Dietrich Rebholz-Schuhmann

167 papers A* 1B 7C 2Misc 1Journal 75Unranked 66

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	Implementing Webby FAIR Digital Objects in MLentory. INFORMATIK Rohitha Ravinder, Nelson Quiñones, Dietrich Rebholz-Schuhmann, Leyla Jael Castro
2025	—	`ed.`	Proceedings of the 8th Workshop on Semantic Web solutions for large-scale biomedical data analytics co-located with The ESWC 2025: Extended Semantic Web Conference (ESWC 2025), Portorož, Slovenia, June 1, 2025. SeWeBMeDa@ESWC Rita Torres de Sousa, Michel Dumontier, Dietrich Rebholz-Schuhmann, Ali Hasnain
2024	—	`conf`	A Lightweight Approach to FDOs via Bioschemas, RO-Crate and Signposting on GitHub Pages. FDO Rohitha Ravinder, Nelson Quiñones, Dietrich Rebholz-Schuhmann, Leyla Jael Castro
2024	J	`jnl`	Enabling personalised disease diagnosis by combining a patient's time-specific gene expression profile with a biomedical knowledge base. BMC Bioinform. Ghanshyam Verma, Dietrich Rebholz-Schuhmann, Michael G. Madden
2024	—	`conf`	From Large Language Models to Knowledge Graphs for Biomarker Discovery in Cancer. HICSS Md. Rezaul Karim, Lina Molinas Comet, Md Shajalal, Paola de Perthuis, Dietrich Rebholz-Schuhmann, Stefan Decker
2024	—	`conf`	MLentory, an FDO registry for machine learning models. SWAT4HCLS Dhwani Solanki, Nelson Quiñones, Dietrich Rebholz-Schuhmann, Leyla Jael Castro
2024	—	`ed.`	Proceedings of the 7th Workshop on Semantic Web solutions for large-scale biomedical data analytics co-located with The ESWC 2024: Extended Semantic Web Conference (ESWC 2024), Hersonissos, Greece, May 26, 2024. SeWeBMeDa@ESWC Ali Hasnain, Alba Catalina Morales Tirado, Michel Dumontier, Dietrich Rebholz-Schuhmann
2023	—	`ed.`	3rd Workshop on Metadata and Research (objects) Management for Linked Open Science - DaMaLOS 2023, co-located with ESWC 2023, Hersonissos, Greece, May 29, 2023. DaMaLOS Leyla Jael Castro, Danilo Dessì, Jens Dierkes, Dietrich Rebholz-Schuhmann, Sonja Schimmler
2023	J	`jnl`	A Biomedical Knowledge Graph for Biomarker Discovery in Cancer. CoRR Md. Rezaul Karim, Lina Molinas Comet, Oya Beyan, Dietrich Rebholz-Schuhmann, Stefan Decker
2023	—	`conf`	A Comparison of Vector-based Approaches for Document Similarity Using the RELISH Corpus. SeWeBMeDA@ESWC Rohitha Ravinder, Tim Fellerhoff, Vishnu Dadi, Lukas Geist, Guillermo Rocamora, Muhammad Talha, Dietrich Rebholz-Schuhmann, Leyla Jael Castro
2023	—	`conf`	A metadata schema for machine-actionable Software Management Plans. DaMaLOS Leyla Jael Castro, Dietrich Rebholz-Schuhmann, Nelson Quiñones, Dimitrios Bampalikis, Olga L. Giraldo, Eva Martín del Pico, Allegra Via, Dhwani Solanki, Lukas Geist, Fotis E. Psomopoulos, Renato Alves, José María Fernández González
2023	—	`conf`	Comparative analysis of protein function text-based embeddings and their applicability to prediction tasks. SWAT4HCLS Rohitha Ravinder, Leyla Jael Castro, Martin Hofmann-Apitius, Dietrich Rebholz-Schuhmann
2023	—	`conf`	DaMaLOS 2023 Editorial Note. DaMaLOS Leyla Jael Castro, Dietrich Rebholz-Schuhmann, Danilo Dessì, Jens Dierkes, Sonja Schimmler
2023	—	`conf`	Document-to-document relevance assessment for TREC Genomics Track 2005. SWAT4HCLS Olga L. Giraldo, María Fernanda Cadena, Andrea Robayo-Gama, Dhwani Solanki, Tim Fellerhoff, Lukas Geist, Rohitha Ravinder, Muhammad Talha, Dietrich Rebholz-Schuhmann, Leyla Jael Castro
2023	J	`jnl`	Explainable AI for Bioinformatics: Methods, Tools and Applications. Briefings Bioinform. Md. Rezaul Karim, Tanhim Islam, Md Shajalal, Oya Beyan, Christoph Lange, Michael Cochez, Dietrich Rebholz-Schuhmann, Stefan Decker
2023	J	`jnl`	From Large Language Models to Knowledge Graphs for Biomarker Discovery in Cancer. CoRR Md. Rezaul Karim, Lina Molinas Comet, Md Shajalal, Oya Beyan, Dietrich Rebholz-Schuhmann, Stefan Decker
2023	—	`conf`	Machine-Actionable Metadata for Software and Software Management Plans for NFDI. CoRDI Olga L. Giraldo, Danilo Dessì, Stefan Dietze, Dietrich Rebholz-Schuhmann, Leyla Jael Castro
2023	—	`conf`	Multilabel-classification task for Medline abstracts. SWAT4HCLS Nelson Quiñones, Cesar Canales, Javier Torres, Dietrich Rebholz-Schuhmann, Leyla Jael Castro, Andrés Aristizábal
2023	—	`conf`	OntoClue, a framework to compare vector-based approaches for document relatedness using the RELISH corpus. SWAT4HCLS Rohitha Ravinder, Tim Fellerhoff, Vishnu Dadi, Lukas Geist, Guillermo Rocamora, Muhammad Talha, Dietrich Rebholz-Schuhmann, Leyla Jael Castro
