Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies
•OwlReady is an ontology-oriented programming module for Python.•It provides automatic classification and high level constructs inspired by medical ontologies.•It has a specific syntax for manipulating classes and role-filler constructs.•It supports some form of local closed world reasoning.•These f...
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| Published in | Artificial intelligence in medicine Vol. 80; pp. 11 - 28 |
|---|---|
| Main Author | |
| Format | Journal Article |
| Language | English |
| Published |
Netherlands
Elsevier B.V
01.07.2017
Elsevier |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0933-3657 1873-2860 1873-2860 |
| DOI | 10.1016/j.artmed.2017.07.002 |
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| Abstract | •OwlReady is an ontology-oriented programming module for Python.•It provides automatic classification and high level constructs inspired by medical ontologies.•It has a specific syntax for manipulating classes and role-filler constructs.•It supports some form of local closed world reasoning.•These features have been useful for reasoning on drug contraindications.
Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies.
From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated “role-filler” constraints. We also propose an algorithm for performing local closed world reasoning in simple situations.
We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning.
Owlready has been successfully used in a medical research project. It has been published as Open-Source software and then used by many other researchers. Future developments will focus on the support of vagueness and additional non-monotonic reasoning feature, and automatic dialog box generation. |
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| AbstractList | Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies.
From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated "role-filler" constraints. We also propose an algorithm for performing local closed world reasoning in simple situations.
We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning.
Owlready has been successfully used in a medical research project. It has been published as Open-Source software and then used by many other researchers. Future developments will focus on the support of vagueness and additional non-monotonic reasoning feature, and automatic dialog box generation. Objective: Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies. Methods: From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated " role-filler " constraints. We also propose an algorithm for performing local closed world reasoning in simple situations. Results: We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning. Conclusion: Owlready has been successfully used in a medical research project. It has been published as Open-Source software and then used by many other researchers. Future developments will focus on the support of vagueness and additional non-monotonic reasoning feature, and automatic dialog box generation. Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies.OBJECTIVEOntologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies.From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated "role-filler" constraints. We also propose an algorithm for performing local closed world reasoning in simple situations.METHODSFrom our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated "role-filler" constraints. We also propose an algorithm for performing local closed world reasoning in simple situations.We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning.RESULTSWe developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning.Owlready has been successfully used in a medical research project. It has been published as Open-Source software and then used by many other researchers. Future developments will focus on the support of vagueness and additional non-monotonic reasoning feature, and automatic dialog box generation.CONCLUSIONOwlready has been successfully used in a medical research project. It has been published as Open-Source software and then used by many other researchers. Future developments will focus on the support of vagueness and additional non-monotonic reasoning feature, and automatic dialog box generation. •OwlReady is an ontology-oriented programming module for Python.