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Biomedical ontology alignment: an approach based on representation learning

Prodromos Kolyvakis, Alexandros Kalousis, Barry Smith, Dimitris Kiritsis
2018 Journal of Biomedical Semantics  
Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task.  ...  Our approach is based on embedding ontological terms in a high-dimensional Euclidean space.  ...  Representation learning has so far limited impact on ontology matching.  ... 
doi:10.1186/s13326-018-0187-8 pmid:30111369 pmcid:PMC6094585 fatcat:x4ojf6uht5g45dke7zmty7slue

Bootstrapping Adversarial Learning of Biomedical Ontology Alignments

Ramon M Maldonado, Sanda M Harabagiu
2020 AMIA Annual Symposium Proceedings  
Learning how to automatically align biomedical ontologies has been a long-standing goal, given their ever-growing content and the many applications that rely on them.  ...  Because the knowledge graphs underlying biomedical ontologies enable neural learning techniques to acquire knowledge embeddings as representations of these ontologies, neural learning can also consider  ...  distinct biomedical ontologies into the same semantic space such that pairs of concepts from different ontologies can be aligned based on their similarity, while also (2) encoding the semantics of both  ... 
pmid:32308857 pmcid:PMC7153069 fatcat:55bsch3b55cflg2oskq63qksmm

SAMBO - A System for Aligning and Merging Biomedical Ontologies

Patrick Lambrix, He Tan
2006 Social Science Research Network  
Further, we developed a system for aligning and merging biomedical ontologies (SAMBO) based on this framework.  ...  Due to the recent explosion of the amount of on-line accessible biomedical data and tools, finding and retrieving the relevant information is not an easy task.  ...  Acknowledgements We thank Vaida Jakonienė for comments on the paper and SAMBO and Bo Servenius for discussions and comments on SAMBO.  ... 
doi:10.2139/ssrn.3199338 fatcat:giumjehjsjayhabgzq4s4hs2zu

SAMBO—A system for aligning and merging biomedical ontologies

Patrick Lambrix, He Tan
2006 Journal of Web Semantics  
Further, we developed a system for aligning and merging biomedical ontologies (SAMBO) based on this framework.  ...  Due to the recent explosion of the amount of on-line accessible biomedical data and tools, finding and retrieving the relevant information is not an easy task.  ...  Acknowledgements We thank Vaida Jakonienė for comments on the paper and SAMBO and Bo Servenius for discussions and comments on SAMBO.  ... 
doi:10.1016/j.websem.2006.05.003 fatcat:4mszk4nh3fdfxhxpiuvixp2uoa

Aligning Biomedical Metadata with Ontologies Using Clustering and Embeddings [article]

Rafael S. Gonçalves, Maulik R. Kamdar, Mark A. Musen
2019 arXiv   pre-print
To that end, we present a new method based on clustering and embeddings (i.e., vector representations of words) to align metadata field names with ontology terms.  ...  We apply our method to biomedical metadata by generating embeddings for terms in biomedical ontologies from the BioPortal repository.  ...  We thank the experts in our evaluation panel: John Graybeal, Josef Hardi, Marcos Martínez-Romero, and Csongor Nyulas (all of whom from the Center for Biomedical Informatics Research at Stanford University  ... 
arXiv:1903.08206v2 fatcat:w55gpodddvcvrbtlahjv45wnbe

Ontology Alignment in the Biomedical Domain Using Entity Definitions and Context [article]

Lucy Lu Wang, Chandra Bhagavatula, Mark Neumann, Kyle Lo, Chris Wilhelm, Waleed Ammar
2018 arXiv   pre-print
We develop a neural architecture capable of encoding the additional information when available, and show that the addition of external data results in an F1-score of 0.69 on the Ontology Alignment Evaluation  ...  We propose a method for enriching entities in an ontology with external definition and context information, and use this additional information for ontology alignment.  ...  Our 100-dimensional pretrained embeddings are learned using the default settings of word2vec based on the Medline corpus.  ... 
arXiv:1806.07976v1 fatcat:fx2xk4e7tvh6johkgddnw4lhoy

Ontology alignment in the biomedical domain using entity definitions and context

Lucy Wang, Chandra Bhagavatula, Mark Neumann, Kyle Lo, Chris Wilhelm, Waleed Ammar
2018 Proceedings of the BioNLP 2018 workshop  
We develop a neural architecture capable of encoding the additional information when available, and show that the addition of external data results in an F1-score of 0.69 on the Ontology Alignment Evaluation  ...  We propose a method for enriching entities in an ontology with external definition and context information, and use this additional information for ontology alignment.  ...  Our 100-dimensional pretrained embeddings are learned using the default settings of word2vec based on the Medline corpus.  ... 
doi:10.18653/v1/w18-2306 dblp:conf/bionlp/WangBNLWA18 fatcat:iqrp6lyhxnhj7inakttrpczymu

Methods in biomedical ontology

Alexander C. Yu
2006 Journal of Biomedical Informatics  
Research on ontologies is becoming widespread in the biomedical informatics community.  ...  This paper reviews current methods in the construction, maintenance, alignment, and evaluation of ontologies.  ...  Acknowledgments The author thanks James Cimino and an anonymous reviewer for their valuable feedback.  ... 
doi:10.1016/j.jbi.2005.11.006 pmid:16387553 fatcat:lejoszoldnhupo7irv6f6c2q5i

