Search Results - "Hahn, Udo"

Medical Information Extraction in the Age of Deep Learning by Hahn, Udo, Oleynik, Michel

“…Summary Objectives : We survey recent developments in medical Information Extraction (IE) as reported in the literature from the past three years. Our focus is…”
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A systems study reveals concurrent activation of AMPK and mTOR by amino acids by Dalle Pezze, Piero, Ruf, Stefanie, Sonntag, Annika G., Langelaar-Makkinje, Miriam, Hall, Philip, Heberle, Alexander M., Razquin Navas, Patricia, van Eunen, Karen, Tölle, Regine C., Schwarz, Jennifer J., Wiese, Heike, Warscheid, Bettina, Deitersen, Jana, Stork, Björn, Fäßler, Erik, Schäuble, Sascha, Hahn, Udo, Horvatovich, Peter, Shanley, Daryl P., Thedieck, Kathrin

“…Amino acids (aa) are not only building blocks for proteins, but also signalling molecules, with the mammalian target of rapamycin complex 1 (mTORC1) acting as…”
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The PI3K and MAPK/p38 pathways control stress granule assembly in a hierarchical manner by Heberle, Alexander Martin, Razquin Navas, Patricia, Langelaar-Makkinje, Miriam, Kasack, Katharina, Sadik, Ahmed, Faessler, Erik, Hahn, Udo, Marx-Stoelting, Philip, Opitz, Christiane A, Sers, Christine, Heiland, Ines, Schäuble, Sascha, Thedieck, Kathrin

“…All cells and organisms exhibit stress-coping mechanisms to ensure survival. Cytoplasmic protein-RNA assemblies termed stress granules are increasingly…”
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Towards valid and reusable reference alignments - ten basic quality checks for ontology alignments and their application to three different reference data sets by Beisswanger, Elena, Hahn, Udo

“…Identifying relationships between hitherto unrelated entities in different ontologies is the key task of ontology alignment. An alignment is either manually…”
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Text mining for biology--the way forward: opinions from leading scientists by Altman, Russ B, Bergman, Casey M, Blake, Judith, Blaschke, Christian, Cohen, Aaron, Gannon, Frank, Grivell, Les, Hahn, Udo, Hersh, William, Hirschman, Lynette, Jensen, Lars Juhl, Krallinger, Martin, Mons, Barend, O'Donoghue, Seán I, Peitsch, Manuel C, Rebholz-Schuhmann, Dietrich, Shatkay, Hagit, Valencia, Alfonso

“…This article collects opinions from leading scientists about how text mining can provide better access to the biological literature, how the scientific…”
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SYNTACTIC SIMPLIFICATION AND SEMANTIC ENRICHMENT-TRIMMING DEPENDENCY GRAPHS FOR EVENT EXTRACTION by Buyko, Ekaterina, Faessler, Erik, Wermter, Joachim, Hahn, Udo

“…In our approach to event extraction, dependency graphs constitute the fundamental data structure for knowledge capture. Two types of trimming operations pave…”
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Part-whole representation and reasoning in formal biomedical ontologies by Schulz, Stefan, Hahn, Udo

“…Objective:Biomedical ontologies are typically structured in a biaxial way, reflecting both a taxonomic ( is-a) and a partonomic ( part-of) hierarchy. Commonly…”
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Spatial location and its relevance for terminological inferences in bio-ontologies by Schulz, Stefan, Markó, Kornél, Hahn, Udo

“…An adequate and expressive ontological representation of biological organisms and their parts requires formal reasoning mechanisms for their relations of…”
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U-Compare bio-event meta-service: compatible BioNLP event extraction services by Kano, Yoshinobu, Björne, Jari, Ginter, Filip, Salakoski, Tapio, Buyko, Ekaterina, Hahn, Udo, Cohen, K Bretonnel, Verspoor, Karin, Roeder, Christophe, Hunter, Lawrence E, Kilicoglu, Halil, Bergler, Sabine, Van Landeghem, Sofie, Van Parys, Thomas, Van de Peer, Yves, Miwa, Makoto, Ananiadou, Sophia, Neves, Mariana, Pascual-Montano, Alberto, Özgür, Arzucan, Radev, Dragomir R, Riedel, Sebastian, Sætre, Rune, Chun, Hong-Woo, Kim, Jin-Dong, Pyysalo, Sampo, Ohta, Tomoko, Tsujii, Jun'ichi