•It provides automatic classification and high level constructs inspired by medical ontologies.•It has a specific syntax for manipulating classes and role-filler constructs.•It supports some form of local closed world reasoning.•These features have been useful for reasoning on drug contraindications. Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies. From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated “role-filler” constraints. We also propose an algorithm for performing local closed world reasoning in simple situations. We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning. Owlready has been successfully used in a medical research project. It has been published as Open-Source software and then used by many other researchers. Future developments will focus on the support of vagueness and additional non-monotonic reasoning feature, and automatic dialog box generation. |
| Author | Lamy, Jean-Baptiste |
| Author_xml | – sequence: 1 givenname: Jean-Baptiste surname: Lamy fullname: Lamy, Jean-Baptiste email: jibalamy@free.fr organization: LIMICS, Université Paris 13, Sorbonne Paris Cité, 93017 Bobigny, INSERM UMRS 1142, UPMC Université Paris 6, Sorbonne Universités, Paris, France |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28818520$$D View this record in MEDLINE/PubMed https://hal.science/hal-01592746$$DView record in HAL |
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| Cites_doi | 10.1007/3-540-45331-8_5 10.1007/11836025_27 10.1613/jair.3872 10.1613/jair.2811 10.1007/978-3-540-39718-2_54 10.1371/journal.pmed.1000352 10.1016/j.jbi.2003.11.007 10.1145/1806907.1806914 10.1016/j.jbi.2005.11.006 10.1038/nbt1346 10.1016/j.jbi.2017.04.019 10.1016/j.jacc.2016.03.600 10.1111/j.1365-2125.2001.01332.x 10.1016/j.ijar.2011.05.003 10.1145/1754399.1754403 10.1613/jair.2763 10.1007/s10489-006-8511-x 10.1093/fampra/20.1.61 10.1186/s13326-015-0035-z 10.1016/S1007-0214(10)70117-6 10.1093/nar/gkm883 10.1109/ICSC.2016.53 10.3233/SW-2011-0025 10.1016/j.jbi.2009.03.003 10.1016/j.artint.2011.01.007 10.1186/1472-6947-8-S1-S8 10.1016/j.artmed.2016.04.003 |
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| Keywords | Semantic web Automatic classification Biomedical ontology Local closed world reasoning OWL Ontology-oriented programming |
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| References | Koide, Aasman, Haflich (bib0120) 2005 Bock, Fokoue, Haase, Hoekstra, Horrocks, Ruttenberg, Sattler, Smith (bib0010) 2012 Lamy, Venot, Duclos (bib0215) 2015; 210 Grimm, Motik (bib0185) 2005 Curé (bib0070) 2012; 4 Krishnadhi, Sengupta, Hitzler (bib0200) 2011 Denecker, Cortés-calabuig, Bruynooghe, Arieli (bib0210) 2010; 35 The Gene Ontology Consortium (bib0040) 2008; 36 Kollia, Glimm (bib0105) 2013; 48 Grimm, Motik, Preist (bib0170) 2006 Patel, Cimino, Dolby, Fokoue, Kalyanpur, Kershenbaum, Ma, Schonberg, Srinivas (bib0080) 2007 Bonatti, Lutz, Wolter (bib0245) 2009; 35 Lamy, Berthelot, Favre, Ugon, Duclos, Venot (bib0240) 2017; 71 McGettigan, Golden, Fryer, Chan, Feely (bib0230) 2000; 51 Doherty, Lukaszewicz, Szalas (bib0175) 2000; 1904 Lamy (bib0065) 2016; 221 Grasso, Joshi, Siegel (bib0260) 2016 Sheridan, Julian (bib0075) 2016; 68 Motik, Shearer, Horrocks (bib0055) 2009; 36 Motik, Horrocks, Sattler (bib0180) 2007 Spurling, Mansfield, Montgomery, Lexchin, Doust, Othman, Vitry (bib0235) 2010; 7 Burgun, Bodenreider, Mougin (bib0085) 2005 Hustadt (bib0165) 1994 Schulz, Jansen (bib0095) 2013 Rector, Horridge, Iannone, Drummond (bib0060) 2008 Bobillo, Straccia (bib0275) 2011; 52 Keet (bib0250) 2017 (bib0100) 2008 Horridge, Bechhofer (bib0110) 2011; 2 Levin, Cowell (bib0115) 2015; 6 Yu (bib0020) 2006; 39 Detwiler, Mejino, Brinkley (bib0050) 2016; 69 Rector, Rogers, Pole (bib0030) 1996 Stevenson, Dobson (bib0160) 2011 Ren, Pan, Zhao (bib0205) 2010; 15 Babik, Hluchy (bib0150) 2006 Rosse, V. Mejino (bib0045) 2003; 36 Goldman (bib0140) 2003 Lassila, Webick (bib0015) 1999 Kalyanpur, Pastor, Battle, Padget (bib0130) 2004 Zhao, Huang, Tian, Wu (bib0265) 2017 Prosser, Almond, Walley (bib0225) 2003; 20 Knublauch, Oberle, Tetlow, Wallace (bib0125) 2006 Knorr, Alferes, Hitzler (bib0195) 2011; 175 Guarino, Oberle, Staab (bib0005) 2009 Rudolph, Krötzsch, Hitzler (bib0090) 2008 Motik, Rosati (bib0190) 2010; 57 Keet, Xakaza, Khumalo (bib0255) 2017 Héja, Surján, Varga (bib0035) 2008; 8 Koide, Takeda (bib0145) 2006; 4185 Calegari, Ciucci (bib0270) 2007; 4578 Zimmermann (bib0135) 2009 Clark, McCabe (bib0155) 2006; 24 Smith, Ashburner, Rosse, Bard, Bug, Ceusters, Goldberg, Eilbeck, Ireland, Mungall, Leontis, Rocca-Serra, Ruttenberg, Sansone, Scheuermann, Shah, Whetzel, Lewis (bib0025) 2007; 25 Zhu, Fan, Baorto, Weng, Cimino (bib0220) 2009; 42 Schulz (10.1016/j.artmed.2017.07.002_bib0095) 2013 Grimm (10.1016/j.artmed.2017.07.002_bib0170) 2006 Bonatti (10.1016/j.artmed.2017.07.002_bib0245) 2009; 35 Knublauch (10.1016/j.artmed.2017.07.002_bib0125) 2006 Keet (10.1016/j.artmed.2017.07.002_bib0250) 2017 Levin (10.1016/j.artmed.2017.07.002_bib0115) 2015; 6 Ren (10.1016/j.artmed.2017.07.002_bib0205) 2010; 15 Patel (10.1016/j.artmed.2017.07.002_bib0080) 2007 Bobillo (10.1016/j.artmed.2017.07.002_bib0275) 2011; 52 Babik (10.1016/j.artmed.2017.07.002_bib0150) 2006 Calegari (10.1016/j.artmed.2017.07.002_bib0270) 2007; 4578 Lamy (10.1016/j.artmed.2017.07.002_bib0065) 2016; 221 Krishnadhi (10.1016/j.artmed.2017.07.002_bib0200) 2011 Motik (10.1016/j.artmed.2017.07.002_bib0190) 2010; 57 Kalyanpur (10.1016/j.artmed.2017.07.002_bib0130) 2004 Lamy (10.1016/j.artmed.2017.07.002_bib0215) 2015; 210 Héja (10.1016/j.artmed.2017.07.002_bib0035) 2008; 8 Zhu (10.1016/j.artmed.2017.07.002_bib0220) 2009; 42 The Gene Ontology Consortium (10.1016/j.artmed.2017.07.002_bib0040) 2008; 36 Knorr (10.1016/j.artmed.2017.07.002_bib0195) 2011; 175 Grasso (10.1016/j.artmed.2017.07.002_bib0260) 2016 Rosse (10.1016/j.artmed.2017.07.002_bib0045) 2003; 36 Zimmermann (10.1016/j.artmed.2017.07.002_bib0135) 2009 Rector (10.1016/j.artmed.2017.07.002_bib0060) 2008 Denecker (10.1016/j.artmed.2017.07.002_bib0210) 2010; 35 Motik (10.1016/j.artmed.2017.07.002_bib0055) 2009; 36 Motik (10.1016/j.artmed.2017.07.002_bib0180) 2007 Lassila (10.1016/j.artmed.2017.07.002_bib0015) 1999 Sheridan (10.1016/j.artmed.2017.07.002_bib0075) 2016; 68 Kollia (10.1016/j.artmed.2017.07.002_bib0105) 2013; 48 (10.1016/j.artmed.2017.07.002_bib0100) 2008 Keet (10.1016/j.artmed.2017.07.002_bib0255) 2017 Zhao (10.1016/j.artmed.2017.07.002_bib0265) 2017 Stevenson (10.1016/j.artmed.2017.07.002_bib0160) 2011 Guarino (10.1016/j.artmed.2017.07.002_bib0005) 2009 Burgun (10.1016/j.artmed.2017.07.002_bib0085) 2005 Grimm (10.1016/j.artmed.2017.07.002_bib0185) 2005 Spurling (10.1016/j.artmed.2017.07.002_bib0235) 2010; 7 Curé (10.1016/j.artmed.2017.07.002_bib0070) 2012; 4 Clark (10.1016/j.artmed.2017.07.002_bib0155) 2006; 24 Lamy (10.1016/j.artmed.2017.07.002_bib0240) 2017; 71 Hustadt (10.1016/j.artmed.2017.07.002_bib0165) 1994 Bock (10.1016/j.artmed.2017.07.002_bib0010) 2012 Rudolph (10.1016/j.artmed.2017.07.002_bib0090) 2008 Horridge (10.1016/j.artmed.2017.07.002_bib0110) 2011; 2 Koide (10.1016/j.artmed.2017.07.002_bib0120) 2005 Goldman (10.1016/j.artmed.2017.07.002_bib0140) 2003 Detwiler (10.1016/j.artmed.2017.07.002_bib0050) 2016; 69 Prosser (10.1016/j.artmed.2017.07.002_bib0225) 2003; 20 McGettigan (10.1016/j.artmed.2017.07.002_bib0230) 2000; 51 Yu (10.1016/j.artmed.2017.07.002_bib0020) 2006; 39 Rector (10.1016/j.artmed.2017.07.002_bib0030) 1996 Koide (10.1016/j.artmed.2017.07.002_bib0145) 2006; 4185 Smith (10.1016/j.artmed.2017.07.002_bib0025) 2007; 25 Doherty (10.1016/j.artmed.2017.07.002_bib0175) 2000; 1904 |
| References_xml | – volume: 221 start-page: 64 year: 2016 end-page: 68 ident: bib0065 article-title: Ontology-oriented programming for biomedical informatics publication-title: Stud Health Technol Inform – volume: 1904 start-page: 49 year: 2000 end-page: 58 ident: bib0175 article-title: Efficient reasoning using the local closed-world assumption, international conference on artificial intelligence: methodology, systems, and applications (AIMSA) publication-title: Lecture notes in computer science – volume: 48 start-page: 253 year: 2013 end-page: 303 ident: bib0105 article-title: Optimizing SPARQL query answering over OWL ontologies publication-title: J Artif Intell Res – year: 2008 ident: bib0100 article-title: SPARQL query language for RDF, W3C recommendation – volume: 24 start-page: 3 year: 2006 end-page: 37 ident: bib0155 article-title: Ontology oriented programming in Go