BFO-Based Data and Information Ontologies: Difference between revisions
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'''The Information Artifact Ontology (IAO)''' | '''The Information Artifact Ontology (IAO)''' | ||
The Information Artifact Ontology (IAO) grew out of the Data Processing Branch of the [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851331/ Ontology for Biomedical Investigations (OBI)] in recognition of the need for domain‐neutral resource for the representation of types of information content entities (ICEs), that would apply to documents and data of all kinds, and not merely to information entities in the domain of biomedicine. IAO is based on the copying and aboutnessrelations: an information content entity is, roughly, an entity that can be copied (in the way, for example, that a gene sequence or a computer file can be copied) and that is about something. The aboutness relation itself has its roots in the mental realm -- an information content entity ''e'' is about something, again roughly speaking, in virtue of the fact that the mental acts which gave rise to or which are used to interpret or communicate with ''e'' are about something. | |||
: | '''Background Information''' | ||
::[ | :[http://www.ontobee.org/ontology/IAO Ontobee] | ||
:[https://github.com/information-artifact-ontology/IAO Github] | |||
:[http://www.obofoundry.org/ontology/iao.html OBO Foundry] | |||
:[http://www.ontobee.org/ontology/IAO?iri=http://purl.obolibrary.org/obo/IAO_0000003 Example IAO term: measurement unit label] | |||
:[https://github.com/obi-ontology/obi/wiki/Data-and-Values Data and values in the Ontology for Biomedical Investigations] | |||
:[https://www.nist.gov/system/files/documents/2019/05/30/nist-ai-rfi-cubrc_inc_003.pdf Modeling Information with the Common Core Ontologies (CCO)] | |||
'''Videos''' | |||
:[https://www.youtube.com/watch?v=PBKsupBquok Aboutness] | |||
:[https://www.youtube.com/watch?v=Jqqq7eBnZvE&list=PLyngZgIl3WTjK-D7L1pdtpqzxIBhjBsb_&index=1 Truth and the Ontology of Maps] | |||
:[https://www.youtube.com/watch?v=5chInYVVypI From Speech Acts to Document Acts] | |||
'''Articles''' | |||
:Werner Ceusters & Barry Smith, "[http://ceur-ws.org/Vol-1515/regular10.pdf Aboutness: Towards Foundations for the Information Artifact Ontology]", ''Proceedings of the Sixth International Conference on Biomedical Ontology (ICBO)'' (CEUR 1515), 2015. | |||
:Werner Ceusters & Barry Smith, "Aboutness: Towards Foundations for the Information Artifact Ontology", '' | |||
Proceedings of the Sixth International Conference on Biomedical Ontology (ICBO)'' (CEUR 1515), 2015 | |||
[ | :Barry Smith, Tatiana Malyuta, Ron Rudnicki, William Mandrick, David Salmen, Peter Morosoff, Danielle K. Duff, James Schoening & Kesny Parent, "[https://philpapers.org/archive/SMII-16.pdf IAO-Intel: An Ontology of Information Artifacts in the Intelligence Domain]", ''Proceedings of the Eighth International Conference on Semantic Technologies for Intelligence, Defense, and Security (STIDS)'', (CEUR 1097), 2013, 33-40. | ||
:Janna Hastings, Christopher Batchelor, Fabian Neuhaus, Christian Steinbeck, "[http://ceur-ws.org/Vol-833/paper26.pdf What's in an 'is about' link? Chemical diagrams and the Information Artifact Ontology]", ''Proceedings of the Second International Conference on Biomedical Ontology'' (ICBO) 2011. | |||
of | |||
:Mary Bone, Mark Blackburn, Benjamin Kruse, John Dzielski, Thomas Hagedorn and Ian Grosse, "[https://www.mdpi.com/2079-8954/6/4/46 Toward an Interoperability and Integration Framework to Enable Digital Thread]", ''Systems'', 2018, 6(4), 46; https://doi.org/10.3390/systems6040046. | :Mary Bone, Mark Blackburn, Benjamin Kruse, John Dzielski, Thomas Hagedorn and Ian Grosse, "[https://www.mdpi.com/2079-8954/6/4/46 Toward an Interoperability and Integration Framework to Enable Digital Thread]", ''Systems'', 2018, 6(4), 46; https://doi.org/10.3390/systems6040046. | ||
'''Examples of ontologies extending IAO''' | |||
