Botanische Knoten von GBIF Deutschland - 3. Workshop Vegetationsdatenbanken - Vegetationsdatenbanken in Landschaftsplanung, Naturschutz, Biomonitoring und Biodiversitätsforschung, 11.-12.03.2004, Fachhochschule Weihenstephan, Freising.

Hahn, A., Kirchhoff A., Berendsohn W.G. 2003: German Botany and the Global Biodiversity Information Facility (GBIF) - Symposium "Sustainable use and conservation of biological diversity", 1.-4.12.2003, Berlin.

Hahn, A., Kirchhoff, A., Stevens A.-D., Berendsohn W.G. 2003: German Botany within the Global Biodiversity Information Facility (GBIF). - EuroGard III Congress, 21.-26.7.2003, Meise, Belgium.

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Agnes Kirchhoff

Publications

Talks

Poster

Botanischer Garten und Botanisches Museum Berlin