Standardized Metadata for Human Pathogen/Vector Genomic Sequences
Publication Date
June 17, 2014
Journal
PLOS ONE
Authors
Vivien G. Dugan, Scott J. Emrich, Gloria I. Giraldo Calderón, Omar S. Harb, et al
Volume
9
Issue
6
Pages
e99979
DOI
https://dx.plos.org/10.1371/journal.pone.0099979
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0099979
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24936976
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4061050
Europe PMC
http://europepmc.org/abstract/MED/24936976
Web of Science
000338503400061
Scopus
84903289157
Mendeley
http://www.mendeley.com/research/standardized-metadata-human-pathogenvector-genomic-sequences
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Mendeley | Further Information

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Florian", "last_name"=>"Fricke", "scopus_author_id"=>"34568855100"}, {"first_name"=>"Maria", "last_name"=>"Giovanni", "scopus_author_id"=>"6701710445"}, {"first_name"=>"Matthew R.", "last_name"=>"Henn", "scopus_author_id"=>"9840790000"}, {"first_name"=>"Erin", "last_name"=>"Hine", "scopus_author_id"=>"57193978647"}, {"first_name"=>"Julie Dunning", "last_name"=>"Hotopp", "scopus_author_id"=>"6506933689"}, {"first_name"=>"Ilene", "last_name"=>"Karsch-Mizrachi", "scopus_author_id"=>"6602299769"}, {"first_name"=>"Jessica C.", "last_name"=>"Kissinger", "scopus_author_id"=>"7003480060"}, {"first_name"=>"Eun Mi", "last_name"=>"Lee", "scopus_author_id"=>"56229999800"}, {"first_name"=>"Punam", "last_name"=>"Mathur", "scopus_author_id"=>"56230162900"}, {"first_name"=>"Emmanuel F.", "last_name"=>"Mongodin", "scopus_author_id"=>"6507813767"}, {"first_name"=>"Cheryl I.", "last_name"=>"Murphy", "scopus_author_id"=>"55018439700"}, {"first_name"=>"Garry", "last_name"=>"Myers", "scopus_author_id"=>"13308677800"}, {"first_name"=>"Daniel E.", "last_name"=>"Neafsey", "scopus_author_id"=>"6507104012"}, {"first_name"=>"Karen E.", "last_name"=>"Nelson", "scopus_author_id"=>"7403227781"}, {"first_name"=>"William C.", "last_name"=>"Nierman", "scopus_author_id"=>"7003633617"}, {"first_name"=>"Julia", "last_name"=>"Puzak", "scopus_author_id"=>"56229505400"}, {"first_name"=>"David", "last_name"=>"Rasko", "scopus_author_id"=>"6602145541"}, {"first_name"=>"David S.", "last_name"=>"Roos", "scopus_author_id"=>"7201570041"}, {"first_name"=>"Lisa", "last_name"=>"Sadzewicz", "scopus_author_id"=>"8773619800"}, {"first_name"=>"Joana C.", "last_name"=>"Silva", "scopus_author_id"=>"7403023173"}, {"first_name"=>"Bruno", "last_name"=>"Sobral", "scopus_author_id"=>"6603924027"}, {"first_name"=>"R. Burke", "last_name"=>"Squires", "scopus_author_id"=>"57069672200"}, {"first_name"=>"Rick L.", "last_name"=>"Stevens", "scopus_author_id"=>"7403202225"}, {"first_name"=>"Luke", "last_name"=>"Tallon", "scopus_author_id"=>"6506732053"}, {"first_name"=>"Herve", "last_name"=>"Tettelin", "scopus_author_id"=>"6603804103"}, {"first_name"=>"David", "last_name"=>"Wentworth", "scopus_author_id"=>"7004800841"}, {"first_name"=>"Owen", "last_name"=>"White", "scopus_author_id"=>"7006065802"}, {"first_name"=>"Rebecca", "last_name"=>"Will", "scopus_author_id"=>"15761443400"}, {"first_name"=>"Jennifer", "last_name"=>"Wortman", "scopus_author_id"=>"7006948361"}, {"first_name"=>"Yun", "last_name"=>"Zhang", "scopus_author_id"=>"56230384400"}, {"first_name"=>"Richard H.", "last_name"=>"Scheuermann", "scopus_author_id"=>"7006976175"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84903289157", "pui"=>"373396708", "doi"=>"10.1371/journal.pone.0099979", "isbn"=>"1932-6203", "sgr"=>"84903289157", "pmid"=>"24936976"}, "id"=>"dfe16b2a-ba49-3a6e-bf53-3e50a1b3879d", "abstract"=>"High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.", "link"=>"http://www.mendeley.com/research/standardized-metadata-human-pathogenvector-genomic-sequences", "reader_count"=>40, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>4, "Librarian"=>1, "Researcher"=>12, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>9, "Student > Master"=>2, "Student > Bachelor"=>5, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>4, "Librarian"=>1, "Researcher"=>12, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>9, "Student > Master"=>2, "Student > Bachelor"=>5, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>9, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Nursing and Health Professions"=>4, "Agricultural and Biological Sciences"=>11, "Medicine and Dentistry"=>5, "Physics and Astronomy"=>1, "Computer Science"=>5, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Computer Science"=>{"Computer Science"=>5}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>9}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>1, "United Kingdom"=>1, "Germany"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1537997"], "description"=>"<p>*Mandatory NCBI BioSample attributes in the “Pathogen: clinical or host-associated” version 1.0 package.</p>", "links"=>[], "tags"=>["biotechnology", "Computational biology", "genome analysis", "Genomic databases", "Biological data management", "bioontologies", "Comparative genomics", "epigenomics", "Evolutionary biology", "population genetics", "Genetic polymorphism", "genetics", "genomics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Zoology", "Entomology", "data management", "Ontology and logic", "Information technology", "databases", "text mining", "Infectious diseases", "Technology regulations"], "article_id"=>1060059, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Vivien G. Dugan", "Scott J. Emrich", "Gloria I. Giraldo-Calderón", "Omar S. Harb", "Ruchi M. Newman", "Brett E. Pickett", "Lynn M. Schriml", "Timothy B. Stockwell", "Christian J. Stoeckert Jr", "Dan E. Sullivan", "Indresh Singh", "Doyle V. Ward", "Alison Yao", "Jie Zheng", "Tanya Barrett", "Bruce Birren", "Lauren Brinkac", "Vincent M. Bruno", "Elizabet Caler", "Sinéad Chapman", "Frank H. Collins", "Christina A. Cuomo", "Valentina Di Francesco", "Scott Durkin", "Mark Eppinger", "Michael Feldgarden", "Claire Fraser", "W. Florian Fricke", "Maria Giovanni", "Matthew R. Henn", "Erin Hine", "Julie Dunning Hotopp", "Ilene Karsch-Mizrachi", "Jessica C. Kissinger", "Eun Mi Lee", "Punam Mathur", "Emmanuel F. Mongodin", "Cheryl I. Murphy", "Garry Myers", "Daniel E. Neafsey", "Karen E. Nelson", "William C. Nierman", "Julia Puzak", "David Rasko", "David S. Roos", "Lisa Sadzewicz", "Joana C. Silva", "Bruno Sobral", "R. Burke Squires", "Rick L. Stevens", "Luke Tallon", "Hervé Tettelin", "David Wentworth", "Owen White", "Rebecca Will", "Jennifer Wortman", "Yun Zhang", "Richard H. Scheuermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099979.t002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Core_Sample_Attributes_/1060059", "title"=>"Core Sample Attributes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-17 03:14:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/1537975"], "description"=>"<p>Coverage of the twelve major data categories in the five data field collections is shown.</p>", "links"=>[], "tags"=>["biotechnology", "Computational biology", "genome analysis", "Genomic databases", "Biological data management", "bioontologies", "Comparative genomics", "epigenomics", "Evolutionary biology", "population genetics", "Genetic polymorphism", "genetics", "genomics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Zoology", "Entomology", "data management", "Ontology and logic", "Information technology", "databases", "text mining", "Infectious diseases", "Technology regulations"], "article_id"=>1060039, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Vivien G. Dugan", "Scott J. Emrich", "Gloria I. Giraldo-Calderón", "Omar S. Harb", "Ruchi M. Newman", "Brett E. Pickett", "Lynn M. Schriml", "Timothy B. Stockwell", "Christian J. Stoeckert Jr", "Dan E. Sullivan", "Indresh Singh", "Doyle V. Ward", "Alison Yao", "Jie Zheng", "Tanya Barrett", "Bruce Birren", "Lauren Brinkac", "Vincent M. Bruno", "Elizabet Caler", "Sinéad Chapman", "Frank H. Collins", "Christina A. Cuomo", "Valentina Di Francesco", "Scott Durkin", "Mark Eppinger", "Michael Feldgarden", "Claire Fraser", "W. Florian Fricke", "Maria Giovanni", "Matthew R. Henn", "Erin Hine", "Julie Dunning Hotopp", "Ilene Karsch-Mizrachi", "Jessica C. Kissinger", "Eun Mi Lee", "Punam Mathur", "Emmanuel F. Mongodin", "Cheryl I. Murphy", "Garry Myers", "Daniel E. Neafsey", "Karen E. Nelson", "William C. Nierman", "Julia Puzak", "David Rasko", "David S. Roos", "Lisa Sadzewicz", "Joana C. Silva", "Bruno Sobral", "R. Burke Squires", "Rick L. Stevens", "Luke Tallon", "Hervé Tettelin", "David Wentworth", "Owen White", "Rebecca Will", "Jennifer Wortman", "Yun Zhang", "Richard H. Scheuermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099979.g001", "stats"=>{"downloads"=>0, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_NIAID_GSCID_BRC_Project_and_Sample_Application_Standard_Overview_/1060039", "title"=>"NIAID GSCID/BRC Project and Sample Application Standard Overview.