Reconstructing prokaryotic transcriptional regulatory networks: lessons from actinobacteria View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-03

AUTHORS

Thiago M Venancio, L Aravind

ABSTRACT

Reconstruction of transcriptional regulatory networks of uncharacterized bacteria is a main challenge for the post-genomic era. Recent studies, including one in BMC Systems Biology, address this problem in the relatively underexplored actinobacteria clade, which includes major pathogenic and economically relevant taxa.

PAGES

29

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/jbiol132

DOI

http://dx.doi.org/10.1186/jbiol132

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1030211728

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19435474


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/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "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"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Actinobacteria", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Regulation, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Regulatory Networks", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transcription Factors", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transcription, Genetic", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "National Center for Biotechnology Information", 
          "id": "https://www.grid.ac/institutes/grid.419234.9", 
          "name": [
            "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 20894, Bethesda, Maryland, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Venancio", 
        "givenName": "Thiago M", 
        "id": "sg:person.0737006745.40", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0737006745.40"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National Center for Biotechnology Information", 
          "id": "https://www.grid.ac/institutes/grid.419234.9", 
          "name": [
            "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 20894, Bethesda, Maryland, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Aravind", 
        "givenName": "L", 
        "id": "sg:person.01106662166.38", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01106662166.38"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1146/annurev.bi.61.070192.005201", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004544236"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-8-293", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007754367", 
          "https://doi.org/10.1186/1471-2105-8-293"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0022-2836(61)80072-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010232058"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng881", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010954918", 
          "https://doi.org/10.1038/ng881"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng881", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010954918", 
          "https://doi.org/10.1038/ng881"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm994", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011544616"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1752-0509-3-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011643872", 
          "https://doi.org/10.1186/1752-0509-3-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm910", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012798639"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jmb.2006.02.019", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018154049"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1272", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018231980", 
          "https://doi.org/10.1038/nrg1272"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1272", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018231980", 
          "https://doi.org/10.1038/nrg1272"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/msb.2008.63", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035608084"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/msb.2008.63", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035608084"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.086595.108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043032853"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00438-003-0952-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050711091", 
          "https://doi.org/10.1007/s00438-003-0952-x"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00438-003-0952-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050711091", 
          "https://doi.org/10.1007/s00438-003-0952-x"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2009-03", 
    "datePublishedReg": "2009-03-01", 
    "description": "Reconstruction of transcriptional regulatory networks of uncharacterized bacteria is a main challenge for the post-genomic era. Recent studies, including one in BMC Systems Biology, address this problem in the relatively underexplored actinobacteria clade, which includes major pathogenic and economically relevant taxa.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/jbiol132", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2726065", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1032884", 
        "issn": [
          "1478-5854", 
          "1741-7007"
        ], 
        "name": "BMC Biology", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "3", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "8"
      }
    ], 
    "name": "Reconstructing prokaryotic transcriptional regulatory networks: lessons from actinobacteria", 
    "pagination": "29", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "8feccc2446e5ae643f005462e95fa69737e08c887bfe1f27c9034d8e27caaffd"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "19435474"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101147570"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/jbiol132"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1030211728"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/jbiol132", 
      "https://app.dimensions.ai/details/publication/pub.1030211728"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T19:57", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8681_00000513.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2Fjbiol132"
  }
]
 

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/jbiol132'

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/jbiol132'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/jbiol132'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/jbiol132'


 

