Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill's critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative.
{"title":"Ontological realism: A methodology for coordinated evolution of scientific ontologies.","authors":"Barry Smith, Werner Ceusters","doi":"10.3233/AO-2010-0079","DOIUrl":"10.3233/AO-2010-0079","url":null,"abstract":"<p><p>Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill's critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative.</p>","PeriodicalId":49238,"journal":{"name":"Applied Ontology","volume":"5 3-4","pages":"139-188"},"PeriodicalIF":1.0,"publicationDate":"2010-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3104413/pdf/nihms-294028.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29910865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This article presents a formal ontology which accounts for the general nature of artefacts. The objective is to help structure application ontologies in areas where specific artefacts are present -...
本文提出了一个形式本体，它解释了工件的一般性质。目标是帮助在存在特定工件的领域构建应用程序本体-…
{"title":"A formal ontology of artefacts","authors":"KasselGilles","doi":"10.5555/1889917.1889918","DOIUrl":"https://doi.org/10.5555/1889917.1889918","url":null,"abstract":"This article presents a formal ontology which accounts for the general nature of artefacts. The objective is to help structure application ontologies in areas where specific artefacts are present -...","PeriodicalId":49238,"journal":{"name":"Applied Ontology","volume":"1 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2010-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71124042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Natalya F Noy, Sherri de Coronado, Harold Solbrig, Gilberto Fragoso, Frank W Hartel, Mark A Musen
The National Cancer Institute's (NCI) Thesaurus is a biomedical reference ontology. The NCI Thesaurus is represented using Description Logic, more specifically Ontylog, a Description logic implemented by Apelon, Inc. We are exploring the use of the DL species of the Web Ontology Language (OWL DL)-a W3C recommended standard for ontology representation-instead of Ontylog for representing the NCI Thesaurus. We have studied the requirements for knowledge representation of the NCI Thesaurus, and considered how OWL DL (and its implementation in Protégé-OWL) satisfies these requirements. In this paper, we discuss the areas where OWL DL was sufficient for representing required components, where tool support that would hide some of the complexity and extra levels of indirection would be required, and where language expressiveness is not sufficient given the representation requirements. Because many of the knowledge-representation issues that we encountered are very similar to the issues in representing other biomedical terminologies and ontologies in general, we believe that the lessons that we learned and the approaches that we developed will prove useful and informative for other researchers.
{"title":"Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages.","authors":"Natalya F Noy, Sherri de Coronado, Harold Solbrig, Gilberto Fragoso, Frank W Hartel, Mark A Musen","doi":"10.3233/AO-2008-0051","DOIUrl":"https://doi.org/10.3233/AO-2008-0051","url":null,"abstract":"<p><p>The National Cancer Institute's (NCI) Thesaurus is a biomedical reference ontology. The NCI Thesaurus is represented using Description Logic, more specifically Ontylog, a Description logic implemented by Apelon, Inc. We are exploring the use of the DL species of the Web Ontology Language (OWL DL)-a W3C recommended standard for ontology representation-instead of Ontylog for representing the NCI Thesaurus. We have studied the requirements for knowledge representation of the NCI Thesaurus, and considered how OWL DL (and its implementation in Protégé-OWL) satisfies these requirements. In this paper, we discuss the areas where OWL DL was sufficient for representing required components, where tool support that would hide some of the complexity and extra levels of indirection would be required, and where language expressiveness is not sufficient given the representation requirements. Because many of the knowledge-representation issues that we encountered are very similar to the issues in representing other biomedical terminologies and ontologies in general, we believe that the lessons that we learned and the approaches that we developed will prove useful and informative for other researchers.</p>","PeriodicalId":49238,"journal":{"name":"Applied Ontology","volume":"3 3","pages":"173-190"},"PeriodicalIF":1.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3233/AO-2008-0051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40043922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
What is needed to enable communication about observation and measurement results in information systems? Information system ontologies make a certain conceptualization explicit and partially account for the meanings of symbols associated with this conceptualization. Yet, the meaning of signs denoting measurement results such as “10 m”, “red” or “high” cannot be specified with currently available ontologies. They fail to separate the ontological nature of some observable quality from the specification of how to observe and name the measurement result. We employ the foundational ontology DOLCE for characterizing the ontological nature of observable magnitudes. This involves dealing with ontological questions like “What kinds of observable qualities exist, in which entity does the observed quality inhere and how are the magnitudes of the observed quality structured?”. Then, in order to capture the semantic aspects of an observation result, we introduce semantic reference spaces, which help deal with semantic questions like “Do the signs “10 m”, “33 feet” or “shallow” have the same meaning? Do these signs refer to the same entity, e.g. the depth magnitude of a lake? How to establish a unit of measure?". We posit that the semantic questions can be approached efficiently only if agreement is reached on the ontological questions, and show that the specification of the meaning of signs denoting measurement results is enabled via the extension of the foundational ontology DOLCE with semantic reference spaces. This work was conducted while the author (Probst) was working at the Institute for Geoinformatics, University of Munster, Germany.
