MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments
Abstract MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (h...
Saved in:
| Published in | Nucleic acids research Vol. 46; no. D1; pp. D684 - D691 |
|---|---|
| Main Authors | , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
04.01.2018
|
| Subjects | |
| Online Access | Get full text |
Cover
Loading…
| Abstract | Abstract
MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical 'strategy' approach. The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples from healthy human subjects in the Human Microbiome Project (http://portal.ihmpdcc.org/). Query results can be statistically analyzed and graphically visualized via interactive web applications launched directly in the browser, providing insight into microbial community diversity and allowing users to identify taxa associated with any experimental covariate. |
|---|---|
| AbstractList | Abstract
MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical 'strategy' approach. The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples from healthy human subjects in the Human Microbiome Project (http://portal.ihmpdcc.org/). Query results can be statistically analyzed and graphically visualized via interactive web applications launched directly in the browser, providing insight into microbial community diversity and allowing users to identify taxa associated with any experimental covariate. MicrobiomeDB ( http://microbiomeDB.org ) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center ( http://EuPathDB.org ) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical ‘strategy’ approach. The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples from healthy human subjects in the Human Microbiome Project ( http://portal.ihmpdcc.org/ ). Query results can be statistically analyzed and graphically visualized via interactive web applications launched directly in the browser, providing insight into microbial community diversity and allowing users to identify taxa associated with any experimental covariate. MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical 'strategy' approach. The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples from healthy human subjects in the Human Microbiome Project (http://portal.ihmpdcc.org/). Query results can be statistically analyzed and graphically visualized via interactive web applications launched directly in the browser, providing insight into microbial community diversity and allowing users to identify taxa associated with any experimental covariate.MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical 'strategy' approach. The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples from healthy human subjects in the Human Microbiome Project (http://portal.ihmpdcc.org/). Query results can be statistically analyzed and graphically visualized via interactive web applications launched directly in the browser, providing insight into microbial community diversity and allowing users to identify taxa associated with any experimental covariate. MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical 'strategy' approach. The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples from healthy human subjects in the Human Microbiome Project (http://portal.ihmpdcc.org/). Query results can be statistically analyzed and graphically visualized via interactive web applications launched directly in the browser, providing insight into microbial community diversity and allowing users to identify taxa associated with any experimental covariate. |
| Author | Zheng, Jie Beiting, Daniel P Kissinger, Jessica C Stoeckert, Christian J Aurrecoechea, Cristina Oliveira, Francislon S Brestelli, John Fischer, Steve Brunk, Brian P Iodice, John Cade, Shon Fernandes, Gabriel R Roos, David S |
