Ontology type: schema:ScholarlyArticle Open Access: True
2020-07-20
AUTHORSAna T. Duggan, Jennifer Klunk, Ashleigh F. Porter, Anna N. Dhody, Robert Hicks, Geoffrey L. Smith, Margaret Humphreys, Andrea M. McCollum, Whitni B. Davidson, Kimberly Wilkins, Yu Li, Amanda Burke, Hanna Polasky, Lowell Flanders, Debi Poinar, Amogelang R. Raphenya, Tammy T. Y. Lau, Brian Alcock, Andrew G. McArthur, G. Brian Golding, Edward C. Holmes, Hendrik N. Poinar
ABSTRACTVaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and diversity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque. We reconstruct and analyse viral vaccine genomes associated with smallpox vaccination from historical artefacts. Significantly, we recover viral molecules through non-destructive sampling of historical materials lacking signs of biological residues. We use the authenticated ancient genomes to reveal the evolutionary relationships of smallpox vaccination viruses within the poxviruses as a whole. More... »
PAGES175
http://scigraph.springernature.com/pub.10.1186/s13059-020-02079-z
DOIhttp://dx.doi.org/10.1186/s13059-020-02079-z
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1129484152
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/32684155
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/05",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Environmental Sciences",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/08",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Information and Computing Sciences",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "American Civil War",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genetic Variation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genome, Viral",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "History, 19th Century",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Humans",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Metagenome",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Smallpox Vaccine",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Vaccination",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Vaccinia virus",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Department of Anthropology, McMaster University, L8S 4L9, Hamilton, Canada",
"id": "http://www.grid.ac/institutes/grid.25073.33",
"name": [
"Department of Anthropology, McMaster University, L8S 4L9, Hamilton, Canada"
],
"type": "Organization"
},
"familyName": "Duggan",
"givenName": "Ana T.",
"id": "sg:person.011727150425.30",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011727150425.30"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Present address: Arbor Biosciences, 48103, Ann Arbor, MI, USA",
"id": "http://www.grid.ac/institutes/None",
"name": [
"Department of Biology, McMaster University, L8S 4L9, Hamilton, Canada",
"Present address: Arbor Biosciences, 48103, Ann Arbor, MI, USA"
],
"type": "Organization"
},
"familyName": "Klunk",
"givenName": "Jennifer",
"id": "sg:person.01252742210.51",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01252742210.51"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, 2006, Sydney, NSW, Australia",
"id": "http://www.grid.ac/institutes/grid.1013.3",
"name": [
"Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, 2006, Sydney, NSW, Australia"
],
"type": "Organization"
},
"familyName": "Porter",
"givenName": "Ashleigh F.",
"id": "sg:person.012536763673.51",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012536763673.51"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "M\u00fctter Museum of The College of Physicians of Philadelphia, 19103, Philadelphia, PA, USA",
"id": "http://www.grid.ac/institutes/grid.418804.1",
"name": [
"M\u00fctter Research Institute, 19103, Philadelphia, PA, USA",
"M\u00fctter Museum of The College of Physicians of Philadelphia, 19103, Philadelphia, PA, USA"
],
"type": "Organization"
},
"familyName": "Dhody",
"givenName": "Anna N.",
"id": "sg:person.01016412266.41",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01016412266.41"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "M\u00fctter Museum of The College of Physicians of Philadelphia, 19103, Philadelphia, PA, USA",
"id": "http://www.grid.ac/institutes/grid.418804.1",
"name": [
"M\u00fctter Research Institute, 19103, Philadelphia, PA, USA",
"M\u00fctter Museum of The College of Physicians of Philadelphia, 19103, Philadelphia, PA, USA"
],
"type": "Organization"
},
"familyName": "Hicks",
"givenName": "Robert",
"id": "sg:person.015376432045.91",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015376432045.91"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Pathology, University of Cambridge, CB2 1QP, Cambridge, UK",
"id": "http://www.grid.ac/institutes/grid.5335.0",
"name": [
"Department of Pathology, University of Cambridge, CB2 1QP, Cambridge, UK"
],
"type": "Organization"
},
"familyName": "Smith",
"givenName": "Geoffrey L.",
"id": "sg:person.0672173502.20",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0672173502.20"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of History, Duke University, 27708, Durham, NC, USA",
