The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-12

AUTHORS

F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, T Paczian, A Rodriguez, R Stevens, A Wilke, J Wilkening, RA Edwards

ABSTRACT

BACKGROUND: Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers. RESULTS: A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats. CONCLUSION: The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis - the availability of high-performance computing for annotating the data. http://metagenomics.nmpdr.org. More... »

PAGES

386

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-9-386

DOI

http://dx.doi.org/10.1186/1471-2105-9-386

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1006083026

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18803844


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/2008/0806", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information Systems", 
        "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": "Algorithms", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Database Management Systems", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Databases, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Information Storage and Retrieval", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Internet", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Phylogeny", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Proteome", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "User-Computer Interface", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Argonne National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.187073.a", 
          "name": [
            "Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, 60439, Argonne, IL, USA", 
            "Computation Institute, University of Chicago, 60637, Chicago, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Meyer", 
        "givenName": "F", 
        "id": "sg:person.0623154651.88", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0623154651.88"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Computation Institute, University of Chicago, 60637, Chicago, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Paarmann", 
        "givenName": "D", 
        "id": "sg:person.0777253413.55", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0777253413.55"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Computation Institute, University of Chicago, 60637, Chicago, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "D'Souza", 
        "givenName": "M", 
        "id": "sg:person.01152724247.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01152724247.02"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Argonne National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.187073.a", 
          "name": [
            "Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, 60439, Argonne, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Olson", 
        "givenName": "R", 
        "id": "sg:person.01021612334.04", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021612334.04"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Argonne National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.187073.a", 
          "name": [
            "Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, 60439, Argonne, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Glass", 
        "givenName": "EM", 
        "id": "sg:person.014362205622.34", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014362205622.34"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Computation Institute, University of Chicago, 60637, Chicago, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kubal", 
        "givenName": "M", 
        "id": "sg:person.0707535617.12", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0707535617.12"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Argonne National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.187073.a", 
          "name": [
            "Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, 60439, Argonne, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Paczian", 
        "givenName": "T", 
        "id": "sg:person.01045366613.60", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01045366613.60"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Computation Institute, University of Chicago, 60637, Chicago, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Rodriguez", 
        "givenName": "A", 
        "id": "sg:person.01040102605.20", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01040102605.20"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Argonne National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.187073.a", 
          "name": [
            "Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, 60439, Argonne, IL, USA", 
            "Computation Institute, University of Chicago, 60637, Chicago, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Stevens", 
        "givenName": "R", 
        "id": "sg:person.0707416220.12", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0707416220.12"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Computation Institute, University of Chicago, 60637, Chicago, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wilke", 
        "givenName": "A", 
        "id": "sg:person.0624451746.13", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0624451746.13"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Argonne National Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.187073.a", 
          "name": [
            "Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, 60439, Argonne, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wilkening", 
        "givenName": "J", 
        "id": "sg:person.01314774340.13", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01314774340.13"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "San Diego State University", 
          "id": "https://www.grid.ac/institutes/grid.263081.e", 
          "name": [
            "Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, 60439, Argonne, IL, USA", 
            "Department of Computer Science, San Diego State University, 5500 Campanile Drive, 92182, San Diego, CA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Edwards", 
        "givenName": "RA", 
        "id": "sg:person.01136331207.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01136331207.33"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/nmeth976", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007149601", 
          "https://doi.org/10.1038/nmeth976"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth976", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007149601", 
          "https://doi.org/10.1038/nmeth976"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh084", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009527553"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gki866", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009961531"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1089/omi.2006.10.100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013157869"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/aem.00358-07", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013422473"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-9-75", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013431920", 
          "https://doi.org/10.1186/1471-2164-9-75"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkl947", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013967033"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-7-57", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020041008", 
          "https://doi.org/10.1186/1471-2164-7-57"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03959", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021574562", 
          "https://doi.org/10.1038/nature03959"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03959", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021574562", 
          "https://doi.org/10.1038/nature03959"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature02340", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023089166", 
          "https://doi.org/10.1038/nature02340"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature02340", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023089166", 
          "https://doi.org/10.1038/nature02340"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1462-2920.2007.01383.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023137141"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkl889", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029901284"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1107851", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032827529"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btl247", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033954668"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/aem.03006-05", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034568952"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2007-8-7-r143", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037510125", 
          "https://doi.org/10.1186/gb-2007-8-7-r143"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-162", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044943589", 
          "https://doi.org/10.1186/1471-2105-7-162"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-162", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044943589", 
          "https://doi.org/10.1186/1471-2105-7-162"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/30.1.183", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045702270"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/25.17.3389", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047265454"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature06810", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047805213", 
          "https://doi.org/10.1038/nature06810"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/28.18.3657", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048342572"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature06513", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052335368", 
          "https://doi.org/10.1038/nature06513"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1093857", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062449306"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2008-12", 
    "datePublishedReg": "2008-12-01", 
    "description": "BACKGROUND: Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers.\nRESULTS: A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats.\nCONCLUSION: The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis - the availability of high-performance computing for annotating the data. http://metagenomics.nmpdr.org.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2105-9-386", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1023786", 
        "issn": [
          "1471-2105"
        ], 
        "name": "BMC Bioinformatics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "9"
      }
    ], 
    "name": "The metagenomics RAST server \u2013 a public resource for the automatic phylogenetic and functional analysis of metagenomes", 
    "pagination": "386", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "1cfa061bb58c96c0e88b8c2d9ae4cf8b0f07280625e4b240dfb8d9bfebcf99c0"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "18803844"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965194"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2105-9-386"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1006083026"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2105-9-386", 
      "https://app.dimensions.ai/details/publication/pub.1006083026"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T13:13", 
    "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_8659_00000503.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1471-2105-9-386"
  }
]
 

