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Embeddings of Gene Ontology (GO) using OWL2Vec* ...
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Abstract:
These embeddings are from the Gene Ontology (GO) [1] downloaded on 19 Oct 2020, were created using OWL2Vec* [2], and are in binary format (output using pickle). Some information about the embedding settings and an example for how they were used are found in Ritchie et al.'s paper "Ontology Clustering with OWL2Vec*" [3]. References [1] The Gene Ontology Consortium. The Gene Ontology Resource: 20 years and still GOing strong, Nucleic Acids Research, Volume 47, 2019. Accessed 9th October 2020. [2] Chen J, Hu P, Jimenez-Ruiz E, Holter OM, Antonyrajah D, Horrocks I. OWL2Vec*: Embedding of OWL Ontologies. Machine Learning, Springer, 2021. https://github.com/KRR-Oxford/OWL2Vec-Star [3] Ritchie, A., Chen, J., Castro, L. J., Rebholz-Schuhmann, D. and Jimenez-Ruiz, E. Ontology Clustering with OWL2Vec* . Paper presented at the Deep Learning meets Ontologies and Natural Language Processing (DeepOntoNLP2021), 6-10 Jun 2021, Online. ... : The naming convention of the files are as follows where each symbol is separated by a dash (e.g. 3-L-R-2-50): First Symbol - Document/Embedding Settings 1 - Structure Document, IRI embeddings [D(s), V(iri)] 2 - Lexical Document, IRI embeddings [D(s,l), V(iri)] 3 - Lexical Document, Word embeddings [D(s,l), V(word)] 4 - Lexical Document, IRI & Word embeddings [D(s,l), V(iri, word)] 5 - Combined Document - random, IRI embeddings [D(s,l,rc), V(iri)] 6 - Combined Document - random, word embeddings [D(s,l,rc), V(word)] 7 - Combined Document - random, IRI & Word embeddings [D(s,l,rc), V(iri, word)] 8 - Combined Document - traversal, IRI embeddings [D(s,l,tc), V(iri)] 9 - Combined Document - traversal, word embeddings [D(s,l,tc), V(word)] 10 - Combined Document - traversal, IRI & Word embeddings [D(s,l,tc), V(iri, word)] Second Symbol - Annotation Settings A - All annotations L - Limited annotations (label, hasExactSynonym) Third Symbol - Walker Type R - Random walker WL - Weisfeiler Lehman sub-tree ...
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Keyword:
Embeddings, Ontology, OWL2Vec*, Gene Ontology, GO
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URL: https://zenodo.org/record/4882682
https://dx.doi.org/10.5281/zenodo.4882682
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Breaking-down the Ontology Alignment Task with a Lexical Index and Neural Embeddings ...
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Evaluating Ontology Matching Systems on Large, Multilingual and Real-world Test Cases ...
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Logic-based assessment of the compatibility of UMLS ontology sources
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