IAO has been used as starting point for a large number of ontologies in the biomedical and bioinformatics domain. We list here some examples of direct or indirect reuse of IAO in non-biomedical fields. | |||
:[http://obofoundry.org/ontology/iao.html Information Artifact Ontology (IAO)] | |||
:[https://pdfs.semanticscholar.org/f424/b88d92bcc00ade3d61acede2ee8732301350.pdf Ceusters W. An information artifact ontology perspective on data collections and associated representational artifacts. Stud Health Technol Inform. 2012;180:68–72.] | :[https://pdfs.semanticscholar.org/f424/b88d92bcc00ade3d61acede2ee8732301350.pdf Ceusters W. An information artifact ontology perspective on data collections and associated representational artifacts. Stud Health Technol Inform. 2012;180:68–72.] | ||
:[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209884/ Barton, Adrien et al. “An ontological analysis of medical Bayesian indicators of performance.” Journal of biomedical semantics vol. 8,1 1. 3 Jan. 2017, doi:10.1186/s13326-016-0099-4] | :[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209884/ Barton, Adrien et al. “An ontological analysis of medical Bayesian indicators of performance.” Journal of biomedical semantics vol. 8,1 1. 3 Jan. 2017, doi:10.1186/s13326-016-0099-4] | ||
:[http://obofoundry.org/ontology/cheminf.html Chemical Information Ontology (CHEMINF)] | |||
:[https://www-spiedigitallibrary-org.gate.lib.buffalo.edu/conference-proceedings-of-spie/10635/106350F/A-common-core-based-cyber-ontology-in-support-of-cross/10.1117/12.2307719.full?SSO=1 Common Core Cyber Ontology (C3O)] | :[https://www-spiedigitallibrary-org.gate.lib.buffalo.edu/conference-proceedings-of-spie/10635/106350F/A-common-core-based-cyber-ontology-in-support-of-cross/10.1117/12.2307719.full?SSO=1 Common Core Cyber Ontology (C3O)] | ||
:[http://www.ncbi.nlm.nih.gov/pubmed/20543345 Communication Standards Ontology (CSO)] | :[http://www.ncbi.nlm.nih.gov/pubmed/20543345 Communication Standards Ontology (CSO)] | ||
:[https://bioportal.bioontology.org/ontologies/CDAO Comparative Data Analysis Ontology (CDAO)] | :[https://bioportal.bioontology.org/ontologies/CDAO Comparative Data Analysis Ontology (CDAO)] | ||
:[http://ceur-ws.org/Vol-833/paper25.pdf Conceptual Model Ontology (CMO)] | :[http://ceur-ws.org/Vol-833/paper25.pdf Conceptual Model Ontology (CMO)] | ||
:[https://www.researchgate.net/publication/263323866_Clinical_Data_Integration_Model_Core_Interoperability_Ontology_for_Research_Using_Primary_Care_Data Core Data Integration Model (CDIM)] | :[https://www.researchgate.net/publication/263323866_Clinical_Data_Integration_Model_Core_Interoperability_Ontology_for_Research_Using_Primary_Care_Data Core Data Integration Model (CDIM)] | ||
:[https://doi.org/10.3390/systems6040046 Decision Ontology] | :[https://doi.org/10.3390/systems6040046 Decision Ontology] | ||
:[https://code.google.com/p/d-acts Document Act Ontology (D-Acts)] | :[https://code.google.com/p/d-acts Document Act Ontology (D-Acts)] | ||
:[http://ncor.buffalo.edu/2013/STIDS/5-Email.pptx Email Ontology] | :[http://ncor.buffalo.edu/2013/STIDS/5-Email.pptx Email Ontology] | ||
:[https://lirias.kuleuven.be/bitstream/123456789/273222/1/sokd10.pdf Exposé: an ontology for data mining experiments] (see also :[https://www.researchgate.net/publication/228525536_Expose_An_ontology_for_data_mining_experiments here]) | |||
:[https://lirias.kuleuven.be/bitstream/123456789/273222/1/sokd10.pdf Exposé: an ontology for data mining experiments] (see also:[https://www.researchgate.net/publication/228525536_Expose_An_ontology_for_data_mining_experiments here]) | |||
:[https://arxiv.org/ftp/arxiv/papers/1805/1805.11050.pdf eXtended Formal Ontology (XFO)] | :[https://arxiv.org/ftp/arxiv/papers/1805/1805.11050.pdf eXtended Formal Ontology (XFO)] | ||
:[http://jamia.bmj.com/content/20/5/986.full General Information Model (GIM)] | :[http://jamia.bmj.com/content/20/5/986.full General Information Model (GIM)] | ||