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.10.1186/1471-2105-9-386'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-386'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-386'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-9-386'


 

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

274 TRIPLES      21 PREDICATES      61 URIs      30 LITERALS      18 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2105-9-386 schema:about N067c8378a8074cafb53b4e87c7b6e7be
2 N186984b079b54e97b85956c7039f8850
3 N1c8880df4d14476ab5ce2146eb3d3429
4 N72b5071d57e140aeb167a032cf1c448f
5 N72c65f75df564621ac41bc8db03ecc42
6 N73be4eb4a5144d5995df952269766ee1
7 N97be7a9d2363451e9162209f2e4333ff
8 N9c71d2760ae44dd4a0b97d586e2d0e16
9 Ne26a8624c6da41abb0ad26d073f6baad
10 anzsrc-for:08
11 anzsrc-for:0806
12 schema:author N4ea9c065c9d840a99f20f01a669599d8
13 schema:citation sg:pub.10.1038/nature02340
14 sg:pub.10.1038/nature03959
15 sg:pub.10.1038/nature06513
16 sg:pub.10.1038/nature06810
17 sg:pub.10.1038/nmeth976
18 sg:pub.10.1186/1471-2105-7-162
19 sg:pub.10.1186/1471-2164-7-57
20 sg:pub.10.1186/1471-2164-9-75
21 sg:pub.10.1186/gb-2007-8-7-r143
22 https://doi.org/10.1089/omi.2006.10.100
23 https://doi.org/10.1093/bioinformatics/btl247
24 https://doi.org/10.1093/nar/25.17.3389
25 https://doi.org/10.1093/nar/28.18.3657
26 https://doi.org/10.1093/nar/30.1.183
27 https://doi.org/10.1093/nar/gkh084
28 https://doi.org/10.1093/nar/gki866
29 https://doi.org/10.1093/nar/gkl889
30 https://doi.org/10.1093/nar/gkl947
31 https://doi.org/10.1111/j.1462-2920.2007.01383.x
32 https://doi.org/10.1126/science.1093857
33 https://doi.org/10.1126/science.1107851
34 https://doi.org/10.1128/aem.00358-07
35 https://doi.org/10.1128/aem.03006-05
36 schema:datePublished 2008-12
37 schema:datePublishedReg 2008-12-01
38 schema:description BACKGROUND: Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers. RESULTS: A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats. CONCLUSION: The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis - the availability of high-performance computing for annotating the data. http://metagenomics.nmpdr.org.
39 schema:genre research_article
40 schema:inLanguage en
41 schema:isAccessibleForFree true
42 schema:isPartOf N374004875bab48bfbc1c772d3083c108
43 N996c11d073ef4149b862363360d7030d
44 sg:journal.1023786
45 schema:name The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
46 schema:pagination 386
47 schema:productId N1f3965386da84c85baa753231d88c25b
48 N6198ea21df3943e49f7768fefa169ff6
49 N7175d5aa50264ff0901bfe33f0d296ef
50 Nc8e67d90413b41ad8434c3917cad875b
51 Ne7383cd550cd431e90017474e58d0ec2
52 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006083026
53 https://doi.org/10.1186/1471-2105-9-386
54 schema:sdDatePublished 2019-04-10T13:13
55 schema:sdLicense https://scigraph.springernature.com/explorer/license/
56 schema:sdPublisher N639d3cf761e843d893a915b53f5e6602
57 schema:url http://link.springer.com/10.1186%2F1471-2105-9-386
58 sgo:license sg:explorer/license/
59 sgo:sdDataset articles
60 rdf:type schema:ScholarlyArticle
61 N067c8378a8074cafb53b4e87c7b6e7be schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
62 schema:name Proteome
63 rdf:type schema:DefinedTerm
64 N08699ace240b4d1696f5dc279aa28061 rdf:first sg:person.0707535617.12
65 rdf:rest N57e70e629ec8492fbfdf71ed1a5feeb4
66 N170bf2a99606498da9aaa34c5b8a02f0 rdf:first sg:person.014362205622.34
67 rdf:rest N08699ace240b4d1696f5dc279aa28061
68 N186984b079b54e97b85956c7039f8850 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
69 schema:name Internet
70 rdf:type schema:DefinedTerm
71 N1c8880df4d14476ab5ce2146eb3d3429 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
72 schema:name Databases, Genetic
