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Janna Hastings

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affiliation: University of Zurich, Faculty of Medicine, Switzerland
affiliation: University of St. Gallen, School of Medicine, Switzerland

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2023
[j34]
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Janna Hastings, John A. Bateman:
Applied ontology: Where are we now and where are we going? Appl. Ontology 18(1): 1-4 (2023)
[j33]
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Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Skoda, Valentina A. M. Tamma:
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. TGDK 1(1): 5:1-5:33 (2023)
2022
[j32]
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Fabian Neuhaus, Janna Hastings:
Ontology development is consensus creation, not (merely) representation. Appl. Ontology 17(4): 495-513 (2022)
2021
[j31]
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Emma Norris, Janna Hastings, Marta M. Marques, Ailbhe N. Finnerty, Silje Zink, Susan Michie:
Why and how to engage expert stakeholders in ontology development: insights from social and behavioural sciences. J. Biomed. Semant. 12(1): 4 (2021)
[j30]
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Janna Hastings, Martin Glauer, Adel Memariani, Fabian Neuhaus, Till Mossakowski:
Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification. J. Cheminformatics 13(1): 23 (2021)
2016
[j29]
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Neil Swainston, Janna Hastings, Adriano Dekker, Venkatesh Muthukrishnan, John W. May, Christoph Steinbeck, Pedro Mendes:
libChEBI: an API for accessing the ChEBI database. J. Cheminformatics 8(1): 11:1-11:6 (2016)
[j28]
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Yannick Djoumbou, Roman Eisner, Craig Knox, Leonid L. Chepelev, Janna Hastings, Gareth I. Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David S. Wishart:
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. J. Cheminformatics 8(1): 61:1-61:20 (2016)
[j27]
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Janna Hastings, Gareth I. Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck:
ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 44(Database-Issue): 1214-1219 (2016)
2015
[j26]
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Janna Hastings, Nina Jeliazkova, Gareth I. Owen, Georgia Tsiliki, Cristian R. Munteanu, Christoph Steinbeck, Egon L. Willighagen:
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. J. Biomed. Semant. 6: 10 (2015)
[j25]
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Pablo A. Moreno, Stephan Beisken, Bhavana Harsha, Venkatesh Muthukrishnan, Ilinca Tudose, Adriano Dekker, Stefanie Dornfeldt, Franziska Taruttis, Ivo Grosse, Janna Hastings, Steffen Neumann, Christoph Steinbeck:
BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology. BMC Bioinform. 16: 56:1-56:7 (2015)
[j24]
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María Herrero-Zazo, Isabel Segura-Bedmar, Janna Hastings, Paloma Martínez:
Application of Domain Ontologies to Natural Language Processing: A Case Study for Drug-Drug Interactions. Int. J. Inf. Retr. Res. 5(3): 19-38 (2015)
[j23]
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Gang Fu, Colin R. Batchelor, Michel Dumontier, Janna Hastings, Egon L. Willighagen, Evan Bolton:
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. J. Cheminformatics 7: 34:1-34:15 (2015)
[j22]
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María Herrero-Zazo, Isabel Segura-Bedmar, Janna Hastings, Paloma Martínez:
DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions and Their Mechanisms. J. Chem. Inf. Model. 55(8): 1698-1707 (2015)
2014
[j21]
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Janna Hastings, Andy Brass, Colin Caine, Caroline Jay, Robert Stevens:
Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference. J. Biomed. Semant. 5: 38 (2014)
[j20]
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Janna Hastings, Gwen A. Frishkoff, Barry Smith, Mark Jensen, Russell A. Poldrack, Jane Lomax, Anita E. Bandrowski, Fahim T. Imam, Jessica A. Turner, Maryann E. Martone:
Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies. Frontiers Neuroinformatics 8: 62 (2014)
2013
[j19]
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Reza M. Salek, Kenneth Haug, Pablo Conesa, Janna Hastings, Mark Williams, Tejasvi Mahendraker, Eamonn Maguire, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Susanna-Assunta Sansone, Christoph Steinbeck:
The MetaboLights repository: curation challenges in metabolomics. Database J. Biol. Databases Curation 2013 (2013)
[j18]
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João D. Ferreira, Janna Hastings, Francisco M. Couto:
