A Gross Anatomy Ontology for Hymenoptera
Publication Date
December 29, 2010
Journal
PLOS ONE
Authors
Matthew J. Yoder, István Mikó, Katja C. Seltmann, Matthew A. Bertone, et al
Volume
5
Issue
12
Pages
e15991
DOI
http://doi.org/10.1371/journal.pone.0015991
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0015991
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/21209921
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012123
Europe PMC
http://europepmc.org/abstract/MED/21209921
Web of Science
000285793200077
Scopus
78650837915
Mendeley
http://www.mendeley.com/research/gross-anatomy-ontology-hymenoptera
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Mendeley | Further Information

{"title"=>"A gross anatomy ontology for hymenoptera", "type"=>"journal", "authors"=>[{"first_name"=>"Matthew J.", "last_name"=>"Yoder", "scopus_author_id"=>"7102996483"}, {"first_name"=>"István", "last_name"=>"Mikó", "scopus_author_id"=>"23569727600"}, {"first_name"=>"Katja C.", "last_name"=>"Seltmann", "scopus_author_id"=>"16043556600"}, {"first_name"=>"Matthew A.", "last_name"=>"Bertone", "scopus_author_id"=>"25122537600"}, {"first_name"=>"Andrew R.", "last_name"=>"Deans", "scopus_author_id"=>"6603925497"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"1000090690", "sgr"=>"78650837915", "arxiv"=>"1203.2655", "pui"=>"361034584", "scopus"=>"2-s2.0-78650837915", "issn"=>"19326203", "isbn"=>"0011-3891", "doi"=>"10.1371/journal.pone.0015991"}, "id"=>"77f252b0-0d53-3026-81f2-d8f6c47087d3", "abstract"=>"Hymenoptera is an extraordinarily diverse lineage, both in terms of species numbers and morphotypes, that includes sawflies, bees, wasps, and ants. These organisms serve critical roles as herbivores, predators, parasitoids, and pollinators, with several species functioning as models for agricultural, behavioral, and genomic research. The collective anatomical knowledge of these insects, however, has been described or referred to by labels derived from numerous, partially overlapping lexicons. The resulting corpus of information--millions of statements about hymenopteran phenotypes--remains inaccessible due to language discrepancies. The Hymenoptera Anatomy Ontology (HAO) was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy. The HAO was built using newly developed interfaces within mx, a Web-based, open source software package, that enables collaborators to simultaneously contribute to an ontology. Over twenty people contributed to the development of this ontology by adding terms, genus differentia, references, images, relationships, and annotations. The database interface returns an Open Biomedical Ontology (OBO) formatted version of the ontology and includes mechanisms for extracting candidate data and for publishing a searchable ontology to the Web. The application tools are subject-agnostic and may be used by others initiating and developing ontologies. The present core HAO data constitute 2,111 concepts, 6,977 terms (labels for concepts), 3,152 relations, 4,361 sensus (links between terms, concepts, and references) and over 6,000 text and graphical annotations. The HAO is rooted with the Common Anatomy Reference Ontology (CARO), in order to facilitate interoperability with and future alignment to other anatomy ontologies, and is available through the OBO Foundry ontology repository and BioPortal. The HAO provides a foundation through which connections between genomic, evolutionary developmental biology, phylogenetic, taxonomic, and morphological research can be actualized. Inherent mechanisms for feedback and content delivery demonstrate the effectiveness of remote, collaborative ontology development and facilitate future refinement of the HAO.", "link"=>"http://www.mendeley.com/research/gross-anatomy-ontology-hymenoptera", "reader_count"=>98, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>9, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>20, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>4, "Student > Master"=>15, "Other"=>7, "Student > Bachelor"=>6, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>9, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>20, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>4, "Student > Master"=>15, "Other"=>7, "Student > Bachelor"=>6, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Environmental Science"=>2, "Agricultural and Biological Sciences"=>79, "Arts and Humanities"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Computer Science"=>9, "Earth and Planetary Sciences"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>79}, "Computer Science"=>{"Computer Science"=>9}, "Linguistics"=>{"Linguistics"=>1}, "Environmental Science"=>{"Environmental Science"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>3}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>13, "Brazil"=>4, "South Africa"=>1, "Malaysia"=>1, "Kenya"=>1, "Australia"=>1, "Germany"=>6}, "group_count"=>13}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/809105"], "description"=>"<p>The term “paramere” (highlighted in blue) is a homonym in this example, since it is used to describe different classes ( = concepts) in various publications. Within the HAO the A, B, C, D, E overlays respectively refer to the concepts HAO:0000707, HAO:0000395, HAO:0000389, (HAO:0000389+HAO: 0001084), and (HAO:0000707+ HAO:0000389+HAO: 0001084). See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015991#s1\" target=\"_blank\">Introduction</a> for citations.