:[https://ieeexplore.ieee.org/abstract/document/8795392 Information Security Domain (ISD) ontology] | :[https://ieeexplore.ieee.org/abstract/document/8795392 Information Security Domain (ISD) ontology] | ||
:[http://ceur-ws.org/Vol-2285/ICBO_2018_paper_59.pdf Informed Consent Ontology (ICO)] | :[http://ceur-ws.org/Vol-2285/ICBO_2018_paper_59.pdf Informed Consent Ontology (ICO)] | ||
:[https://onlinelibrary.wiley.com/doi/full/10.1002/lrh2.10054 Knowledge Object Reference Ontology (KORO)] | :[https://onlinelibrary.wiley.com/doi/full/10.1002/lrh2.10054 Knowledge Object Reference Ontology (KORO)] | ||
:[http://obofoundry.org/ontology/mf.html Mental Functioning Ontology (MF)] | :[http://obofoundry.org/ontology/mf.html Mental Functioning Ontology (MF)] | ||
:[http://obofoundry.org/ontology/obi.html Ontology for Biomedical Investigations (OBI)] | :[http://obofoundry.org/ontology/obi.html Ontology for Biomedical Investigations (OBI)] | ||
:[http://ceur-ws.org/Vol-2427/SEPDA_2019_paper_15.pdf Ontology for Documentation of Variable/Data Source Selection (ODVDS)] | :[http://ceur-ws.org/Vol-2427/SEPDA_2019_paper_15.pdf Ontology for Documentation of Variable/Data Source Selection (ODVDS)] | ||
:[http://www.ontodm.com/ Ontology of Data Mining (OntoDM)] | :[http://www.ontodm.com/ Ontology of Data Mining (OntoDM)] | ||
:[http://www.ontodt.com/ Ontology of Datatypes (OntoDT)] (see also :[http://www.sciencedirect.com/science/article/pii/S0020025515005800 here]) | |||
:[https://bioportal.bioontology.org/ontologies/OOEVV Ontology of Experimental Variables and Values (OOEVV)] | :[http://www.ontodt.com/ Ontology of Datatypes (OntoDT)] (see also:[http://www.sciencedirect.com/science/article/pii/S0020025515005800 here]) | ||
:[https://bioportal.bioontology.org/ontologies/OOEVV Ontology of Experimental Variables and Values (OOEVV)] (see also: [https://www.isi.edu/projects/kefed_ooevv/kefed_ooevv_technology here]) | |||
:[https://www.researchgate.net/publication/299534658_OntoforInfoScience_a_detailed_methodology_for_construction_of_ontologies_and_its_application_in_the_blood_domain Ontology for Information Science (OntoforInforScience)] | :[https://www.researchgate.net/publication/299534658_OntoforInfoScience_a_detailed_methodology_for_construction_of_ontologies_and_its_application_in_the_blood_domain Ontology for Information Science (OntoforInforScience)] | ||
:[http://www.sciencedirect.com.gate.lib.buffalo.edu/science/article/pii/S1570826815000165 Ontology-Based Data Access (OBDA)] | :[http://www.sciencedirect.com.gate.lib.buffalo.edu/science/article/pii/S1570826815000165 Ontology-Based Data Access (OBDA)] | ||
:[http://www.ncbi.nlm.nih.gov/pubmed/20460173 Ontology-Based eXtensible Data Model (OBX)] | :[http://www.ncbi.nlm.nih.gov/pubmed/20460173 Ontology-Based eXtensible Data Model (OBX)] | ||
:[http://www.sciencedirect.com/science/article/pii/S0952197615000913 Ontology-Driven Information System (ODIS) / Ontology-Driven Scenario Generator (ODSG)] | :[http://www.sciencedirect.com/science/article/pii/S0952197615000913 Ontology-Driven Information System (ODIS) / Ontology-Driven Scenario Generator (ODSG)] | ||
:[https://code.google.com/p/proper-name-ontology Proper Name Ontology (PNO)] | :[https://code.google.com/p/proper-name-ontology Proper Name Ontology (PNO)] | ||
:[http://cci.case.edu/cci/images/a/aa/Janus.pdf Provenir ontology for provenance modeling] | :[http://cci.case.edu/cci/images/a/aa/Janus.pdf Provenir ontology for provenance modeling] | ||
:[http://ceur-ws.org/Vol-1747/IT605_ICBO2016.pdf Scientific Evidence and Provenance Information Ontology (SEPIO)] | :[http://ceur-ws.org/Vol-1747/IT605_ICBO2016.pdf Scientific Evidence and Provenance Information Ontology (SEPIO)] | ||
:[http://code.google.com/p/semanticscience/wiki/SIO Semanticscience Integrated Ontology (SIO)] | :[http://code.google.com/p/semanticscience/wiki/SIO Semanticscience Integrated Ontology (SIO)] | ||