publication-title: Appl Intell – start-page: 98 year: 2004 end-page: 103 ident: bib0130 article-title: Automatic mapping of OWL ontologies into Java publication-title: Proceedings of the sixteenth international conference on software engineering & knowledge engineering (SEKE’2004) – volume: 68 start-page: 204 year: 2016 end-page: 213 ident: bib0075 article-title: Achievements and limitations of evidence-based medicine publication-title: J Am Coll Cardiol – year: 2005 ident: bib0185 article-title: Closed world reasoning in the semantic web through epistemic operators publication-title: Proceedings of the OWLED 2005 workshop on OWL: experiences and directions – volume: 51 start-page: 184 year: 2000 end-page: 189 ident: bib0230 article-title: Prescribers prefer people: the sources of information used by doctors for prescribing suggest that the medium is more important than the message publication-title: Br J Clin Pharmacol – volume: 8 start-page: 8 year: 2008 ident: bib0035 article-title: Ontological analysis of SNOMED CT publication-title: BMC Med Inform Decis Mak – volume: 35 start-page: 717 year: 2009 end-page: 773 ident: bib0245 article-title: The complexity of circumscription in description logic publication-title: J Artif Intell Res – start-page: 91 year: 2005 end-page: 95 ident: bib0085 article-title: Classifying diseases with respect to anatomy: a study in SNOMED CT. publication-title: AMIA Annu Symp Proc – start-page: 1 year: 2005 end-page: 15 ident: bib0120 article-title: OWL vs. object oriented programming publication-title: the 4th international semantic web conference (ISWC 2005), workshop on semantic web enabled software engineering (SWESE) – start-page: 58 year: 2017 end-page: 73 ident: bib0250 article-title: Representing and aligning similar relations: parts and wholes in isiZulu vs. English publication-title: Proceedings of the first international conference on language, data and knowledge, lecture notes in artificial intelligence, vol. 10318 – year: 2017 ident: bib0265 article-title: Knowledge system for helicopter transmission design based on ontology publication-title: Proceedings of the 2017 international conference on management engineering, software engineering and service sciences, vol. 321–325 – volume: 69 start-page: 12 year: 2016 end-page: 21 ident: bib0050 article-title: From frames to OWL2: converting the foundational model of anatomy publication-title: Artif Intell Med – year: 2009 ident: bib0135 article-title: OWL2Java: a java code generator for OWL – start-page: 24 year: 1994 end-page: 26 ident: bib0165 article-title: Do we need the closed-world assumption in knowledge representation publication-title: Working notes of the KI’94 workshop: reasoning about structured objects, knowledge representation meets databases (KRDB’94), vol. D-94-11 – year: 2016 ident: bib0260 article-title: Visualization of pain severity events in clinical records using semantic structures publication-title: IEEE tenth international conference on semantic computing (ICSC), vol. 321–324 – volume: 210 start-page: 924 year: 2015 end-page: 928 ident: bib0215 article-title: PyMedTermino: an open-source generic API for advanced terminology services publication-title: Stud Health Technol Inform – volume: 36 start-page: D440 year: 2008 end-page: D444 ident: bib0040 article-title: The gene ontology project in 2008 publication-title: Nucleic Acids Res – year: 2006 ident: bib0170 article-title: Matching semantic service descriptions with local closed-world reasoning publication-title: European semantic web conference, vol. 575–589 – volume: 25 start-page: 1251 year: 2007 end-page: 1255 ident: bib0025 article-title: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration publication-title: Nat Biotechnol – volume: 7 start-page: e1000352 year: 2010 ident: bib0235 article-title: Information from pharmaceutical companies and the quality, quantity, and cost of physicians’ prescribing: a systematic review publication-title: PLoS Med – volume: 35 start-page: 22 year: 2010 ident: bib0210 article-title: Towards a logical reconstruction of a theory for locally closed databases publication-title: ACM Trans Database Syst (TODS) – start-page: 850 year: 2003 end-page: 865 ident: bib0140 article-title: Ontology-oriented programming: static typing for the inconsistent