Ontology type: schema:ScholarlyArticle Open Access: True
2013-12
AUTHORSAlireza Hadj Khodabakhshi, Anthony P Fejes, Inanc Birol, Steven JM Jones
ABSTRACTBACKGROUND: In the past decade, bioinformatics tools have matured enough to reliably perform sophisticated primary data analysis on Next Generation Sequencing (NGS) data, such as mapping, assemblies and variant calling, however, there is still a dire need for improvements in the higher level analysis such as NGS data organization, analysis of mutation patterns and Genome Wide Association Studies (GWAS). RESULTS: We present a high throughput pipeline for identifying cancer mutation targets, capable of processing billions of variations across thousands of samples. This pipeline is coupled with our Human Variation Database to provide more complex down stream analysis on the variations hosted in the database. Most notably, these analysis include finding significantly mutated regions across multiple genomes and regions with mutational preferences within certain types of cancers. The results of the analysis is presented in HTML summary reports that incorporate gene annotations from various resources for the reported regions. CONCLUSION: MuteProc is available for download through the Vancouver Short Read Analysis Package on Sourceforge: http://vancouvershortr.sourceforge.net. Instructions for use and a tutorial are provided on the accompanying wiki pages at https://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=Pipeline_introduction. More... »
PAGES167
http://scigraph.springernature.com/pub.10.1186/1471-2105-14-167
DOIhttp://dx.doi.org/10.1186/1471-2105-14-167
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1020733634
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/23714400
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": "DNA Mutational Analysis",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genes, Neoplasm",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "High-Throughput Nucleotide Sequencing",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Humans",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Molecular Sequence Annotation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Mutation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Neoplasms",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Software",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "BC Cancer Agency",
"id": "https://www.grid.ac/institutes/grid.248762.d",
"name": [
"Genome Sciences Centre, BC Cancer Agency, Suite 100 - 570 West 7th Ave, V5Z 4S6, Vancouver, British Columbia, Canada"
],
"type": "Organization"
},
"familyName": "Hadj Khodabakhshi",
"givenName": "Alireza",
"id": "sg:person.01237475163.06",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01237475163.06"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "BC Cancer Agency",
"id": "https://www.grid.ac/institutes/grid.248762.d",
"name": [
"Genome Sciences Centre, BC Cancer Agency, Suite 100 - 570 West 7th Ave, V5Z 4S6, Vancouver, British Columbia, Canada"
],
"type": "Organization"
},
"familyName": "Fejes",
"givenName": "Anthony P",
"id": "sg:person.0672053321.72",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0672053321.72"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "BC Cancer Agency",
"id": "https://www.grid.ac/institutes/grid.248762.d",
"name": [
"Genome Sciences Centre, BC Cancer Agency, Suite 100 - 570 West 7th Ave, V5Z 4S6, Vancouver, British Columbia, Canada"
],
"type": "Organization"
},
"familyName": "Birol",
"givenName": "Inanc",
"id": "sg:person.01120102220.26",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01120102220.26"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "BC Cancer Agency",
"id": "https://www.grid.ac/institutes/grid.248762.d",
"name": [
"Genome Sciences Centre, BC Cancer Agency, Suite 100 - 570 West 7th Ave, V5Z 4S6, Vancouver, British Columbia, Canada"
],
"type": "Organization"
},
"familyName": "Jones",
"givenName": "Steven JM",
"id": "sg:person.011076371162.80",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011076371162.80"
],
"type": "Person"
}
],
"citation": [
{
"id": "https://doi.org/10.1182/blood-2009-06-225839",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001613916"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/29.1.308",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1005817660"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkp265",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1012288743"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/35085588",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1013839107",
"https://doi.org/10.1038/35085588"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/35085588",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1013839107",
"https://doi.org/10.1038/35085588"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2006-7-s1-s1",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1015572447",
"https://doi.org/10.1186/gb-2006-7-s1-s1"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkl996",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018548414"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.18632/oncotarget.653",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031285896"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1101/gr.107524.110",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1032096953"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btr100",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042699958"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1101/gr.134635.111",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1044550376"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2006-7-s1-s12",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050280568",
"https://doi.org/10.1186/gb-2006-7-s1-s12"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.95.20.11816",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050643010"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1126/science.1229259",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1062467132"
],
"type": "CreativeWork"
}
],
"datePublished": "2013-12",
"datePublishedReg": "2013-12-01",
"description": "BACKGROUND: In the past decade, bioinformatics tools have matured enough to reliably perform sophisticated primary data analysis on Next Generation Sequencing (NGS) data, such as mapping, assemblies and variant calling, however, there is still a dire need for improvements in the higher level analysis such as NGS data organization, analysis of mutation patterns and Genome Wide Association Studies (GWAS).\nRESULTS: We present a high throughput pipeline for identifying cancer mutation targets, capable of processing billions of variations across thousands of samples. This pipeline is coupled with our Human Variation Database to provide more complex down stream analysis on the variations hosted in the database. Most notably, these analysis include finding significantly mutated regions across multiple genomes and regions with mutational preferences within certain types of cancers. The results of the analysis is presented in HTML summary reports that incorporate gene annotations from various resources for the reported regions.\nCONCLUSION: MuteProc is available for download through the Vancouver Short Read Analysis Package on Sourceforge: http://vancouvershortr.sourceforge.net. Instructions for use and a tutorial are provided on the accompanying wiki pages at https://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=Pipeline_introduction.",
"genre": "research_article",
"id": "sg:pub.10.1186/1471-2105-14-167",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isPartOf": [
{
"id": "sg:journal.1023786",
"issn": [
"1471-2105"
],
"name": "BMC Bioinformatics",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "14"
}
],
"name": "Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline",
"pagination": "167",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"62ca360657ff6bede9113fe954b6cd6f8e29fc8d9b96caf653372e267204ca61"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"23714400"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"100965194"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/1471-2105-14-167"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1020733634"
]
}
],
"sameAs": [
"https://doi.org/10.1186/1471-2105-14-167",
"https://app.dimensions.ai/details/publication/pub.1020733634"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-11T00:14",
"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_8695_00000505.jsonl",
"type": "ScholarlyArticle",
"url": "http://link.springer.com/10.1186/1471-2105-14-167"
}
]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.10.1186/1471-2105-14-167'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-14-167'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-14-167'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-14-167'
This table displays all metadata directly associated to this object as RDF triples.
163 TRIPLES
21 PREDICATES
50 URIs
29 LITERALS
17 BLANK NODES