"id": "http://www.grid.ac/institutes/grid.26009.3d",
"name": [
"Department of History, Duke University, 27708, Durham, NC, USA"
],
"type": "Organization"
},
"familyName": "Humphreys",
"givenName": "Margaret",
"id": "sg:person.011177703225.13",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011177703225.13"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, 30333, Atlanta, GA, USA",
"id": "http://www.grid.ac/institutes/grid.416738.f",
"name": [
"U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, 30333, Atlanta, GA, USA"
],
"type": "Organization"
},
"familyName": "McCollum",
"givenName": "Andrea M.",
"id": "sg:person.0762410731.53",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0762410731.53"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, 30333, Atlanta, GA, USA",
"id": "http://www.grid.ac/institutes/grid.416738.f",
"name": [
"U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, 30333, Atlanta, GA, USA"
],
"type": "Organization"
},
"familyName": "Davidson",
"givenName": "Whitni B.",
"id": "sg:person.01103423603.63",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01103423603.63"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, 30333, Atlanta, GA, USA",
"id": "http://www.grid.ac/institutes/grid.416738.f",
"name": [
"U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, 30333, Atlanta, GA, USA"
],
"type": "Organization"
},
"familyName": "Wilkins",
"givenName": "Kimberly",
"id": "sg:person.0607551331.93",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0607551331.93"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, 30333, Atlanta, GA, USA",
"id": "http://www.grid.ac/institutes/grid.416738.f",
"name": [
"U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, 30333, Atlanta, GA, USA"
],
"type": "Organization"
},
"familyName": "Li",
"givenName": "Yu",
"id": "sg:person.01300742102.05",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01300742102.05"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "M\u00fctter Museum of The College of Physicians of Philadelphia, 19103, Philadelphia, PA, USA",
"id": "http://www.grid.ac/institutes/grid.418804.1",
"name": [
"M\u00fctter Museum of The College of Physicians of Philadelphia, 19103, Philadelphia, PA, USA"
],
"type": "Organization"
},
"familyName": "Burke",
"givenName": "Amanda",
"type": "Person"
},
{
"affiliation": {
"alternateName": "M\u00fctter Museum of The College of Physicians of Philadelphia, 19103, Philadelphia, PA, USA",
"id": "http://www.grid.ac/institutes/grid.418804.1",
"name": [
"M\u00fctter Museum of The College of Physicians of Philadelphia, 19103, Philadelphia, PA, USA"
],
"type": "Organization"
},
"familyName": "Polasky",
"givenName": "Hanna",
"type": "Person"
},
{
"affiliation": {
"alternateName": "M\u00fctter Museum of The College of Physicians of Philadelphia, 19103, Philadelphia, PA, USA",
"id": "http://www.grid.ac/institutes/grid.418804.1",
"name": [
"M\u00fctter Museum of The College of Physicians of Philadelphia, 19103, Philadelphia, PA, USA"
],
"type": "Organization"
},
"familyName": "Flanders",
"givenName": "Lowell",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Anthropology, McMaster University, L8S 4L9, Hamilton, Canada",
"id": "http://www.grid.ac/institutes/grid.25073.33",
"name": [
"Department of Anthropology, McMaster University, L8S 4L9, Hamilton, Canada"
],
"type": "Organization"
},
"familyName": "Poinar",
"givenName": "Debi",
"id": "sg:person.0705307675.33",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0705307675.33"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Present address: BC Cancer Research Centre, V5Z 1G1, Vancouver, Canada",
"id": "http://www.grid.ac/institutes/grid.248762.d",
"name": [
"Present address: BC Cancer Research Centre, V5Z 1G1, Vancouver, Canada"
],
"type": "Organization"
},
"familyName": "Raphenya",
"givenName": "Amogelang R.",
"id": "sg:person.016102111511.02",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016102111511.02"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, L8S 4K1, Hamilton, Canada",
"id": "http://www.grid.ac/institutes/grid.25073.33",
"name": [
"Present address: BC Cancer Research Centre, V5Z 1G1, Vancouver, Canada",
"M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, L8S 4K1, Hamilton, Canada"
],
"type": "Organization"
},
"familyName": "Lau",
"givenName": "Tammy T. Y.",
"id": "sg:person.07375434463.89",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07375434463.89"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Present address: BC Cancer Research Centre, V5Z 1G1, Vancouver, Canada",
"id": "http://www.grid.ac/institutes/grid.248762.d",
"name": [
"Present address: BC Cancer Research Centre, V5Z 1G1, Vancouver, Canada"
],
"type": "Organization"
},
"familyName": "Alcock",
"givenName": "Brian",
"id": "sg:person.01053507016.78",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01053507016.78"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Present address: BC Cancer Research Centre, V5Z 1G1, Vancouver, Canada",
"id": "http://www.grid.ac/institutes/grid.248762.d",
"name": [
"Present address: BC Cancer Research Centre, V5Z 1G1, Vancouver, Canada"
],
"type": "Organization"
},
"familyName": "McArthur",
"givenName": "Andrew G.",
"id": "sg:person.01153756704.13",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01153756704.13"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Biology, McMaster University, L8S 4L9, Hamilton, Canada",
"id": "http://www.grid.ac/institutes/grid.25073.33",
"name": [
"Department of Biology, McMaster University, L8S 4L9, Hamilton, Canada"
],
"type": "Organization"
},
"familyName": "Golding",
"givenName": "G. Brian",
"id": "sg:person.01207473736.33",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01207473736.33"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, 2006, Sydney, NSW, Australia",
"id": "http://www.grid.ac/institutes/grid.1013.3",
"name": [
"Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, 2006, Sydney, NSW, Australia"
],
"type": "Organization"
},
"familyName": "Holmes",
"givenName": "Edward C.",
"id": "sg:person.012501436222.04",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012501436222.04"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Biochemistry, McMaster University, L8S 4L9, Hamilton, Canada",
"id": "http://www.grid.ac/institutes/grid.25073.33",
"name": [
"Department of Anthropology, McMaster University, L8S 4L9, Hamilton, Canada",
"Present address: BC Cancer Research Centre, V5Z 1G1, Vancouver, Canada",
"Department of Biochemistry, McMaster University, L8S 4L9, Hamilton, Canada"
],
"type": "Organization"
},
"familyName": "Poinar",
"givenName": "Hendrik N.",
"id": "sg:person.0676355246.40",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676355246.40"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1007/bf01319903",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1020032461",
"https://doi.org/10.1007/bf01319903"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-3-319-24277-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1028525626",
"https://doi.org/10.1007/978-3-319-24277-4"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-1-4939-7290-6_28",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1092014726",
"https://doi.org/10.1007/978-1-4939-7290-6_28"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13059-015-0776-0",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1025994099",
"https://doi.org/10.1186/s13059-015-0776-0"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2105-12-385",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1037780208",
"https://doi.org/10.1186/1471-2105-12-385"
],
"type": "CreativeWork"
}
],
"datePublished": "2020-07-20",
"datePublishedReg": "2020-07-20",
"description": "Vaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and diversity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque. We reconstruct and analyse viral vaccine genomes associated with smallpox vaccination from historical artefacts. Significantly, we recover viral molecules through non-destructive sampling of historical materials lacking signs of biological residues. We use the authenticated ancient genomes to reveal the evolutionary relationships of smallpox vaccination viruses within the poxviruses as a whole.",
"genre": "article",
"id": "sg:pub.10.1186/s13059-020-02079-z",
"isAccessibleForFree": true,
"isPartOf": [
{
"id": "sg:journal.1023439",
"issn": [
"1474-760X",
"1465-6906"
],
"name": "Genome Biology",
"publisher": "Springer Nature",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "21"
}
],
"keywords": [
"smallpox vaccination",
"historical materials",
"twentieth century",
"historical artifacts",
"ancient genomes",
"historical importance",
"eradication of smallpox",
"vaccine genome",
"non-destructive sampling",
"biological residues",
"century",
"origin",
"smallpox vaccine",
"smallpox",
"artifacts",
"whole",
"diversity",
"public health",
"source",
"genomic diversity",
"importance",
"relationship",
"viral molecules",
"materials",
"signs",
"eradication",
"evolutionary relationships",
"health",
"genome",
"sampling",
"method",
"vaccination",
"poxviruses",
"virus",
"residues",
"molecules",
"vaccine"
],
"name": "The origins and genomic diversity of American Civil War Era smallpox vaccine strains",
"pagination": "175",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1129484152"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/s13059-020-02079-z"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"32684155"
]
}
],
"sameAs": [
"https://doi.org/10.1186/s13059-020-02079-z",
"https://app.dimensions.ai/details/publication/pub.1129484152"
],
"sdDataset": "articles",
"sdDatePublished": "2022-08-04T17:08",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-springernature-scigraph/baseset/20220804/entities/gbq_results/article/article_833.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1186/s13059-020-02079-z"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13059-020-02079-z'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13059-020-02079-z'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-020-02079-z'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13059-020-02079-z'
This table displays all metadata directly associated to this object as RDF triples.
332 TRIPLES
21 PREDICATES
77 URIs
63 LITERALS
16 BLANK NODES