</p>", "links"=>[], "tags"=>["defined"], "article_id"=>479473, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physiology", "Evolutionary Biology"], "users"=>["Matthew J. Yoder", "István Mikó", "Katja C. Seltmann", "Matthew A. Bertone", "Andrew R. Deans"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015991.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Usage_of_the_term_8220_paramere_8221_as_defined_in_different_publications_/479473", "title"=>"Usage of the term “paramere” as defined in different publications.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 21:31:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/809590"], "description"=>"<p>*Indicates the complexity of each ontology, with respect to the number of concepts with >1 or relationships.</p><p>**Estimate of presently described species/Estimated total world species (if notably different).</p>", "links"=>[], "tags"=>["arthropod", "anatomy", "ontologies", "reported"], "article_id"=>479955, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physiology", "Evolutionary Biology"], "users"=>["Matthew J. Yoder", "István Mikó", "Katja C. Seltmann", "Matthew A. Bertone", "Andrew R. Deans"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015991.t001", "stats"=>{"downloads"=>6, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_comparison_of_existing_arthropod_anatomy_ontologies_as_reported_from_OBOEdit_/479955", "title"=>"A comparison of existing arthropod anatomy ontologies as reported from OBOEdit.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 21:34:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/809378"], "description"=>"<p>A <i>sensu</i> is the combination of a reference, concept and term. Given this model, independent observations (e.g. A–D) can be inferred across to compute synonyms (terms sharing classes), homonyms (a term with many classes), and acts of synonymy and homonymy. For example, given A–D, we can infer that: 1) T1, T2, and T3 are synonyms (all referenced C1); 2) T3 is homonymous (it refers to C1 and C2); and that 3) the author of R1 synonymized T2 and T3. An example from the HAO is provided in E. Here two sensus are defined both referencing the same class, the result being that the labels “phallobase” and “gonocoxite IX” are synonyms.</p>", "links"=>[], "tags"=>["physiology", "Computational biology", "computer science", "Evolutionary biology"], "article_id"=>479748, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physiology", "Evolutionary Biology"], "users"=>["Matthew J. Yoder", "István Mikó", "Katja C. Seltmann", "Matthew A. Bertone", "Andrew R. Deans"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015991.g004", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_sensu_model_/479748", "title"=>"The <i>sensu</i> model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 21:33:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/809197"], "description"=>"<p>The class with labels “propodeum” and “abdominal tergum 1” is illustrated.</p>", "links"=>[], "tags"=>["curatorial", "interface", "ontology"], "article_id"=>479560, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physiology", "Evolutionary Biology"], "users"=>["Matthew J. Yoder", "István Mikó", "Katja C. Seltmann", "Matthew A. Bertone", "Andrew R. Deans"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015991.g002", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Screenshot_of_the_curatorial_interface_for_ontology_classes_/479560", "title"=>"Screenshot of the curatorial interface for ontology classes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 21:32:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/809304"], "description"=>"<p>Above- 6 of the 7 major data types, the 7th, a “sensu”, is described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015991#pone-0015991-g004\" target=\"_blank\">Fig. 4</a>. Below- an example with data from the HAO. A tag is a text annotation that references a keyword (from a configurable controlled vocabulary) and which may have additional notes, in this case the alternative definition. References can be associated in various places to provide additional context, as here in the relationship to a tag.</p>", "links"=>[], "tags"=>["types"], "article_id"=>479676, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physiology", "Evolutionary Biology"], "users"=>["Matthew J. Yoder", "István Mikó", "Katja C. Seltmann", "Matthew A. Bertone", "Andrew R. Deans"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015991.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Simplified_model_of_the_data_types_in_the_HAO_/479676", "title"=>"Simplified model of the data types in the HAO.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 21:33:00"}
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Relative Metric

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