“…Bio-molecular event extraction from literature is recognized as an important task of bio text mining and, as such, many relevant systems have been developed…”
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Assessment of NER solutions against the first and second CALBC Silver Standard Corpus by Rebholz-Schuhmann, Dietrich, Jimeno Yepes, Antonio, Li, Chen, Kafkas, Senay, Lewin, Ian, Kang, Ning, Corbett, Peter, Milward, David, Buyko, Ekaterina, Beisswanger, Elena, Hornbostel, Kerstin, Kouznetsov, Alexandre, Witte, René, Laurila, Jonas B, Baker, Christopher Jo, Kuo, Cheng-Ju, Clematide, Simone, Rinaldi, Fabio, Farkas, Richárd, Móra, György, Hara, Kazuo, Furlong, Laura I, Rautschka, Michael, Neves, Mariana Lara, Pascual-Montano, Alberto, Wei, Qi, Collier, Nigel, Chowdhury, Md Faisal Mahbub, Lavelli, Alberto, Berlanga, Rafael, Morante, Roser, Van Asch, Vincent, Daelemans, Walter, Marina, José Luís, van Mulligen, Erik, Kors, Jan, Hahn, Udo

“…Competitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus…”
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Towards the ontological foundations of symbolic biological theories by Schulz, Stefan, Hahn, Udo

“…Summary Objective Support for the symbolic representation of the physical structure of living organisms by an ontologically solid and logically sound…”
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Influence of Context in Transformer-Based Medication Relation Extraction by Modersohn, Luise, Hahn, Udo

“…The extraction of medication information from unstructured clinical documents has been a major application of clinical NLP in the past decade as evidenced by…”
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GePI: large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions by Faessler, Erik, Hahn, Udo, Schäuble, Sascha

“…Abstract We present GePI, a novel Web server for large-scale text mining of molecular interactions from the scientific biomedical literature. GePI leverages…”
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High-performance gene name normalization with GeNo by Wermter, Joachim, Tomanek, Katrin, Hahn, Udo

“…Motivation: The recognition and normalization of textual mentions of gene and protein names is both particularly important and challenging. Its importance lies…”
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IL4I1 Is a Metabolic Immune Checkpoint that Activates the AHR and Promotes Tumor Progression by Sadik, Ahmed, Somarribas Patterson, Luis F., Öztürk, Selcen, Mohapatra, Soumya R., Panitz, Verena, Secker, Philipp F., Pfänder, Pauline, Loth, Stefanie, Salem, Heba, Prentzell, Mirja Tamara, Berdel, Bianca, Iskar, Murat, Faessler, Erik, Reuter, Friederike, Kirst, Isabelle, Kalter, Verena, Foerster, Kathrin I., Jäger, Evelyn, Guevara, Carina Ramallo, Sobeh, Mansour, Hielscher, Thomas, Poschet, Gernot, Reinhardt, Annekathrin, Hassel, Jessica C., Zapatka, Marc, Hahn, Udo, von Deimling, Andreas, Hopf, Carsten, Schlichting, Rita, Escher, Beate I., Burhenne, Jürgen, Haefeli, Walter E., Ishaque, Naveed, Böhme, Alexander, Schäuble, Sascha, Thedieck, Kathrin, Trump, Saskia, Seiffert, Martina, Opitz, Christiane A.

“…Aryl hydrocarbon receptor (AHR) activation by tryptophan (Trp) catabolites enhances tumor malignancy and suppresses anti-tumor immunity. The context…”
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A Vector Space Approach for Measuring Relationality and Multidimensionality of Meaning in Large Text Collections by Poschmann, Philipp, Goldenstein, Jan, Büchel, Sven, Hahn, Udo

“…In this article, we develop a methodological approach for organizational research regarding the construction of multidimensional and relational similarity…”
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Final Report on the German Clinical Reference Corpus 3000PA by Hahn, Udo, Modersohn, Luise, Faller, Jakob, Lohr, Christina

“…We here report on one of the outcomes of a large-scale German research program, the Medical Informatics Initiative (MII), aiming at the development of a solid…”
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3000PA-Towards a National Reference Corpus of German Clinical Language by Hahn, Udo, Matthies, Franz, Lohr, Christina, Löffler, Markus

“…We introduce 3000PA, a clinical document corpus composed of 3,000 EPRs from three different clinical sites, which will serve as the backbone of a national…”
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Exploiting parallel corpora to scale up multilingual biomedical terminologies by Hellrich, Johannes, Hahn, Udo

“…Creating and maintaining biomedical terminologies for multiple natural languages is a resource-expensive task, typically carried out by human domain experts…”
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Phosphoproteomics Profiling Defines a Target Landscape of the Basophilic Protein Kinases AKT, S6K, and RSK in Skeletal Myotubes by Fricke, Anna L., Mühlhäuser, Wignand W. D., Reimann, Lena, Zimmermann, Johannes P., Reichenbach, Christa, Knapp, Bettina, Peikert, Christian D., Heberle, Alexander M., Faessler, Erik, Schäuble, Sascha, Hahn, Udo, Thedieck, Kathrin, Radziwill, Gerald, Warscheid, Bettina

“…Phosphorylation-dependent signal transduction plays an important role in regulating the functions and fate of skeletal muscle cells. Central players in the…”
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