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-17 03:14:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/1537993"], "description"=>"<p>*Mandatory NCBI BioProject attributes.</p>", "links"=>[], "tags"=>["biotechnology", "Computational biology", "genome analysis", "Genomic databases", "Biological data management", "bioontologies", "Comparative genomics", "epigenomics", "Evolutionary biology", "population genetics", "Genetic polymorphism", "genetics", "genomics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Zoology", "Entomology", "data management", "Ontology and logic", "Information technology", "databases", "text mining", "Infectious diseases", "Technology regulations"], "article_id"=>1060055, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Vivien G. Dugan", "Scott J. Emrich", "Gloria I. Giraldo-Calderón", "Omar S. Harb", "Ruchi M. Newman", "Brett E. Pickett", "Lynn M. Schriml", "Timothy B. Stockwell", "Christian J. Stoeckert Jr", "Dan E. Sullivan", "Indresh Singh", "Doyle V. Ward", "Alison Yao", "Jie Zheng", "Tanya Barrett", "Bruce Birren", "Lauren Brinkac", "Vincent M. Bruno", "Elizabet Caler", "Sinéad Chapman", "Frank H. Collins", "Christina A. Cuomo", "Valentina Di Francesco", "Scott Durkin", "Mark Eppinger", "Michael Feldgarden", "Claire Fraser", "W. Florian Fricke", "Maria Giovanni", "Matthew R. Henn", "Erin Hine", "Julie Dunning Hotopp", "Ilene Karsch-Mizrachi", "Jessica C. Kissinger", "Eun Mi Lee", "Punam Mathur", "Emmanuel F. Mongodin", "Cheryl I. Murphy", "Garry Myers", "Daniel E. Neafsey", "Karen E. Nelson", "William C. Nierman", "Julia Puzak", "David Rasko", "David S. Roos", "Lisa Sadzewicz", "Joana C. Silva", "Bruno Sobral", "R. Burke Squires", "Rick L. Stevens", "Luke Tallon", "Hervé Tettelin", "David Wentworth", "Owen White", "Rebecca Will", "Jennifer Wortman", "Yun Zhang", "Richard H. Scheuermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099979.t001", "stats"=>{"downloads"=>6, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Core_Project_Attributes_/1060055", "title"=>"Core Project Attributes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-17 03:14:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/1537990"], "description"=>"<p>A semantic representation of the entities relevant to describe infectious disease samples based on the OBI and other OBO Foundry ontologies is shown. Distinctions are made between material entities (blue outlines), information entities and qualities (black outlines), and processes (red outlines). Entities are connected by standard semantic relations, in <i>italic</i>. The subset of entities selected as Core Sample fields are noted with ovals containing the respective Field ID. For example, the OBI:organism <i>has_quality</i> “Specimen Source Gender” (CS5), which is equivalent to the PATO:biological sex, and <i>has_quality</i> PATO:age, and <i>has_quality</i> “Specimen Source Health Status” (CS8), which is equivalent to PATO:organismal status. PATO:age <i>is_quality_measured_as</i> OBI:age since birth measurement datum, which <i>has_measurement_value</i> “Specimen Source Age – Value” (CS6) and <i>has_measurement_unit_label</i> “Specimen Source Age – Unit” (CS7).