Environmental metagenome classification for constructing a microbiome fingerprint.
Identifieur interne : 000595 ( Main/Curation ); précédent : 000594; suivant : 000596Environmental metagenome classification for constructing a microbiome fingerprint.
Auteurs : Jolanta Kawulok [Pologne] ; Michal Kawulok [Pologne] ; Sebastian Deorowicz [Pologne]Source :
- Biology direct [ 1745-6150 ] ; 2019.
Abstract
Nowadays, not only are single genomes commonly analyzed, but also metagenomes, which are sets of, DNA fragments (reads) derived from microbes living in a given environment. Metagenome analysis is aimed at extracting crucial information on the organisms that have left their traces in an investigated environmental sample.In this study we focus on the MetaSUB Forensics Challenge (organized within the CAMDA 2018 conference) which consists in predicting the geographical origin of metagenomic samples. Contrary to the existing methods for environmental classification that are based on taxonomic or functional classification, we rely on the similarity between a sample and the reference database computed at a reads level.
DOI: 10.1186/s13062-019-0251-z
PubMed: 31722729
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000366
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :000366
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000581
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :002398
- to stream Ncbi, to step Curation: Pour aller vers cette notice dans l'étape Curation :002398
- to stream Ncbi, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :002398
- to stream Main, to step Merge: Pour aller vers cette notice dans l'étape Curation :000598
Links to Exploration step
pubmed:31722729Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Environmental metagenome classification for constructing a microbiome fingerprint.</title>
<author><name sortKey="Kawulok, Jolanta" sort="Kawulok, Jolanta" uniqKey="Kawulok J" first="Jolanta" last="Kawulok">Jolanta Kawulok</name>
<affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland. jolanta.kawulok@polsl.pl.</nlm:affiliation>
<country xml:lang="fr">Pologne</country>
<wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea>
<wicri:noRegion>Gliwice</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kawulok, Michal" sort="Kawulok, Michal" uniqKey="Kawulok M" first="Michal" last="Kawulok">Michal Kawulok</name>
<affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
<country xml:lang="fr">Pologne</country>
<wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea>
<wicri:noRegion>Gliwice</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name>
<affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
<country xml:lang="fr">Pologne</country>
<wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea>
<wicri:noRegion>Gliwice</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2019">2019</date>
<idno type="RBID">pubmed:31722729</idno>
<idno type="pmid">31722729</idno>
<idno type="doi">10.1186/s13062-019-0251-z</idno>
<idno type="wicri:Area/PubMed/Corpus">000366</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000366</idno>
<idno type="wicri:Area/PubMed/Curation">000366</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000366</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000581</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000581</idno>
<idno type="wicri:Area/Ncbi/Merge">002398</idno>
<idno type="wicri:Area/Ncbi/Curation">002398</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">002398</idno>
<idno type="wicri:Area/Main/Merge">000598</idno>
<idno type="wicri:Area/Main/Curation">000595</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Environmental metagenome classification for constructing a microbiome fingerprint.</title>
<author><name sortKey="Kawulok, Jolanta" sort="Kawulok, Jolanta" uniqKey="Kawulok J" first="Jolanta" last="Kawulok">Jolanta Kawulok</name>
<affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland. jolanta.kawulok@polsl.pl.</nlm:affiliation>
<country xml:lang="fr">Pologne</country>
<wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea>
<wicri:noRegion>Gliwice</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kawulok, Michal" sort="Kawulok, Michal" uniqKey="Kawulok M" first="Michal" last="Kawulok">Michal Kawulok</name>
<affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
<country xml:lang="fr">Pologne</country>
<wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea>
<wicri:noRegion>Gliwice</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name>
<affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation>
<country xml:lang="fr">Pologne</country>
<wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea>
<wicri:noRegion>Gliwice</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Biology direct</title>
<idno type="eISSN">1745-6150</idno>
<imprint><date when="2019" type="published">2019</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Nowadays, not only are single genomes commonly analyzed, but also metagenomes, which are sets of, DNA fragments (reads) derived from microbes living in a given environment. Metagenome analysis is aimed at extracting crucial information on the organisms that have left their traces in an investigated environmental sample.In this study we focus on the MetaSUB Forensics Challenge (organized within the CAMDA 2018 conference) which consists in predicting the geographical origin of metagenomic samples. Contrary to the existing methods for environmental classification that are based on taxonomic or functional classification, we rely on the similarity between a sample and the reference database computed at a reads level.</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000595 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Curation/biblio.hfd -nk 000595 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Main |étape= Curation |type= RBID |clé= pubmed:31722729 |texte= Environmental metagenome classification for constructing a microbiome fingerprint. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Curation/RBID.i -Sk "pubmed:31722729" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Curation/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |