Minimum Information about any (x) Sequence
Names
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Minimum Information about any (x) Sequence
metasource: Fairsharing.org
version: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
MIxS
metasource: Fairsharing.org
version: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Names
More detailed information about this field from each metasource.
Minimum Information about any (x) Sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
MIxS
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Names
More detailed information about this field from each metasource.
Minimum Information about any (x) Sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
MIxS
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
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The minimum information about any (x) sequence (MIxS) is an overarching framework of sequence metadata, that includes technology-specific checklists from the previous MIGS and MIMS standards, provides a way of introducing additional checklists such as MIMARKS, and also allows annotation of sample data using environmental packages.
Description
More detailed information about this field from each metasource.
The minimum information about any (x) sequence (MIxS) is an overarching framework of sequence metadata, that includes technology-specific checklists from the previous MIGS and MIMS standards, provides a way of introducing additional checklists such as MIMARKS, and also allows annotation of sample data using environmental packages.
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Webpage:
http://gensc.org/mixs/Webpage
More detailed information about this field from each metasource.
http://gensc.org/mixs/
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
PMID: 21552244
metasource: Fairsharing.org
version: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Publications
More detailed information about this field from each metasource.
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
PMID: 21552244
metasource: Fairsharing.org
version: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
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Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
PubMed citations: 264.
264 articles citing: Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake. PMID:35902092
The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. PMID:35889831
Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods. PMID:35852418
Ecosystem-specific microbiota and microbiome databases in the era of big data. PMID:35842686
Metadata harmonization-Standards are the key for a better usage of omics data for integrative microbiome analysis. PMID:35751093
A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses. PMID:35739325
Examining the Relationships Between Sleep Physiology and the Gut Microbiome in Preclinical and Translational Research: Protocol for a Scoping Review. PMID:35727619
A Simple Standard for Sharing Ontological Mappings (SSSOM). PMID:35616100
Availability of vitamin B12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems. PMID:35585186
A decade of GigaScience: 10 years of the evolving genomic and biomedical standards landscape. PMID:35579551
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata. PMID:35576001
Enhancing Data Integration, Interoperability, and Reuse to Address Complex and Emerging Environmental Health Problems. PMID:35549252
Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter. PMID:35545619
met v1: expanding on old estimations of biodiversity from eDNA with a new database framework. PMID:35543254
Sugars dominate the seagrass rhizosphere. PMID:35501482
PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types. PMID:35208748
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. PMID:35169842
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences. PMID:35134858
The crewed journey to Mars and its implications for the human microbiome. PMID:35125119
Biological manganese-dependent sulfide oxidation impacts elemental gradients in redox-stratified systems: indications from the Black Sea water column. PMID:35124702
Bacterial Indicators Are Ubiquitous Members of Pelagic Microbiome in Anthropogenically Impacted Coastal Ecosystem. PMID:35111137
Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies. PMID:35106579
Significance of gene variants for the functional biogeography of the near-surface Atlantic Ocean microbiome. PMID:35075131
Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems. PMID:34956127
Ancient Metagenomic Studies: Considerations for the Wider Scientific Community. PMID:34931883
Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation. PMID:34859349
Insights into the bacterial community composition of farmed Caulerpa lentillifera: A comparison between contrasting health states. PMID:34821475
Reporting guidelines for human microbiome research: the STORMS checklist. PMID:34789871
An Aniline-Substituted Bile Salt Analog Protects both Mice and Hamsters from Multiple Clostridioides difficile Strains. PMID:34780262
RESCRIPt: Reproducible sequence taxonomy reference database management. PMID:34748542
Tracking, Synthesizing, and Sharing Global Batrachochytrium Data at AmphibianDisease.org. PMID:34692807
Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil. PMID:34531836
Associations of the gut microbiome with hepatic adiposity in the Multiethnic Cohort Adiposity Phenotype Study. PMID:34491886
Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota. PMID:34460815
Opportunities and challenges of macrogenetic studies. PMID:34408318
Draft Genome Sequences of the Three Massilia Strains AB1, ST3, and ZL223. PMID:34323604
Forming Consensus To Advance Urobiome Research. PMID:34282932
An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities. PMID:34012005
A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers. PMID:33983435
Deep-sea mussels from a hybrid zone on the Mid-Atlantic Ridge host genetically indistinguishable symbionts. PMID:33972724
Specialized pro-resolving mediator lipidome and 16S rRNA bacterial microbiome data associated with human chronic rhinosinusitis. PMID:33937456
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox. PMID:33785070
DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions. PMID:33673098