Exploiting disjointness axioms to improve semantic similarity measures. Bioinform. 29(21): 2781-2787 (2013)
[j17]
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Ilinca Tudose, Janna Hastings, Venkatesh Muthukrishnan, Gareth I. Owen, Steve Turner, Adriano Dekker, Namrata Kale, Marcus Ennis, Christoph Steinbeck:
OntoQuery: easy-to-use web-based OWL querying. Bioinform. 29(22): 2955-2957 (2013)
[j16]
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Jon Chambers, Mark Davies, Anna Gaulton, Anne Hersey, Sameer Velankar, Robert Petryszak, Janna Hastings, Louisa J. Bellis, Shaun McGlinchey, John P. Overington:
UniChem: a unified chemical structure cross-referencing and identifier tracking system. J. Cheminformatics 5: 3 (2013)
[j15]
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Andrew Dalke, Janna Hastings:
FMCS: a novel algorithm for the multiple MCS problem. J. Cheminformatics 5(S-1): 6 (2013)
[j14]
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Egon L. Willighagen, Andra Waagmeester, Ola Spjuth, Peter Ansell, Antony J. Williams, Valery Tkachenko, Janna Hastings, Bin Chen, David J. Wild:
The ChEMBL database as linked open data. J. Cheminformatics 5: 23 (2013)
[j13]
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Janna Hastings, Pablo Conesa, Adriano Dekker, Marcus Ennis, Kenneth Haug, Kalai Vanii Jayaseelan, Namrata Kale, Tejasvi Mahendraker, Pablo A. Moreno, Venkatesh Muthukrishnan, Gareth I. Owen, Reza M. Salek, Steve Turner, Christoph Steinbeck:
Expanding natural product chemistry resources at the EBI. J. Cheminformatics 5(S-1): 43 (2013)
[j12]
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Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Bhavana Harsha, Namrata Kale, Venkatesh Muthukrishnan, Gareth I. Owen, Steve Turner, Mark Williams, Christoph Steinbeck:
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 41(Database-Issue): 456-463 (2013)
[j11]
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Kenneth Haug, Reza M. Salek, Pablo Conesa, Janna Hastings, Paula de Matos, Mark Rijnbeek, Tejasvi Mahendraker, Mark Williams, Steffen Neumann, Philippe Rocca-Serra, Eamonn Maguire, Alejandra N. González-Beltrán, Susanna-Assunta Sansone, Julian L. Griffin, Christoph Steinbeck:
MetaboLights - an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res. 41(Database-Issue): 781-786 (2013)
2012
[j10]
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Leonid L. Chepelev, Janna Hastings, Marcus Ennis, Christoph Steinbeck, Michel Dumontier:
Self-organizing ontology of biochemically relevant small molecules. BMC Bioinform. 13: 3 (2012)
[j9]
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André Queiroz de Andrade, Ward Blondé, Janna Hastings, Stefan Schulz:
Process attributes in bio-ontologies. BMC Bioinform. 13: 217 (2012)
[j8]
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Jörg K. Wegner, Aaron D. Sterling, Rajarshi Guha, Andreas Bender, Jean-Loup Faulon, Janna Hastings, Noel M. O'Boyle, John P. Overington, Herman van Vlijmen, Egon L. Willighagen:
Cheminformatics. Commun. ACM 55(11): 65-75 (2012)
[j7]
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Lian Duan, Janna Hastings, Paula de Matos, Marcus Ennis, Christoph Steinbeck:
Structured chemical class definitions and automated matching for chemical ontology evolution. J. Cheminformatics 4(S-1): 5 (2012)
[j6]
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Janna Hastings, Despoina Magka, Colin R. Batchelor, Lian Duan, Robert Stevens, Marcus Ennis, Christoph Steinbeck:
Structure-based classification and ontology in chemistry. J. Cheminformatics 4: 8 (2012)
2011
[j5]
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Martin Boeker, Ilinca Tudose, Janna Hastings, Daniel Schober, Stefan Schulz:
Unintended consequences of existential quantifications in biomedical ontologies. BMC Bioinform. 12: 456 (2011)
[j4]
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Janna Hastings, Nico Adams, Marcus Ennis, Duncan Hull, Christoph Steinbeck:
Chemical ontologies: what are they, what are they for and what are the challenges. J. Cheminformatics 3(S-1): 4 (2011)
2010
[j3]
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Paula de Matos, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Steve Turner, Christoph Steinbeck:
ChEBI: a chemistry ontology and database. J. Cheminformatics 2(S-1): 6 (2010)
[j2]
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Paula de Matos, Rafael Alcántara, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Inmaculada Spiteri, Steve Turner, Christoph Steinbeck:
Chemical Entities of Biological Interest: an update. Nucleic Acids Res. 38(Database-Issue): 249-254 (2010)
2008
[j1]
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Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, Michael Ashburner:
ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36(Database-Issue): 344-350 (2008)