2023	—	`ed.`	Proceedings of the 6th Workshop on Semantic Web Solutions for Large-Scale Biomedical Data Analytics co-located with ESWC 2023, Hersonissos, Greece, May 29, 2023. SeWeBMeDa@ESWC Ali Hasnain, Tracy Robson, Michel Dumontier, Alba Catalina Morales Tirado, Dietrich Rebholz-Schuhmann
2023	—	`conf`	RO-Crates Meets FAIR Digital Objects. CoRDI Leyla Jael Castro, Stian Soiland-Reyes, Dietrich Rebholz-Schuhmann
2023	—	`conf`	Schema.org as a Lightweight Harmonization Approach for NFDI. CoRDI Leyla Jael Castro, Juliane Fluck, Daniel Arend, Matthias Lange, Daniel Martini, Steffen Neumann, Sonja Schimmler, Dietrich Rebholz-Schuhmann
2022	J	`jnl`	Adversary-Aware Multimodal Neural Networks for Cancer Susceptibility Prediction From Multiomics Data. IEEE Access Md. Rezaul Karim, Tanhim Islam, Christoph Lange, Dietrich Rebholz-Schuhmann, Stefan Decker
2022	J	`jnl`	Convolutional Embedded Networks for Population Scale Clustering and Bio-Ancestry Inferencing. IEEE ACM Trans. Comput. Biol. Bioinform. Md. Rezaul Karim, Michael Cochez, Achille Zappa, Ratnesh Sahay, Dietrich Rebholz-Schuhmann, Oya Beyan, Stefan Decker
2022	J	`jnl`	Explainable AI for Bioinformatics: Methods, Tools, and Applications. CoRR Md. Rezaul Karim, Tanhim Islam, Oya Beyan, Christoph Lange, Michael Cochez, Dietrich Rebholz-Schuhmann, Stefan Decker
2022	—	`conf`	NFDI4DataScience registry for reproducible Data Science and Artificial Intelligence. WOOC Leyla Jael Castro, Zeyd Boukhers, Olga L. Giraldo, Adamantios Koumpis, Oya Beyan, Dietrich Rebholz-Schuhmann
2022	J	`jnl`	Ontology-based identification and prioritization of candidate drugs for epilepsy from literature. J. Biomed. Semant. Bernd Müller, Leyla Jael Castro, Dietrich Rebholz-Schuhmann
2021	—	`ed.`	DaMaLOS - Second Workshop on Data and Research Objects Management for Linked Open Science, Co-located at the International Semantic Web Conference ISWC 2021, Virtual Conference, October 24, 2021. DaMaLOS Leyla Jael Castro, Markus Stocker, Dietrich Rebholz-Schuhmann
2021	J	`jnl`	Deep learning-based clustering approaches for bioinformatics. Briefings Bioinform. Md. Rezaul Karim, Oya Beyan, Achille Zappa, Ivan G. Costa, Dietrich Rebholz-Schuhmann, Michael Cochez, Stefan Decker
2021	J	`jnl`	DeepKneeExplainer: Explainable Knee Osteoarthritis Diagnosis From Radiographs and Magnetic Resonance Imaging. IEEE Access Md. Rezaul Karim, Jiao Jiao, Till Döhmen, Michael Cochez, Oya Beyan, Dietrich Rebholz-Schuhmann, Stefan Decker
2021	—	`conf`	Ontology Clustering with OWL2Vec. DeepOntoNLP/X-SENTIMENT@ESWC Ashley Ritchie, Jiaoyan Chen, Leyla Jael Castro, Dietrich Rebholz-Schuhmann, Ernesto Jiménez-Ruiz
2020	—	`ed.`	DaMaLOS - First Workshop on Data and Research Objects Management for Linked Open Science, Co-located at the International Semantic Web Conference ISWC 2020, Virtual Conference, November 2-3, 2020. DaMaLOS Leyla Jael García Castro, Sören Auer, Maria-Esther Vidal, Dietrich Rebholz-Schuhmann
2020	—	`conf`	DeepCOVIDExplainer: Explainable COVID-19 Diagnosis from Chest X-ray Images. BIBM Md. Rezaul Karim, Till Döhmen, Michael Cochez, Oya Beyan, Dietrich Rebholz-Schuhmann, Stefan Decker
2020	J	`jnl`	DeepCOVIDExplainer: Explainable COVID-19 Predictions Based on Chest X-ray Images. CoRR Md. Rezaul Karim, Till Döhmen, Dietrich Rebholz-Schuhmann, Stefan Decker, Michael Cochez, Oya Beyan
2019	J	`jnl`	Predicting knee osteoarthritis severity: comparative modeling based on patient's data and plain X-ray images. CoRR Jaynal Abedin, Joseph Antony, Kevin McGuinness, Kieran Moran, Noel E. O'Connor, Dietrich Rebholz-Schuhmann, John Newell
2019	J	`jnl`	Predicting links between tumor samples and genes using 2-Layered graph based diffusion approach. BMC Bioinform. Mohan Timilsina, Haixuan Yang, Ratnesh Sahay, Dietrich Rebholz-Schuhmann
2019	—	`ed.`	Proceedings of the Workshop on Semantic Web Solutions for Large-Scale Biomedical Data Analytics co-located with 18th International Semantic Web Conference (ISWC 2019), Auckland, New Zealand, October 27th, 2019. SeWeBMeDa@ISWC Ali Hasnain, Vít Novácek, Michel Dumontier, Dietrich Rebholz-Schuhmann
2019	C	`conf`	Ranked MSD: A New Feature Ranking and Feature Selection Approach for Biomarker Identification. CD-MAKE Ghanshyam Verma, Alokkumar Jha, Dietrich Rebholz-Schuhmann, Michael G. Madden
2019	—	`conf`	Selected Approaches Ranking Contextual Term for the BioASQ Multi-label Classification (Task6a and 7a). PKDD/ECML Workshops (2) Bernd Müller, Dietrich Rebholz-Schuhmann
