Contextual Cross-Referencing of Species Names for Fiddler Crabs (Genus Uca): An Experiment in Cyber-Taxonomy
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{"title"=>"Contextual cross-referencing of species names for fiddler crabs (genus Uca): An experiment in cyber-taxonomy", "type"=>"journal", "authors"=>[{"first_name"=>"Michael S.", "last_name"=>"Rosenberg", "scopus_author_id"=>"7402654254"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84903888707", "issn"=>"19326203", "pmid"=>"25004097", "pui"=>"373472047", "sgr"=>"84903888707", "doi"=>"10.1371/journal.pone.0101704"}, "id"=>"5b22450a-8d34-3596-933b-afc2ed66878e", "abstract"=>"Cyber-taxonomy of name usage has focused primarily on producing authoritative lists of names or cross-linking names and data across disparate databases. A feature missing from much of this work is the recording and analysis of the context in which a name was used-context which can be critical for understanding not only what name an author used, but to which currently recognized species they actually refer. An experiment on recording contextual information associated with name usage was conducted for the fiddler crabs (genus Uca). Data from approximately one quarter of all publications that mention fiddler crabs, including 95% of those published prior to 1924 and 67% of those published prior to 1976, have currently been recorded in a database. Approaches and difficulties in recording and analyzing the context of name use are discussed. These results are not meant to be a full solution, rather to highlight problems which have not been previously investigated and may act as a springboard for broader approaches and discussion. Some data on the accessibility of the literature, including in particular electronic forms of publication, are also presented. The resulting data has been integrated for general browsing into the website http://www.fiddlercrab.info; the raw data and code used to construct the website is available at https://github.com/msrosenberg/fiddlercrab.info.", "link"=>"http://www.mendeley.com/research/contextual-crossreferencing-species-names-fiddler-crabs-genus-uca-experiment-cybertaxonomy", "reader_count"=>24, "reader_count_by_academic_status"=>{"Researcher"=>7, "Student > Postgraduate"=>3, "Student > Master"=>3, "Student > Bachelor"=>8, "Professor"=>2, "Student > Doctoral Student"=>1}, "reader_count_by_user_role"=>{"Researcher"=>7, "Student > Postgraduate"=>3, "Student > Master"=>3, "Student > Bachelor"=>8, "Professor"=>2, "Student > Doctoral Student"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Agricultural and Biological Sciences"=>20, "Medicine and Dentistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>20}, "Computer Science"=>{"Computer Science"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Denmark"=>1, "Brazil"=>1, "Spain"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1584792"], "description"=>"<p>The columns represent: (1) a unique key to identify a publication; (2) a numeric key for separating different names used in a single publication and in different contexts; (3) the exact name as used in the publication; (4) where in the publication the name occurs or is applied; (5) the context of the use; (6–7) additional information on the context, with details depending on the type of context (described in text); (8) the “actual species”: either the accepted species (as we now understand it) which the authors was referring to or an equals sign (for citation contexts) indicating the accepted species should be computationally determined; (9) notes on the name usage. A period generally indicates no data (columns could not be left blank). Two additional columns of data were also recorded: the common name(s) used in the publication and notes on the publication in general. These columns were rarely used and were left out of the figure to save space. Specific records indicated with letters in circles are discussed further in the text.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary biology", "Evolutionary systematics", "taxonomy", "Animal taxonomy", "Zoology", "Information technology", "text mining", "contextual", "taxonomic", "recorded", "publications"], "article_id"=>1097104, "categories"=>["Biological Sciences"], "users"=>["Michael S. Rosenberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101704.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_of_contextual_taxonomic_name_data_recorded_for_three_publications_12_14_/1097104", "title"=>"An example of contextual taxonomic name data recorded for three publications [12]–[14].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-08 03:13:24"}
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  • {"files"=>["https://ndownloader.figshare.com/files/1584796"], "description"=>"<p>The long tail of publications prior to 1924 are not included for clarity. a) Representation of the literature currently included in the name database versus those still pending. Approximately one quarter of all publications are in the database, including 95% of those published prior to 1924 (not shown) and two thirds of those published through 1975. The inset figure shows the cumulative number of publications in the database, by year, illustrating the explosion of literature over the past 40 years. b) Representation of the literature by accessibility. While the specific distribution is unique to my own circumstances, it generally illustrates the type of pattern one might expect to find with respect to accessibility of the primary literature.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary biology", "Evolutionary systematics", "taxonomy", "Animal taxonomy", "Zoology", "Information technology", "text mining", "illustrating", "publications", "names", "fiddler", "crabs", "90"], "article_id"=>1097107, "categories"=>["Biological Sciences"], "users"=>["Michael S. Rosenberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101704.g002", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Histograms_of_literature_illustrating_pattern_of_publications_using_names_associated_with_fiddler_crabs_over_the_past_90_years_/1097107", "title"=>"Histograms of literature illustrating pattern of publications using names associated with fiddler crabs over the past 90 years.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-08 03:13:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/1584804"], "description"=>"<p>Underlined text represents links. Contrast the style and content of this output with the raw data records for the same paper illustrated in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101704#pone-0101704-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary biology", "Evolutionary systematics", "taxonomy", "Animal taxonomy", "Zoology", "Information technology", "text mining", "contained", "1966", "webpage"], "article_id"=>1097115, "categories"=>["Biological Sciences"], "users"=>["Michael S. Rosenberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101704.g005", "stats"=>{"downloads"=>3, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_of_the_output_contained_on_publication_pages_in_this_case_for_Macnae_1966_12_the_full_webpage_can_be_found_at_http_www_fiddlercrab_info_references_Macnae1966_html_/1097115", "title"=>"An example of the output contained on publication pages, in this case for Macnae, 1966 [12] (the full webpage can be found at http://www.fiddlercrab.info/references/Macnae1966.html).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-08 03:13:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/1584799"], "description"=>"<p>Underlined text represents links.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary biology", "Evolutionary systematics", "taxonomy", "Animal taxonomy", "Zoology", "Information technology", "text mining", "contained", "webpage"], "article_id"=>1097110, "categories"=>["Biological Sciences"], "users"=>["Michael S. Rosenberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101704.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_of_the_output_contained_on_specific_name_pages_in_this_case_for_the_name_marionis_the_full_webpage_can_be_found_at_http_www_fiddlercrab_info_names_sn_marionis_html_/1097110", "title"=>"An example of the output contained on specific name pages, in this case for the name <i>marionis</i> (the full webpage can be found at http://www.fiddlercrab.info/names/sn_marionis.html).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-08 03:13:24"}

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