Automatically Populating a Preclinical Spinal Cord Injury Knowledge Base to Support Clinical Translation

Akronym
PSINK
Koordinator
Philipp Cimiano
Einrichtung(en)
Center of Excellence - Cognitive Interaction Technology CITEC
Beschreibung
In this BMBF-funded project, we apply ontology-based information extraction from textual data to large collections of scientific publications reporting on pre-clinical studies in the context of spinal cord injury (SCI). Our goal is to create the first comprehensive SCI knowledge base in order to foster translation from pre-clinicial research into therapeutic concepts that are likely to be effective in human patients. Our approach to information extraction is based on probabilistic graphical models. We apply techniques from active learning and distant supervision in order to reduce manual annotation and curation efforts to a minimum.
Förderer
BMBF

8 Publikationen

2018 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2914075
What Coreference Chains Tell about Experimental Groups in (Pre-)Clinical Trials
Schwitteck A, ter Horst H, Hartung M (2018)
In: Proceedings of DGfS/CL Poster Session. Stuttgart.
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2017 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2910336
Joint Entity Recognition and Linking in Technical Domains Using Undirected Probabilistic Graphical Models
ter Horst H, Hartung M, Cimiano P (2017)
In: Language, Data, and Knowledge (Proceedings of the 1st International LDK Conference). Gracia J, Bond F, McCrae JP, Buitelaar P, Chiarcos C, Hellmann S (Eds); Lecture Notes in Artificial Intelligence, 10318. Springer: 166-180.
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2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2918981
Assessing the Impact of Single and Pairwise Slot Constraints in a Factor Graph Model for Template-based Information Extraction
ter Horst H, Hartung M, Klinger R, Brazda N, Müller HW, Cimiano P (2018)
In: Proceedings of the 23rd International Conference on Natural Language & Information Systems (NLDB). Silberztein M, Atigui F, Kornyshova E, Métais E, Meziane F (Eds); Lecture Notes in Computer Science, 10859. Cham: Springer International Publishing: 179-190.
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2016 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2905448
SCIO: The Spinal Cord Injury Ontology, a Prerequisite for Automated Data Extraction from Publications on Research in Spinal Cord Injury
Brazda N, Estrada V, Kirchhoffer T, ter Horst H, Hartung M, Wiljes C, Klinger R, Cimiano P, Müller HW (2016)
In: Proceedings of the 18th Spinal Research Network Meeting (ISRT 2016). London.
PUB
 
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2930952
Cold-Start Knowledge Base Population Using Ontology-Based Information Extraction with Conditional Random Fields
ter Horst H, Hartung M, Cimiano P (2018)
In: Reasoning Web. Learning, Uncertainty, Streaming, and Scalability. d'Amato C, Theobald M (Eds); Lecture Notes in Computer Science, 11078. Springer: 78-109.
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913482
Ontology-driven Visual Exploration of Preclinical Research Data in the Spinal Cord Injury Domain
Borowi A, ter Horst H, Hartung M, Estrada V, Brazda N, Müller HW, Cimiano P (2017)
In: Proceedings of the SEMANTICS 2017 Poster and Demo Track. CEUR Workshop proceedings, 2044. Aachen: RWTH.
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913603
SCIO: An Ontology to Support the Formalization of Pre-Clinical Spinal Cord Injury Experiments
Brazda N, ter Horst H, Hartung M, Wiljes C, Estrada V, Klinger R, Kuchinke W, Müller HW, Cimiano P (2017)
In: Proceedings of the 3rd Joint Ontology Workshops (JOWO): Ontologies and Data in the Life Sciences. CEUR Workshop proceedings, 2050. Aachen: RWTH.
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2018 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2919923
SANTO: A Web-based Annotation Tool for Ontology-driven Slot Filling
Hartung M, ter Horst H, Grimm F, Diekmann T, Klinger R, Cimiano P (2018)
In: Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics (System Demonstrations). Association for Computational Linguistics.
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