| AuthorAffiliation | Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA Department of Genetics, University of Georgia, Athens, GA 30602, USA Instituto René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA |
| AuthorAffiliation_xml | – name: Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA – name: Instituto René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil – name: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – name: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA – name: Department of Genetics, University of Georgia, Athens, GA 30602, USA – name: Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA – name: Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil – name: Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – name: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA |
| Author_xml | – sequence: 1 givenname: Francislon S surname: Oliveira fullname: Oliveira, Francislon S organization: Instituto René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil – sequence: 2 givenname: John surname: Brestelli fullname: Brestelli, John organization: Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 3 givenname: Shon surname: Cade fullname: Cade, Shon organization: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 4 givenname: Jie surname: Zheng fullname: Zheng, Jie organization: Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 5 givenname: John surname: Iodice fullname: Iodice, John organization: Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 6 givenname: Steve surname: Fischer fullname: Fischer, Steve organization: Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 7 givenname: Cristina surname: Aurrecoechea fullname: Aurrecoechea, Cristina organization: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA – sequence: 8 givenname: Jessica C surname: Kissinger fullname: Kissinger, Jessica C organization: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA – sequence: 9 givenname: Brian P surname: Brunk fullname: Brunk, Brian P organization: Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 10 givenname: Christian J surname: Stoeckert fullname: Stoeckert, Christian J organization: Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 11 givenname: Gabriel R surname: Fernandes fullname: Fernandes, Gabriel R organization: Instituto René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil – sequence: 12 givenname: David S surname: Roos fullname: Roos, David S email: dsroos@sas.upenn.edu organization: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 13 givenname: Daniel P surname: Beiting fullname: Beiting, Daniel P email: beiting@upenn.edu organization: Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29106667$$D View this record in MEDLINE/PubMed |
| BookMark | eNp9UUlv1DAUtlARnZaeuCOfEFIJ9Yu3hANSFzapiAs9W7bjCS6JHexM1emvx6OZVoAqDvbTs7_F_t4B2gsxOIReAHkLpKUnQaeT_uctkFo-QQugoq5YK-o9tCCU8AoIa_bRQc7XhAADzp6h_boFIoSQC-S-epui8XF0F2fvsMZ5nWc3ZlyOhtiv8TToeRnTiMuGfZhdn_TsQ_8Gjz6UinXoytLD-m7TjQ9y2N1OLvnRhTk_R0-XesjuaFcP0dXHD9_PP1eX3z59OT-9rCyDeq6Y7ZxZMt6aRhBChbTAheSuM0ZKkB0zxFgDpjaW8fLHRsrayE40ttCAanqI3m91p5UZXWeLd9KDmsozdFqrqL36-yb4H6qPN4pLTikTReD1TiDFXyuXZzX6bN0w6ODiKitoBRAqG76BvvzT68HkPtsCgC2gJJJzcktl_VyyixtrPyggajM_VeandvMrnON_OPeyj6NfbdFxNf0X-BuOo62C |