2019	—	`conf`	Unsupervised Classification of Health Content on Reddit. PDH Joana M. Barros, Paul Buitelaar, Jim Duggan, Dietrich Rebholz-Schuhmann
2019	J	`jnl`	Where to search top-K biomedical ontologies? Briefings Bioinform. Daniela Oliveira, Anila Sahar Butt, Armin Haller, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
2018	B	`conf`	A 2-Layered Graph Based Diffusion Approach for Altmetric Analysis. ASONAM Mohan Timilsina, Haixuan Yang, Dietrich Rebholz-Schuhmann
2018	—	`conf`	Assessing FAIR Data Principles Against the 5-Star Open Data Principles. ESWC (Satellite Events) Ali Hasnain, Dietrich Rebholz-Schuhmann
2018	C	`conf`	Deep Convolution Neural Network Model to Predict Relapse in Breast Cancer. ICMLA Alokkumar Jha, Ghanshyam Verma, Yasar Khan, Qaiser Mehmood, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
2018	J	`jnl`	Disease mentions in airport and hospital geolocations expose dominance of news events for disease concerns. J. Biomed. Semant. Joana M. Barros, Jim Duggan, Dietrich Rebholz-Schuhmann
2018	—	`conf`	Extending LargeRDFBench for Multi-Source Data at Scale for SPARQL Endpoint Federation. ISWC (Best Workshop Papers) Ali Hasnain, Muhammad Saleem, Axel-Cyrille Ngonga Ngomo, Dietrich Rebholz-Schuhmann
2018	—	`conf`	Extending LargeRDFBench for Multi-Source Data at Scale for SPARQL Endpoint Federation. SSWS@ISWC Ali Hasnain, Muhammad Saleem, Axel-Cyrille Ngonga Ngomo, Dietrich Rebholz-Schuhmann
2018	B	`conf`	FedS: Towards Traversing Federated RDF Graphs. DaWaK Qaiser Mehmood, Alokkumar Jha, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
2018	J	`jnl`	Improving data workflow systems with cloud services and use of open data for bioinformatics research. Briefings Bioinform. Md. Rezaul Karim, Audrey M. Michel, Achille Zappa, Pavel V. Baranov, Ratnesh Sahay, Dietrich Rebholz-Schuhmann
2018	—	`conf`	Linked Data Based Multi-omics Integration and Visualization for Cancer Decision Networks. DILS Alokkumar Jha, Yasar Khan, Qaiser Mehmood, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
2018	J	`jnl`	Recurrent Deep Embedding Networks for Genotype Clustering and Ethnicity Prediction. CoRR Md. Rezaul Karim, Michael Cochez, Oya Beyan, Achille Zappa, Ratnesh Sahay, Stefan Decker, Dietrich Rebholz-Schuhmann
2018	—	`conf`	Using Machine Learning to Distinguish Infected from Non-infected Subjects at an Early Stage Based on Viral Inoculation. DILS Ghanshyam Verma, Alokkumar Jha, Dietrich Rebholz-Schuhmann, Michael G. Madden
2017	—	`conf`	A Deep Learning Approach to Genomics Data for Population Scale Clustering and Ethnicity Prediction. SeWeBMeDA@ESWC Md. Rezaul Karim, Achille Zappa, Ratnesh Sahay, Dietrich Rebholz-Schuhmann
2017	J	`jnl`	BioFed: federated query processing over life sciences linked open data. J. Biomed. Semant. Ali Hasnain, Qaiser Mehmood, Syeda Sana e Zainab, Muhammad Saleem, Claude N. Warren Jr., Durre Zehra, Stefan Decker, Dietrich Rebholz-Schuhmann
2017	—	`conf`	Biomedical Semantic Resources for Drug Discovery Platforms. ESWC (Satellite Events) Ali Hasnain, Dietrich Rebholz-Schuhmann
2017	—	`conf`	Federated Query Formulation and Processing through BioFed. SeWeBMeDA@ESWC Ali Hasnain, Syeda Sana e Zainab, Durre Zehra, Qaiser Mehmood, Muhammad Saleem, Dietrich Rebholz-Schuhmann
2017	—	`ed.`	Proceedings of the Workshop on Semantic Web Solutions for Large-scale Biomedical Data Analytics co-located with 14th Extended Semantic Web Conference, SeWeBMeDA@ESWC 2017, Portoroz, Slovenia, May 28, 2017. SeWeBMeDA@ESWC Ali Hasnain, Amit P. Sheth, Michel Dumontier, Dietrich Rebholz-Schuhmann
2017	—	`conf`	Quantifying the Content of Biomedical Semantic Resources as a Core for Drug Discovery Platforms. SeWeBMeDA@ESWC Ali Hasnain, Dietrich Rebholz-Schuhmann
2017	—	`conf`	Querying web polystores. IEEE BigData Yasar Khan, Antoine Zimmermann, Alokkumar Jha, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
2017	J	`jnl`	SAFE: SPARQL Federation over RDF Data Cubes with Access Control. J. Biomed. Semant. Yasar Khan, Muhammad Saleem, Muntazir Mehdi, Aidan Hogan, Qaiser Mehmood, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
2017	J	`jnl`	Towards precision medicine: discovering novel gynecological cancer biomarkers and pathways using linked data. J. Biomed. Semant. Alokkumar Jha, Yasar Khan, Muntazir Mehdi, Md. Rezaul Karim, Qaiser Mehmood, Achille Zappa, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
2016	—	`conf`	Drug Dosage Balancing Using Large Scale Multi-omics Datasets. DMAH@VLDB Alokkumar Jha, Muntazir Mehdi, Yasar Khan, Qaiser Mehmood, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
2016	—	`conf`	PrEVIEw: Clustering and Visualising PubMed using Visual Interface. VOILA@ISWC Syeda Sana e Zainab, Qaiser Mehmood, Durre Zehra, Dietrich Rebholz-Schuhmann, Ali Hasnain
2016	—	`ed.`	Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine, SMBM 2016, Potsdam, Germany, August 4-5, 2016. SMBM Mariana L. Neves, Fabio Rinaldi, Goran Nenadic, Dietrich Rebholz-Schuhmann
2016	J	`jnl`	The digital revolution in phenotyping. Briefings Bioinform. Anika Oellrich, Nigel Collier, Tudor Groza, Dietrich Rebholz-Schuhmann, Nigam Shah, Olivier Bodenreider, Mary Regina Boland, Ivo I. Georgiev, Hongfang Liu, Kevin M. Livingston, Augustin Luna, Ann-Marie Mallon, Prashanti Manda, Peter N. Robinson, Gabriella Rustici, Michelle Simon, Liqin Wang, Rainer Winnenburg, Michel Dumontier
2015	J	`jnl`	A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC. J. Am. Medical Informatics Assoc. Jan A. Kors, Simon Clematide, Saber A. Akhondi, Erik M. van Mulligen, Dietrich Rebholz-Schuhmann
2015	J	`jnl`	Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task. BMC Bioinform. Jin-Dong Kim, Jung-Jae Kim, Xu Han, Dietrich Rebholz-Schuhmann
2015	—	`conf`	Linked Functional Annotation For Differentially Expressed Gene (DEG) Demonstrated using Illumina Body Map 2.0. SWAT4LS Alokkumar Jha, Yasar Khan, Aftab Iqbal, Achille Zappa, Muntazir Mehdi, Ratnesh Sahay, Dietrich Rebholz-Schuhmann
2015	J	`jnl`	PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. Database J. Biol. Databases Curation Nigel Collier, Tudor Groza, Damian Smedley, Peter N. Robinson, Anika Oellrich, Dietrich Rebholz-Schuhmann
2015	J	`jnl`	The semantic web in translational medicine: current applications and future directions. Briefings Bioinform. Catia M. Machado, Dietrich Rebholz-Schuhmann, Ana T. Freitas, Francisco M. Couto
2014	J	`jnl`	Biological network extraction from scientific literature: state of the art and challenges. Briefings Bioinform. Chen Li, Maria Liakata, Dietrich Rebholz-Schuhmann
2014	B	`conf`	Collaboratively Annotating Multilingual Parallel Corpora in the Biomedical Domain―some MANTRAs. LREC Johannes Hellrich, Simon Clematide, Udo Hahn, Dietrich Rebholz-Schuhmann
2014	J	`jnl`	The functional therapeutic chemical classification system. Bioinform. Samuel Croset, John P. Overington, Dietrich Rebholz-Schuhmann
2014	J	`jnl`	Thematic series on biomedical ontologies in JBMS: challenges and new directions. J. Biomed. Semant. Robert Hoehndorf, Dietrich Rebholz-Schuhmann, Melissa A. Haendel, Robert Stevens
2013	A*	`conf`	A Discourse-Driven Content Model for Summarising Scientific Articles Evaluated in a Complex Question Answering Task. EMNLP Maria Liakata, Simon Dobnik, Shyamasree Saha, Colin R. Batchelor, Dietrich Rebholz-Schuhmann
2013	—	`conf`	An Evaluation of the Concept Retrieval Annotation for Spanish-English CLEFER Parallel Corpora. CLEF (Working Notes) Rafael Berlanga Llavori, Antonio Jimeno-Yepes, María Pérez Catalán, Dietrich Rebholz-Schuhmann
2013	—	`conf`	An Overview of Terminological Resources available for French bioNLP. CLEF (Working Notes) Aurélie Névéol, Dietrich Rebholz-Schuhmann, Pierre Zweigenbaum
2013	J	`jnl`	Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP. J. Biomed. Semant. Anika Oellrich, Christoph Grabmüller, Dietrich Rebholz-Schuhmann
2013	—	`conf`	Brain, Biomedical Knowledge Manipulation. ICBO Samuel Croset, John P. Overington, Dietrich Rebholz-Schuhmann
2013	—	`conf`	Brain, a Library for the OWL2 EL profile. OWLED Samuel Croset, John P. Overington, Dietrich Rebholz-Schuhmann
2013	J	`jnl`	Brain: biomedical knowledge manipulation. Bioinform. Samuel Croset, John P. Overington, Dietrich Rebholz-Schuhmann
2013	—	`conf`	Connections across Scientific Publications based on Semantic Annotations. SePublica Leyla Jael García Castro, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann, Alexander García Castro
2013	—	`conf`	Context-Dependent Semantic Annotation in Cross-Lingual Biomedical Resources. CLEF Rafael Berlanga Llavori, Antonio Jimeno-Yepes, María Pérez Catalán, Dietrich Rebholz-Schuhmann
2013	—	`conf`	Creating Multilingual Gold Standard Corpora for Biomedical Concept Recognition. CLEF (Working Notes) Jan A. Kors, Simon Clematide, Saber A. Akhondi, Erik M. van Mulligen, Dietrich Rebholz-Schuhmann