</p>", "links"=>[], "tags"=>["biotechnology", "Computational biology", "genome analysis", "Genomic databases", "Biological data management", "bioontologies", "Comparative genomics", "epigenomics", "Evolutionary biology", "population genetics", "Genetic polymorphism", "genetics", "genomics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Zoology", "Entomology", "data management", "Ontology and logic", "Information technology", "databases", "text mining", "Infectious diseases", "Technology regulations"], "article_id"=>1060054, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Vivien G. Dugan", "Scott J. Emrich", "Gloria I. Giraldo-Calderón", "Omar S. Harb", "Ruchi M. Newman", "Brett E. Pickett", "Lynn M. Schriml", "Timothy B. Stockwell", "Christian J. Stoeckert Jr", "Dan E. Sullivan", "Indresh Singh", "Doyle V. Ward", "Alison Yao", "Jie Zheng", "Tanya Barrett", "Bruce Birren", "Lauren Brinkac", "Vincent M. Bruno", "Elizabet Caler", "Sinéad Chapman", "Frank H. Collins", "Christina A. Cuomo", "Valentina Di Francesco", "Scott Durkin", "Mark Eppinger", "Michael Feldgarden", "Claire Fraser", "W. Florian Fricke", "Maria Giovanni", "Matthew R. Henn", "Erin Hine", "Julie Dunning Hotopp", "Ilene Karsch-Mizrachi", "Jessica C. Kissinger", "Eun Mi Lee", "Punam Mathur", "Emmanuel F. Mongodin", "Cheryl I. Murphy", "Garry Myers", "Daniel E. Neafsey", "Karen E. Nelson", "William C. Nierman", "Julia Puzak", "David Rasko", "David S. Roos", "Lisa Sadzewicz", "Joana C. Silva", "Bruno Sobral", "R. Burke Squires", "Rick L. Stevens", "Luke Tallon", "Hervé Tettelin", "David Wentworth", "Owen White", "Rebecca Will", "Jennifer Wortman", "Yun Zhang", "Richard H. Scheuermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099979.g003", "stats"=>{"downloads"=>2, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Semantic_Network_of_the_Core_Sample_Data_Fields_/1060054", "title"=>"Semantic Network of the Core Sample Data Fields.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-17 03:14:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/1537986"], "description"=>"<p>A semantic representation of the entities relevant to describe infectious disease projects based on the OBI and other OBO Foundry ontologies is shown. Distinctions are made between material entities (blue outlines), information entities and qualities (black outlines), and processes (red outlines). Entities are connected by standard semantic relations, in <i>italic</i>. The subset of entities selected as Core Project fields are noted with ovals containing the respective Field ID. For example, both the “Project Title” (CP1) and “Project ID” (CP2) <i>denote</i> an OBI:Investigation; the “Project Description” (CP3) <i>is_about</i> the same OBI:Investigation.</p>", "links"=>[], "tags"=>["biotechnology", "Computational biology", "genome analysis", "Genomic databases", "Biological data management", "bioontologies", "Comparative genomics", "epigenomics", "Evolutionary biology", "population genetics", "Genetic polymorphism", "genetics", "genomics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Zoology", "Entomology", "data management", "Ontology and logic", "Information technology", "databases", "text mining", "Infectious diseases", "Technology regulations"], "article_id"=>1060050, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Vivien G. Dugan", "Scott J. Emrich", "Gloria I. Giraldo-Calderón", "Omar S. Harb", "Ruchi M. Newman", "Brett E. Pickett", "Lynn M. Schriml", "Timothy B. Stockwell", "Christian J. Stoeckert Jr", "Dan E. Sullivan", "Indresh Singh", "Doyle V. Ward", "Alison Yao", "Jie Zheng", "Tanya Barrett", "Bruce Birren", "Lauren Brinkac", "Vincent M. Bruno", "Elizabet Caler", "Sinéad Chapman", "Frank H. Collins", "Christina A. Cuomo", "Valentina Di Francesco", "Scott Durkin", "Mark Eppinger", "Michael Feldgarden", "Claire Fraser", "W. Florian Fricke", "Maria Giovanni", "Matthew R. Henn", "Erin Hine", "Julie Dunning Hotopp", "Ilene Karsch-Mizrachi", "Jessica C. Kissinger", "Eun Mi Lee", "Punam Mathur", "Emmanuel F. Mongodin", "Cheryl I. Murphy", "Garry Myers", "Daniel E. Neafsey", "Karen E. Nelson", "William C. Nierman", "Julia Puzak", "David Rasko", "David S. Roos", "Lisa Sadzewicz", "Joana C. Silva", "Bruno Sobral", "R. Burke Squires", "Rick L. Stevens", "Luke Tallon", "Hervé Tettelin", "David Wentworth", "Owen White", "Rebecca Will", "Jennifer Wortman", "Yun Zhang", "Richard H. Scheuermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099979.g002", "stats"=>{"downloads"=>3, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Semantic_Network_of_the_Core_Project_Data_Fields_/1060050", "title"=>"Semantic Network of the Core Project Data Fields.