Fraunhofer-Gesellschaft

Publica

Hier finden Sie wissenschaftliche Publikationen aus den Fraunhofer-Instituten.
2019The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track
Madan, S.; Szostak, J.; Elayavilli, R.K.; Tsai, R.T.H.; Ali, M.; Qian, L.H.; Rastegar-Mojarad, M.; Hoeng, J.; Fluck, J.
Journal Article
2019PSB 2019 Workshop on Text Mining and Visualization for Precision Medicine
Gonzalez-Hernandez, G.; Lu, Z.Y.; Leaman, R.; Weissenbacher, D.; Boland, M.R.; Chen, Y.; Du, J.C.; Fluck, J.; Greene, C.S.; Holmes, J.; Kashyap, A.; Nielsen, R.L.; Ouyang, Z.Q.; Schaaf, S.; Taroni, J.N.; Tao, C.; Zhang, Y.P.; Liu, H.F.
Conference Paper
2018Graph based discovery in biomedical information systems connecting scientific texts with structured expert knowledge
Dörpinghaus, J.; Jacobs, M.; Fluck, J.
Conference Paper
2017Automatic extraction of BEL-statements based on neural networks
Ali, Mehdi; Madan, Sumit; Fischer, Asja; Petzka, Henning; Fluck, Juliane
Conference Paper
2017The cloud4health Project. Secondary use of clinical data with secure cloud-based text mining services
Fluck, Juliane; Senger, Philipp; Ziegler, Wolfgang; Claus, Steffen; Schwichtenberg, Horst
Book Article
2017Document clustering using a graph covering with pseudostable sets
Dörpinghaus, Jens; Schaaf, Sebastian; Fluck, Juliane; Jacobs, Marc
Conference Paper
2017Overview of BEL track: Extraction of complex relationships and their conversion to BEL
Madan, Sumit; Szostak, Justyna; Dörpinghaus, Jens; Hoeng, Julia; Fluck, Juliane
Conference Paper
2017Recent improvements of the BEL Information Extraction workFlow (BELIEF) for biomedical text mining and curation
Szostak, Justyna; Madan, Sumit; Hayes, William; Doerpinghaus, Jens; Fluck, Juliane; Talikka, Marja; Peitsch, Manuel C.; Hoeng, Julia
Poster
2016The BEL information extraction workflow (BELIEF): Evaluation in the BioCreative V BEL and IAT track
Madan, Sumit; Hodapp, Sven; Senger, Philipp; Ansari, Sam; Szostak, Justyna; Hoeng, Julia; Peitsch, Manuel; Fluck, Juliane
Journal Article
2016BioCreative V track 4: A shared task for the extraction of causal network information using the Biological Expression Language
Rinaldi, Fabio; Ellendorff, Tilia Renate; Madan, Sumit; Clematide, Simon; Lek, Adrian van der; Mevissen, Theo; Fluck, Juliane
Journal Article
2016Integration of UIMA text mining components into an event-based asynchronous microservice architecture
Hodapp, Sven; Madan, Sumit; Fluck, Juliane; Zimmermann, Marc
Conference Paper
2016Overview of the interactive task in BioCreative V
Wang, Q.; Abdul, S.S.; Almeida, L.; Ananiadou, S.; Balderas-Martínez, Y.I.; Batista-Navarro, R.; Campos, D.; Chilton, L.; Chou, H.-J.; Contreras, G.; Cooper, L.; Dai, H.-J.; Ferrell, B.; Fluck, J.; Gama-Castro, S.; George, N.; Gkoutos, G.; Irin, A.K.; Jensen, L.J.; Jimenez, S.; Jue, T.R.; Keseler, I.; Madan, S.; Matos, S.; McQuilton, P.; Milacic, M.; Mort, M.; Natarajan, J.; Pafilis, E.; Pereira, E.; Rao, S.; Rinaldi, F.; Rothfels, K.; Salgado, D.; Silva, R.M.; Singh, O.; Stefancsik, R.; Su, C.-H.; Subramani, S.; Tadepally, H.D.; Tsaprouni, L.; Vasilevsky, N.; Wang, X.; Chatr-Aryamontri, A.; Laulederkind, S.J.F.; Matis-Mitchell, S.; McEntyre, J.; Orchard, S.; Pundir, S.; Rodriguez-Esteban, R.; Auken, K. van; Lu, Z.; Schaeffer, M.; Wu, C.H.; Hirschman, L.; Arighi, C.N.
Journal Article
2016Towards a pathway inventory of the human brain for modeling disease mechanisms underlying neurodegeneration
Iyappan, A.; Gündel, M.; Shahid, M.; Wang, J.; Li, H.; Mevissen, H.-T.; Müller, B.; Fluck, J.; Jirsa, V.; Domide, L.; Younesi, E.; Hofmann-Apitius, M.
