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2020 – today
- 2020
[j55]Maxat Kulmanov
, Robert Hoehndorf:
DeepGOPlus: improved protein function prediction from sequence. Bioinform. 36(2): 422-429 (2020)- [j54]Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. Bioinform. 36(7): 2229-2236 (2020) - [j53]Sara Althubaiti, Senay Kafkas, Marwa Abdelhakim, Robert Hoehndorf:
Combining lexical and context features for automatic ontology extension. J. Biomed. Semant. 11(1): 1 (2020) - [i8]Jun Chen, Robert Hoehndorf, Mohamed Elhoseiny, Xiangliang Zhang:
Efficient long-distance relation extraction with DG-SpanBERT. CoRR abs/2004.03636 (2020)
2010 – 2019
- 2019
- [j52]Senay Kafkas, Robert Hoehndorf:
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. Database J. Biol. Databases Curation 2019: baz019 (2019) - [j51]Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. Bioinform. 35(12): 2133-2140 (2019) - [j50]Senay Kafkas, Robert Hoehndorf:
Ontology based mining of pathogen-disease associations from literature. J. Biomed. Semant. 10(1): 15:1-15:5 (2019) - [c28]Maxat Kulmanov, Wang Liu-Wei, Yuan Yan, Robert Hoehndorf:
EL Embeddings: Geometric Construction of Models for the Description Logic EL++. IJCAI 2019: 6103-6109 - [c27]Shichao Pei, Lu Yu, Robert Hoehndorf, Xiangliang Zhang:
Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference. WWW 2019: 3130-3136 - [i7]Maxat Kulmanov, Wang Liu-Wei, Yuan Yan, Robert Hoehndorf:
EL Embeddings: Geometric construction of models for the Description Logic EL ++. CoRR abs/1902.10499 (2019) - 2018
- [j49]Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knüpfer, Wolfram Liebermeister, Dagmar Waltemath:
Notions of similarity for systems biology models. Briefings Bioinform. 19(1): 77-88 (2018) - [j48]Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
The anatomy of phenotype ontologies: principles, properties and applications. Briefings Bioinform. 19(5): 1008-1021 (2018) - [j47]Maxat Kulmanov, Mohammad Asif Khan, Robert Hoehndorf:
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. Bioinform. 34(4): 660-668 (2018) - [j46]Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. Bioinform. 34(13): i52-i60 (2018) - [j45]Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf:
Ontology-based validation and identification of regulatory phenotypes. Bioinform. 34(17): i857-i865 (2018) - [j44]Mona Alshahrani, Robert Hoehndorf:
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes. Bioinform. 34(17): i901-i907 (2018) - [j43]Miguel Ángel Rodríguez-García, Robert Hoehndorf:
Inferring ontology graph structures using OWL reasoning. BMC Bioinform. 19(1): 7:1-7:9 (2018) - [c26]Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic, Georgios V. Gkoutos, Michel Dumontier, Robert Hoehndorf:
Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings. SWAT4LS 2018 - [p1]Robert Hoehndorf, Claus Weiland, Marco Schmidt, Quentin Groom, George Gosline, Stefan Dressler, Thomas Hamann:
The Flora Phenotype Ontology (FLOPO) and the FLOPO Knowledgebase. Application of Semantic Technology in Biodiversity Science 2018: 107-119 - [i6]Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. CoRR abs/1802.00864 (2018) - [i5]Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. CoRR abs/1804.10922 (2018) - 2017
- [j42]Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knüpfer, Wolfram Liebermeister, Dagmar Waltemath:
Notions of similarity for systems biology models. Briefings Bioinform. 18(5): 902 (2017) - [j41]Mona Alshahrani, Mohammad Asif Khan, Omar Maddouri, Akira R. Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf:
