publication . Preprint . 2013

A pattern-driven approach to biomedical ontology engineering

Warrender, Jennifer D.; Lord, Phillip;
Open Access English
  • Published: 02 Dec 2013
Abstract
Developing ontologies can be expensive, time-consuming, as well as difficult to develop and maintain. This is especially true for more expressive and/or larger ontologies. Some ontologies are, however, relatively repetitive, reusing design patterns; building these with both generic and bespoke patterns should reduce duplication and increase regularity which in turn should impact on the cost of development. Here we report on the usage of patterns applied to two biomedical ontologies: firstly a novel ontology for karyotypes which has been built ground-up using a pattern based approach; and, secondly, our initial refactoring of the SIO ontology to make explicit use...
Subjects
free text keywords: Computer Science - Computational Engineering, Finance, and Science, Computer Science - Digital Libraries
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27 references, page 1 of 2

1. Stevens, R., Lord, P.: Application of Ontologies in Bioinformatics. In Staab, S., Studer, R., eds.: Handbook on Ontologies. International Handbooks on Information Systems. Springer Berlin Heidelberg (2009) 735-756

2. Warren, P.: Ontology Users Survey Summary of Results. Technical report, The Knowledge Media Institute (KMi), The Open University (2013)

3. Mungall, C., Ruttenberg, A., Horrocks, I., Osumi-Sutherland, D.: OBO Flat File Format 1.4 Syntax and Semantics [DRAFT]. http://oboformat.googlecode.com/svn/branches/2011-11-29/doc/obo-syntax.html

4. W3C OWL Working Group: OWL 2 Web Ontology Language Document Overview (Second Edition). http://www.w3.org/TR/owl2-overview/ (2012)

5. Tirmizi, S., Aitken, S., Moreira, D., Mungall, C., Sequeda, J., Shah, N., Miranker, D.: Mapping between the OBO and OWL ontology languages. Journal of Biomedical Semantics 2(1) (2011) 1-16

6. Gamma, E., Helm, R., Johnson, R., Vlissides, J.: Design patterns: elements of reusable object-oriented software. Addison-Wesley Longman Publishing Co., Inc., Boston, MA, USA (1995) [OpenAIRE]

7. Egaa, M., Rector, A., Stevens, R., Antezana, E.: Applying Ontology Design Patterns in Bio-ontologies. In Gangemi, A., Euzenat, J., eds.: Knowledge Engineering: Practice and Patterns. Volume 5268 of Lecture Notes in Computer Science. Springer Berlin Heidelberg (2008) 7-16

8. Rector, A.: Representing Specified Values in OWL: value partitions and value sets. http://www.w3.org/TR/swbp-specified-values/ (2005)

9. Drummond, N., Rector, A., Stevens, R., Moulton, G., Horridge, M., Wang, H.H., Seidenberg, J.: Putting OWL in order: Patterns for sequences in OWL. Concrete (2006) 1-10

10. Egana Aranguren, M., Stevens, R., Antezana, E.: Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language. Nature Precedings (Dec 2009) [OpenAIRE]

11. Mungall, C., Ruttenberg, A., Osumi-Sutherland, D.: Taking shortcuts with OWL using safe macros. Nature Preceedings (2010)

12. Wolstencroft, K., Owen, S., Horridge, M., Krebs, O., Mueller, W., Snoep, J.L., du Preez, F., Goble, C.: RightField: embedding ontology annotation in spreadsheets. Bioinformatics 27(14) (2011) 2021-2022

13. Jupp, S., Horridge, M., Iannone, L., Klein, J., Owen, S., Schanstra, J., Stevens, R., Wolstencroft, K.: Populous: A Tool for Populating Templates for OWL Ontologies. In Burger, A., Marshall, M.S., 0001, P.R., Paschke, A., Splendiani, A., eds.: SWAT4LS. Volume 698 of CEUR Workshop Proceedings., CEUR-WS.org (2010)

14. Rocca-Serra, P., Ruttenberg, A., O'Connor, M.J., Whetzel, P.L., Schober, D., Greenbaum, J., Courtot, M., Brinkman, R.R., Sansone, S.A., Scheuermann, R., Scheuermann, R., Peters, B.: Overcoming the ontology enrichment bottleneck with Quick Term Templates. Appl. Ontol. 6(1) (January 2011) 13-22

15. OConnor, M., Halaschek-Wiener, C., Musen, M.: Mapping Master: A Flexible Approach for Mapping Spreadsheets to OWL. In Patel-Schneider, P., Pan, Y., Hitzler, P., Mika, P., Zhang, L., Pan, J., Horrocks, I., Glimm, B., eds.: The Semantic Web ISWC 2010. Volume 6497 of Lecture Notes in Computer Science. Springer Berlin Heidelberg (2010) 194-208 [OpenAIRE]