Journal Article
2016Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL)
Fluck, Juliane; Madan, Sumit; Ansari, Sam; Kodamullil, Alpha T.; Karki, Reagon; Rastegar-Mojarad, Majid; Catelett, Natalie L.; Hayes, William; Szostak, Justyna; Hoeng, Julia; Peitsch, Manuel C.
Journal Article
2015BELIEF dashboard - a web-based curation interface to support generation of BEL networks
Madan, Sumit; Hodapp, Sven; Fluck, Juliane
Conference Paper
2015BioCreative V a new challenge in text mining for biocuration
Arighi, Cecilia N.; Chatraryamontri, Andrew; Kevin, Cohen B.; Comeau, Donald; Fluck, Juliane; Dogan, Rezarta Islamaj; Hirschman, Lynette; Kim, Sun; Krallinger, Martin; Leitner, Florian; Lu, Zhiyong; Oyarzabal, Julen; Rabal, Obdulia; Rinaldi, Fabio; Tudor, Catalina O.; Valencia, Alfonso; Wiegers, Thomas; Wilbur, John; Wu, Cathy H.
Abstract
2015Construction of biological networks from unstructured information based on a semi-automated curation workflow
Szostak, Justyna; Ansari, Sam; Madan, Sumit; Fluck, Juliane; Talikka, Marja; Iskandar, Anita; Leon, Hector de; Hofmann-Apitius, Martin; Peitsch, Manuel C.; Hoeng, Julia
Journal Article
2015Data management and processing in toxicoinformatics - from chemical databases to automatic extraction of unstructured resources
Fluck, Juliane; Zimmermann, Marc
Book Article
2015Detecting miRNA mentions and relations in biomedical literature
Bagewadi, S.; Bobic, T.; Hofmann-Apitius, M.; Fluck, J.; Klinger, R.
Journal Article
2015Interpretation of large scale biological data facilitated by curated causal biological network models
Szostak, Justyna; Ansari, Sam; Boue, Stephanie; Talikka, Marja; Fluck, Juliane; Peitsch, Manuel; Hoeng, Julia
Abstract
2015Overview of the interactive task in BioCreative V
Wang, Qinghua; Abdul, Shabbir Syed; Almeida, Lara; Ananiadou, Sophia; Balderas-Martínez, Yalbi Itzel; BatistaNavarro, Riza; Campos, David; Chilton, Lucy; Chou, Hui-Jou; Contreras, Gabriela; Cooper, Laurel; Dai, Hong-Jie; Fluck, Juliane; Gama, Socorro; Gkoutos, Georgios; Irin, Afroza Khanam; Jensen, Lars Juhl; Jimenez, Silvia; Jue, Toni Rose; Keseler, Ingrid; Madan, Sumit; Matos, Sérgio; McQuilton, Peter; Mort, Matthew; Natarajan, Jeyakumar; Pafilis, Evangelos; Pereira, Emiliano; Rao, Shruti; Rinaldi, Fabio; Salgado, David; Singh, Onkar; Stefancsik, Raymund; Su, Chu-Hsien; Subramani, Suresh; Tadepally, Hamsa Dhwani; Tsaprouni, Loukia; Vasilevsky, Nicole; Wang, Xiaodong; Chatr-aryamontri, Andrew; Laulederkind, Stan; Matis-Mitchell, Sherri; McEntyre, Johanna; Orchard, Sandra; Pundir, Sangya; Rodriguez-Esteban, Raul; Auken, Kimberly Van; Lu, Zhiyong; Schaeffer, Mary; Hirschman, Lynette; Arighi, Cecilia
Conference Paper
2015Track 4 overview: Extraction of causal network information in biological expression language (BEL)
Fluck, Juliane; Madan, Sumit; Ellendorf, Tilia; Mevissen, Heinz-Theodor; Clematide, Simon; Lek, Adrian van der; Rinaldi, Fabio
Conference Paper
2014BELIEF - a semiautomatic workflow for BEL network creation
Fluck, Juliane; Madan, Sumit; Ansari, Sam; Szostak, Justyna; Hoeng, Julia; Zimmermann, Marc; Hofmann-Apitius, Martin; Peitsch, Manuel C
Conference Paper
2014Text mining for systems biology
Fluck, Juliane; Hofman-Apitius, Martin
Journal Article
2013BEL networks derived from qualitative translations of BioNLP shared task annotations
Fluck, Juliane; Klenner, Alexander; Madan, Sumit; Ansari, Sam; Bobic, Tamara; Hoeng, Julia; Hofman-Apitius, Martin; Peitsch, Manuel
Conference Paper
2013A business logic system for mining German patient records
Senger, Philipp; Klenner, Alexander; Fluck, Juliane
Abstract
