Horizontal gene transfer is not a hallmark of the human genome View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2017-05-08

AUTHORS

Steven L. Salzberg

ABSTRACT

Crisp et al. recently reported that 145 human genes have been horizontally transferred from distant species. Here, I re-analyze those genes listed by Crisp et al. as having the highest certainty of having been horizontally transferred, as well as 17 further genes from the 2001 human genome article, and find little or no evidence to support claims of horizontal gene transfer (HGT).Please see related Research article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0607-3 More... »

PAGES

85

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13059-017-1214-2

DOI

http://dx.doi.org/10.1186/s13059-017-1214-2

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1085212334

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/28482857


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

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/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Transfer, Horizontal", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Human", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Invertebrates", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Vertebrates", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Departments of Biomedical Engineering, Computer Science and Biostatistics, Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA", 
          "id": "http://www.grid.ac/institutes/grid.21107.35", 
          "name": [
            "Departments of Biomedical Engineering, Computer Science and Biostatistics, Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Salzberg", 
        "givenName": "Steven L.", 
        "id": "sg:person.01223441713.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01223441713.02"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/35057062", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042854081", 
          "https://doi.org/10.1038/35057062"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35082058", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052379739", 
          "https://doi.org/10.1038/35082058"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-015-0607-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037904253", 
          "https://doi.org/10.1186/s13059-015-0607-3"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2017-05-08", 
    "datePublishedReg": "2017-05-08", 
    "description": "Crisp et al. recently reported that 145 human genes have been horizontally transferred from distant species. Here, I re-analyze those genes listed by Crisp et al. as having the highest certainty of having been horizontally transferred, as well as 17 further genes from the 2001 human genome article, and find little or no evidence to support claims of horizontal gene transfer (HGT).Please see related Research article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0607-3", 
    "genre": "article", 
    "id": "sg:pub.10.1186/s13059-017-1214-2", 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2519905", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2529453", 
        "type": "MonetaryGrant"
      }
    ], 
    "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": "18"
      }
    ], 
    "keywords": [
      "horizontal gene transfer", 
      "gene transfer", 
      "distant species", 
      "human genes", 
      "further genes", 
      "human genome", 
      "genes", 
      "genome", 
      "species", 
      "hallmark", 
      "transfer", 
      "evidence", 
      "high certainty", 
      "research articles", 
      "et al", 
      "certainty", 
      "al", 
      "article", 
      "claims"
    ], 
    "name": "Horizontal gene transfer is not a hallmark of the human genome", 
    "pagination": "85", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1085212334"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/s13059-017-1214-2"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "28482857"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/s13059-017-1214-2", 
      "https://app.dimensions.ai/details/publication/pub.1085212334"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-09-02T16:00", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220902/entities/gbq_results/article/article_730.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/s13059-017-1214-2"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

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/s13059-017-1214-2'

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/s13059-017-1214-2'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-017-1214-2'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13059-017-1214-2'


 

This table displays all metadata directly associated to this object as RDF triples.

