title: Standardized metadata for human pathogen/vector genomic sequences.
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.
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America; National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America.
authors.forename: Vivien G
authors.initials: VG
authors.lastname: Dugan
authors.affiliation: University of Notre Dame, Notre Dame, Indiana, United States of America.
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Emrich
authors.affiliation: University of Notre Dame, Notre Dame, Indiana, United States of America.
authors.forename: Gloria I
authors.initials: GI
authors.lastname: Giraldo-Calderón
authors.affiliation: University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: Omar S
authors.initials: OS
authors.lastname: Harb
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Ruchi M
authors.initials: RM
authors.lastname: Newman
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America.
authors.forename: Brett E
authors.initials: BE
authors.lastname: Pickett
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Lynn M
authors.initials: LM
authors.lastname: Schriml
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America.
authors.forename: Timothy B
authors.initials: TB
authors.lastname: Stockwell
authors.affiliation: University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Stoeckert
authors.affiliation: Cyberinfrastructure Division, Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America.
authors.forename: Dan E
authors.initials: DE
authors.lastname: Sullivan
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America.
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authors.lastname: Singh
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Doyle V
authors.initials: DV
authors.lastname: Ward
authors.affiliation: National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America.
authors.forename: Alison
authors.initials: A
authors.lastname: Yao
authors.affiliation: University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: Jie
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authors.lastname: Zheng
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, United States of America.
authors.forename: Tanya
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authors.lastname: Barrett
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Bruce
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authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America.
authors.forename: Lauren
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authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Vincent M
authors.initials: VM
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authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America.
authors.forename: Elizabet
authors.initials: E
authors.lastname: Caler
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Sinéad
authors.initials: S
authors.lastname: Chapman
authors.affiliation: University of Notre Dame, Notre Dame, Indiana, United States of America.
authors.forename: Frank H
authors.initials: FH
authors.lastname: Collins
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Christina A
authors.initials: CA
authors.lastname: Cuomo
authors.affiliation: National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America.
authors.forename: Valentina
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authors.lastname: Di Francesco
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America.
authors.forename: Scott
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authors.lastname: Durkin
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
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authors.lastname: Eppinger
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Michael
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authors.lastname: Feldgarden
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Claire
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authors.lastname: Fraser
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: W Florian
authors.initials: WF
authors.lastname: Fricke
authors.affiliation: National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America.
authors.forename: Maria
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authors.lastname: Giovanni
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Henn
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Erin
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authors.lastname: Hine
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Julie Dunning
authors.initials: JD
authors.lastname: Hotopp
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, United States of America.
authors.forename: Ilene
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authors.lastname: Karsch-Mizrachi
authors.affiliation: University of Georgia, Athens, Georgia, United States of America.
authors.forename: Jessica C
authors.initials: JC
authors.lastname: Kissinger
authors.affiliation: National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America.
authors.forename: Eun Mi
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authors.affiliation: National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America.
authors.forename: Punam
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authors.lastname: Mathur
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Emmanuel F
authors.initials: EF
authors.lastname: Mongodin
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Cheryl I
authors.initials: CI
authors.lastname: Murphy
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
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authors.lastname: Myers
authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Neafsey
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America.
authors.forename: Karen E
authors.initials: KE
authors.lastname: Nelson
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America.
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authors.initials: WC
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authors.affiliation: Kelly Government Solutions, Rockville, Maryland, United States of America.
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authors.lastname: Puzak
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
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authors.lastname: Rasko
authors.affiliation: University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: David S
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authors.lastname: Roos
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
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authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
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authors.affiliation: Cyberinfrastructure Division, Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America.
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authors.affiliation: National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America.
authors.forename: R Burke
authors.initials: RB
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authors.affiliation: Argonne National Laboratory, Lemont, Illinois, United States of America.
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authors.initials: RL
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authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
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authors.lastname: Tallon
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
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authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America.
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authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
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authors.affiliation: Cyberinfrastructure Division, Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America.
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authors.affiliation: Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Jennifer
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authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America.
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authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America; Department of Pathology, University of California San Diego, San Diego, California, United States of America.
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authors.initials: RH
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mesh_terms: D000818:Animals; D003141:Communicable Diseases / Q000382:microbiology / Q000469:parasitology; D030541:Databases, Genetic / Q000592:standards*; D066264:Datasets as Topic; D004199:Disease Vectors; D063990:Gene Ontology; D016678:Genome; D006801:Humans; D012015:Reference Standards; D017422:Sequence Analysis, DNA; D014774:Virulence / Q000235:genetics