Conference and Workshop Papers

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2023
[c33]
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Marie Wosny, Livia Strasser, Janna Hastings:
Human Factors Influencing the Experience of Healthcare Professionals Using Digital Tools. ICIMTH 2023: 224-225
[c32]
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Martin Glauer, Fabian Neuhaus, Till Mossakowski, Janna Hastings:
Ontology Pre-training for Poison Prediction. KI 2023: 31-45
2022
[c31]
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Martin Glauer, Robert West, Susan Michie, Janna Hastings:
ESC-Rules: Explainable, Semantically Constrained Rule Sets. NeSy 2022: 94-103
2021
[c30]
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Guy Divita, Maryanne Sacco, Janna Hastings, Piper Ranallo:
Mental Functioning Ontologies. AMIA 2021
[c29]
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Adel Memariani, Martin Glauer, Fabian Neuhaus, Till Mossakowski, Janna Hastings:
Automated and Explainable Ontology Extension based on Deep Learning: A Case Study in the Chemical Domain. DAO-XAI 2021
[c28]
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Janna Hastings, Robert West, Susan Michie, Caitlin Notley, Sharon Cox:
Ontologies for the Behavioural and Social Sciences: Opportunities and Challenges. ICBO 2021: 155-161
[c27]
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Simon Flügel, Anna Kleinau, Fabian Neuhaus, Martin Glauer, Janna Hastings:
FOWL - An OWL to FOL Translator. JOWO 2021
[c26]
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Janna Hastings:
Scientific Ontologies, Digital Curation and the Learning Knowledge Ecosystem. Qurator 2021
2019
[c25]
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Janna Hastings, Stefan Schulz:
Representing Literary Characters and their Attributes in an Ontology. JOWO 2019
[c24]
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Paul Sheridan, Mikael Onsjö, Janna Hastings:
The Literary Theme Ontology for Media Annotation and Information Retrieval. JOWO 2019
2015
[c23]
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Janna Hastings, Neil Swainston, Venkatesh Muthukrishnan, Namrata Kale, Adriano Dekker, Gareth I. Owen, Steve Turner, Pedro Mendes, Christoph Steinbeck:
ChEBI for systems biology and metabolic modelling. ICBO 2015
2014
[c22]
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Nina Jeliazkova, Philip Doganis, Bengt Fadeel, Roland Grafstrom, Janna Hastings, Vedrin Jeliazkov, Pekka Kohonen, Cristian R. Munteanu, Haralambos Sarimveis, Bart Smeets, Georgia Tsiliki, David Vorgrimmler, Egon L. Willighagen:
The first eNanoMapper prototype: A substance database to support safe-by-design. BIBM 2014: 1-9
2013
[c21]
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Janna Hastings, Colin R. Batchelor, Mitsuhiro Okada:
Shape Perception in Chemistry. SHAPES 2013: 83-94
[c20]
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María Herrero-Zazo, Janna Hastings, Isabel Segura-Bedmar, Samuel Croset, Paloma Martínez, Christoph Steinbeck:
An Ontology for Drug-drug Interactions. SWAT4LS 2013
2012
[c19]
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Oliver Kutz, Janna Hastings, Till Mossakowski:
Modelling Highly Symmetrical Molecules: Linking Ontologies and Graphs. AIMSA 2012: 103-111
[c18]
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Colin R. Batchelor, Janna Hastings:
Waves and fields in bio-ontologies. ICBO 2012
[c17]
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Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Venkatesh Muthukrishnan, Steve Turner, Gareth I. Owen, Christoph Steinbeck:
Modular Extensions to the ChEBI Ontology. ICBO 2012