| CitedBy_id | crossref_primary_10_1093_bib_bbaa082 crossref_primary_10_1016_j_scitotenv_2024_170010 crossref_primary_10_1109_JBHI_2022_3148672 crossref_primary_10_1186_s40168_020_00987_7 crossref_primary_10_1007_s00335_021_09871_7 crossref_primary_10_1016_j_lfs_2022_121118 crossref_primary_10_1161_STROKEAHA_121_034792 crossref_primary_10_1038_s41467_022_28034_z crossref_primary_10_1186_s12859_024_05803_9 crossref_primary_10_3389_fbinf_2021_774631 crossref_primary_10_3389_fmicb_2022_837396 crossref_primary_10_1021_jasms_9b00035 crossref_primary_10_1007_s41745_023_00370_z crossref_primary_10_1128_msphere_00670_20 crossref_primary_10_1371_journal_pntd_0011058 crossref_primary_10_1093_database_baac033 crossref_primary_10_1371_journal_pcbi_1006102 crossref_primary_10_1016_j_ymgme_2021_11_355 crossref_primary_10_1093_genetics_iyae035 crossref_primary_10_1186_s13326_019_0217_1 crossref_primary_10_1038_s41598_025_87256_5 crossref_primary_10_1093_jas_skz208 crossref_primary_10_5604_01_3001_0054_8093 crossref_primary_10_3389_fmicb_2022_1085079 crossref_primary_10_12688_gatesopenres_13087_2 crossref_primary_10_1093_nar_gkab929 crossref_primary_10_20517_mrr_2023_80 crossref_primary_10_1093_bib_bbad168 crossref_primary_10_1186_s40168_021_01089_8 crossref_primary_10_3390_app13031614 crossref_primary_10_1093_nar_gky136 crossref_primary_10_1016_j_csbj_2025_02_034 crossref_primary_10_12688_gatesopenres_13087_1 crossref_primary_10_1186_s40168_019_0740_4 crossref_primary_10_1093_gigascience_giad017 crossref_primary_10_1016_j_cois_2021_11_008 crossref_primary_10_1186_s40168_023_01505_1 |
| Cites_doi | 10.1126/science.1254529 10.1128/AEM.01541-09 10.1038/nature11234 10.1186/2047-217X-1-7 10.1038/ismej.2012.8 10.1038/nmeth.f.303 10.1093/nar/gkn741 10.7554/eLife.00458 10.1371/journal.pone.0061217 10.1126/scitranslmed.aad7121 10.1128/AEM.01043-13 10.1147/sj.402.0512 10.1186/gb-2011-12-6-r60 10.1186/s13059-014-0550-8 10.1038/ismej.2011.39 10.1186/2041-1480-4-43 10.1093/nar/gkp440 10.1371/journal.pone.0154556 10.1093/bioinformatics/btq415 10.1093/nar/gkw1017 10.1038/ismej.2011.139 10.1093/nar/gkw1105 10.1038/s41598-017-06665-3 10.1186/gb-2014-15-3-r46 10.1128/AEM.03006-05 10.1038/nbt1346 |
| ContentType | Journal Article |
| Copyright | The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. 2018 The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| Copyright_xml | – notice: The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. 2018 – notice: The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| DBID | TOX AAYXX CITATION CGR CUY CVF ECM EIF NPM 7X8 5PM |
| DOI | 10.1093/nar/gkx1027 |
| DatabaseName | Oxford Journals Open Access Collection CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE - Academic MEDLINE |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database – sequence: 3 dbid: TOX name: Oxford Journals Open Access Collection url: https://academic.oup.com/journals/ sourceTypes: Publisher |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Anatomy & Physiology Chemistry |
| DocumentTitleAlternate | Database issue |
| EISSN | 1362-4962 |
| EndPage | D691 |
| ExternalDocumentID | PMC5753346 29106667 10_1093_nar_gkx1027 10.1093/nar/gkx1027 |
| Genre | Journal Article |
| GroupedDBID | --- -DZ -~X .I3 0R~ 123 18M 1TH 29N 2WC 4.4 482 53G 5VS 5WA 70E 85S A8Z AAFWJ AAHBH AAMVS AAOGV AAPXW AAUQX AAVAP ABEJV ABGNP ABPTD ABQLI ABXVV ACGFO ACGFS ACIWK ACNCT ACPRK ACUTJ ADBBV ADHZD AEGXH AENEX AENZO AFFNX AFPKN AFRAH AFYAG AHMBA AIAGR ALMA_UNASSIGNED_HOLDINGS ALUQC AMNDL AOIJS BAWUL BAYMD BCNDV CAG CIDKT CS3 CZ4 DIK DU5 D~K E3Z EBD EBS EJD EMOBN F5P GROUPED_DOAJ GX1 H13 HH5 HYE HZ~ IH2 KAQDR KQ8 KSI M49 OAWHX OBC OBS OEB OES OJQWA P2P PEELM PQQKQ R44 RD5 RNS ROL ROZ RPM RXO SV3 TN5 TOX TR2 WG7 WOQ X7H XSB YSK ZKX ~91 ~D7 ~KM AAYXX CITATION OVT CGR CUY CVF ECM EIF NPM 7X8 5PM |
| ID | FETCH-LOGICAL-c412t-4cdebf459b8600367c15675edbb7717d4b0bcb1b2bc454968772b7d68cebf13a3 |
| IEDL.DBID | TOX |
| ISSN | 0305-1048 1362-4962 |
| IngestDate | Thu Aug 21 18:16:17 EDT 2025 Thu Jul 10 19:09:50 EDT 2025 Mon Jul 21 06:05:48 EDT 2025 Thu Apr 24 23:08:50 EDT 2025 Tue Jul 01 02:07:11 EDT 2025 Wed Apr 02 07:01:49 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | D1 |
| Language | English |