{"title":"Ontological foundations for conceptual modelling","authors":"Giancarlo Guizzardi, Terry A. Halpin","doi":"10.3233/AO-2008-0046","DOIUrl":"https://doi.org/10.3233/AO-2008-0046","url":null,"abstract":"What is needed to enable communication about observation and measurement results in information systems? Information system ontologies make a certain conceptualization explicit and partially account for the meanings of symbols associated with this conceptualization. Yet, the meaning of signs denoting measurement results such as “10 m”, “red” or “high” cannot be specified with currently available ontologies. They fail to separate the ontological nature of some observable quality from the specification of how to observe and name the measurement result. We employ the foundational ontology DOLCE for characterizing the ontological nature of observable magnitudes. This involves dealing with ontological questions like “What kinds of observable qualities exist, in which entity does the observed quality inhere and how are the magnitudes of the observed quality structured?”. Then, in order to capture the semantic aspects of an observation result, we introduce semantic reference spaces, which help deal with semantic questions like “Do the signs “10 m”, “33 feet” or “shallow” have the same meaning? Do these signs refer to the same entity, e.g. the depth magnitude of a lake? How to establish a unit of measure?\". We posit that the semantic questions can be approached efficiently only if agreement is reached on the ontological questions, and show that the specification of the meaning of signs denoting measurement results is enabled via the extension of the foundational ontology DOLCE with semantic reference spaces. This work was conducted while the author (Probst) was working at the Institute for Geoinformatics, University of Munster, Germany.","PeriodicalId":49238,"journal":{"name":"Applied Ontology","volume":"3 1","pages":"1-12"},"PeriodicalIF":1.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3233/AO-2008-0046","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69755761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Johanna Völker, Denny Vrandečić, York Sure, A. Hotho
OntoClean is an approach towards the formal evaluation of taxonomic relations in ontologies. The application of OntoClean consists of two main steps. First, concepts are tagged according to meta-properties known as rigidity, unity, dependency and identity. Second, the tagged concepts are checked according to predefined constraints to discover taxonomic errors. Although OntoClean is well documented in numerous publications, it is still used rather infrequently due to the high costs of application. Especially, the manual tagging of concepts with the correct meta-properties requires substantial efforts of highly experienced ontology engineers. In order to facilitate the use of OntoClean and to enable the evaluation of real-world ontologies, we provide AEON, a tool which automatically tags concepts with appropriate OntoClean meta-properties and performs the constraint checking. We use the Web as an embodiment of world knowledge, where we search for patterns that indicate how to properly tag concepts. We thoroughly evaluated our approach against a manually created gold standard. The evaluation shows the competitiveness of our approach while at the same time significantly lowering the costs. All of our results, i.e. the tool AEON as well as the experiment data, are publicly available.
{"title":"AEON --An approach to the automatic evaluation of ontologies","authors":"Johanna Völker, Denny Vrandečić, York Sure, A. Hotho","doi":"10.3233/AO-2008-0048","DOIUrl":"https://doi.org/10.3233/AO-2008-0048","url":null,"abstract":"OntoClean is an approach towards the formal evaluation of taxonomic relations in ontologies. The application of OntoClean consists of two main steps. First, concepts are tagged according to meta-properties known as rigidity, unity, dependency and identity. Second, the tagged concepts are checked according to predefined constraints to discover taxonomic errors. Although OntoClean is well documented in numerous publications, it is still used rather infrequently due to the high costs of application. Especially, the manual tagging of concepts with the correct meta-properties requires substantial efforts of highly experienced ontology engineers. In order to facilitate the use of OntoClean and to enable the evaluation of real-world ontologies, we provide AEON, a tool which automatically tags concepts with appropriate OntoClean meta-properties and performs the constraint checking. We use the Web as an embodiment of world knowledge, where we search for patterns that indicate how to properly tag concepts. We thoroughly evaluated our approach against a manually created gold standard. The evaluation shows the competitiveness of our approach while at the same time significantly lowering the costs. All of our results, i.e. the tool AEON as well as the experiment data, are publicly available.","PeriodicalId":49238,"journal":{"name":"Applied Ontology","volume":"3 1","pages":"41-62"},"PeriodicalIF":1.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3233/AO-2008-0048","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69755819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Role is a commonly used concept in software development, but a concept with divergent definitions. This paper discusses the characteristics of roles in software organizations, and contrasts such or...
{"title":"Roles, players and adaptable organizations","authors":"ColmanAlan, Han-jun","doi":"10.5555/1412401.1412404","DOIUrl":"https://doi.org/10.5555/1412401.1412404","url":null,"abstract":"Role is a commonly used concept in software development, but a concept with divergent definitions. This paper discusses the characteristics of roles in software organizations, and contrasts such or...","PeriodicalId":49238,"journal":{"name":"Applied Ontology","volume":"31 11 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2007-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71117493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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