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-17 03:14:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/1537999"], "description"=>"<div><p>High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium’s minimal information (MIxS) and NCBI’s BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.</p></div>", "links"=>[], "tags"=>["biotechnology", "Computational biology", "genome analysis", "Genomic databases", "Biological data management", "bioontologies", "Comparative genomics", "epigenomics", "Evolutionary biology", "population genetics", "Genetic polymorphism", "genetics", "genomics", "microbiology", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Zoology", "Entomology", "data management", "Ontology and logic", "Information technology", "databases", "text mining", "Infectious diseases", "Technology regulations", "metadata", "genomic"], "article_id"=>1060063, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Vivien G. Dugan", "Scott J. Emrich", "Gloria I. Giraldo-Calderón", "Omar S. Harb", "Ruchi M. Newman", "Brett E. Pickett", "Lynn M. Schriml", "Timothy B. Stockwell", "Christian J. Stoeckert Jr", "Dan E. Sullivan", "Indresh Singh", "Doyle V. Ward", "Alison Yao", "Jie Zheng", "Tanya Barrett", "Bruce Birren", "Lauren Brinkac", "Vincent M. Bruno", "Elizabet Caler", "Sinéad Chapman", "Frank H. Collins", "Christina A. Cuomo", "Valentina Di Francesco", "Scott Durkin", "Mark Eppinger", "Michael Feldgarden", "Claire Fraser", "W. Florian Fricke", "Maria Giovanni", "Matthew R. Henn", "Erin Hine", "Julie Dunning Hotopp", "Ilene Karsch-Mizrachi", "Jessica C. Kissinger", "Eun Mi Lee", "Punam Mathur", "Emmanuel F. Mongodin", "Cheryl I. Murphy", "Garry Myers", "Daniel E. Neafsey", "Karen E. Nelson", "William C. Nierman", "Julia Puzak", "David Rasko", "David S. Roos", "Lisa Sadzewicz", "Joana C. Silva", "Bruno Sobral", "R. Burke Squires", "Rick L. Stevens", "Luke Tallon", "Hervé Tettelin", "David Wentworth", "Owen White", "Rebecca Will", "Jennifer Wortman", "Yun Zhang", "Richard H. Scheuermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099979", "stats"=>{"downloads"=>16, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Standardized_Metadata_for_Human_Pathogen_Vector_Genomic_Sequences_/1060063", "title"=>"Standardized Metadata for Human Pathogen/Vector Genomic Sequences", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-17 03:14:04"}

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  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"7", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"11", "full-text"=>"12", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"11", "full-text"=>"13", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"9", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"5", "full-text"=>"2", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"18", "full-text"=>"20", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"10", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
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  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"13", "full-text"=>"14", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"5", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[291]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[306, 482]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[310]}, {"subject_area"=>"/Computer and information sciences", "average_usage"=>[327, 511]}, {"subject_area"=>"/Computer and information sciences/Data management", "average_usage"=>[365, 545]}]}
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Net::HTTPTooManyRequests

Source
Scopus
Time
2019-09-26 20:09:21 UTC
Target URL
https://api.elsevier.com/content/search/index:SCOPUS?query=DOI(10.1371%2Fjournal.pone.0099979)
Trace

/app/models/concerns/networkable.rb:21:in `get_result'
/app/models/source.rb:165:in `get_data'
/app/models/retrieval_status.rb:47:in `perform_get_data'
/app/jobs/source_job.rb:52:in `block (2 levels) in perform'
/app/jobs/source_job.rb:51:in `block in perform'
/app/jobs/source_job.rb:35:in `each'
/app/jobs/source_job.rb:35:in `perform'