:[http://ieeexplore.ieee.org/document/8232468/ Sentinel: Platform for Semantic Enrichment of Social Media Streams] | :[http://ieeexplore.ieee.org/document/8232468/ Sentinel: Platform for Semantic Enrichment of Social Media Streams] | ||
:[http://link.springer.com/article/10.1007/s10489-016-0834-7 Situation Awareness Ontology (SAO)] | :[http://link.springer.com/article/10.1007/s10489-016-0834-7 Situation Awareness Ontology (SAO)] | ||
:[https://www.tandfonline.com/doi/abs/10.1080/13658816.2017.1309043?journalCode=tgis20 Sketch Map Ontology] | :[https://www.tandfonline.com/doi/abs/10.1080/13658816.2017.1309043?journalCode=tgis20 Sketch Map Ontology] | ||
:[http://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-5-25 Software Ontology (SWO)] | :[http://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-5-25 Software Ontology (SWO)] | ||
:[http://obofoundry.org/ontology/stato.html Statistics Ontology (STATO)] | :[http://obofoundry.org/ontology/stato.html Statistics Ontology (STATO)] | ||
:[https://www.scitepress.org/papers/2017/65827/65827.pdf Survey Ontology] | :[https://www.scitepress.org/papers/2017/65827/65827.pdf Survey Ontology] | ||
:[https://unsceb-hlcm.github.io/onto-undo/ United Nations System Document Ontology (ONTO-UNDO)] | :[https://unsceb-hlcm.github.io/onto-undo/ United Nations System Document Ontology (ONTO-UNDO)] | ||
:[https://openreview.net/forum?id=SkgyVa-coV VIVO Ontology] | :[https://openreview.net/forum?id=SkgyVa-coV VIVO Ontology] | ||
Latest revision as of 21:24, 5 April 2020
The Information Artifact Ontology (IAO)
The Information Artifact Ontology (IAO) grew out of the Data Processing Branch of the Ontology for Biomedical Investigations (OBI) in recognition of the need for domain‐neutral resource for the representation of types of information content entities (ICEs), that would apply to documents and data of all kinds, and not merely to information entities in the domain of biomedicine. IAO is based on the copying and aboutnessrelations: an information content entity is, roughly, an entity that can be copied (in the way, for example, that a gene sequence or a computer file can be copied) and that is about something. The aboutness relation itself has its roots in the mental realm -- an information content entity e is about something, again roughly speaking, in virtue of the fact that the mental acts which gave rise to or which are used to interpret or communicate with e are about something.
Background Information
- Ontobee
- Github
- OBO Foundry
- Example IAO term: measurement unit label
- Data and values in the Ontology for Biomedical Investigations
- Modeling Information with the Common Core Ontologies (CCO)
Videos
Articles
- Werner Ceusters & Barry Smith, "Aboutness: Towards Foundations for the Information Artifact Ontology", Proceedings of the Sixth International Conference on Biomedical Ontology (ICBO) (CEUR 1515), 2015.
- Barry Smith, Tatiana Malyuta, Ron Rudnicki, William Mandrick, David Salmen, Peter Morosoff, Danielle K. Duff, James Schoening & Kesny Parent, "IAO-Intel: An Ontology of Information Artifacts in the Intelligence Domain", Proceedings of the Eighth International Conference on Semantic Technologies for Intelligence, Defense, and Security (STIDS), (CEUR 1097), 2013, 33-40.
- Janna Hastings, Christopher Batchelor, Fabian Neuhaus, Christian Steinbeck, "What's in an 'is about' link? Chemical diagrams and the Information Artifact Ontology", Proceedings of the Second International Conference on Biomedical Ontology (ICBO) 2011.
- Mary Bone, Mark Blackburn, Benjamin Kruse, John Dzielski, Thomas Hagedorn and Ian Grosse, "Toward an Interoperability and Integration Framework to Enable Digital Thread", Systems, 2018, 6(4), 46; https://doi.org/10.3390/systems6040046.
Examples of ontologies extending IAO
IAO has been used as starting point for a large number of ontologies in the biomedical and bioinformatics domain. We list here some examples of direct or indirect reuse of IAO in non-biomedical fields.
- Ontology of Datatypes (OntoDT) (see also:here)