120 TRIPLES      21 PREDICATES      52 URIs      41 LITERALS      13 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/s13059-017-1214-2 schema:about N123e6569c94d49e6a8c696e418f2fef2
2 N181c17c9e0ae45768d0115e76d9bd27f
3 N1e3cfc08f7434476a2ee82dd62144164
4 N466555dcb00948979677f0a19b8a0f8b
5 N87fad2f9156b4d4296a88bb1b1ac9df9
6 Nb36dd5ef078241ea866ef92400df5414
7 anzsrc-for:06
8 anzsrc-for:0604
9 schema:author Na0ec2d0e1639495d9af5d2d628fa5927
10 schema:citation sg:pub.10.1038/35057062
11 sg:pub.10.1038/35082058
12 sg:pub.10.1186/s13059-015-0607-3
13 schema:datePublished 2017-05-08
14 schema:datePublishedReg 2017-05-08
15 schema:description Crisp et al. recently reported that 145 human genes have been horizontally transferred from distant species. Here, I re-analyze those genes listed by Crisp et al. as having the highest certainty of having been horizontally transferred, as well as 17 further genes from the 2001 human genome article, and find little or no evidence to support claims of horizontal gene transfer (HGT).Please see related Research article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0607-3
16 schema:genre article
17 schema:isAccessibleForFree true
18 schema:isPartOf N0f23bc1703eb4ce6a8392e1421dea387
19 Nefe912fd7d5d4b528d41fca1887e4d01
20 sg:journal.1023439
21 schema:keywords al
22 article
23 certainty
24 claims
25 distant species
26 et al
27 evidence
28 further genes
29 gene transfer
30 genes
31 genome
32 hallmark
33 high certainty
34 horizontal gene transfer
35 human genes
36 human genome
37 research articles
38 species
39 transfer
40 schema:name Horizontal gene transfer is not a hallmark of the human genome
41 schema:pagination 85
42 schema:productId N0f452022228747a7b252836555914a0f
43 N9442978386a3435d96639caa594284cd
44 Nf2549d4035d246b09ea0fbe290356801
45 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085212334
46 https://doi.org/10.1186/s13059-017-1214-2
47 schema:sdDatePublished 2022-09-02T16:00
48 schema:sdLicense https://scigraph.springernature.com/explorer/license/
49 schema:sdPublisher N1ae970ae0cad473e8c31337f53724047
50 schema:url https://doi.org/10.1186/s13059-017-1214-2
51 sgo:license sg:explorer/license/
52 sgo:sdDataset articles
53 rdf:type schema:ScholarlyArticle
54 N0f23bc1703eb4ce6a8392e1421dea387 schema:volumeNumber 18
55 rdf:type schema:PublicationVolume
56 N0f452022228747a7b252836555914a0f schema:name dimensions_id
57 schema:value pub.1085212334
58 rdf:type schema:PropertyValue
59 N123e6569c94d49e6a8c696e418f2fef2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
60 schema:name Invertebrates
61 rdf:type schema:DefinedTerm
62 N181c17c9e0ae45768d0115e76d9bd27f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
63 schema:name Vertebrates
64 rdf:type schema:DefinedTerm
65 N1ae970ae0cad473e8c31337f53724047 schema:name Springer Nature - SN SciGraph project
66 rdf:type schema:Organization
67 N1e3cfc08f7434476a2ee82dd62144164 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
68 schema:name Humans
69 rdf:type schema:DefinedTerm
70 N466555dcb00948979677f0a19b8a0f8b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
71 schema:name Genome, Human
72 rdf:type schema:DefinedTerm
73 N87fad2f9156b4d4296a88bb1b1ac9df9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
74 schema:name Gene Transfer, Horizontal
75 rdf:type schema:DefinedTerm
76 N9442978386a3435d96639caa594284cd schema:name pubmed_id
77 schema:value 28482857
78 rdf:type schema:PropertyValue
79 Na0ec2d0e1639495d9af5d2d628fa5927 rdf:first sg:person.01223441713.02
80 rdf:rest rdf:nil
81 Nb36dd5ef078241ea866ef92400df5414 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
82 schema:name Animals
83 rdf:type schema:DefinedTerm
84 Nefe912fd7d5d4b528d41fca1887e4d01 schema:issueNumber 1
85 rdf:type schema:PublicationIssue
86 Nf2549d4035d246b09ea0fbe290356801 schema:name doi
87 schema:value 10.1186/s13059-017-1214-2
88 rdf:type schema:PropertyValue
89 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
90 schema:name Biological Sciences
91 rdf:type schema:DefinedTerm
92 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
93 schema:name Genetics
94 rdf:type schema:DefinedTerm
95 sg:grant.2519905 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-017-1214-2
96 rdf:type schema:MonetaryGrant
97 sg:grant.2529453 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-017-1214-2
98 rdf:type schema:MonetaryGrant
99 sg:journal.1023439 schema:issn 1465-6906
100 1474-760X
101 schema:name Genome Biology
102 schema:publisher Springer Nature
103 rdf:type schema:Periodical
104 sg:person.01223441713.02 schema:affiliation grid-institutes:grid.21107.35
105 schema:familyName Salzberg
106 schema:givenName Steven L.
107 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01223441713.02
108 rdf:type schema:Person
109 sg:pub.10.1038/35057062 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042854081
110 https://doi.org/10.1038/35057062
111 rdf:type schema:CreativeWork
112 sg:pub.10.1038/35082058 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052379739
113 https://doi.org/10.1038/35082058
114 rdf:type schema:CreativeWork
115 sg:pub.10.1186/s13059-015-0607-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037904253
116 https://doi.org/10.1186/s13059-015-0607-3
117 rdf:type schema:CreativeWork
118 grid-institutes:grid.21107.35 schema:alternateName Departments of Biomedical Engineering, Computer Science and Biostatistics, Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
119 schema:name Departments of Biomedical Engineering, Computer Science and Biostatistics, Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
120 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...