The Ontology for Biomedical Investigations

Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel (+33 others)
2016 PLoS ONE  
OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived  ...  The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are  ...  In order to garner the experience and knowledge to describe biomedicine, we have taken a community-based approach. Authors on this paper, for example, cover many disciplines within biomedicine.  ... 
doi:10.1371/journal.pone.0154556 pmid:27128319 pmcid:PMC4851331 fatcat:cxeglm5tynfszjthzt7ebbsjhe

The SWAN biomedical discourse ontology

Paolo Ciccarese, Elizabeth Wu, Gwen Wong, Marco Ocana, June Kinoshita, Alan Ruttenberg, Tim Clark
2008 Journal of Biomedical Informatics  
In this paper, we present and discuss the SWAN ontology of biomedical discourse.  ...  SWAN (Semantic Web Applications in Neuromedicine) is an interdisciplinary project to develop a practical, common, semantically structured, framework for biomedical discourse initially applied, but not  ...  Acknowledgements We are grateful to the Ellison Medical Foundation, the Alzheimer Association, Eli Lilly and Company, and to an anonymous foundation, for their generous support of the SWAN project.  ... 
doi:10.1016/j.jbi.2008.04.010 pmid:18583197 pmcid:PMC4536833 fatcat:mtq6hvo565g65dtwuvdifo7e5y

DAEOM: A Deep Attentional Embedding Approach for Biomedical Ontology Matching

Jifang Wu, Jianghua Lv, Haoming Guo, Shilong Ma
2020 Applied Sciences  
Firstly, these methods only focus on the terminological-based features to learn word vectors for discovering mappings, ignoring the network structure of ontology.  ...  The preliminary result on real-world biomedical ontologies indicates that DAEOM is competitive with several OAEI top-ranked systems in terms of F-measure.  ...  [23] proposed an entity representation learning algorithm based on Stacked Auto-Encoders to learn the general representation of the entities.  ... 
doi:10.3390/app10217909 fatcat:zqpshggw5jel5dqtuzwsqkboxy

Using Compact Coevolutionary Algorithm for Matching Biomedical Ontologies

Xingsi Xue, Jie Chen, Junfeng Chen, Dongxu Chen
2018 Computational Intelligence and Neuroscience  
To implement the cooperation between intelligent applications based on biomedical ontologies, it is crucial to establish correspondences between the heterogeneous biomedical concepts in different ontologies  ...  , which is so-called biomedical ontology matching.  ...  To implement the cooperation between intelligent applications based on biomedical ontologies, it is crucial to establish correspondences between the heterogeneous biomedical concepts in different ontologies  ... 
doi:10.1155/2018/2309587 pmid:30405706 pmcid:PMC6199880 fatcat:3banmvgle5gzhputmvdd3tgfee

Experiences from the anatomy track in the ontology alignment evaluation initiative

Zlatan Dragisic, Valentina Ivanova, Huanyu Li, Patrick Lambrix
2017 Journal of Biomedical Semantics  
This paper is an overall presentation of the OAEI 2014 campaign.  ...  This paper improves on the "Preliminary results" initially published in the on-site proceedings of the ISWC workshop on Ontology Matching (OM-2014).  ...  We are also grateful to Martin Ringwald and Terry Hayamizu for providing the reference alignment for the anatomy ontologies and thank Elena Beisswanger for her thorough support on improving the quality  ... 
doi:10.1186/s13326-017-0166-5 pmid:29202830 pmcid:PMC5715990 fatcat:zvet5vb6zncxnlgd225ndhcik4

Multilingual Mapping Reconciliation between English-French Biomedical Ontologies

Unknown
2016 Proceedings of the 6th International Conference on Web Intelligence, Mining and Semantics - WIMS '16  
In this paper, we propose an approach to represent translation mappings between ontologies based on the NCBO BioPortal format.  ...  Even if multilingual ontologies are now more common, for historical reasons, in the biomedical domain, many ontologies or terminologies have been translated from one natural language to another resulting  ...  We thanks the NCBO (Stanford University) and the CISMeF group (Rouen CHU Hospital) for the availability of the ontologies used in this work.  ... 
doi:10.1145/2912845.2912847 dblp:conf/wims/AnnaneEAJ16 fatcat:3eyb73bgnfbi7pysomirfsei54

The African wildlife ontology tutorial ontologies

C. Maria Keet
2020 Journal of Biomedical Semantics  
Most tutorial ontologies focus on illustrating one aspect of ontology development, notably language features and automated reasoners, but ignore ontology development factors, such as emergent modelling  ...  It assists in demonstrating tasks concerning ontology quality, such as alignment to a foundational ontology and satisfying competency questions, versioning, and multilingual ontologies.  ...  Acknowledgements The author would like to thank previous ontology engineering course participants on their feedback, which assisted in refining some of the examples and exercises with the AWO, and Ludger  ... 
doi:10.1186/s13326-020-00224-y pmid:32576239 fatcat:jvpkw63rpjaxfoeixhjpbrrzki
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