Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning

Luke Slater; Miguel Ángel Rodríguez-García; Keiron O’Shea; Paul N. Schofield; Georgios V. Gkoutos; Robert Hoehndorf

doi:10.1007/978-3-319-33245-1_8

Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning

Luke Slater, Miguel Ángel Rodríguez-García, Keiron O’Shea, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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Abstract

Ontologies are widely used in biology and biomedicine for the annotation and integration of data, and hundreds of ontologies have been developed for this purpose. These ontologies also constitute large volumes of formalized domain knowledge, usually expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within them relies on the use of automated reasoning. We have developed Aber-OWL, an ontology repository that provides OWL EL reasoning to answer queries and verify the consistency of ontologies. Aber-OWL also provides a set of web services which provide ontology-based access to scientific literature in Pubmed and Pubmed Central, SPARQL query expansion to retrieve linked data, and integration with Bio2RDF. Here, we report on our experiences with Aber-OWL and outline a roadmap for future development. Aber-OWL is freely available at http://aber-owl.net.

Original language	English
Title of host publication	Ontology Engineering
Subtitle of host publication	12th International Experiences and Directions Workshop on OWL, OWLED 2015, co-located with ISWC 2015 Bethlehem, PA, USA, October 9–10, 2015 Revised Selected Papers
Editors	Valentina Tamma, Mauro Dragoni, Rafael Gonçalves, Agnieszka Ławrynowicz
Publisher	Springer
Pages	81-86
Number of pages	6
ISBN (Electronic)	978-3-319-33245-1
ISBN (Print)	978-3-319-33244-4
DOIs	https://doi.org/10.1007/978-3-319-33245-1_8
Publication status	E-pub ahead of print - 20 Apr 2016
Event	OWLED 2015 12th OWL: Experiences and Directions Workshop - Bethlehem, United States Duration: 9 Oct 2015 → 10 Oct 2015

Publication series

Name	Lecture Notes in Computer Science
Publisher	Springer
Volume	9557
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	OWLED 2015 12th OWL: Experiences and Directions Workshop
Abbreviated title	OWLED 2015
Country/Territory	United States
City	Bethlehem
Period	9/10/15 → 10/10/15

Keywords

Biomedical ontology
Semantic web
Literature search
Semantic indexing
Query expansion

Access to Document

10.1007/978-3-319-33245-1_8Licence: None: All rights reserved

Luke_Slater_et_al_Experiences_with_Aber-OWL_Ontology_Engineering_2015
Checked for eligibility: 04/04/2019 The final authenticated version is: available online at https://doi.org/10.1007/978-3-319-33245-1_8.
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Cite this

Slater, L., Rodríguez-García, M. Á., O’Shea, K., Schofield, P. N., Gkoutos, G. V., & Hoehndorf, R. (2016). Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning. In V. Tamma, M. Dragoni, R. Gonçalves, & A. Ławrynowicz (Eds.), Ontology Engineering: 12th International Experiences and Directions Workshop on OWL, OWLED 2015, co-located with ISWC 2015 Bethlehem, PA, USA, October 9–10, 2015 Revised Selected Papers (pp. 81-86). (Lecture Notes in Computer Science; Vol. 9557). Springer. Advance online publication. https://doi.org/10.1007/978-3-319-33245-1_8

Slater, Luke ; Rodríguez-García, Miguel Ángel ; O’Shea, Keiron et al. / Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning. Ontology Engineering: 12th International Experiences and Directions Workshop on OWL, OWLED 2015, co-located with ISWC 2015 Bethlehem, PA, USA, October 9–10, 2015 Revised Selected Papers. editor / Valentina Tamma ; Mauro Dragoni ; Rafael Gonçalves ; Agnieszka Ławrynowicz. Springer, 2016. pp. 81-86 (Lecture Notes in Computer Science).

@inproceedings{465e7a98f9d2404fb839521cc37e3e5f,

title = "Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning",

abstract = "Ontologies are widely used in biology and biomedicine for the annotation and integration of data, and hundreds of ontologies have been developed for this purpose. These ontologies also constitute large volumes of formalized domain knowledge, usually expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within them relies on the use of automated reasoning. We have developed Aber-OWL, an ontology repository that provides OWL EL reasoning to answer queries and verify the consistency of ontologies. Aber-OWL also provides a set of web services which provide ontology-based access to scientific literature in Pubmed and Pubmed Central, SPARQL query expansion to retrieve linked data, and integration with Bio2RDF. Here, we report on our experiences with Aber-OWL and outline a roadmap for future development. Aber-OWL is freely available at http://aber-owl.net.",

keywords = "Biomedical ontology, Semantic web, Literature search, Semantic indexing, Query expansion",

author = "Luke Slater and Rodr{\'i}guez-Garc{\'i}a, {Miguel {\'A}ngel} and Keiron O{\textquoteright}Shea and Schofield, {Paul N.} and Gkoutos, {Georgios V.} and Robert Hoehndorf",

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doi = "10.1007/978-3-319-33245-1_8",

language = "English",

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series = "Lecture Notes in Computer Science",

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booktitle = "Ontology Engineering",

note = "OWLED 2015 12th OWL: Experiences and Directions Workshop, OWLED 2015 ; Conference date: 09-10-2015 Through 10-10-2015",

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Slater, L, Rodríguez-García, MÁ, O’Shea, K, Schofield, PN, Gkoutos, GV & Hoehndorf, R 2016, Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning. in V Tamma, M Dragoni, R Gonçalves & A Ławrynowicz (eds), Ontology Engineering: 12th International Experiences and Directions Workshop on OWL, OWLED 2015, co-located with ISWC 2015 Bethlehem, PA, USA, October 9–10, 2015 Revised Selected Papers. Lecture Notes in Computer Science, vol. 9557, Springer, pp. 81-86, OWLED 2015 12th OWL: Experiences and Directions Workshop, Bethlehem, Pennsylvania, United States, 9/10/15. https://doi.org/10.1007/978-3-319-33245-1_8

Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning. / Slater, Luke; Rodríguez-García, Miguel Ángel; O’Shea, Keiron et al.
Ontology Engineering: 12th International Experiences and Directions Workshop on OWL, OWLED 2015, co-located with ISWC 2015 Bethlehem, PA, USA, October 9–10, 2015 Revised Selected Papers. ed. / Valentina Tamma; Mauro Dragoni; Rafael Gonçalves; Agnieszka Ławrynowicz. Springer, 2016. p. 81-86 (Lecture Notes in Computer Science; Vol. 9557).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning

AU - Slater, Luke

AU - Rodríguez-García, Miguel Ángel

AU - O’Shea, Keiron

AU - Schofield, Paul N.

AU - Gkoutos, Georgios V.

AU - Hoehndorf, Robert

PY - 2016/4/20

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N2 - Ontologies are widely used in biology and biomedicine for the annotation and integration of data, and hundreds of ontologies have been developed for this purpose. These ontologies also constitute large volumes of formalized domain knowledge, usually expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within them relies on the use of automated reasoning. We have developed Aber-OWL, an ontology repository that provides OWL EL reasoning to answer queries and verify the consistency of ontologies. Aber-OWL also provides a set of web services which provide ontology-based access to scientific literature in Pubmed and Pubmed Central, SPARQL query expansion to retrieve linked data, and integration with Bio2RDF. Here, we report on our experiences with Aber-OWL and outline a roadmap for future development. Aber-OWL is freely available at http://aber-owl.net.

AB - Ontologies are widely used in biology and biomedicine for the annotation and integration of data, and hundreds of ontologies have been developed for this purpose. These ontologies also constitute large volumes of formalized domain knowledge, usually expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within them relies on the use of automated reasoning. We have developed Aber-OWL, an ontology repository that provides OWL EL reasoning to answer queries and verify the consistency of ontologies. Aber-OWL also provides a set of web services which provide ontology-based access to scientific literature in Pubmed and Pubmed Central, SPARQL query expansion to retrieve linked data, and integration with Bio2RDF. Here, we report on our experiences with Aber-OWL and outline a roadmap for future development. Aber-OWL is freely available at http://aber-owl.net.

KW - Biomedical ontology

KW - Semantic web

KW - Literature search

KW - Semantic indexing

KW - Query expansion

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M3 - Conference contribution

SN - 978-3-319-33244-4

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BT - Ontology Engineering

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A2 - Dragoni, Mauro

A2 - Gonçalves, Rafael

A2 - Ławrynowicz, Agnieszka

PB - Springer

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Y2 - 9 October 2015 through 10 October 2015

ER -

Slater L, Rodríguez-García MÁ, O’Shea K, Schofield PN, Gkoutos GV, Hoehndorf R. Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning. In Tamma V, Dragoni M, Gonçalves R, Ławrynowicz A, editors, Ontology Engineering: 12th International Experiences and Directions Workshop on OWL, OWLED 2015, co-located with ISWC 2015 Bethlehem, PA, USA, October 9–10, 2015 Revised Selected Papers. Springer. 2016. p. 81-86. (Lecture Notes in Computer Science). Epub 2016 Apr 20. doi: 10.1007/978-3-319-33245-1_8

Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning

Abstract

Publication series

Conference

Keywords

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