| License | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com http://creativecommons.org/licenses/by-nc/4.0 The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c412t-4cdebf459b8600367c15675edbb7717d4b0bcb1b2bc454968772b7d68cebf13a3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors contributed equally to this work as first authors. |
| OpenAccessLink | https://dx.doi.org/10.1093/nar/gkx1027 |
| PMID | 29106667 |
| PQID | 1961037856 |
| PQPubID | 23479 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_5753346 proquest_miscellaneous_1961037856 pubmed_primary_29106667 crossref_citationtrail_10_1093_nar_gkx1027 crossref_primary_10_1093_nar_gkx1027 oup_primary_10_1093_nar_gkx1027 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2018-01-04 |
| PublicationDateYYYYMMDD | 2018-01-04 |
| PublicationDate_xml | – month: 01 year: 2018 text: 2018-01-04 day: 04 |
| PublicationDecade | 2010 |
| PublicationPlace | England |
| PublicationPlace_xml | – name: England |
| PublicationTitle | Nucleic acids research |
| PublicationTitleAlternate | Nucleic Acids Res |
| PublicationYear | 2018 |
| Publisher | Oxford University Press |
| Publisher_xml | – name: Oxford University Press |
| References | ( key 20180103185554_B21) 2011; 5 ( key 20180103185554_B24) 2016; 11 ( key 20180103185554_B29) 2009; 37 ( key 20180103185554_B36) 2014; 15 ( key 20180103185554_B5) 2011; 12 ( key 20180103185554_B27) 2010; 26 ( key 20180103185554_B13) 2017; 45 ( key 20180103185554_B6) 2014; 15 key 20180103185554_B12 ( key 20180103185554_B19) 2006; 72 ( key 20180103185554_B22) 2007; 25 ( key 20180103185554_B1) 2013; 79 ( key 20180103185554_B35) 2013; 8 key 20180103185554_B7 key 20180103185554_B11 key 20180103185554_B9 key 20180103185554_B10 ENVO Consortium ( key 20180103185554_B23) 2013; 4 ( key 20180103185554_B20) 2012; 6 ( key 20180103185554_B31) 2017 R Core Team ( key 20180103185554_B33) 2017 Human Microbiome Project Consortium ( key 20180103185554_B14) 2012; 486 ( key 20180103185554_B4) 2010; 7 ( key 20180103185554_B3) 2009; 75 ( key 20180103185554_B18) 2012; 1 ( key 20180103185554_B28) 2001; 40 ( key 20180103185554_B30) 2017; 45 ( key 20180103185554_B34) 2009 ( key 20180103185554_B2) 2012; 6 ( key 20180103185554_B8) 2017 ( key 20180103185554_B25) 2016 RStudio Team ( key 20180103185554_B32) 2016 ( key 20180103185554_B17) 2014; 345 ( key 20180103185554_B37) 2017; 7 ( key 20180103185554_B16) 2013; 2 ( key 20180103185554_B26) 2009; 37 ( key 20180103185554_B15) 2016; 8 |
| References_xml | – year: 2017 ident: key 20180103185554_B8 article-title: The microbiome and big data publication-title: Curr. Opin. Syst. Biol. – volume: 345 start-page: 1048 year: 2014 ident: key 20180103185554_B17 article-title: Longitudinal analysis of microbial interaction between humans and the indoor environment publication-title: Science doi: 10.1126/science.1254529 – volume: 75 start-page: 7537 year: 2009 ident: key 20180103185554_B3 article-title: Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.01541-09 – volume: 486 start-page: 207 year: 2012 ident: key 20180103185554_B14 article-title: Structure, function and diversity of the healthy human microbiome publication-title: Nature doi: 10.1038/nature11234 – year: 2016 ident: key 20180103185554_B32 article-title: RStudio: Integrated Development Environment for R – volume: 1 start-page: 7 year: 2012 ident: key 20180103185554_B18 article-title: The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome publication-title: Gigascience doi: 10.1186/2047-217X-1-7 – volume: 6 start-page: 1621 year: 2012 ident: key 20180103185554_B2 article-title: Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms publication-title: ISME J. doi: 10.1038/ismej.2012.8 – volume: 7 start-page: 335 year: 2010 ident: key 20180103185554_B4 article-title: QIIME allows analysis of high-throughput community sequencing data publication-title: Nat. Methods doi: 