73 rdf:type schema:DefinedTerm
74 N1f3965386da84c85baa753231d88c25b schema:name nlm_unique_id
75 schema:value 100965194
76 rdf:type schema:PropertyValue
77 N25e2277f6e6a4fba870dfc6da3b3f7c8 rdf:first sg:person.01152724247.02
78 rdf:rest N43f85c2d9bea4255a435c9200608f68b
79 N2ba26e65c78d40218d7f59d98ee3d75c rdf:first sg:person.0624451746.13
80 rdf:rest N5c64b842870444a3b21ae942cf718505
81 N2d1c98487e3e435a9fba0a5d6ce2911f schema:name Computation Institute, University of Chicago, 60637, Chicago, IL, USA
82 rdf:type schema:Organization
83 N374004875bab48bfbc1c772d3083c108 schema:volumeNumber 9
84 rdf:type schema:PublicationVolume
85 N42aaa9d696cf4f2cba18543449d2e231 schema:name Computation Institute, University of Chicago, 60637, Chicago, IL, USA
86 rdf:type schema:Organization
87 N43f85c2d9bea4255a435c9200608f68b rdf:first sg:person.01021612334.04
88 rdf:rest N170bf2a99606498da9aaa34c5b8a02f0
89 N4ea9c065c9d840a99f20f01a669599d8 rdf:first sg:person.0623154651.88
90 rdf:rest Nc5a8b443da8548b5a6f3ded341035f0c
91 N57e70e629ec8492fbfdf71ed1a5feeb4 rdf:first sg:person.01045366613.60
92 rdf:rest N5caeb5c0b5484cea86fd12e928bf88ed
93 N5c64b842870444a3b21ae942cf718505 rdf:first sg:person.01314774340.13
94 rdf:rest Naba53436b6794d3ba8660bca36aed784
95 N5caeb5c0b5484cea86fd12e928bf88ed rdf:first sg:person.01040102605.20
96 rdf:rest Ndd3c76dbe91f44298f119545a3ca7cbf
97 N6198ea21df3943e49f7768fefa169ff6 schema:name doi
98 schema:value 10.1186/1471-2105-9-386
99 rdf:type schema:PropertyValue
100 N639d3cf761e843d893a915b53f5e6602 schema:name Springer Nature - SN SciGraph project
101 rdf:type schema:Organization
102 N7175d5aa50264ff0901bfe33f0d296ef schema:name pubmed_id
103 schema:value 18803844
104 rdf:type schema:PropertyValue
105 N72b5071d57e140aeb167a032cf1c448f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
106 schema:name User-Computer Interface
107 rdf:type schema:DefinedTerm
108 N72c65f75df564621ac41bc8db03ecc42 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
109 schema:name Information Storage and Retrieval
110 rdf:type schema:DefinedTerm
111 N73be4eb4a5144d5995df952269766ee1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
112 schema:name Database Management Systems
113 rdf:type schema:DefinedTerm
114 N794a0faf042549cfa4688ba61a04c3c2 schema:name Computation Institute, University of Chicago, 60637, Chicago, IL, USA
115 rdf:type schema:Organization
116 N96d013b9477c4a6d90da70c95a87dad1 schema:name Computation Institute, University of Chicago, 60637, Chicago, IL, USA
117 rdf:type schema:Organization
118 N97be7a9d2363451e9162209f2e4333ff schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
119 schema:name Algorithms
120 rdf:type schema:DefinedTerm
121 N996c11d073ef4149b862363360d7030d schema:issueNumber 1
122 rdf:type schema:PublicationIssue
123 N9c71d2760ae44dd4a0b97d586e2d0e16 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
124 schema:name Phylogeny
125 rdf:type schema:DefinedTerm
126 Naba53436b6794d3ba8660bca36aed784 rdf:first sg:person.01136331207.33
127 rdf:rest rdf:nil
128 Nb6d6cdc487dd4978980fb69c8d82d156 schema:name Computation Institute, University of Chicago, 60637, Chicago, IL, USA
129 rdf:type schema:Organization
130 Nc5a8b443da8548b5a6f3ded341035f0c rdf:first sg:person.0777253413.55
131 rdf:rest N25e2277f6e6a4fba870dfc6da3b3f7c8
132 Nc8e67d90413b41ad8434c3917cad875b schema:name dimensions_id
133 schema:value pub.1006083026
134 rdf:type schema:PropertyValue
135 Ndd3c76dbe91f44298f119545a3ca7cbf rdf:first sg:person.0707416220.12
136 rdf:rest N2ba26e65c78d40218d7f59d98ee3d75c
137 Ne26a8624c6da41abb0ad26d073f6baad schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
138 schema:name Software
139 rdf:type schema:DefinedTerm
140 Ne7383cd550cd431e90017474e58d0ec2 schema:name readcube_id
