A document-centric approach for developing the tolAPC ontology
Abstract Background There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometimes, an understanding of the philosophical b...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2017-11-01
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| Series: | Journal of Biomedical Semantics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13326-017-0159-4 |
| _version_ | 1818081518224932864 |
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| author | Aisha Blfgeh Jennifer Warrender Catharien M. U. Hilkens Phillip Lord |
| author_facet | Aisha Blfgeh Jennifer Warrender Catharien M. U. Hilkens Phillip Lord |
| author_sort | Aisha Blfgeh |
| collection | DOAJ |
| description | Abstract Background There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometimes, an understanding of the philosophical background. In practice, it is very rare that an ontology can be completed by a single person, as they are unlikely to combine all of these skills. So people with these skills must collaborate. One solution to this is to use face-to-face meetings, but these can be expensive and time-consuming for teams that are not co-located. Remote collaboration is possible, of course, but one difficulty here is that domain specialists use a wide-variety of different “formalisms” to represent and share their data – by the far most common, however, is the “office file” either in the form of a word-processor document or a spreadsheet. Here we describe the development of an ontology of immunological cell types; this was initially developed by domain specialists using an Excel spreadsheet for collaboration. We have transformed this spreadsheet into an ontology using highly-programmatic and pattern-driven ontology development. Critically, the spreadsheet remains part of the source for the ontology; the domain specialists are free to update it, and changes will percolate to the end ontology. Results We have developed a new ontology describing immunological cell lines built by instantiating ontology design patterns written programmatically, using values from a spreadsheet catalogue. Conclusions This method employs a spreadsheet that was developed by domain experts. The spreadsheet is unconstrained in its usage and can be freely updated resulting in a new ontology. This provides a general methodology for ontology development using data generated by domain specialists. |
| first_indexed | 2024-12-10T19:07:29Z |
| format | Article |
| id | doaj.art-05b11a2fe35e453f9966e5956786d4f4 |
| institution | Directory Open Access Journal |
| issn | 2041-1480 |
| language | English |
| last_indexed | 2024-12-10T19:07:29Z |
| publishDate | 2017-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Biomedical Semantics |
| spelling | doaj.art-05b11a2fe35e453f9966e5956786d4f42022-12-22T01:36:50ZengBMCJournal of Biomedical Semantics2041-14802017-11-01811910.1186/s13326-017-0159-4A document-centric approach for developing the tolAPC ontologyAisha Blfgeh0Jennifer Warrender1Catharien M. U. Hilkens2Phillip Lord3School of Computing Science, Newcastle UniversitySchool of Computing Science, Newcastle UniversityInstitute of Cellular Medicine, Newcastle UniversitySchool of Computing Science, Newcastle UniversityAbstract Background There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometimes, an understanding of the philosophical background. In practice, it is very rare that an ontology can be completed by a single person, as they are unlikely to combine all of these skills. So people with these skills must collaborate. One solution to this is to use face-to-face meetings, but these can be expensive and time-consuming for teams that are not co-located. Remote collaboration is possible, of course, but one difficulty here is that domain specialists use a wide-variety of different “formalisms” to represent and share their data – by the far most common, however, is the “office file” either in the form of a word-processor document or a spreadsheet. Here we describe the development of an ontology of immunological cell types; this was initially developed by domain specialists using an Excel spreadsheet for collaboration. We have transformed this spreadsheet into an ontology using highly-programmatic and pattern-driven ontology development. Critically, the spreadsheet remains part of the source for the ontology; the domain specialists are free to update it, and changes will percolate to the end ontology. Results We have developed a new ontology describing immunological cell lines built by instantiating ontology design patterns written programmatically, using values from a spreadsheet catalogue. Conclusions This method employs a spreadsheet that was developed by domain experts. The spreadsheet is unconstrained in its usage and can be freely updated resulting in a new ontology. This provides a general methodology for ontology development using data generated by domain specialists.http://link.springer.com/article/10.1186/s13326-017-0159-4Tawny-OWLDocument-centricOntologyExcel workflow |
| spellingShingle | Aisha Blfgeh Jennifer Warrender Catharien M. U. Hilkens Phillip Lord A document-centric approach for developing the tolAPC ontology Journal of Biomedical Semantics Tawny-OWL Document-centric Ontology Excel workflow |
| title | A document-centric approach for developing the tolAPC ontology |
| title_full | A document-centric approach for developing the tolAPC ontology |
| title_fullStr | A document-centric approach for developing the tolAPC ontology |
| title_full_unstemmed | A document-centric approach for developing the tolAPC ontology |
| title_short | A document-centric approach for developing the tolAPC ontology |
| title_sort | document centric approach for developing the tolapc ontology |
| topic | Tawny-OWL Document-centric Ontology Excel workflow |
| url | http://link.springer.com/article/10.1186/s13326-017-0159-4 |
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