programmer publication-title: Lecture notes in computer science: the SemanticWeb, ISWC, vol. 2870 – start-page: 132 year: 2013 end-page: 146 ident: bib0095 article-title: Formal ontologies in biomedical knowledge representation publication-title: Yearbook of medical informatics, vol. 8 – volume: 71 start-page: 58 year: 2017 end-page: 69 ident: bib0240 article-title: Using visual analytics for presenting comparative information on new drugs publication-title: J Biomed Inform – start-page: 1 year: 2006 end-page: 5 ident: bib0150 article-title: Deep integration of python with web ontology language publication-title: Proceedings of the 2nd workshop on scripting for the semantic web – year: 1996 ident: bib0030 article-title: The GALEN high level ontology publication-title: Fourteenth international congress of the European federation for medical informatics (MIE-96) – year: 2007 ident: bib0080 article-title: Ch. Matching patient records to clinical trials using ontologies publication-title: The semantic web, vol. 816–829 – volume: 15 start-page: 692 year: 2010 end-page: 701 ident: bib0205 article-title: Closed world reasoning for OWL2 with NBox publication-title: Tsinghua Sci Technol – start-page: 1 year: 2009 end-page: 17 ident: bib0005 article-title: Ch. What is an ontology? publication-title: Handbook on ontologies – volume: 4578 start-page: 118 year: 2007 end-page: 126 ident: bib0270 article-title: Fuzzy ontology, fuzzy description logics and fuzzy-OWL publication-title: International workshop on fuzzy logic and applications (WILF), lecture notes in computer science – volume: 42 start-page: 413 year: 2009 end-page: 425 ident: bib0220 article-title: A review of auditing methods applied to the content of controlled biomedical terminologies publication-title: J Biomed Inform – start-page: 425 year: 2011 end-page: 436 ident: bib0160 article-title: Sapphire: generating java runtime artefacts from OWL ontologies publication-title: Lecture notes in business information processing, advanced information systems engineering workshops, vol. 83 – volume: 4 start-page: 20 year: 2012 ident: bib0070 article-title: Improving the data quality of drug databases using conditional dependencies and ontologies publication-title: J Data Inf Qual – year: 2008 ident: bib0090 article-title: All elephants are bigger than all mice, technical report – year: 2012 ident: bib0010 article-title: OWL 2 web ontology language, W3C recommendation – volume: 36 start-page: 165 year: 2009 end-page: 228 ident: bib0055 article-title: Hypertableau reasoning for description logics publication-title: J Artif Intell Res – volume: 20 start-page: 61 year: 2003 end-page: 68 ident: bib0225 article-title: Influences on GPs’ decision to prescribe new drugs-the importance of who says what publication-title: Fam Pract – volume: 6 start-page: 35 year: 2015 ident: bib0115 article-title: owlcpp: a C++ library for working with OWL ontologies publication-title: J Biomed Semant – year: 1999 ident: bib0015 article-title: Resource Description Framework (RDF) model and syntax specification, W3C recommendation – volume: 2 start-page: 11 year: 2011 end-page: 21 ident: bib0110 article-title: The OWL API: a java API for OWL ontologies publication-title: Semant Web – volume: 39 start-page: 252 year: 2006 end-page: 266 ident: bib0020 article-title: Methods in biomedical ontology publication-title: J Biomed Inform – volume: 175 start-page: 1528 year: 2011 end-page: 1554 ident: bib0195 article-title: Local closed world reasoning with description logics under the well-founded semantics publication-title: Artif Intell – year: 2017 ident: bib0255 article-title: Verbalising OWL ontologies in isiZulu with Python publication-title: Demo at the 14th extended semantic web conference (ESWC17) – year: 2008 ident: bib0060 article-title: Use cases for building OWL ontologies as modules: localizing, ontology and programming interfaces & extensions publication-title: 4th int. workshop on semantic web enabled software engineering (SWESE-08) – volume: 52 start-page: 1073 year: 2011 end-page: 1094 ident: bib0275 article-title: Fuzzy ontology representation using OWL 2 publication-title: Int J Approx Reason – year: 2007 ident: bib0180 article-title: Adding integrity constraints to OWL publication-title: Proceedings of the OWLED 2007 