2013	—	`conf`	Entity Recognition in Parallel Multi-lingual Biomedical Corpora: The CLEF-ER Laboratory Overview. CLEF Dietrich Rebholz-Schuhmann, Simon Clematide, Fabio Rinaldi, Senay Kafkas, Erik M. van Mulligen, Quoc-Chinh Bui, Johannes Hellrich, Ian Lewin, David Milward, Michael Poprat, Antonio Jimeno-Yepes, Udo Hahn, Jan A. Kors
2013	J	`jnl`	Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. J. Biomed. Semant. Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno-Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin
2013	—	`conf`	Exploiting BabelNet for Multilingual Biomedical Synonym Expansion. CLEF (Working Notes) Simon Clematide, Martin Davtyan, Fabio Rinaldi, Dietrich Rebholz-Schuhmann
2013	—	`conf`	GRO Task: Populating the Gene Regulation Ontology with events and relations. BioNLP@ACL (Shared Task) Jung-Jae Kim, Xu Han, Vivian Lee, Dietrich Rebholz-Schuhmann
2013	J	`jnl`	Literature Mining Solutions for Life Science Research. Adv. Bioinformatics Jörg Hakenberg, Goran Nenadic, Dietrich Rebholz-Schuhmann, Jin-Dong Kim
2013	J	`jnl`	Monitoring named entity recognition: the League Table. J. Biomed. Semant. Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Antonio Jimeno-Yepes, Ian Lewin
2013	—	`conf`	Multilingual Semantic Resources and Parallel Corpora in the Biomedical Domain: the CLEF-ER Challenge. CLEF (Working Notes) Dietrich Rebholz-Schuhmann, Simon Clematide, Fabio Rinaldi, Senay Kafkas, Erik M. van Mulligen, Quoc-Chinh Bui, Johannes Hellrich, Ian Lewin, David Milward, Michael Poprat, Antonio Jimeno-Yepes, Udo Hahn, Jan A. Kors
2013	J	`jnl`	PCorral - interactive mining of protein interactions from MEDLINE. Database J. Biol. Databases Curation Chen Li, Antonio Jimeno-Yepes, Miguel Arregui, Harald Kirsch, Dietrich Rebholz-Schuhmann
2013	—	`conf`	The Functional Therapeutic Chemical Classification System. ICBO Samuel Croset, John P. Overington, Dietrich Rebholz-Schuhmann
2012	B	`conf`	A Hybrid Approach to Finding Phenotype Candidates in Genetic Texts. COLING Nigel Collier, Mai-Vu Tran, Hoang-Quynh Le, Anika Oellrich, Ai Kawazoe, Martin Hall-May, Dietrich Rebholz-Schuhmann
2012	J	`jnl`	Automatic recognition of conceptualization zones in scientific articles and two life science applications. Bioinform. Maria Liakata, Shyamasree Saha, Simon Dobnik, Colin R. Batchelor, Dietrich Rebholz-Schuhmann
2012	B	`conf`	CALBC: Releasing the Final Corpora. LREC Senay Kafkas, Ian Lewin, David Milward, Erik M. van Mulligen, Jan A. Kors, Udo Hahn, Dietrich Rebholz-Schuhmann
2012	B	`conf`	Centroids: Gold standards with distributional variation. LREC Ian Lewin, Senay Kafkas, Dietrich Rebholz-Schuhmann
2012	—	`conf`	Finding small molecule and protein pairs in scientific literature using a bootstrapping method. BioNLP@HLT-NAACL Ying Yan, Jee-Hyub Kim, Samuel Croset, Dietrich Rebholz-Schuhmann
2012	J	`jnl`	Harmonization of gene/protein annotations: towards a gold standard MEDLINE. Bioinform. David Campos, Sérgio Matos, Ian Lewin, José Luís Oliveira, Dietrich Rebholz-Schuhmann
2012	Misc	`conf`	Linking PharmGKB to Phenotype Studies and Animal Models of Disease for Drug Repurposing. Pacific Symposium on Biocomputing Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos
2012	J	`jnl`	Poseidon: An information retrieval and extraction system for metagenomic marine science. Ecol. Informatics Marcin Radom, Agnieszka Rybarczyk, Renzo Kottmann, Piotr Formanowicz, Marta Szachniuk, Frank Oliver Glöckner, Dietrich Rebholz-Schuhmann, Jacek Blazewicz
2012	—	`ed.`	Proceedings of the Workshop on Annotation, Interpretation and Management of Mutations, Basel, Switzerland, September 9, 2012. AIMM Christopher J. O. Baker, Dietrich Rebholz-Schuhmann
2012	J	`jnl`	Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology. J. Biomed. Semant. Anika Oellrich, Georgios V. Gkoutos, Robert Hoehndorf, Dietrich Rebholz-Schuhmann
2011	J	`jnl`	A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinform. Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala M. Wimalaratne, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos
2011	J	`jnl`	Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. J. Biomed. Semant. Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter T. Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, René Witte, Jonas B. Laurila, Christopher J. O. Baker, Cheng-Ju Kuo, Simon Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura Inés Furlong, Michael Rautschka, Mariana L. Neves, Alberto D. Pascual-Montano, Qi Wei, Nigel Collier, Md. Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga Llavori, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik M. van Mulligen, Jan A. Kors, Udo Hahn