2013Experience made using public cloud infrastructure to analyse clinical patient data
Ziegler, Wolfgang; Ihle, Matthias; Claus, Steffen; Senger, Philipp; Mohebbi, Pooya; Khan, Zakir; Fluck, Juliane; Griebel, Lena; Sedlmayr, Martin; Berger, Florian; Laufer, Julian; Chatziastros, Astros; Drepper, Johannes
Conference Paper
2013SCAI: Extracting drug-drug interactions using a rich feature vector
Bobic, Tamara; Fluck, Juliane; Hofmann-Apitius, Martin
Conference Paper
2012Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports
Gurulingappa, Harsha; Rajput, Abdul-Mateen; Roberts, Angus; Fluck, Juliane; Hofmann-Apitius, Martin; Toldo, Luca
Journal Article
2012Mining biomarker information in biomedical literature
Younesi, Erfan; Toldo, Luca; Müller, Bernd; Friedrich, Christoph M.; Novac, Natalia; Scheer, Alexander; Hofmann-Apitius, Martin; Fluck, Juliane
Journal Article
2012Text mining in livestock animal science: Introducing the potential of text mining to animal sciences
Sahadevan, S.; Hofmann-Apitius, M.; Schellander, K.; Tesfaye, D.; Fluck, J.; Friedrich, C.M.
Journal Article
2011Information retrieval framework for technology survey in biomedical and chemistry literature
Gurulingappa, Harsha; Müller, Bernd; Hofmann-Apitius, Martin; Fluck, Juliane
Conference Paper
2011Overview of the TREC 2011 Chemical IR Track
Lupu, Mihai; Jiashu, Zhao; Huang, Jimmy; Gurulingappa, Harsha; Fluck, Juliane; Zimmermann, Marc; Filippov, Igor; Tait, John
Conference Paper
2011A semantic platform for information retrieval from e-health records
Gurulingappa, Harsha; Müller, Bernd; Hofmann-Apitius, Martin; Fluck, Juliane
Conference Paper
2010Abstracts versus full texts and patents: A quantitative analysis of biomedical entities
Müller, B.; Klinger, R.; Gurulingappa, H.; Mevissen, H.-T.; Hofmann-Apitius, M.; Fluck, J.; Friedrich, C.M.
Conference Paper
2010Concept identification and assertion classification in patient health records
Gurulingappa, H.; Hofmann-Apitius, M.; Fluck, J.
Conference Paper
2010An empirical evaluation of resources for the identification of diseases and adverse effects in biomedical literature
Gurulingappa, H.; Klinger, R.; Hofmann-Apitius, M.; Fluck, J.
Conference Paper
2010Prior art search in chemistry patents based on semantic concepts and co-citation analysis
Gurulingappa, H.; Müller, B.; Klinger, R.; Mevissen, H.-T.; Hofmann-Apitius, M.; Friedrich, C.M.; Fluck, J.
Conference Paper
2009Concept-based semi-automatic classification of drugs
Gurulingappa, H.; Kolarik, C.; Hofmann-Apitius, M.; Fluck, J.
Journal Article
2009Patent retrieval in chemistry based on semantically tagged named entities
Gurulingappa, H.; Müller, B.; Klinger, R.; Mevissen, H.-T.; Hofmann-Apitius, M.; Fluck, J.; Friedrich, C.M.
Conference Paper
2009Text mining in full text articles- methodical and representation issues
Klinger, R.; Pesch, R.; Mevissen, T.; Fluck, J.
Poster
2008Chemical names: Terminological resources and corpora annotation
Kolarik, C.; Klinger, R.; Friedrich, C.M.; Hofmann-Apitius, M.; Fluck, J.
Conference Paper
2008Detection of IUPAC and IUPAC-like chemical names
Klinger, R.; Kolarik, C.; Fluck, J.; Hofmann-Apitius, M.; Friedrich, C.M.
Journal Article
2008Knowledge environments representing molecular entities for the virtual physiological human
Hofmann-Apitius, M.; Fluck, J.; Furlong, L.I.; Fornes, O.; Kolarik, C.; Hanser, S.; Boeker, M.; Schulz, S.; Sanz, F.; Klinger, R.; Mevissen, T.; Gattermayer, T.; Oliva, B.; Friedrich, C.M.
Journal Article
2008Knowledge structuring and retrieval for intracranial aneurysm research
Hanser, S.; Fluck, J.; Furlong, L.I.; Friedrich, C.M.; Hofmann-Apitius, M.; Stenzhorn, H.; Boeker, M.