workshop on OWL: experiences and directions – volume: 57 start-page: 93 year: 2010 end-page: 154 ident: bib0190 article-title: Reconciling description logics and rules publication-title: J ACM – volume: 4185 start-page: 263 year: 2006 end-page: 277 ident: bib0145 article-title: OWL-full reasoning from an object oriented perspective, lecture notes in computer science publication-title: ASWC 2006 – volume: 36 start-page: 478 year: 2003 end-page: 500 ident: bib0045 article-title: A reference ontology for biomedical informatics: the foundational model of anatomy publication-title: J Biomed Inform – year: 2011 ident: bib0200 article-title: Local closed world semantics: keep it simple, stupid!. publication-title: Proceedings of the 2011 international workshop on description logics (DL2011), vol. 745–756 – year: 2006 ident: bib0125 article-title: A semantic web primer for object-oriented software developers, W3C working group note – year: 2009 ident: 10.1016/j.artmed.2017.07.002_bib0135 – year: 2005 ident: 10.1016/j.artmed.2017.07.002_bib0185 article-title: Closed world reasoning in the semantic web through epistemic operators – volume: 1904 start-page: 49 year: 2000 ident: 10.1016/j.artmed.2017.07.002_bib0175 article-title: Efficient reasoning using the local closed-world assumption, international conference on artificial intelligence: methodology, systems, and applications (AIMSA) publication-title: Lecture notes in computer science doi: 10.1007/3-540-45331-8_5 – volume: 4185 start-page: 263 year: 2006 ident: 10.1016/j.artmed.2017.07.002_bib0145 article-title: OWL-full reasoning from an object oriented perspective, lecture notes in computer science publication-title: ASWC 2006 doi: 10.1007/11836025_27 – year: 2008 ident: 10.1016/j.artmed.2017.07.002_bib0100 – volume: 48 start-page: 253 year: 2013 ident: 10.1016/j.artmed.2017.07.002_bib0105 article-title: Optimizing SPARQL query answering over OWL ontologies publication-title: J Artif Intell Res doi: 10.1613/jair.3872 – volume: 36 start-page: 165 year: 2009 ident: 10.1016/j.artmed.2017.07.002_bib0055 article-title: Hypertableau reasoning for description logics publication-title: J Artif Intell Res doi: 10.1613/jair.2811 – start-page: 850 year: 2003 ident: 10.1016/j.artmed.2017.07.002_bib0140 article-title: Ontology-oriented programming: static typing for the inconsistent programmer publication-title: Lecture notes in computer science: the SemanticWeb, ISWC, vol. 2870 doi: 10.1007/978-3-540-39718-2_54 – volume: 7 start-page: e1000352 issue: 10 year: 2010 ident: 10.1016/j.artmed.2017.07.002_bib0235 article-title: Information from pharmaceutical companies and the quality, quantity, and cost of physicians’ prescribing: a systematic review publication-title: PLoS Med doi: 10.1371/journal.pmed.1000352 – start-page: 91 year: 2005 ident: 10.1016/j.artmed.2017.07.002_bib0085 article-title: Classifying diseases with respect to anatomy: a study in SNOMED CT. publication-title: AMIA Annu Symp Proc – year: 2008 ident: 10.1016/j.artmed.2017.07.002_bib0090 – volume: 36 start-page: 478 year: 2003 ident: 10.1016/j.artmed.2017.07.002_bib0045 article-title: A reference ontology for biomedical informatics: the foundational model of anatomy publication-title: J Biomed Inform doi: 10.1016/j.jbi.2003.11.007 – volume: 35 start-page: 22 issue: 3 year: 2010 ident: 10.1016/j.artmed.2017.07.002_bib0210 article-title: Towards a logical reconstruction of a theory for locally closed databases publication-title: ACM Trans Database Syst (TODS) doi: 10.1145/1806907.1806914 – volume: 39 start-page: 252 issue: 3 year: 2006 ident: 10.1016/j.artmed.2017.07.002_bib0020 article-title: Methods in biomedical ontology publication-title: J Biomed Inform doi: 10.1016/j.jbi.2005.11.006 – start-page: 98 year: 2004 ident: 10.1016/j.artmed.2017.07.002_bib0130 article-title: Automatic mapping of OWL ontologies into Java publication-title: Proceedings of the sixteenth international conference on software engineering & knowledge engineering (SEKE’2004) – year: 2011 ident: 10.1016/j.artmed.2017.07.002_bib0200 article-title: Local closed world semantics: keep it simple, stupid!. publication-title: Proceedings of the 2011 international workshop on description logics (DL2011), vol. 745–756 – year: 2006 ident: 10.1016/j.artmed.2017.07.002_bib0170 article-title: Matching semantic service descriptions with local closed-world reasoning – year: 1999 ident: 10.1016/j.artmed.2017.07.002_bib0015 – start-page: 24 year: 1994 ident: 10.1016/j.artmed.2017.07.002_bib0165 article-title: Do we need the closed-world assumption in knowledge representation publication-title: Working notes of the KI’94 workshop: reasoning about structured objects, knowledge representation meets databases (KRDB’94), vol. D-94-11 – volume: 25 start-page: 1251 issue: 11 year: 2007 ident: 10.1016/j.artmed.2017.07.002_bib0025 article-title: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration publication-title: Nat Biotechnol doi: 10.1038/nbt1346 – volume: 71 start-page: 58 year: 2017 ident: 10.1016/j.artmed.2017.07.002_bib0240 article-title: Using visual analytics for presenting comparative information on new drugs publication-title: J Biomed Inform doi: 10.1016/j.jbi.2017.04.019 – start-page: 1 year: 2009 ident: 10.1016/j.artmed.2017.07.002_bib0005 article-title: Ch. What is an ontology? – volume: 68 start-page: 204 issue: 2 year: 2016 ident: 10.1016/j.artmed.2017.07.002_bib0075 article-title: Achievements and limitations of evidence-based medicine publication-title: J Am Coll Cardiol doi: 10.1016/j.jacc.2016.03.600 – volume: 51 start-page: 184 year: 2000 ident: 10.1016/j.artmed.2017.07.002_bib0230 article-title: Prescribers prefer people: the sources of information used by doctors for prescribing suggest that the medium is more important than the message publication-title: Br J Clin Pharmacol doi: 10.1111/j.1365-2125.2001.01332.x – volume: 52 start-page: 1073 issue: 7 year: 2011 ident: 10.1016/j.artmed.2017.07.002_bib0275 article-title: Fuzzy ontology representation using OWL 2 publication-title: Int J Approx Reason doi: 10.1016/j.ijar.2011.05.003 – year: 1996 ident: 10.1016/j.artmed.2017.07.002_bib0030 article-title: The GALEN high level ontology – year: 2007 ident: 10.1016/j.artmed.2017.07.002_bib0080 article-title: Ch. Matching patient records to clinical trials using ontologies – volume: 57 start-page: 93 issue: 5 year: 2010 ident: 10.1016/j.artmed.2017.07.002_bib0190 article-title: Reconciling description logics and rules publication-title: J ACM doi: 10.1145/1754399.1754403 – volume: 4578 start-page: 118 year: 2007 ident: 10.1016/j.artmed.2017.07.002_bib0270 article-title: Fuzzy ontology, fuzzy description logics and fuzzy-OWL publication-title: International workshop on fuzzy logic and applications (WILF), lecture notes in computer science – volume: 35 start-page: 717 year: 2009 ident: 10.1016/j.artmed.2017.07.002_bib0245 article-title: The complexity of circumscription in description logic publication-title: J Artif Intell Res doi: 10.1613/jair.2763 – volume: 4 start-page: 20 issue: 1 year: 2012 ident: 10.1016/j.artmed.2017.07.002_bib0070 article-title: Improving the data quality of drug databases using conditional dependencies and ontologies publication-title: J Data Inf Qual – volume: 24 start-page: 3 year: 2006 ident: 10.1016/j.artmed.2017.07.002_bib0155 article-title: Ontology oriented programming in Go publication-title: Appl Intell doi: 10.1007/s10489-006-8511-x – year: 2017 ident: 10.1016/j.artmed.2017.07.002_bib0265 article-title: Knowledge system for helicopter transmission design based on ontology – start-page: 1 year: 2005 ident: 10.1016/j.artmed.2017.07.002_bib0120 article-title: OWL vs. object oriented programming publication-title: the 4th international semantic web conference (ISWC 2005), workshop on semantic web enabled software engineering (SWESE) – volume: 20 start-page: 61 issue: 1 year: 2003 ident: 10.1016/j.artmed.2017.07.002_bib0225 article-title: Influences on GPs’ decision to prescribe new drugs-the importance of who says what publication-title: Fam Pract doi: 10.1093/fampra/20.1.61 – volume: 221 start-page: 64 year: 2016 ident: 10.1016/j.artmed.2017.07.002_bib0065 article-title: Ontology-oriented programming for biomedical informatics publication-title: Stud Health Technol Inform – volume: 6 start-page: 35 year: 2015 ident: 10.1016/j.artmed.2017.07.002_bib0115 article-title: owlcpp: a C++ library for working with OWL ontologies publication-title: J Biomed Semant doi: 10.1186/s13326-015-0035-z – start-page: 58 year: 2017 ident: 10.1016/j.artmed.2017.07.002_bib0250 article-title: Representing and