Neuro-symbolic representation learning on biological knowledge graphs. Bioinform. 33(17): 2723-2730 (2017) - [j40]Maxat Kulmanov, Robert Hoehndorf:
Evaluating the effect of annotation size on measures of semantic similarity. J. Biomed. Semant. 8(1): 7:1-7:10 (2017) - [j39]Miguel Ángel Rodríguez-García, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
Integrating phenotype ontologies with PhenomeNET. J. Biomed. Semant. 8(1): 58:1-58:11 (2017) - [j38]Senay Kafkas, Sirarat Sarntivijai, Robert Hoehndorf:
Usage of cell nomenclature in biomedical literature. BMC Bioinform. 18(S-17): 17-24 (2017) - [j37]Robert Hoehndorf, Núria Queralt-Rosinach:
Data Science and symbolic AI: Synergies, challenges and opportunities. Data Sci. 1(1-2): 27-38 (2017) - [j36]Imane Boudellioua, Rozaimi B. Mahamad Razali, Maxat Kulmanov, Yasmeen Hashish, Vladimir B. Bajic, Eva Goncalves-Serra, Nadia Schoenmakers, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
Semantic prioritization of novel causative genomic variants. PLoS Comput. Biol. 13(4) (2017) - [i4]Maxat Kulmanov, Mohammad Asif Khan, Robert Hoehndorf:
DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier. CoRR abs/1705.05919 (2017) - 2016
- [j35]Hannah M. Fisher, Robert Hoehndorf, Bruno S. Bazelato, Soheil S. Dadras, Lloyd E. King, Georgios V. Gkoutos, John P. Sundberg, Paul N. Schofield:
DermO; an ontology for the description of dermatologic disease. J. Biomed. Semant. 7: 38 (2016) - [j34]Jerven T. Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul Jean Pierre Bonnal, Robert M. Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama, Peter J. A. Cock:
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. J. Biomed. Semant. 7: 39 (2016) - [j33]Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
Using AberOWL for fast and scalable reasoning over BioPortal ontologies. J. Biomed. Semant. 7: 49 (2016) - [j32]Robert Hoehndorf, Mona Alshahrani, Georgios V. Gkoutos, George Gosline, Quentin Groom, Thomas Hamann, Jens Kattge, Sylvia Mota de Oliveira, Marco Schmidt, Soraya Sierra, Erik Smets, Rutger A. Vos, Claus Weiland:
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. J. Biomed. Semant. 7: 65:1-65:11 (2016) - [j31]Adil Salhi, Magbubah Essack, Aleksandar Radovanovic, Benoit Marchand, Salim Bougouffa, André Antunes, Marta Filipa Simões, Feras F. Lafi, Olaa A. Motwalli, Ameerah Bokhari, Tariq Malas, Soha Al Amoudi, Ghofran Othum, Intikhab Alam, Katsuhiko Mineta, Xin Gao, Robert Hoehndorf, John A. C. Archer, Takashi Gojobori, Vladimir B. Bajic:
DESM: portal for microbial knowledge exploration systems. Nucleic Acids Res. 44(Database-Issue): 624-633 (2016) - [c25]Robert Hoehndorf, Liam Mencel, Georgios V. Gkoutos, Paul N. Schofield:
Large-Scale Reasoning over Functions in Biomedical Ontologies. FOIS 2016: 299-312 - [c24]Mona Alshahrani, Hussein Almashouq, Robert Hoehndorf:
SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL. ICBO/BioCreative 2016 - [c23]Emma J. Griffiths, Damion M. Dooley, Pier Luigi Buttigieg, Robert Hoehndorf, Fiona S. L. Brinkman, William W. L. Hsiao:
FoodON: A Global Farm-to-Fork Food Ontology. ICBO/BioCreative 2016 - [c22]Miguel Ángel Rodríguez-García, Luke T. Slater, Imane Boudellioua, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf:
Updates to the AberOWL Ontology Repository. ICBO/BioCreative 2016 - [c21]Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