141 schema:value 1cfa061bb58c96c0e88b8c2d9ae4cf8b0f07280625e4b240dfb8d9bfebcf99c0
142 rdf:type schema:PropertyValue
143 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
144 schema:name Information and Computing Sciences
145 rdf:type schema:DefinedTerm
146 anzsrc-for:0806 schema:inDefinedTermSet anzsrc-for:
147 schema:name Information Systems
148 rdf:type schema:DefinedTerm
149 sg:journal.1023786 schema:issn 1471-2105
150 schema:name BMC Bioinformatics
151 rdf:type schema:Periodical
152 sg:person.01021612334.04 schema:affiliation https://www.grid.ac/institutes/grid.187073.a
153 schema:familyName Olson
154 schema:givenName R
155 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01021612334.04
156 rdf:type schema:Person
157 sg:person.01040102605.20 schema:affiliation N96d013b9477c4a6d90da70c95a87dad1
158 schema:familyName Rodriguez
159 schema:givenName A
160 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01040102605.20
161 rdf:type schema:Person
162 sg:person.01045366613.60 schema:affiliation https://www.grid.ac/institutes/grid.187073.a
163 schema:familyName Paczian
164 schema:givenName T
165 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01045366613.60
166 rdf:type schema:Person
167 sg:person.01136331207.33 schema:affiliation https://www.grid.ac/institutes/grid.263081.e
168 schema:familyName Edwards
169 schema:givenName RA
170 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01136331207.33
171 rdf:type schema:Person
172 sg:person.01152724247.02 schema:affiliation N2d1c98487e3e435a9fba0a5d6ce2911f
173 schema:familyName D'Souza
174 schema:givenName M
175 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01152724247.02
176 rdf:type schema:Person
177 sg:person.01314774340.13 schema:affiliation https://www.grid.ac/institutes/grid.187073.a
178 schema:familyName Wilkening
179 schema:givenName J
180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01314774340.13
181 rdf:type schema:Person
182 sg:person.014362205622.34 schema:affiliation https://www.grid.ac/institutes/grid.187073.a
183 schema:familyName Glass
184 schema:givenName EM
185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014362205622.34
186 rdf:type schema:Person
187 sg:person.0623154651.88 schema:affiliation https://www.grid.ac/institutes/grid.187073.a
188 schema:familyName Meyer
189 schema:givenName F
190 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0623154651.88
191 rdf:type schema:Person
192 sg:person.0624451746.13 schema:affiliation N42aaa9d696cf4f2cba18543449d2e231
193 schema:familyName Wilke
194 schema:givenName A
195 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0624451746.13
196 rdf:type schema:Person
197 sg:person.0707416220.12 schema:affiliation https://www.grid.ac/institutes/grid.187073.a
198 schema:familyName Stevens
199 schema:givenName R
200 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0707416220.12
201 rdf:type schema:Person
202 sg:person.0707535617.12 schema:affiliation Nb6d6cdc487dd4978980fb69c8d82d156
203 schema:familyName Kubal
204 schema:givenName M
205 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0707535617.12
206 rdf:type schema:Person
207 sg:person.0777253413.55 schema:affiliation N794a0faf042549cfa4688ba61a04c3c2
208 schema:familyName Paarmann
209 schema:givenName D
210 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0777253413.55
211 rdf:type schema:Person
212 sg:pub.10.1038/nature02340 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023089166
213 https://doi.org/10.1038/nature02340
214 rdf:type schema:CreativeWork
215 sg:pub.10.1038/nature03959 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021574562
216 https://doi.org/10.1038/nature03959
217 rdf:type schema:CreativeWork