[c16]
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Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan, Barry Smith:
Wanting what we don't want to want: Representing addiction in interoperable bio-ontologies. ICBO 2012
2011
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Janna Hastings, Werner Ceusters, Barry Smith, Kevin Mulligan:
The Emotion Ontology: Enabling Interdisciplinary Research in the Affective Sciences. CONTEXT 2011: 119-123
[c14]
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Janna Hastings, Colin R. Batchelor, Fabian Neuhaus, Christoph Steinbeck:
What's in an 'is about' Link? Chemical Diagrams and the Information Artifact Ontology. ICBO 2011
[c13]
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Janna Hastings, Werner Ceusters, Barry Smith, Kevin Mulligan:
Dispositions and Processes in the Emotion Ontology. ICBO 2011
[c12]
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Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Kenneth Haug, Zara Josephs, Gareth I. Owen, Steve Turner, Christoph Steinbeck:
Recent Developments in the ChEBI Ontology. ICBO 2011
[c11]
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Oliver Kutz, Till Mossakowski, Janna Hastings, Alexander García Castro, Aleksandra Sojic:
Hyperontology for the Biomedical Ontologist: A Sketch and Some Examples. ICBO 2011
[c10]
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Ying Yan, Janna Hastings, Jee-Hyub Kim, Stefan Schulz, Christoph Steinbeck, Dietrich Rebholz-Schuhmann:
Use of Multiple Ontologies to Characterize the Bioactivity of Small Molecules. ICBO 2011
[c9]
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Martin Boeker, Janna Hastings, Daniel Schober, Stefan Schulz:
A T-Box Generator for Testing Scalability of OWL Mereotopological Patterns. OWLED 2011
[c8]
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Janna Hastings, Ludger Jansen, Christoph Steinbeck, Stefan Schulz:
Modelling Threshold Phenomena in OWL: Metabolite Concentrations as Evidence For Disorders. OWLED 2011
[c7]
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Janna Hastings, Colin R. Batchelor, Stefan Schulz:
Parts and Wholes, Shapes and Holes in Living Beings. SHAPES 2011
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Janna Hastings, Colin R. Batchelor, Christoph Steinbeck, Stefan Schulz:
Modularization Requirements in Bio-Ontologies: A Case Study of ChEbi. WoMO 2011: 63-70
2010
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Janna Hastings, Colin R. Batchelor, Christoph Steinbeck, Stefan Schulz:
What are chemical structures and their relations? FOIS 2010: 257-270
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Colin R. Batchelor, Janna Hastings, Christoph Steinbeck:
Ontological dependence, dispositions and institutional reality in chemistry. FOIS 2010: 271-284
[c3]
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Janna Hastings, Michel Dumontier, Duncan Hull, Matthew Horridge, Christoph Steinbeck, Robert Stevens, Ulrike Sattler, Tertia Hörne, Katarina Britz:
Representing Chemicals Using OWL, Description Graphs and Rules. OWLED 2010
2009
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Nico Adams, Paula de Matos, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Duncan Hull, Zara Josephs, Pablo A. Moreno, Steve Turner, Christoph Steinbeck:
Semantic access to chemistry data with the ChEBI ontology and web services. SWAT4LS 2009
2008
[c1]
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Janna Hastings, Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Christoph Steinbeck:
The ChEBI Ontology: An Ontology for Chemistry within a Biological Context. SWAT4LS 2008