10.1038/nmeth.f.303 – ident: key 20180103185554_B12 article-title: Phinch: an interactive, exploratory data visualization framework for –Omic datasets – volume: 37 start-page: D5 year: 2009 ident: key 20180103185554_B29 article-title: Database resources of the National Center for Biotechnology Information publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkn741 – volume: 2 start-page: e00458 year: 2013 ident: key 20180103185554_B16 article-title: Cohabiting family members share microbiota with one another and with their dogs publication-title: elife doi: 10.7554/eLife.00458 – volume: 8 start-page: e61217 year: 2013 ident: key 20180103185554_B35 article-title: phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data publication-title: PLoS ONE doi: 10.1371/journal.pone.0061217 – volume: 8 start-page: 343ra82 year: 2016 ident: key 20180103185554_B15 article-title: Antibiotics, birth mode, and diet shape microbiome maturation during early life publication-title: Sci. Transl. Med. doi: 10.1126/scitranslmed.aad7121 – ident: key 20180103185554_B11 article-title: Human Microbiome Project publication-title: Data Portal. – volume-title: ICBO/BioCreative year: 2016 ident: key 20180103185554_B25 article-title: Malaria Study Data Integration and Information Retrieval Based on OBO Foundry Ontologies – ident: key 20180103185554_B9 article-title: Office of Cyber Infrastructure and Computational Biology (OCICB), National Institute of Allergy and Infectious Diseases (NIAID) publication-title: Nephele. – volume: 79 start-page: 5112 year: 2013 ident: key 20180103185554_B1 article-title: Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.01043-13 – volume: 40 start-page: 512 year: 2001 ident: key 20180103185554_B28 article-title: K2/Kleisli and GUS: Experiments in integrated access to genomic data sources publication-title: IBM Syst. J. doi: 10.1147/sj.402.0512 – ident: key 20180103185554_B10 article-title: Metaviz: interactive statistical and visual analysis of metagenomic data – volume: 12 start-page: R60 year: 2011 ident: key 20180103185554_B5 article-title: Metagenomic biomarker discovery and explanation publication-title: Genome Biol. doi: 10.1186/gb-2011-12-6-r60 – volume-title: R Foundation for Statistical Computing year: 2017 ident: key 20180103185554_B33 article-title: R: A Language and Environment for Statistical Computing – start-page: c2009 volume-title: ggplot2: Elegant Graphics for Data Analysis Springer year: 2009 ident: key 20180103185554_B34 – volume: 15 start-page: 550 year: 2014 ident: key 20180103185554_B36 article-title: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 publication-title: Genome Biol. doi: 10.1186/s13059-014-0550-8 – volume: 5 start-page: 1565 year: 2011 ident: key 20180103185554_B21 article-title: The genomic standards consortium: bringing standards to life for microbial ecology publication-title: ISME J. doi: 10.1038/ismej.2011.39 – volume: 4 start-page: 43 year: 2013 ident: key 20180103185554_B23 article-title: The environment ontology: contextualising biological and biomedical entities publication-title: J. Biomed. Semantics doi: 10.1186/2041-1480-4-43 – volume: 37 start-page: W170 year: 2009 ident: key 20180103185554_B26 article-title: BioPortal: ontologies and integrated data resources at the click of a mouse publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkp440 – year: 2017 ident: key 20180103185554_B31 article-title: shiny: Web Application Framework for R – volume: 11 start-page: e0154556 year: 2016 ident: key 20180103185554_B24 article-title: The ontology for biomedical investigations publication-title: PLoS ONE doi: 10.1371/journal.pone.0154556 – volume: 26 start-page: 2354 year: 2010 ident: key 20180103185554_B27 article-title: ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq415 – volume: 