27 references, page 1 of 2
Abstract
Developing ontologies can be expensive, time-consuming, as well as difficult to develop and maintain. This is especially true for more expressive and/or larger ontologies. Some ontologies are, however, relatively repetitive, reusing design patterns; building these with both generic and bespoke patterns should reduce duplication and increase regularity which in turn should impact on the cost of development. Here we report on the usage of patterns applied to two biomedical ontologies: firstly a novel ontology for karyotypes which has been built ground-up using a pattern based approach; and, secondly, our initial refactoring of the SIO ontology to make explicit use...
Subjects
free text keywords: Computer Science - Computational Engineering, Finance, and Science, Computer Science - Digital Libraries
Download from
27 references, page 1 of 2

1. Stevens, R., Lord, P.: Application of Ontologies in Bioinformatics. In Staab, S., Studer, R., eds.: Handbook on Ontologies. International Handbooks on Information Systems. Springer Berlin Heidelberg (2009) 735-756

2. Warren, P.: Ontology Users Survey Summary of Results. Technical report, The Knowledge Media Institute (KMi), The Open University (2013)

3. Mungall, C., Ruttenberg, A., Horrocks, I., Osumi-Sutherland, D.: OBO Flat File Format 1.4 Syntax and Semantics [DRAFT]. http://oboformat.googlecode.com/svn/branches/2011-11-29/doc/obo-syntax.html

4. W3C OWL Working Group: OWL 2 Web Ontology Language Document Overview (Second Edition). http://www.w3.org/TR/owl2-overview/ (2012)

5. Tirmizi, S., Aitken, S., Moreira, D., Mungall, C., Sequeda, J., Shah, N., Miranker, D.: Mapping between the OBO and OWL ontology languages. Journal of Biomedical Semantics 2(1) (2011) 1-16

6. Gamma, E., Helm, R., Johnson, R., Vlissides, J.: Design patterns: elements of reusable object-oriented software. Addison-Wesley Longman Publishing Co., Inc., Boston, MA, USA (1995) [OpenAIRE]

7. Egaa, M., Rector, A., Stevens, R., Antezana, E.: Applying Ontology Design Patterns in Bio-ontologies. In Gangemi, A., Euzenat, J., eds.: Knowledge Engineering: Practice and Patterns. Volume 5268 of Lecture Notes in Computer Science. Springer Berlin Heidelberg (2008) 7-16

8. Rector, A.: Representing Specified Values in OWL: value partitions and value sets. http://www.w3.org/TR/swbp-specified-values/ (2005)

9. Drummond, N., Rector, A., Stevens, R., Moulton, G., Horridge, M., Wang, H.H., Seidenberg, J.: Putting OWL in order: Patterns for sequences in OWL. Concrete (2006) 1-10

10. Egana Aranguren, M., Stevens, R., Antezana, E.: Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language. Nature Precedings (Dec 2009) [OpenAIRE]

11. Mungall, C., Ruttenberg, A., Osumi-Sutherland, D.: Taking shortcuts with OWL using safe macros. Nature Preceedings (2010)

12. Wolstencroft, K., Owen, S., Horridge, M., Krebs, O., Mueller, W., Snoep, J.L., du Preez, F., Goble, C.: RightField: embedding ontology annotation in spreadsheets. Bioinformatics 27(14) (2011) 2021-2022

13. Jupp, S., Horridge, M., Iannone, L., Klein, J., Owen, S., Schanstra, J., Stevens, R., Wolstencroft, K.: Populous: A Tool for Populating Templates for OWL Ontologies. In Burger, A., Marshall, M.S., 0001, P.R., Paschke, A., Splendiani, A., eds.: SWAT4LS. Volume 698 of CEUR Workshop Proceedings., CEUR-WS.org (2010)

14. Rocca-Serra, P., Ruttenberg, A., O'Connor, M.J., Whetzel, P.L., Schober, D., Greenbaum, J., Courtot, M., Brinkman, R.R., Sansone, S.A., Scheuermann, R., Scheuermann, R., Peters, B.: Overcoming the ontology enrichment bottleneck with Quick Term Templates. Appl. Ontol. 6(1) (January 2011) 13-22

15. OConnor, M., Halaschek-Wiener, C., Musen, M.: Mapping Master: A Flexible Approach for Mapping Spreadsheets to OWL. In Patel-Schneider, P., Pan, Y., Hitzler, P., Mika, P., Zhang, L., Pan, J., Horrocks, I., Glimm, B., eds.: The Semantic Web ISWC 2010. Volume 6497 of Lecture Notes in Computer Science. Springer Berlin Heidelberg (2010) 194-208 [OpenAIRE]

27 references, page 1 of 2
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