To MIREOT or not to MIREOT? A Case Study of the Impact of Using MIREOT in the Experimental Factor Ontology (EFO). ICBO/BioCreative 2016 - [c20]Miguel Ángel Rodríguez-García, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
Integrating phenotype ontologies with PhenomeNET. OM@ISWC 2016: 201-209 - [c19]Claus Weiland, Robert Hoehndorf, George Gosline, Quentin Groom, Thomas Hamann, Marco Schmidt:
FLOPO - An Ontology for the Integration of Trait Data from Digitized Floras and Plant Image Collections. SWAT4LS 2016 - [e2]Pankaj Jaiswal, Robert Hoehndorf, Cecilia N. Arighi, Austin Meier:
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016. CEUR Workshop Proceedings 1747, CEUR-WS.org 2016 [contents] - [i3]Mona Alshahrani, Mohammad Asif Khan, Omar Maddouri, Akira R. Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf:
Neuro-symbolic representation learning on biological knowledge graphs. CoRR abs/1612.04256 (2016) - 2015
- [j30]Robert Hoehndorf, Paul N. Schofield, Georgios V. Gkoutos:
The role of ontologies in biological and biomedical research: a functional perspective. Briefings Bioinform. 16(6): 1069-1080 (2015) - [j29]Robert Hoehndorf, Michael Gruenberger, Georgios V. Gkoutos, Paul N. Schofield:
Similarity-based search of model organism, disease and drug effect phenotypes. J. Biomed. Semant. 6: 6 (2015) - [j28]Robert Hoehndorf, Luke T. Slater, Paul N. Schofield, Georgios V. Gkoutos:
Aber-OWL: a framework for ontology-based data access in biology. BMC Bioinform. 16: 26:1-26:9 (2015) - [c18]Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies. ICBO 2015 - [c17]Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
AberOWL: an ontology portal with OWL EL reasoning. ICBO 2015 - [c16]Luke T. Slater, Miguel Ángel Rodríguez-García, Keiron O'Shea, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf:
Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning. OWLED 2015: 81-86 - [c15]Miguel Ángel Rodríguez-García, Luke T. Slater, Keiron O'Shea, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf:
Visualising Ontologies with AberOWL. SWAT4LS 2015: 183-192 - 2014
- [j27]Robert Hoehndorf, Tanya Hiebert, Nigel W. Hardy, Paul N. Schofield, Georgios V. Gkoutos, Michel Dumontier:
Mouse model phenotypes provide information about human drug targets. Bioinform. 30(5): 719-725 (2014) - [j26]Michel Dumontier, Christopher J. O. Baker, Joachim Baran, Alison Callahan, Leonid L. Chepelev, Jose Cruz-Toledo, Nicholas R. Del Rio, Geraint Duck, Laura Inés Furlong, Nichealla Keath, Dana Klassen, James P. McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D. Wilkinson, Robert Hoehndorf:
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. J. Biomed. Semant. 5: 14 (2014) - [j25]Robert Hoehndorf, Dietrich Rebholz-Schuhmann, Melissa A. Haendel, Robert Stevens:
Thematic series on biomedical ontologies in JBMS: challenges and new directions. J. Biomed. Semant. 5: 15 (2014) - [c14]Robert Hoehndorf, Luke T. Slater, Paul N. Schofield, Georgios V. Gkoutos:
Aber-OWL: A Framework for Ontology-based Data Access in Biology. SWAT4LS 2014 - [i2]Robert Hoehndorf, Luke T. Slater, Paul N. Schofield, Georgios V. Gkoutos:
Aber-OWL: a framework for ontology-based data access in biology. CoRR abs/1407.6812 (2014) - 2013
- [j24]Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos:
Evaluation of research in biomedical ontologies. Briefings Bioinform. 14(6): 696-712 (2013) - [j23]Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno-Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin:
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. J. Biomed. Semant. 4: 28 (2013) - [j22]Daniel L. Cook, Maxwell Lewis Neal, Robert Hoehndorf, Georgios V. Gkoutos, John H. Gennari:
