Ontology type: schema:ScholarlyArticle Open Access: True
2011-10-26
AUTHORSOrion J Buske, Michael M Hoffman, Nadia Ponts, Karine G Le Roch, William Stafford Noble
ABSTRACTBackgroundAs genome-wide experiments and annotations become more prevalent, researchers increasingly require tools to help interpret data at this scale. Many functional genomics experiments involve partitioning the genome into labeled segments, such that segments sharing the same label exhibit one or more biochemical or functional traits. For example, a collection of ChlP-seq experiments yields a compendium of peaks, each labeled with one or more associated DNA-binding proteins. Similarly, manually or automatically generated annotations of functional genomic elements, including cis-regulatory modules and protein-coding or RNA genes, can also be summarized as genomic segmentations.ResultsWe present a software toolkit called Segtools that simplifies and automates the exploration of genomic segmentations. The software operates as a series of interacting tools, each of which provides one mode of summarization. These various tools can be pipelined and summarized in a single HTML page. We describe the Segtools toolkit and demonstrate its use in interpreting a collection of human histone modification data sets and Plasmodium falciparum local chromatin structure data sets.ConclusionsSegtools provides a convenient, powerful means of interpreting a genomic segmentation. More... »
PAGES415
http://scigraph.springernature.com/pub.10.1186/1471-2105-12-415
DOIhttp://dx.doi.org/10.1186/1471-2105-12-415
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1032875039
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/22029426
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": "Gene Expression",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genome, Human",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genomics",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Histone Code",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Histones",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Humans",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Plasmodium falciparum",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Software",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Department of Genome Sciences, University of Washington, PO Box 355065, 98195-5065, Seattle, WA, USA",
"id": "http://www.grid.ac/institutes/grid.34477.33",
"name": [
"Department of Genome Sciences, University of Washington, PO Box 355065, 98195-5065, Seattle, WA, USA"
],
"type": "Organization"
},
"familyName": "Buske",
"givenName": "Orion J",
"id": "sg:person.01104055172.55",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01104055172.55"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Genome Sciences, University of Washington, PO Box 355065, 98195-5065, Seattle, WA, USA",
"id": "http://www.grid.ac/institutes/grid.34477.33",
"name": [
"Department of Genome Sciences, University of Washington, PO Box 355065, 98195-5065, Seattle, WA, USA"
],
"type": "Organization"
},
"familyName": "Hoffman",
"givenName": "Michael M",
"id": "sg:person.01152170372.27",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01152170372.27"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "The Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, 92521, Riverside, CA, USA",
"id": "http://www.grid.ac/institutes/grid.266097.c",
"name": [
"The Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, 92521, Riverside, CA, USA"
],
"type": "Organization"
},
"familyName": "Ponts",
"givenName": "Nadia",
"id": "sg:person.01220303572.09",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01220303572.09"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "The Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, 92521, Riverside, CA, USA",
"id": "http://www.grid.ac/institutes/grid.266097.c",
"name": [
"The Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, 92521, Riverside, CA, USA"
],
"type": "Organization"
},
"familyName": "Le Roch",
"givenName": "Karine G",
"id": "sg:person.01032342213.12",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01032342213.12"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Computer Science and Engineering, University of Washington, PO Box 352350, 98195-2350, Seattle, WA, USA",
"id": "http://www.grid.ac/institutes/grid.34477.33",
"name": [
"Department of Genome Sciences, University of Washington, PO Box 355065, 98195-5065, Seattle, WA, USA",
"Department of Computer Science and Engineering, University of Washington, PO Box 352350, 98195-2350, Seattle, WA, USA"
],
"type": "Organization"
},
"familyName": "Noble",
"givenName": "William Stafford",
"id": "sg:person.01334532172.13",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01334532172.13"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1186/gb-2010-11-8-r86",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1046347776",
"https://doi.org/10.1186/gb-2010-11-8-r86"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2006-7-s1-s4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003630706",
"https://doi.org/10.1186/gb-2006-7-s1-s4"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nsmb.1659",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031385080",