2011	—	`conf`	Exploitation of Cross-References between Terminological Resources within the CALBC Context. DEXA Workshops Ernesto Jiménez-Ruiz, Dietrich Rebholz-Schuhmann, Ian Lewin
2011	—	`conf`	Exploring the Generation and Integration of Publishable Scientific Facts Using the Concept of Nano-publications. SePublica Amanda Clare, Samuel Croset, Christoph Grabmüller, Senay Kafkas, Maria Liakata, Anika Oellrich, Dietrich Rebholz-Schuhmann
2011	J	`jnl`	Improving the extraction of complex regulatory events from scientific text by using ontology-based inference. J. Biomed. Semant. Jung-Jae Kim, Dietrich Rebholz-Schuhmann
2011	J	`jnl`	Ontology design patterns to disambiguate relations between genes and gene products in GENIA. J. Biomed. Semant. Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann
2011	—	`ed.`	Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine, Cambridge, United Kingdom, October, 2010 Semantic Mining in Biomedicine Nigel Collier, Udo Hahn, Dietrich Rebholz-Schuhmann, Fabio Rinaldi, Sampo Pyysalo
2011	J	`jnl`	The BioLexicon: a large-scale terminological resource for biomedical text mining. BMC Bioinform. Paul Thompson, John McNaught, Simonetta Montemagni, Nicoletta Calzolari, Riccardo Del Gratta, Vivian Lee, Simone Marchi, Monica Monachini, Piotr Pezik, Valeria Quochi, C. J. Rupp, Yutaka Sasaki, Giulia Venturi, Dietrich Rebholz-Schuhmann, Sophia Ananiadou
2011	J	`jnl`	Towards mature use of semantic resources for biomedical analyses. J. Biomed. Semant. Dietrich Rebholz-Schuhmann, Fabio Rinaldi, Sampo Pyysalo, Nigel Collier, Udo Hahn
2011	J	`jnl`	UKPMC: a full text article resource for the life sciences. Nucleic Acids Res. Johanna R. McEntyre, Sophia Ananiadou, Stephen Andrews, William J. Black, Richard Boulderstone, Paula Buttery, David Chaplin, Sandeepreddy Chevuru, Norman Cobley, Lee-Ann Coleman, Paul Davey, Bharti Gupta, Lesley Haji-Gholam, Craig Hawkins, Alan Horne, Simon J. Hubbard, Jee-Hyub Kim, Ian Lewin, Vic Lyte, Ross MacIntyre, Sami Mansoor, Linda Mason, John McNaught, Elizabeth Newbold, Chikashi Nobata, Ernest Ong, Sharmila Pillai, Dietrich Rebholz-Schuhmann, Heather Rosie, Rob Rowbotham, C. J. Rupp, Peter Stoehr, Philip Vaughan
2011	—	`conf`	Use of Multiple Ontologies to Characterize the Bioactivity of Small Molecules. ICBO Ying Yan, Janna Hastings, Jee-Hyub Kim, Stefan Schulz, Christoph Steinbeck, Dietrich Rebholz-Schuhmann
2010	—	`ch.`	Applications of Ontologies and Text Mining in the Biomedical Domain. Ontology Theory, Management and Design Antonio Jimeno-Yepes, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann
2010	—	`conf`	Applying ontology design patterns to the implementation of relations in GENIA. Semantic Mining in Biomedicine Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann
2010	—	`conf`	Assessment of NER solutions against the first and second CALBC silver standard corpus. Semantic Mining in Biomedicine Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter T. Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, René Witte, Jonas B. Laurila, Christopher J. O. Baker, Cheng-Ju Kuo, Simon Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura Inés Furlong, Michael Rautschka, Mariana L. Neves, Alberto D. Pascual-Montano, Qi Wei, Nigel Collier, Md. Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga Llavori, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik M. van Mulligen, Jan A. Kors, Udo Hahn
2010	J	`jnl`	Biomedical Semantics: the Hub for Biomedical Research 2.0. J. Biomed. Semant. Dietrich Rebholz-Schuhmann, Goran Nenadic
2010	J	`jnl`	Calbc Silver Standard Corpus. J. Bioinform. Comput. Biol. Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Erik M. van Mulligen, Ning Kang, Jan A. Kors, David Milward, Peter T. Corbett, Ekaterina Buyko, Elena Beisswanger, Udo Hahn
2010	—	`conf`	First Steps in the Logic-based Assessment of Post-composed Phenotypic Descriptions. SWAT4LS Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann
2010	J	`jnl`	First steps in the logic-based assessment of post-composed phenotypic descriptions CoRR Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann
2010	J	`jnl`	Functional variation of alternative splice forms in their protein interaction networks: a literature mining approach. BMC Bioinform. Senay Kafkas, Ekrem Varoglu, Dietrich Rebholz-Schuhmann, Bahar Taneri