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

147 TRIPLES      21 PREDICATES      48 URIs      28 LITERALS      16 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/jbiol132 schema:about N22c5aceebb35493f8fba777ebdcda284
2 N267b6639e48840a69de895e006f9abce
3 N2bf11c611d0c4f439f0714f74df1e0df
4 N77696f99e491489c995fb5dee1f7233b
5 N934e527a0ce644278c207501ce798e23
6 Nab275f4c496a4e52affaf65007c75e0b
7 Nfa4d48a9500c4d3d93e08820ec345e4b
8 anzsrc-for:06
9 anzsrc-for:0604
10 schema:author Nc529a8ad42bb4eb9804c70abfcf02645
11 schema:citation sg:pub.10.1007/s00438-003-0952-x
12 sg:pub.10.1038/ng881
13 sg:pub.10.1038/nrg1272
14 sg:pub.10.1186/1471-2105-8-293
15 sg:pub.10.1186/1752-0509-3-8
16 https://doi.org/10.1016/j.jmb.2006.02.019
17 https://doi.org/10.1016/s0022-2836(61)80072-7
18 https://doi.org/10.1038/msb.2008.63
19 https://doi.org/10.1093/nar/gkm910
20 https://doi.org/10.1093/nar/gkm994
21 https://doi.org/10.1101/gr.086595.108
22 https://doi.org/10.1146/annurev.bi.61.070192.005201
23 schema:datePublished 2009-03
24 schema:datePublishedReg 2009-03-01
25 schema:description Reconstruction of transcriptional regulatory networks of uncharacterized bacteria is a main challenge for the post-genomic era. Recent studies, including one in BMC Systems Biology, address this problem in the relatively underexplored actinobacteria clade, which includes major pathogenic and economically relevant taxa.
26 schema:genre research_article
27 schema:inLanguage en
28 schema:isAccessibleForFree true
29 schema:isPartOf N3f94ffabb2f74d0b91de1f3aeec765d1
30 Nc09b708e4aad4c038ec1983292b30460
31 sg:journal.1032884
32 schema:name Reconstructing prokaryotic transcriptional regulatory networks: lessons from actinobacteria
33 schema:pagination 29
34 schema:productId N27427b30832b4cb8bf464b8984c9a8d3
35 N95ed3c11c1a9408aab3c6b6648ffd2a8
36 Nc17c427893344ac9b2ab62d99bda3d5a
37 Ne9934495e83444e8b2881a366182c6da
38 Nf7a6b11f594e4f658ce3d86145947b35
39 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030211728
40 https://doi.org/10.1186/jbiol132
41 schema:sdDatePublished 2019-04-10T19:57
42 schema:sdLicense https://scigraph.springernature.com/explorer/license/
43 schema:sdPublisher Nc3550a1c854f4179a4cddca702740c66
44 schema:url http://link.springer.com/10.1186%2Fjbiol132
45 sgo:license sg:explorer/license/
46 sgo:sdDataset articles
47 rdf:type schema:ScholarlyArticle
48 N150bfbedcbdc4470ae6a6016050c4e3a rdf:first sg:person.01106662166.38
49 rdf:rest rdf:nil
50 N22c5aceebb35493f8fba777ebdcda284 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
51 schema:name Genome, Bacterial
52 rdf:type schema:DefinedTerm
53 N267b6639e48840a69de895e006f9abce schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
54 schema:name Transcription Factors
55 rdf:type schema:DefinedTerm
56 N27427b30832b4cb8bf464b8984c9a8d3 schema:name dimensions_id
57 schema:value pub.1030211728
58 rdf:type schema:PropertyValue
59 N2bf11c611d0c4f439f0714f74df1e0df schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
60 schema:name Gene Regulatory Networks
61 rdf:type schema:DefinedTerm
62 N3f94ffabb2f74d0b91de1f3aeec765d1 schema:issueNumber 3
63 rdf:type schema:PublicationIssue
64 N77696f99e491489c995fb5dee1f7233b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
65 schema:name Genes, Bacterial
66 rdf:type schema:DefinedTerm
67 N934e527a0ce644278c207501ce798e23 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
68 schema:name Actinobacteria
69 rdf:type schema:DefinedTerm
70 N95ed3c11c1a9408aab3c6b6648ffd2a8 schema:name doi
71 schema:value 10.1186/jbiol132
72 rdf:type schema:PropertyValue
73 Nab275f4c496a4e52affaf65007c75e0b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
74 schema:name Gene Expression Regulation, Bacterial
75 rdf:type schema:DefinedTerm
76 Nc09b708e4aad4c038ec1983292b30460 schema:volumeNumber 8
77 rdf:type schema:PublicationVolume