"https://doi.org/10.1038/nsmb.1659"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-3-642-02008-7_12",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1036683792",
"https://doi.org/10.1007/978-3-642-02008-7_12"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng.154",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018442414",
"https://doi.org/10.1038/ng.154"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng.322",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051265360",
"https://doi.org/10.1038/ng.322"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature05329",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1052925490",
"https://doi.org/10.1038/nature05329"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-1-61779-292-2_11",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1034460467",
"https://doi.org/10.1007/978-1-61779-292-2_11"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.1630",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023421025",
"https://doi.org/10.1038/nbt.1630"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-1-60327-367-1_15",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1012763673",
"https://doi.org/10.1007/978-1-60327-367-1_15"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature09725",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023233286",
"https://doi.org/10.1038/nature09725"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature07667",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003950085",
"https://doi.org/10.1038/nature07667"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.1662",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050061238",
"https://doi.org/10.1038/nbt.1662"
],
"type": "CreativeWork"
}
],
"datePublished": "2011-10-26",
"datePublishedReg": "2011-10-26",
"description": "BackgroundAs genome-wide experiments and annotations become more prevalent, researchers increasingly require tools to help interpret data at this scale. Many functional genomics experiments involve partitioning the genome into labeled segments, such that segments sharing the same label exhibit one or more biochemical or functional traits. For example, a collection of ChlP-seq experiments yields a compendium of peaks, each labeled with one or more associated DNA-binding proteins. Similarly, manually or automatically generated annotations of functional genomic elements, including cis-regulatory modules and protein-coding or RNA genes, can also be summarized as genomic segmentations.ResultsWe present a software toolkit called Segtools that simplifies and automates the exploration of genomic segmentations. The software operates as a series of interacting tools, each of which provides one mode of summarization. These various tools can be pipelined and summarized in a single HTML page. We describe the Segtools toolkit and demonstrate its use in interpreting a collection of human histone modification data sets and Plasmodium falciparum local chromatin structure data sets.ConclusionsSegtools provides a convenient, powerful means of interpreting a genomic segmentation.",
"genre": "article",
"id": "sg:pub.10.1186/1471-2105-12-415",
"inLanguage": "en",
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.2691261",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2458833",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1023786",
"issn": [
"1471-2105"
],
"name": "BMC Bioinformatics",
"publisher": "Springer Nature",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "12"
}
],
"keywords": [
"functional genomic elements",
"cis-regulatory modules",
"genome-wide experiments",
"DNA-binding proteins",
"functional genomics experiments",
"functional traits",
"RNA genes",
"genomic elements",
"genomics experiments",
"structure data sets",
"exhibit one",
"annotation",
"genome",
"genes",
"powerful means",
"traits",
"protein",
"data sets",
"compendium",
"segments",
"toolkit",
"experiments",
"collection",
"tool",
"analysis",
"elements",
"set",
"ResultsWe",
"module",
"data",
"HTML pages",
"software toolkit",
"example",
"pages",
"segmentation",
"scale",
"mode",
"exploration",
"one",
"use",
"peak",
"series",
"means",
"researchers",
"summarization",
"software",
"exploratory analysis",
"simplifies"
],
"name": "Exploratory analysis of genomic segmentations with Segtools",
"pagination": "415",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1032875039"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/1471-2105-12-415"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"22029426"
]
}
],
"sameAs": [
"https://doi.org/10.1186/1471-2105-12-415",
"https://app.dimensions.ai/details/publication/pub.1032875039"
],
"sdDataset": "articles",
"sdDatePublished": "2022-05-10T10:01",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-springernature-scigraph/baseset/20220509/entities/gbq_results/article/article_539.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1186/1471-2105-12-415"
}
]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.10.1186/1471-2105-12-415'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-12-415'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-12-415'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-12-415'
This table displays all metadata directly associated to this object as RDF triples.
230 TRIPLES
22 PREDICATES
95 URIs
74 LITERALS
15 BLANK NODES