2010	—	`conf`	Improving the extraction of complex regulatory events from scientific text by using ontology-based inference. Semantic Mining in Biomedicine Jung-Jae Kim, Dietrich Rebholz-Schuhmann
2010	J	`jnl`	Interoperability between phenotype and anatomy ontologies. Bioinform. Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann
2010	J	`jnl`	Measuring prediction capacity of individual verbs for the identification of protein interactions. J. Biomed. Informatics Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Miguel Arregui, Harald Kirsch
2010	J	`jnl`	Ontology refinement for improved information retrieval. Inf. Process. Manag. Antonio Jimeno-Yepes, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann
2010	J	`jnl`	PaperMaker: validation of biomedical scientific publications. Bioinform. Dietrich Rebholz-Schuhmann, Silvestras Kavaliauskas, Piotr Pezik
2010	—	`conf`	Relational Patterns in OWL and Their Application to OBO. OWLED Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Heinrich Herre, Dietrich Rebholz-Schuhmann
2010	J	`jnl`	Relations as patterns: bridging the gap between OBO and OWL. BMC Bioinform. Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Dietrich Rebholz-Schuhmann, Heinrich Herre
2010	—	`conf`	The CALBC RDF Triple Store: Retrieval over Large Literature Content. SWAT4LS Samuel Croset, Christoph Grabmüller, Chen Li, Silvestras Kavaliauskas, Dietrich Rebholz-Schuhmann
2010	J	`jnl`	The CALBC RDF Triple Store: retrieval over large literature content CoRR Samuel Croset, Christoph Grabmüller, Chen Li, Silvestras Kavaliauskas, Dietrich Rebholz-Schuhmann
2010	B	`conf`	The CALBC Silver Standard Corpus for Biomedical Named Entities - A Study in Harmonizing the Contributions from Four Independent Named Entity Taggers. LREC Dietrich Rebholz-Schuhmann, Antonio José Jimeno-Yepes, Erik M. van Mulligen, Ning Kang, Jan A. Kors, David Milward, Peter T. Corbett, Ekaterina Buyko, Katrin Tomanek, Elena Beisswanger, Udo Hahn
2010	J	`jnl`	Wrestling with Biomedical Research Results: Language Resources and Literature Analysis. J. Bioinform. Comput. Biol. Dietrich Rebholz-Schuhmann, Nigel Collier, Jong C. Park, Limsoon Wong
2009	J	`jnl`	Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb. BMC Bioinform. Kevin Nagel, Antonio Jimeno-Yepes, Dietrich Rebholz-Schuhmann
2009	J	`jnl`	Between proteins and phenotypes: annotation and interpretation of mutations. BMC Bioinform. Christopher J. O. Baker, Dietrich Rebholz-Schuhmann
2009	—	`conf`	How Feasible and Robust is the Automatic Extraction of Gene Regulation Events? A Cross-Method Evaluation under Lab and Real-Life Conditions. BioNLP@HLT-NAACL Udo Hahn, Katrin Tomanek, Ekaterina Buyko, Jung-Jae Kim, Dietrich Rebholz-Schuhmann
2009	—	`conf`	Identification of Chemical Entities in Patent Documents. IWANN (2) Tiago Grego, Piotr Pezik, Francisco M. Couto, Dietrich Rebholz-Schuhmann
2009	J	`jnl`	MeSH Up: effective MeSH text classification for improved document retrieval. Bioinform. Dolf Trieschnigg, Piotr Pezik, Vivian Lee, Franciska de Jong, Wessel Kraaij, Dietrich Rebholz-Schuhmann
2009	J	`jnl`	Response to comment on 'MeSH-up: effective MeSH text classification for improved document retrieval'. Bioinform. Dolf Trieschnigg, Piotr Pezik, Vivian Lee, Franciska de Jong, Wessel Kraaij, Dietrich Rebholz-Schuhmann
2009	J	`jnl`	Reuse of terminological resources for efficient ontological engineering in Life Sciences. BMC Bioinform. Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann
2009	—	`conf`	Support tools for literature-based information access in molecular biology. IUCS Fabio Rinaldi, Dietrich Rebholz-Schuhmann
2009	—	`ch.`	Using Biomedical Terminological Resources for Information Retrieval. Information Retrieval in Biomedicine Piotr Pezik, Antonio Jimeno-Yepes, Dietrich Rebholz-Schuhmann
2008	—	`conf`	08131 Executive Summary -- Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives. Ontologies and Text Mining for Life Sciences Michael Ashburner, Ulf Leser, Dietrich Rebholz-Schuhmann
2008	—	`conf`	Annotation of protein residues based on a literature analysis: cross-validation against UniProtKB. AIMM Kevin Nagel, Antonio Jimeno-Yepes, Dietrich Rebholz-Schuhmann
2008	J	`jnl`	Assessment of disease named entity recognition on a corpus of annotated sentences. BMC Bioinform. Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann
2008	J	`jnl`	Categorization of services for seeking information in biomedical literature: a typology for improvement of practice. Briefings Bioinform. Jung-Jae Kim, Dietrich Rebholz-Schuhmann