aligning similar relations: parts and wholes in isiZulu vs. English – year: 2006 ident: 10.1016/j.artmed.2017.07.002_bib0125 – volume: 15 start-page: 692 issue: 6 year: 2010 ident: 10.1016/j.artmed.2017.07.002_bib0205 article-title: Closed world reasoning for OWL2 with NBox publication-title: Tsinghua Sci Technol doi: 10.1016/S1007-0214(10)70117-6 – start-page: 132 year: 2013 ident: 10.1016/j.artmed.2017.07.002_bib0095 article-title: Formal ontologies in biomedical knowledge representation – volume: 36 start-page: D440 issue: Database issue year: 2008 ident: 10.1016/j.artmed.2017.07.002_bib0040 article-title: The gene ontology project in 2008 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkm883 – year: 2016 ident: 10.1016/j.artmed.2017.07.002_bib0260 article-title: Visualization of pain severity events in clinical records using semantic structures publication-title: IEEE tenth international conference on semantic computing (ICSC), vol. 321–324 doi: 10.1109/ICSC.2016.53 – year: 2017 ident: 10.1016/j.artmed.2017.07.002_bib0255 article-title: Verbalising OWL ontologies in isiZulu with Python publication-title: Demo at the 14th extended semantic web conference (ESWC17) – volume: 2 start-page: 11 year: 2011 ident: 10.1016/j.artmed.2017.07.002_bib0110 article-title: The OWL API: a java API for OWL ontologies publication-title: Semant Web doi: 10.3233/SW-2011-0025 – volume: 42 start-page: 413 issue: 3 year: 2009 ident: 10.1016/j.artmed.2017.07.002_bib0220 article-title: A review of auditing methods applied to the content of controlled biomedical terminologies publication-title: J Biomed Inform doi: 10.1016/j.jbi.2009.03.003 – start-page: 1 year: 2006 ident: 10.1016/j.artmed.2017.07.002_bib0150 article-title: Deep integration of python with web ontology language – start-page: 425 year: 2011 ident: 10.1016/j.artmed.2017.07.002_bib0160 article-title: Sapphire: generating java runtime artefacts from OWL ontologies publication-title: Lecture notes in business information processing, advanced information systems engineering workshops, vol. 83 – volume: 175 start-page: 1528 year: 2011 ident: 10.1016/j.artmed.2017.07.002_bib0195 article-title: Local closed world reasoning with description logics under the well-founded semantics publication-title: Artif Intell doi: 10.1016/j.artint.2011.01.007 – year: 2012 ident: 10.1016/j.artmed.2017.07.002_bib0010 – volume: 8 start-page: 8 issue: Suppl. 1 year: 2008 ident: 10.1016/j.artmed.2017.07.002_bib0035 article-title: Ontological analysis of SNOMED CT publication-title: BMC Med Inform Decis Mak doi: 10.1186/1472-6947-8-S1-S8 – year: 2008 ident: 10.1016/j.artmed.2017.07.002_bib0060 article-title: Use cases for building OWL ontologies as modules: localizing, ontology and programming interfaces & extensions publication-title: 4th int. workshop on semantic web enabled software engineering (SWESE-08) – year: 2007 ident: 10.1016/j.artmed.2017.07.002_bib0180 article-title: Adding integrity constraints to OWL – volume: 210 start-page: 924 year: 2015 ident: 10.1016/j.artmed.2017.07.002_bib0215 article-title: PyMedTermino: an open-source generic API for advanced terminology services publication-title: Stud Health Technol Inform – volume: 69 start-page: 12 year: 2016 ident: 10.1016/j.artmed.2017.07.002_bib0050 article-title: From frames to OWL2: converting the foundational model of anatomy publication-title: Artif Intell Med doi: 10.1016/j.artmed.2016.04.003 |
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| Snippet | •OwlReady is an ontology-oriented programming module for Python.•It provides automatic classification and high level constructs inspired by medical... Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been... Objective: Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions... |
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| SubjectTerms | Artificial Intelligence Automatic classification Biological Ontologies Biomedical ontology Computer Science Gene Ontology Humans Life Sciences Local closed world reasoning Ontology-oriented programming OWL Programming Languages Santé publique et épidémiologie Semantic web Software |
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| Title | Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies |
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