Whole Genome Sequencing Applied to Pathogen Source Tracking in Food Industry: Key Considerations for Robust Bioinformatics Data Analysis and Reliable Results Interpretation. PMID:33671973
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities. PMID:33622857
Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium. PMID:33522965
Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. PMID:33500403
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. PMID:33494105
Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis. PMID:33432777
Host-parasitoid associations in marine planktonic time series: Can metabarcoding help reveal them? PMID:33411833
Extensive Microbial Processing of Polysaccharides in the South Pacific Gyre via Selfish Uptake and Extracellular Hydrolysis. PMID:33391202
Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods. PMID:33363701
HMPDACC: a Human Microbiome Project Multi-omic data resource. PMID:33305317
Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea. PMID:33304331
The Taxon Hypothesis Paradigm-On the Unambiguous Detection and Communication of Taxa. PMID:33266327
Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting. PMID:33226702
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. PMID:33221926
Towards a unified data infrastructure to support European and global microbiome research: a call to action. PMID:33196130
Genomes OnLine Database (GOLD) v.8: overview and updates. PMID:33152092
Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems. PMID:33082281
A P4 Medicine Perspective of Gut Microbiota and Prediabetes: Systems Analysis and Personalized Intervention. PMID:33062587
Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements. PMID:32883786
"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI's sequence read archive". PMID:32883210
The archives are half-empty: an assessment of the availability of microbial community sequencing data. PMID:32859925
FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results. PMID:32815545
Method development for cross-study microbiome data mining: Challenges and opportunities. PMID:32802279
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data. PMID:32735679
High-Quality Draft Genome Sequences of the Uncultured Delta3 Endosymbiont (Deltaproteobacteria) Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis. PMID:32732238
The Oral and Gut Bacterial Microbiomes: Similarities, Differences, and Connections. PMID:32691605
Structure and co-occurrence patterns of bacterial communities associated with white faeces disease outbreaks in Pacific white-leg shrimp Penaeus vannamei aquaculture. PMID:32686764
COVID-19 pandemic reveals the peril of ignoring metadata standards. PMID:32561801
Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea. PMID:32494090
The promise and challenge of cancer microbiome research. PMID:32487228
Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB). PMID:32463383
Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. PMID:32451471
Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. PMID:32416615
A practical guide to amplicon and metagenomic analysis of microbiome data. PMID:32394199
QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data. PMID:32343490
"Candidatus Ethanoperedens," a Thermophilic Genus of Archaea Mediating the Anaerobic Oxidation of Ethane. PMID:32317322
High-Quality Draft Genome Sequences of Two Deltaproteobacterial Endosymbionts, Delta1a and Delta1b, from the Uncultured Sva0081 Clade, Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis. PMID:32299882
Repositories for Taxonomic Data: Where We Are and What is Missing. PMID:32298457
Niche-based assembly of bacterial consortia on the diatom Thalassiosira rotula is stable and reproducible. PMID:32203123
A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile. PMID:32111201
Integrating Computational Methods to Investigate the Macroecology of Microbiomes. PMID:32010196
Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata. PMID:31960040
Transgenic Testing Does Not Support a Role for Additional Candidate Genes in Wolbachia Male Killing or Cytoplasmic Incompatibility. PMID:31937677
OHMI: the ontology of host-microbiome interactions. PMID:31888755
The COMPARE Data Hubs. PMID:31868882
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes. PMID:31728526
The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation. PMID:31685817
Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels. PMID:31611646
Advances and Challenges in Metatranscriptomic Analysis. PMID:31608125
Parasite microbiome project: Grand challenges. PMID:31600339
Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019. PMID:31594828
Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity. PMID:31488541
Anaerobic Degradation of Non-Methane Alkanes by "Candidatus Methanoliparia" in Hydrocarbon Seeps of the Gulf of Mexico. PMID:31431553
Transcriptomic analysis of Pacific white shrimp (Litopenaeus vannamei, Boone 1931) in response to acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus. PMID:31408485
redbiom: a Rapid Sample Discovery and Feature Characterization System. PMID:31239397
Global diversity and biogeography of bacterial communities in wastewater treatment plants. PMID:31086312
On-Site Analysis of Bacterial Communities of the Ultraoligotrophic South Pacific Gyre. PMID:31076426
MIReAD, a minimum information standard for reporting arthropod abundance data. PMID:31024009
Habitat-dependent composition of bacterial and fungal communities in biological soil crusts from Oman. PMID:31015576
The Plastisphere - Uncovering tightly attached plastic "specific" microorganisms. PMID:31013334
A human gut bacterial genome and culture collection for improved metagenomic analyses. PMID:30718869
Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research. PMID:30715273
OMeta: an ontology-based, data-driven metadata tracking system. PMID:30612540
Minimum Information about an Uncultivated Virus Genome (MIUViG). PMID:30556814
Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions. PMID:30533298
Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System. PMID:30532746
Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation. PMID:30531893
GLOSSary: the GLobal Ocean 16S subunit web accessible resource. PMID:30497362
Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. PMID:30467310
Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018. PMID:30396371
The European Nucleotide Archive in 2018. PMID:30395270