2008	J	`jnl`	Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text. EURASIP J. Bioinform. Syst. Biol. Sylvain Gaudan, Antonio Jimeno-Yepes, Vivian Lee, Dietrich Rebholz-Schuhmann
2008	J	`jnl`	Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. BMC Bioinform. Irena Spasic, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas B. Kell, Norman W. Paton
2008	—	`conf`	Gene Regulation Ontology (GRO): Design Principles and Use Cases. MIE Elena Beisswanger, Vivian Lee, Jung-Jae Kim, Dietrich Rebholz-Schuhmann, Andrea Splendiani, Olivier Dameron, Stefan Schulz, Udo Hahn
2008	J	`jnl`	Integrating protein-protein interactions and text mining for protein function prediction. BMC Bioinform. Samira Jaeger, Sylvain Gaudan, Ulf Leser, Dietrich Rebholz-Schuhmann
2008	J	`jnl`	MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline. Bioinform. Jung-Jae Kim, Piotr Pezik, Dietrich Rebholz-Schuhmann
2008	—	`ed.`	Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, 24.03. - 28.03.2008 Ontologies and Text Mining for Life Sciences Michael Ashburner, Ulf Leser, Dietrich Rebholz-Schuhmann
2008	—	`ed.`	Proceedings of the ECCB 2008 Workshop: Annotation, Interpretation and Management of Mutations ( AIMM ) Cagliari, Sardinia, Italy, September, June 22, 2008. AIMM Christopher J. O. Baker, Dietrich Rebholz-Schuhmann
2008	J	`jnl`	Text processing through Web services: calling Whatizit. Bioinform. Dietrich Rebholz-Schuhmann, Miguel Arregui, Sylvain Gaudan, Harald Kirsch, Antonio Jimeno-Yepes
2008	—	`conf`	Towards Knowledge in the Cloud. OTM Workshops Davide Cerri, Emanuele Della Valle, David de Francisco Marcos, Fausto Giunchiglia, Dalit Naor, Lyndon J. B. Nixon, Kia Teymourian, Philipp Obermeier, Dietrich Rebholz-Schuhmann, Reto Krummenacher, Elena Paslaru Bontas Simperl
2008	—	`conf`	Use of Shared Lexical Resources for Efficient Ontological Engineering. SWAT4LS Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann
2007	J	`jnl`	EBIMed - text crunching to gather facts for proteins from Medline. Bioinform. Dietrich Rebholz-Schuhmann, Harald Kirsch, Miguel Arregui, Sylvain Gaudan, Mark Riethoven, Peter Stoehr
2007	J	`jnl`	Medical Informatics and Bioinformatics: A Bibliometric Study. IEEE Trans. Inf. Technol. Biomed. Jean-Yves Bansard, Dietrich Rebholz-Schuhmann, Graham Cameron, Dominic Clark, Erik M. van Mulligen, Francesco Beltrame, Eva del Hoyo-Barbolla, Fernando Martín-Sánchez, Luciano Milanesi, Ioannis G. Tollis, Johan van der Lei, Jean-Louis Coatrieux
2007	J	`jnl`	SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics - exploring current scientific literature for emerging topics. BMC Bioinform. Dietrich Rebholz-Schuhmann, Graham Cameron, Dominic Clark, Erik M. van Mulligen, Jean-Louis Coatrieux, Eva del Hoyo-Barbolla, Fernando Martín-Sánchez, Luciano Milanesi, Ivan Porro, Francesco Beltrame, Ioannis G. Tollis, Johan van der Lei
2007	J	`jnl`	Using argumentation to extract key sentences from biomedical abstracts. Int. J. Medical Informatics Patrick Ruch, Célia Boyer, Christine Chichester, Imad Tbahriti, Antoine Geissbühler, Paul Fabry, Julien Gobeill, Violaine Pillet, Dietrich Rebholz-Schuhmann, Christian Lovis, Anne-Lise Veuthey
2006	—	`conf`	Annotation and Disambiguation of Semantic Types in Biomedical Text: A Cascaded Approach to Named Entity Recognition. NLPXML@EACL Dietrich Rebholz-Schuhmann, Harald Kirsch, Sylvain Gaudan, Miguel Arregui, Goran Nenadic
2006	—	`conf`	Collecting a Large Corpus from all of Medline. SMBM Jörg Hakenberg, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann
2006	J	`jnl`	Dealing with repetitions in sequencing by hybridization. Comput. Biol. Chem. Jacek Blazewicz, Fred W. Glover, Marta Kasprzak, Wojciech T. Markiewicz, Ceyda Oguz, Dietrich Rebholz-Schuhmann, Aleksandra Swiercz
2006	J	`jnl`	Distributed modules for text annotation and IE applied to the biomedical domain. Int. J. Medical Informatics Harald Kirsch, Sylvain Gaudan, Dietrich Rebholz-Schuhmann
2005	—	`conf`	Extracting Key Sentences with Latent Argumentative Structuring. MIE Patrick Ruch, Robert H. Baud, Christine Chichester, Antoine Geissbühler, Frédérique Lisacek, Johan Marty, Dietrich Rebholz-Schuhmann, Imad Tbahriti, Anne-Lise Veuthey
2005	J	`jnl`	Resolving abbreviations to their senses in Medline. Bioinform. Sylvain Gaudan, Harald Kirsch, Dietrich Rebholz-Schuhmann
2004	—	`conf`	Distributed Modules for Text Annotation and IE Applied to the Biomedical Domain. NLPBA/BioNLP Harald Kirsch, Dietrich Rebholz-Schuhmann