78 Nc17c427893344ac9b2ab62d99bda3d5a schema:name pubmed_id
79 schema:value 19435474
80 rdf:type schema:PropertyValue
81 Nc3550a1c854f4179a4cddca702740c66 schema:name Springer Nature - SN SciGraph project
82 rdf:type schema:Organization
83 Nc529a8ad42bb4eb9804c70abfcf02645 rdf:first sg:person.0737006745.40
84 rdf:rest N150bfbedcbdc4470ae6a6016050c4e3a
85 Ne9934495e83444e8b2881a366182c6da schema:name nlm_unique_id
86 schema:value 101147570
87 rdf:type schema:PropertyValue
88 Nf7a6b11f594e4f658ce3d86145947b35 schema:name readcube_id
89 schema:value 8feccc2446e5ae643f005462e95fa69737e08c887bfe1f27c9034d8e27caaffd
90 rdf:type schema:PropertyValue
91 Nfa4d48a9500c4d3d93e08820ec345e4b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
92 schema:name Transcription, Genetic
93 rdf:type schema:DefinedTerm
94 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
95 schema:name Biological Sciences
96 rdf:type schema:DefinedTerm
97 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
98 schema:name Genetics
99 rdf:type schema:DefinedTerm
100 sg:grant.2726065 http://pending.schema.org/fundedItem sg:pub.10.1186/jbiol132
101 rdf:type schema:MonetaryGrant
102 sg:journal.1032884 schema:issn 1478-5854
103 1741-7007
104 schema:name BMC Biology
105 rdf:type schema:Periodical
106 sg:person.01106662166.38 schema:affiliation https://www.grid.ac/institutes/grid.419234.9
107 schema:familyName Aravind
108 schema:givenName L
109 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01106662166.38
110 rdf:type schema:Person
111 sg:person.0737006745.40 schema:affiliation https://www.grid.ac/institutes/grid.419234.9
112 schema:familyName Venancio
113 schema:givenName Thiago M
114 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0737006745.40
115 rdf:type schema:Person
116 sg:pub.10.1007/s00438-003-0952-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1050711091
117 https://doi.org/10.1007/s00438-003-0952-x
118 rdf:type schema:CreativeWork
119 sg:pub.10.1038/ng881 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010954918
120 https://doi.org/10.1038/ng881
121 rdf:type schema:CreativeWork
122 sg:pub.10.1038/nrg1272 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018231980
123 https://doi.org/10.1038/nrg1272
124 rdf:type schema:CreativeWork
125 sg:pub.10.1186/1471-2105-8-293 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007754367
126 https://doi.org/10.1186/1471-2105-8-293
127 rdf:type schema:CreativeWork
128 sg:pub.10.1186/1752-0509-3-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011643872
129 https://doi.org/10.1186/1752-0509-3-8
130 rdf:type schema:CreativeWork
131 https://doi.org/10.1016/j.jmb.2006.02.019 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018154049
132 rdf:type schema:CreativeWork
133 https://doi.org/10.1016/s0022-2836(61)80072-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010232058
134 rdf:type schema:CreativeWork
135 https://doi.org/10.1038/msb.2008.63 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035608084
136 rdf:type schema:CreativeWork
137 https://doi.org/10.1093/nar/gkm910 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012798639
138 rdf:type schema:CreativeWork
139 https://doi.org/10.1093/nar/gkm994 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011544616
140 rdf:type schema:CreativeWork
141 https://doi.org/10.1101/gr.086595.108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043032853
142 rdf:type schema:CreativeWork
143 https://doi.org/10.1146/annurev.bi.61.070192.005201 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004544236
144 rdf:type schema:CreativeWork
145 https://www.grid.ac/institutes/grid.419234.9 schema:alternateName National Center for Biotechnology Information
146 schema:name National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 20894, Bethesda, Maryland, USA
147 rdf:type schema:Organization
 




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


...