Predicting the Extension of Biomedical Ontologies
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{"title"=>"Predicting the Extension of Biomedical Ontologies", "type"=>"journal", "authors"=>[{"first_name"=>"Catia", "last_name"=>"Pesquita", "scopus_author_id"=>"24467133700"}, {"first_name"=>"Francisco M.", "last_name"=>"Couto", "scopus_author_id"=>"6603489917"}], "year"=>2012, "source"=>"PLoS Computational Biology", "identifiers"=>{"doi"=>"10.1371/journal.pcbi.1002630", "scopus"=>"2-s2.0-84866932669", "pui"=>"365755947", "isbn"=>"1553-7358", "pmid"=>"23028267", "issn"=>"1553734X", "sgr"=>"84866932669"}, "id"=>"9f2dfd1a-daa2-3da8-86b9-d408e96f9697", "abstract"=>"Biomedical knowledge is complex and in constant evolution and growth, making it difficult for researchers to keep up with novel discoveries. Ontologies have become essential to help with this issue since they provide a standardized format to describe knowledge that facilitates its storing, sharing and computational analysis. However, the effort to keep a biomedical ontology up-to-date is a demanding and costly task involving several experts. Much of this effort is dedicated to the addition of new elements to extend the ontology to cover new areas of knowledge. We have developed an automated methodology to identify areas of the ontology that need extension based on past versions of the ontology as well as external data such as references in scientific literature and ontology usage. This can be a valuable help to semi-automated ontology extension systems, since they can focus on the subdomains of the identified ontology areas thus reducing the amount of information to process, which in turn releases ontology developers to focus on more complex ontology evolution tasks. By contributing to a faster rate of ontology evolution, we hope to positively impact ontology-based applications such as natural language processing, computer reasoning, information integration or semantic querying of heterogenous data.", "link"=>"http://www.mendeley.com/research/predicting-extension-biomedical-ontologies", "reader_count"=>29, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>13, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>13, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>11, "Medicine and Dentistry"=>1, "Neuroscience"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Chemistry"=>3, "Computer Science"=>6}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Computer Science"=>{"Computer Science"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "United States"=>2, "Norway"=>1, "United Kingdom"=>3}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/577562"], "description"=>"<p>Extension was predicted for the root term and occurred at a distance of one edge, with the addition of a whole new branch.</p>", "links"=>[], "tags"=>["cellular"], "article_id"=>248066, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Catia Pesquita", "Francisco M. Couto"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002630.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_predicted_extension_in_the_Cellular_Component_hierarchy_/248066", "title"=>"Example of predicted extension in the Cellular Component hierarchy.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-13 02:14:26"}
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  • {"files"=>["https://ndownloader.figshare.com/files/577898"], "description"=>"*<p>in the <i>is_a</i> and <i>part_of</i> hierarchies</p>", "links"=>[], "tags"=>["sets", "supervised"], "article_id"=>248402, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Catia Pesquita", "Francisco M. Couto"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002630.t002", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Features_and_feature_sets_used_for_supervised_learning_/248402", "title"=>"Features and feature sets used for supervised learning.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-13 02:20:02"}
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  • {"files"=>["https://ndownloader.figshare.com/files/577213"], "description"=>"<p><b>, </b>F<b>C</b><b> and </b><b>TT</b><b>.</b></p>", "links"=>[], "tags"=>["ontology", "versions"], "article_id"=>247711, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Catia Pesquita", "Francisco M. Couto"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002630.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_ontology_versions_to_use_for_training_and_testing_with_/247711", "title"=>"Example of ontology versions to use for training and testing with", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-13 02:08:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/577727"], "description"=>"<p>Values are average and standard deviation f-measure for all runs using the 15 ontology versions and a Decision Table algorithm. Time parameters: , FC, TT.</p>", "links"=>[], "tags"=>["sets", "molecular"], "article_id"=>248224, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Catia Pesquita", "Francisco M. Couto"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002630.t009", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_feature_and_feature_sets_performance_for_molecular_function_/248224", "title"=>"Summary of feature and feature sets performance for molecular function.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-13 02:17:04"}
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  • {"files"=>["https://ndownloader.figshare.com/files/577807"], "description"=>"<p>Values are average and standard deviation f-measure for all runs using the 15 ontology versions and a Decision Table algorithm, in the biological process hierarchy. Extension mode: refinement, indirect.</p>", "links"=>[], "tags"=>["Computational biology", "computer science"], "article_id"=>248306, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Catia Pesquita", "Francisco M. Couto"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002630.t006", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_time_parameters_/248306", "title"=>"Comparison of time parameters.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-13 02:18:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/577490"], "description"=>"<p>Extension was predicted for the root term and occurred at a distance of two edges, in every subclass.</p>", "links"=>[], "tags"=>["molecular"], "article_id"=>247991, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Catia Pesquita", "Francisco M. Couto"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002630.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_predicted_extension_in_the_Molecular_Function_hierarchy_/247991", "title"=>"Example of predicted extension in the Molecular Function hierarchy.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-13 02:13:11"}
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Relative Metric

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