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2023
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Martin Glauer, Till Mossakowski, Fabian Neuhaus, Adel Memariani, Janna Hastings:
Neuro-Symbolic Semantic Learning for Chemistry. Compendium of Neurosymbolic Artificial Intelligence 2023: 460-484

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2023
[e6]
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Fumiaki Toyoshima, Megan Katsumi, Guendalina Righetti, Stefano De Giorgis, Maria M. Hedblom, Oliver Kutz, Boyan Brodaric, Michael Grüninger, Torsten Hahmann, Damion Dooley Simon, Matthew Lange, Hande Küçük-McGinty, Anoosha Sehar Simon, Rhiannon Cameron, Bart Gajderowicz, Daniela Rosu, Janna Hastings, Davide Audrito, Luigi Di Caro, Francesca Grasso, Roberto Nai, Emilio Sulis, Loris Bozzato, Cogan Shimizu, Antoine Zimmermann, Riccardo Baratella, Stefano Borgo, Sergio de Cesare, Tiago Prince Sales:
Proceedings of the Joint Ontology Workshops 2023 Episode IX: The Quebec Summer of Ontology co-located with the 13th International Conference on Formal Ontology in Information Systems (FOIS 2023), Sherbrooke, Québec, Canada, July 19-20, 2023. CEUR Workshop Proceedings 3637, CEUR-WS.org 2023 [contents]
2022
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Janna Hastings, Adrien Barton:
Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), Bozen-Bolzano, Italy, 16-18 September, 2021. CEUR Workshop Proceedings 3073, CEUR-WS.org 2022 [contents]
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Tiago Prince Sales, Maria M. Hedblom, He Tan, Guendalina Righetti, Oliver Kutz, Martin Glauer, Janna Hastings, Till Mossakowski, Fabian Neuhaus, Lucía Gómez Álvarez, Rafael Peñaloza, Srdjan Vesic, Claudenir Morais Fonseca, Jona Thai, Stefano Borgo, Damion M. Dooley, Rhiannon Cameron, Lauren E. Chan, Duccio Cavalieri, Robert Warren, Hande Küçük-McGinty, Matthew Lange, Fernanda Forea, Francesco Vitali, Bart Gajderowicz, Daniela Rosu, Aldo Gangemi, Robert Porzel, Daniel Beßler, Mihai Pomarlan, Mohammed Diab, Alberto Olivares Alarcos:
Proceedings of the Joint Ontology Workshops 2022 Episode VIII: The Svear Sommar of Ontology, Jönköping, Sweden, August 15-19, 2022. CEUR Workshop Proceedings 3249, CEUR-WS.org 2022 [contents]
2021
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Janna Hastings, Frank Loebe:
Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) joint with the 10th Workshop on Ontologies and Data in Life Sciences (ODLS) and part of the Bolzano Summer of Knowledge (BoSK 2020), Virtual conference hosted in Bolzano, Italy, September 17, 2020. CEUR Workshop Proceedings 2807, CEUR-WS.org 2021 [contents]
2015
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Francisco M. Couto, Janna Hastings:
Proceedings of the International Conference on Biomedical Ontology, ICBO 2015, Lisbon, Portugal, July 27-30, 2015. CEUR Workshop Proceedings 1515, CEUR-WS.org 2015 [contents]
2011
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Janna Hastings, Oliver Kutz, Mehul Bhatt, Stefano Borgo:
Proceedings of the First Interdisciplinary Workshop on SHAPES, Karlsruhe, Germany, September 27, 2011. CEUR Workshop Proceedings 812, CEUR-WS.org 2011 [contents]

Informal and Other Publications

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2023
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Martin Glauer, Fabian Neuhaus, Till Mossakowski, Janna Hastings:
Ontology Pre-training for Poison Prediction. CoRR abs/2301.08577 (2023)
[i8]
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Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Skoda, Valentina A. M. Tamma:
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. CoRR abs/2309.17255 (2023)
2022
[i7]
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Martin Glauer, Robert West, Susan Michie, Janna Hastings:
ESC-Rules: Explainable, Semantically Constrained Rule Sets. CoRR abs/2208.12523 (2022)
[i6]
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  - journals/corr/abs-2210-03497
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Simon Flügel, Martin Glauer, Fabian Neuhaus, Janna Hastings:
When one Logic is Not Enough: Integrating First-order Annotations in OWL Ontologies. CoRR abs/2210.03497 (2022)
[i5]
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  - journals/corr/abs-2210-12026
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Fabian Neuhaus, Janna Hastings:
Ontology Development is Consensus Creation, Not (Merely) Representation. CoRR abs/2210.12026 (2022)
2021
[i4]
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  - journals/corr/abs-2109-09202
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Adel Memariani, Martin Glauer, Fabian Neuhaus, Till Mossakowski, Janna Hastings:
Automated and Explainable Ontology Extension Based on Deep Learning: A Case Study in the Chemical Domain. CoRR abs/2109.09202 (2021)
2019
[i3]
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Paul Sheridan, Mikael Onsjö, Janna Hastings:
The Literary Theme Ontology for Media Annotation and Information Retrieval. CoRR abs/1905.00522 (2019)
2015
[i2]
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Alexander García Castro, Janna Hastings, Robert Stevens, Erich Weichselgartner:
Digital Scholarship and Open Science in Psychology and the Behavioral Sciences (Dagstuhl Perpectives Workshop 15302). Dagstuhl Reports 5(7): 42-68 (2015)
2012
[i1]
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Janna Hastings, Colin R. Batchelor, Fabian Neuhaus, Christoph Steinbeck:
What's in an 'is about' link? Chemical diagrams and the Information Artifact Ontology. CoRR abs/1204.4805 (2012)

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