45 start-page: D535 year: 2017 ident: key 20180103185554_B30 article-title: Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw1017 – ident: key 20180103185554_B7 article-title: QIITA: an open-source microbial study management platform – volume: 6 start-page: 610 year: 2012 ident: key 20180103185554_B20 article-title: An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea publication-title: ISME J. doi: 10.1038/ismej.2011.139 – volume: 45 start-page: D581 year: 2017 ident: key 20180103185554_B13 article-title: EuPathDB: the eukaryotic pathogen genomics database resource publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw1105 – volume: 7 start-page: 6589 year: 2017 ident: key 20180103185554_B37 article-title: Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing publication-title: Sci. Rep. doi: 10.1038/s41598-017-06665-3 – volume: 15 start-page: R46 year: 2014 ident: key 20180103185554_B6 article-title: Kraken: ultrafast metagenomic sequence classification using exact alignments publication-title: Genome Biol. doi: 10.1186/gb-2014-15-3-r46 – volume: 72 start-page: 5069 year: 2006 ident: key 20180103185554_B19 article-title: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB publication-title: Appl. Environ. Microbiol. doi: 10.1128/AEM.03006-05 – volume: 25 start-page: 1251 year: 2007 ident: key 20180103185554_B22 article-title: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration publication-title: Nat. Biotechnol. doi: 10.1038/nbt1346 |
| SSID | ssj0014154 |
| Score | 2.4641767 |
| Snippet | Abstract
MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to... MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to... MicrobiomeDB ( http://microbiomeDB.org ) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to... |
| SourceID | pubmedcentral proquest pubmed crossref oup |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | D684 |
| SubjectTerms | Animals Computer Simulation Data Mining - methods Database Issue Databases, Genetic Datasets as Topic Environmental Microbiology Genetic Variation Humans Internet Microbiota Mobile Applications Systems Biology User-Computer Interface Workflow |
| Title | MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/29106667 https://www.proquest.com/docview/1961037856 https://pubmed.ncbi.nlm.nih.gov/PMC5753346 |
| Volume | 46 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwhV1LS8NAEF7Ui17Et_VRVxAPYjCP3WTjzVcpQvWi0FvIPqLFZlvaFNRf7-wmja2IHhIImQ1hv5D5ZmfnG4ROIuExyTzlKOpyBzye63AvjR0aeyoLXRkoK6bTeQjbz-S-S7vVBtnxLyn8OLjQ6eji5e0dPKEpGgf3ayTynx67dbIAfFCpEmVFNQmryvB-jJ1zPHPFbDOc8ufWyBlf01pDqxVJxFclqutoQekNtHmlIUDOP_Aptts27Xr4Blq-mbZs20Sq0yt1lXJ1e32JU1zqNI9xJbWEh_20MCwVwwlPlSLAeZ3j3DaKwKmWcKT9j09zldePw9-dAMZb6Ll193TTdqo-Co4gnl84REjFM0JjzkKjPwP4UIgTlOQ8gmhOEu5ywT3uc0EgXAwZMG4eyZAJGOYFabCNlvRAq12EeZwFHDhKJlxGhBczmWVMRZSG0heMZg10Np3kRFQi46bXRT8pk91BAogkFSINdFIbD0ttjd_NjgCtvy2Op0gmMOMm5ZFqNZiME_i_mEJIRsMG2imRrR_kA1OC4A1GR3OY1wZGeXv-ju69WgVu4LhBQMK9f99sH60Aw2J2zYYcoKViNFGHwGIK3kSLkXvXtGsATfs9fwHFN_VZ |
| linkProvider | Oxford University Press |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=MicrobiomeDB%3A+a+systems+biology+platform+for+integrating%2C+mining+and+analyzing+microbiome+experiments&rft.jtitle=Nucleic+acids+research&rft.au=Oliveira%2C+Francislon+S&rft.au=Brestelli%2C+John&rft.au=Cade%2C+Shon&rft.au=Zheng%2C+Jie&rft.date=2018-01-04&rft.pub=Oxford+University+Press&rft.issn=0305-1048&rft.eissn=1362-4962&rft.volume=46&rft.issue=Database+issue&rft.spage=D684&rft.epage=D691&rft_id=info:doi/10.1093%2Fnar%2Fgkx1027&rft_id=info%3Apmid%2F29106667&rft.externalDocID=PMC5753346 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0305-1048&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0305-1048&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0305-1048&client=summon |