218 sg:pub.10.1038/nature06513 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052335368
219 https://doi.org/10.1038/nature06513
220 rdf:type schema:CreativeWork
221 sg:pub.10.1038/nature06810 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047805213
222 https://doi.org/10.1038/nature06810
223 rdf:type schema:CreativeWork
224 sg:pub.10.1038/nmeth976 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007149601
225 https://doi.org/10.1038/nmeth976
226 rdf:type schema:CreativeWork
227 sg:pub.10.1186/1471-2105-7-162 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044943589
228 https://doi.org/10.1186/1471-2105-7-162
229 rdf:type schema:CreativeWork
230 sg:pub.10.1186/1471-2164-7-57 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020041008
231 https://doi.org/10.1186/1471-2164-7-57
232 rdf:type schema:CreativeWork
233 sg:pub.10.1186/1471-2164-9-75 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013431920
234 https://doi.org/10.1186/1471-2164-9-75
235 rdf:type schema:CreativeWork
236 sg:pub.10.1186/gb-2007-8-7-r143 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037510125
237 https://doi.org/10.1186/gb-2007-8-7-r143
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1089/omi.2006.10.100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013157869
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1093/bioinformatics/btl247 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033954668
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1093/nar/25.17.3389 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047265454
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1093/nar/28.18.3657 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048342572
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1093/nar/30.1.183 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045702270
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1093/nar/gkh084 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009527553
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1093/nar/gki866 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009961531
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1093/nar/gkl889 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029901284
254 rdf:type schema:CreativeWork
255 https://doi.org/10.1093/nar/gkl947 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013967033
256 rdf:type schema:CreativeWork
257 https://doi.org/10.1111/j.1462-2920.2007.01383.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1023137141
258 rdf:type schema:CreativeWork
259 https://doi.org/10.1126/science.1093857 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062449306
260 rdf:type schema:CreativeWork
261 https://doi.org/10.1126/science.1107851 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032827529
262 rdf:type schema:CreativeWork
263 https://doi.org/10.1128/aem.00358-07 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013422473
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1128/aem.03006-05 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034568952
266 rdf:type schema:CreativeWork
267 https://www.grid.ac/institutes/grid.187073.a schema:alternateName Argonne National Laboratory
268 schema:name Computation Institute, University of Chicago, 60637, Chicago, IL, USA
269 Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, 60439, Argonne, IL, USA
270 rdf:type schema:Organization
271 https://www.grid.ac/institutes/grid.263081.e schema:alternateName San Diego State University
272 schema:name Department of Computer Science, San Diego State University, 5500 Campanile Drive, 92182, San Diego, CA, USA
273 Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, 60439, Argonne, IL, USA
274 rdf:type schema:Organization
 




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


...