Poster
2008Overview of BioCreative II gene normalization
Morgan, A.A.; Lu, Z.; Wang, X.; Cohen, A.M.; Fluck, J.; Ruch, P.; Divoli, A.; Fundel, K.; Leaman, R.; Hakenberg, J.; Sun, C.; Liu, H.-h.; Rorres, R.; Krauthammer, M.; Lau, W.W.; Liu, H.; Hsu, C.-N.; Schuemie, M.; Cohen, K.B.; Hirschman, L.
Journal Article, Conference Paper
2007Identification of new drug classification terms in textual resources
Kolarik, C.; Hofmann-Apitius, M.; Zimmermann, M.; Fluck, J.
Journal Article
2007Identifying gene specific variants in biomedical text
Klinger, R.; Furlong, L.I.; Friedrich, C.M.; Mevissen, H.-T.; Fluck, J.; Sanz, F.; Hofmann-Apitius, M.
Journal Article
2007Named entity recognition with combinations of conditional random fields
Klinger, R.; Friedrich, C.M.; Fluck, J.; Hofmann-Apitius, M.
Conference Paper
2007ProMiner: Recognition of human gene and protein names using regularly updated dictionaries
Fluck, J.; Mevissen, T.H.; Dach, H.; Oster, M.; Hofmann-Apitius, M.
Conference Paper
2006The autoimmune disease database. A dynamically compiled literature-derived database
Karopka, T.; Fluck, J.; Mevissen, H.-T.; Glass, Ä.
Journal Article
2006Biomedical and chemical named entity recognition with conditional random fields: The advantages of dictionary features
Friedrich, C.M.; Revillion, T.; Hofmann, M.; Fluck, J.
Presentation
2006Proceedings of the Second International Symposium for Semantic Mining in Biomedicine. Introduction
Ananiadou, S.; Fluck, J.
Conference Paper
2006Second International Symposium on Semantic Mining in Biomedicine, SMBM 2006. Proceedings
: Ananiadou, S.; Fluck, J.
Conference Proceedings
2005Biological and chemical entity recognition from text using conditional random fields (CRF)
Revillion, T.; Friedrich, C.M.; Fluck, J.; Hofmann, M.
Poster
2005Information extraction in the life sciences: Perspectives for medicinal chemistry, pharmacology and toxicology
Zimmermann, M.; Fluck, J.; Thi, L.T.B.; Kolarik, C.; Kumpf, K.; Hofmann, M.
Journal Article
2005Information extraction technologies for the life science industry
Fluck, J.; Zimmermann, M.; Kurapkat, G.; Hofmann, M.
Journal Article
2005ProMiner: Rule-based protein and gene entity recognition
Hanisch, D.; Fundel, K.; Mevissen, H.-T.; Zimmer, R.; Fluck, J.
Journal Article
2005Recognizing noun phrases in biomedical text
Wermter, J.; Fluck, J.; Strötgen, J.; Geißler, S.; Hahn, U.
Conference Paper
2005Text mining in den Life Sciences
Fluck, J.; Hofmann, M.; Hahn, U.; Wermter, J.; Schulz, S.
Journal Article
2005Text mining in life sciences
Fluck, J.; Deneke, H.; Gieger, C.
Book Article
2005Using named entity recognition for ontology annotation
Fluck, J.; Stitt, M.; Selbig, J.; Hofmann, M.; Thimm, O.
Conference Paper
2004ProMiner: Organism specific protein name detection using approximate string matching
Hanisch, D.; Fundel, K.; Mevissen, H.-T.; Zimmer, R.; Fluck, J.
Conference Paper
2004Using text mining networks for the context specific interpretation of gene expression data
Gieger, C.; Hanisch, D.; Fluck, J.; Mevissen, H.-T.; Tresch, A.; Deneke, H.
Journal Article
2003The Future of Text Mining in Genome-based Clinical Research
Gieger, C.; Deneke, H.; Fluck, J.
Journal Article
2003Microarrays: How Many Do You Need?
Zien, A.; Fluck, J.; Zimmer, R.; Lengauer, T.
Journal Article
2003Playing biology's name game: Identifying protein names in scientific text
Hanisch, D.; Fluck, J.; Mevissen, H.; Zimmer, R.
Conference Paper
2002Microarrays: How Many Do You Need?
Zien, A.; Fluck, J.; Zimmer, R.; Lengauer, T.
Conference Paper
2001Contraction-dependent apoptosis of normal dermal fibroblasts
Niland, S.; Cremer, A.; Fluck, J.; Eble, J.A.; Krieg, T.; Sollberg, S.
Journal Article