Representing physiological processes and their participants with PhysioMaps. J. Biomed. Semant. 4(S-1): S2 (2013) - [e1]Michel Dumontier, Robert Hoehndorf, Christopher J. O. Baker:
Proceedings of the 4th International Conference on Biomedical Ontology, ICBO 2013, Montreal, Canada, July 7-12, 2013. CEUR Workshop Proceedings 1060, CEUR-WS.org 2013 [contents] - 2012
- [j21]Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
The Units Ontology: a tool for integrating units of measurement in science. Database J. Biol. Databases Curation 2012 (2012) - [j20]Sarala M. Wimalaratne, Pierre Grenon, Robert Hoehndorf, Georgios V. Gkoutos, Bernard de Bono:
An infrastructure for ontology-based information systems in biomedicine: RICORDO case study. Bioinform. 28(3): 448-450 (2012) - [j19]Robert Hoehndorf, Midori A. Harris, Heinrich Herre, Gabriella Rustici, Georgios V. Gkoutos:
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. Bioinform. 28(13): 1783-1789 (2012) - [j18]Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos:
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. Bioinform. 28(16): 2169-2175 (2012) - [j17]Simon Jupp, Robert Stevens, Robert Hoehndorf:
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. J. Biomed. Semant. 3(S-1): S3 (2012) - [j16]Anika Oellrich, Georgios V. Gkoutos, Robert Hoehndorf, Dietrich Rebholz-Schuhmann:
Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology. J. Biomed. Semant. 3(S-2): S1 (2012) - [j15]Frank Loebe, Frank Stumpf, Robert Hoehndorf, Heinrich Herre:
Towards improving phenotype representation in OWL. J. Biomed. Semant. 3(S-2): S5 (2012) - [j14]Georgios V. Gkoutos, Robert Hoehndorf:
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. J. Biomed. Semant. 3(S-2): S6 (2012) - [c13]Adam Z. Wyner, Luke Riley, Robert Hoehndorf, Samuel Croset:
Argumentation to Represent and Reason over Biological Systems. ITBAM 2012: 124-138 - [c12]Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos:
Linking PharmGKB to Phenotype Studies and Animal Models of Disease for Drug Repurposing. Pacific Symposium on Biocomputing 2012: 388-399 - [c11]Jens Hollunder, Vladimir Mironov, Erick Antezana, Robert Hoehndorf, Martin Kuiper:
Profiling of Semantically Annotated Proteins. SWAT4LS 2012 - [i1]Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos:
Towards quantitative measures in applied ontology. CoRR abs/1202.3602 (2012) - 2011
- [j13]Robert Hoehndorf, Colin R. Batchelor, Thomas Bittner, Michel Dumontier, Karen Eilbeck, Rob Knight, Chris Mungall, Jane S. Richardson, Jesse Stombaugh, Eric Westhof, Craig L. Zirbel, Neocles Leontis:
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. Appl. Ontology 6(1): 53-89 (2011) - [j12]Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Sarala M. Wimalaratne, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos:
A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinform. 27(7): 1001-1008 (2011) - [j11]Nico Adams, Robert Hoehndorf, Georgios V. Gkoutos, Gesine Hansen, Christian Hennig:
PIDO: the primary immunodeficiency disease ontology. Bioinform. 27(22): 3193-3199 (2011) - [j10]Heinrich Herre, Robert Hoehndorf, Janet Kelso, Frank Loebe, Stefan Schulz:
OBML - Ontologies in Biomedicine and Life Sciences. J. Biomed. Semant. 2(S-4): I1 (2011) - [j9]Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann:
Ontology design patterns to disambiguate relations between genes and gene products in GENIA. J. Biomed. Semant. 2(S-5): S1 (2011) - [j8]Robert Hoehndorf, Michel Dumontier, John H. Gennari, Sarala M. Wimalaratne, Bernard de Bono, Daniel L. Cook, Georgios V. Gkoutos:
Integrating systems biology models and biomedical ontologies. BMC Syst. Biol. 5: 124 (2011) - [c10]Hiroshi Masuya, Georgios V. Gkoutos, Nobuhiko Tanaka, Kazunori Waki, Yoshihiro Okuda, Tatsuya Kushida, Norio Kobayashi, Koji Doi, Kouji Kozaki, Robert Hoehndorf, Shigeharu Wakana, Tetsuro Toyoda, Riichiro Mizoguchi:
An Advanced Strategy for Integration of Biological Measurement Data. ICBO 2011 - [c9]Stefan Schulz, Mathias Brochhausen, Robert Hoehndorf:
Higgs Bosons, Mars Missions, and Unicorn Delusions: How to Deal with Terms of Dubious Reference in Scientific Ontologies. ICBO 2011 - 2010
- [j7]Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann:
Interoperability between phenotype and anatomy ontologies. Bioinform. 26(24): 3112-3118 (2010) - [j6]Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Janet Kelso:
Applying the functional abnormality ontology pattern to anatomical functions. J. Biomed. Semant. 1: 4 (2010) - [j5]Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Dietrich Rebholz-Schuhmann, Heinrich Herre:
Relations as patterns: bridging the gap between OBO and OWL. BMC Bioinform. 11: 441 (2010) - [c8]Michel Dumontier, Robert Hoehndorf:
Realism for scientific ontologies. FOIS 2010: 387-399 - [c7]Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Heinrich Herre, Dietrich Rebholz-Schuhmann:
Relational Patterns in OWL and Their Application to OBO. OWLED 2010 - [c6]Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann:
Applying ontology design patterns to the implementation of relations in GENIA. Semantic Mining in Biomedicine 2010
2000 – 2009
- 2009
- [b1]Robert Hoehndorf:
Basic considerations for improving interoperability between ontology based biological information systems. University of Leipzig, 2009, pp. 1-242 - [j4]Robert Hoehndorf, Joshua Bacher, Michael Backhaus, Sergio E. Gregorio Jr., Frank Loebe, Kay Prüfer, Alexandr Uciteli, Johann Visagie, Heinrich Herre, Janet Kelso:
BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology. BMC Bioinform. 10(S-5) (2009) - [j3]Robert Hoehndorf, Janet Kelso, Heinrich Herre:
The ontology of biological sequences. BMC Bioinform. 10: 377 (2009) - [c5]Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Heinrich Herre:
Developing Consistent and Modular Software Models with Ontologies. SoMeT 2009: 399-412 - 2008
- [j2]Robert Hoehndorf, Frank Loebe, Roberto Poli, Heinrich Herre, Janet Kelso:
GFO-Bio: A biological core ontology. Appl. Ontology 3(4): 219-227 (2008) - [c4]Joshua Bacher, Robert Hoehndorf, Janet Kelso:
BOWiki: Ontology-based Semantic Wiki with ABox Reasoning. SemWiki 2008 - 2007
- [j1]Robert Hoehndorf, Frank Loebe, Janet Kelso, Heinrich Herre:
Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies. BMC Bioinform. 8 (2007) - [c3]Michael Backhaus, Janet Kelso, Joshua Bacher, Heinrich Herre, Robert Hoehndorf, Frank Loebe, Johann Visagie:
BOWiki - a Collaborative Annotation and Ontology Curation Framework. CKC 2007 - 2006
- [c2]Patryk Burek, Robert Hoehndorf, Frank Loebe, Johann Visagie, Heinrich Herre, Janet Kelso:
A top-level ontology of functions and its application in the Open Biomedical Ontologies. ISMB (Supplement of Bioinformatics) 2006: 66-73 - [c1]Robert Hoehndorf, Kay Prüfer, Michael Backhaus, Heinrich Herre, Janet Kelso, Frank Loebe, Johann Visagie:
A Proposal for a Gene Functions Wiki. OTM Workshops (1) 2006: 669-678
Coauthor Index
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