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. PMID:30371820
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data. PMID:30365027
Genomes OnLine database (GOLD) v.7: updates and new features. PMID:30357420
Functional and taxonomic classification of a greenhouse water drain metagenome. PMID:30323887
Qiita: rapid, web-enabled microbiome meta-analysis. PMID:30275573
Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. PMID:30240894
EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PMID:30222734
MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources. PMID:30212909
Over 2.5 million COI sequences in GenBank and growing. PMID:30192752
Microbial Community and Potential Pathogen Shifts Along an Ornamental Fish Supply Chain. PMID:30149657
Are microbiome studies ready for hypothesis-driven research? PMID:30059804
A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences. PMID:30008988
Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean. PMID:29875749
A Genomic Outlook on Bioremediation: The Case of Arsenic Removal. PMID:29755441
The international nucleotide sequence database collaboration. PMID:29190397
Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula. PMID:29163409
Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish. PMID:29124129
A communal catalogue reveals Earth's multiscale microbial diversity. PMID:29088705
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. PMID:29069476
Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences. PMID:29038749
MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. PMID:29028869
DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient. PMID:28986575
Shotgun metagenomics, from sampling to analysis. PMID:28898207
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. PMID:28787424
The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples. PMID:28771471
Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture. PMID:28738824
Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance. PMID:28694792
The metagenomic data life-cycle: standards and best practices. PMID:28637310
Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access. PMID:28588568
Plant specimen contextual data consensus. PMID:28369359
MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota. PMID:28077565
Performing Skin Microbiome Research: A Method to the Madness. PMID:28063650
Metagenome phylogenetic profiling of microbial community evolution in a tetrachloroethene-contaminated aquifer responding to enhanced reductive dechlorination protocols. PMID:27980706
European Nucleotide Archive in 2016. PMID:27899630
Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula. PMID:27857708
cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies. PMID:27822516
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. PMID:27794040
MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources. PMID:27777648
The Global Genome Biodiversity Network (GGBN) Data Standard specification. PMID:27694206
Using a Control to Better Understand Phyllosphere Microbiota. PMID:27669159
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. PMID:27664130
Pathogen metadata platform: software for accessing and analyzing pathogen strain information. PMID:27634291
Toward Accurate and Quantitative Comparative Metagenomics. PMID:27565341
Standardization for natural product synthetic biology. PMID:27313083
Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets. PMID:27296526
Influence of Fishmeal-Free Diets on Microbial Communities in Atlantic Salmon (Salmo salar) Recirculation Aquaculture Systems. PMID:27129964
myPhyloDB: a local web server for the storage and analysis of metagenomic data. PMID:27022159
Interdisciplinary approach towards a systems medicine toolbox using the example of inflammatory diseases. PMID:27016392
Expanding the World of Marine Bacterial and Archaeal Clades. PMID:26779174
Emerging semantics to link phenotype and environment. PMID:26713234
The International Nucleotide Sequence Database Collaboration. PMID:26657633
The MG-RAST metagenomics database and portal in 2015. PMID:26656948
Cross-biome comparison of microbial association networks. PMID:26579106
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. PMID:26578582
Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes. PMID:26536666
Context and the human microbiome. PMID:26530830
Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities. PMID:26458130
BaMBa: towards the integrated management of Brazilian marine environmental data. PMID:26454874
Computational approaches to natural product discovery. PMID:26284671
Minimum Information about a Biosynthetic Gene cluster. PMID:26284661
Standardizing metadata and taxonomic identification in metabarcoding studies. PMID:26236474
Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data. PMID:26226014
Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards. PMID:26203332
SaDA: From Sampling to Data Analysis-An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data. PMID:26047146
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. PMID:25983555
Metazen - metadata capture for metagenomes. PMID:25780508
Ecology and exploration of the rare biosphere. PMID:25730701
ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. PMID:25619994
A RESTful API for accessing microbial community data for MG-RAST. PMID:25569221
Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. PMID:25500508
Assessing the accuracy of quantitative molecular microbial profiling. PMID:25421243
Content discovery and retrieval services at the European Nucleotide Archive. PMID:25404130
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. PMID:25348409
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. PMID:25348402
Advancing the microbiome research community. PMID:25303518
Discovering new indicators of fecal pollution. PMID:25199597
Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records. PMID:25197497
Genomic standards consortium projects. PMID:25197446
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. PMID:25197443
Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PMID:25093819
Conducting a microbiome study. PMID:25036628
Exploring neighborhoods in the metagenome universe. PMID:25026170
Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. PMID:24995004
Standardized metadata for human pathogen/vector genomic sequences. PMID:24936976
Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics. PMID:24634890
GigaDB: promoting data dissemination and reproducibility. PMID:24622612
History and impact of RDP: a legacy from Carl Woese to microbiology. PMID:24607969
All hail reproducibility in microbiome research. PMID:24602292
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. PMID:24595056
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. PMID:24564732
The microbiome in inflammatory bowel disease: current status and the future ahead. PMID:24560869
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. PMID:24456465
Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants. PMID:24450928
The environment ontology: contextualising biological and biomedical entities. PMID:24330602
Ribosomal Database Project: data and tools for high throughput rRNA analysis. PMID:24288368
BacDive--the Bacterial Diversity Metadatabase. PMID:24214959
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data. PMID:24165880
MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. PMID:24152717
Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered Antarctic lakes. PMID:24152712
Analytical tools and databases for metagenomics in the next-generation sequencing era. PMID:24124405
Microbial communities of deep-sea methane seeps at Hikurangi continental margin (New Zealand). PMID:24098632
Patterns and processes of microbial community assembly. PMID:24006468
Clarifying concepts and terms in biodiversity informatics. PMID:23991264
Interactions in the microbiome: communities of organisms and communities of genes. PMID:23909933
Meta-analyses of studies of the human microbiota. PMID:23861384
High abundance of heterotrophic prokaryotes in hydrothermal springs of the Azores as revealed by a network of 16S rRNA gene-based methods. PMID:23708551
AXIOME: automated exploration of microbial diversity. PMID:23587322
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. PMID:23587224
A call for an international network of genomic observatories (GOs). PMID:23587188
Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales. PMID:23550823
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. PMID:23479348
RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011. PMID:23451294
The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. PMID:23409217
Changes in assembly processes in soil bacterial communities following a wildfire disturbance. PMID:23407312
Widespread colonization of the lung by Tropheryma whipplei in HIV infection. PMID:23392441
FANTOM: Functional and taxonomic analysis of metagenomes. PMID:23375020
Eukaryotic diversity at pH extremes. PMID:23335919
Marine bacteria exhibit a bipolar distribution. PMID:23324742
Comparative molecular microbial ecology of the spring haptophyte bloom in a greenland arctic oligosaline lake. PMID:23251134
Bioinformatics for the Human Microbiome Project. PMID:23209389
DDBJ new system and service refactoring. PMID:23180790
Gene Fusion Markup Language: a prototype for exchanging gene fusion data. PMID:23072312
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. PMID:22966151
The Human Microbiome Project: a community resource for the healthy human microbiome. PMID:22904687
Defining the human microbiome. PMID:22861806
Global Biodiversity of Aquatic Ammonia-Oxidizing Archaea is Partitioned by Habitat. PMID:22826704
Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012. PMID:22768370
High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. PMID:22685131
Unlocking the potential of metagenomics through replicated experimental design. PMID:22678395
Metagenomics - a guide from sampling to data analysis. PMID:22587947
Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes. PMID:22587903
Predicting bacterial community assemblages using an artificial neural network approach. PMID:22504588
Carbon, metals, and grain size correlate with bacterial community structure in sediments of a high arsenic aquifer. PMID:22470368
Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils. PMID:22378536
Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life. PMID:22308073
Sequencing our way towards understanding global eukaryotic biodiversity. PMID:22244672
Darwin Core: an evolving community-developed biodiversity data standard. PMID:22238640
Minimum Information about a Genotyping Experiment (MIGEN). PMID:22180825
Open resource metagenomics: a model for sharing metagenomic libraries. PMID:22180823
Experimental and analytical tools for studying the human microbiome. PMID:22179717
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. PMID:22139929
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. PMID:22135293
Major submissions tool developments at the European Nucleotide Archive. PMID:22080548
CDinFusion--submission-ready, on-line integration of sequence and contextual data. PMID:21935468
An all-taxon microbial inventory of the Moorea coral reef ecosystem. PMID:21900967
Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. PMID:21872475
Switching between raltegravir resistance pathways analyzed by deep sequencing. PMID:21832937
Context is key for sequence data. PMID:21728275
The Genomic Standards Consortium. PMID:21713030
The genomic standards consortium: bringing standards to life for microbial ecology. PMID:21472015
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More detailed information about this field from each metasource.
dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
genetic marker
metasource: Fairsharing.org
version: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
metagenome
metasource: Fairsharing.org
version: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
pathogen
metasource: Fairsharing.org
version: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Tags
More detailed information about this field from each metasource.
dna sequence data
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
genetic marker
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
metagenome
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
pathogen
metasource: Fairsharing.orgversion: FAIRsharing.org: MIxS; Minimum Information about any (x) Sequence; DOI: https://doi.org/10.25504/FAIRsharing.9aa0zp; Last edited: Jan. 8, 2019, 1:37 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
dna sequences dna genetic marker genome metagenome pathogen
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