The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept.
PMID:35889831
Establishing a Common Nutritional Vocabulary - From Food Production to Diet.
PMID:35811979
Alleviating Environmental Health Disparities Through Community Science and Data Integration.
PMID:35664667
Biological Microbial Interactions from Cooccurrence Networks in a High Mountain Lacustrine District.
PMID:35642514
Data standardization of plant-pollinator interactions.
PMID:35639882
Past and future uses of text mining in ecology and evolution.
PMID:35582795
Darling: A Web Application for Detecting Disease-Related Biomedical Entity Associations with Literature Mining.
PMID:35454109
Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems.
PMID:34956127
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis.
PMID:34632381
Catalyzing Knowledge-Driven Discovery in Environmental Health Sciences through a Community-Driven Harmonized Language.
PMID:34501574
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies.
PMID:33991093
Semantic standards of external exposome data.
PMID:33901445
Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.
PMID:33500403
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems.
PMID:33205138
Genomes OnLine Database (GOLD) v.8: overview and updates.
PMID:33152092
Development of an Intervention Setting Ontology for behaviour change: Specifying where interventions take place.
PMID:32964137
"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI's sequence read archive".
PMID:32883210
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
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data.
PMID:32735679
The African wildlife ontology tutorial ontologies.
PMID:32576239
Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).
PMID:32463383
Enabling reusability of plant phenomic datasets with MIAPPE 1.1.
PMID:32171029
OHMI: the ontology of host-microbiome interactions.
PMID:31888755
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.
PMID:31728526
Phenotype annotation with the ontology of microbial phenotypes (OMP).
PMID:31307550
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration.
PMID:31304272
Modeling Crop Genetic Resources Phenotyping Information Systems.
PMID:31281323
Global diversity and biogeography of bacterial communities in wastewater treatment plants.
PMID:31086312
Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions.
PMID:30918448
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy.
PMID:30500839
Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research.
PMID:30412219
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
An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights.
PMID:30065857
Latent environment allocation of microbial community data.
PMID:29874232
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments.
PMID:29106667
A communal catalogue reveals Earth's multiscale microbial diversity.
PMID:29088705
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
Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture.
PMID:28738824
Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access.
PMID:28588568
Dead simple OWL design patterns.
PMID:28583177
The anatomy of phenotype ontologies: principles, properties and applications.
PMID:28387809
Seqenv: linking sequences to environments through text mining.
PMID:28028456
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
PMID:28025348
The importance of digitized biocollections as a source of trait data and a new VertNet resource.
PMID:28025346
Macrobenthic molluscs from a marine - lagoonal environmental transition in Lesvos Island (Greece).
PMID:27932914
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.
PMID:27842607
MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources.
PMID:27777648
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.
PMID:27664130
Biodiversity analysis in the digital era.
PMID:27481789
Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research.
PMID:27458549
A method for exploring implicit concept relatedness in biomedical knowledge network.
PMID:27454167
Location and foraging as basis for classification of biotic interactions.
PMID:27160993
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.
PMID:27076900
Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy.
PMID:27065954
MyOSD 2014: Evaluating Oceanographic Measurements Contributed by Citizen Scientists in Support of Ocean Sampling Day.
PMID:27047614
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.
PMID:26896844
Value, but high costs in post-deposition data curation.
PMID:26861660
Expanding the World of Marine Bacterial and Archaeal Clades.
PMID:26779174
Emerging semantics to link phenotype and environment.
PMID:26713234
The MG-RAST metagenomics database and portal in 2015.
PMID:26656948
Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities.
PMID:26458130
Open science resources for the discovery and analysis of Tara Oceans data.
PMID:26029378
Bacterial diversity along a 2600 km river continuum.
PMID:25922985
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.
PMID:25815161
Piecing together the biogeographic history of Chenopodium vulvaria L. using botanical literature and collections.
PMID:25653906
Describing the breakbone fever: IDODEN, an ontology for dengue fever.
PMID:25646954
ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life.
PMID:25619994
TypOn: the microbial typing ontology.
PMID:25584183
Finding our way through phenotypes.
PMID:25562316
Thematic series on biomedical ontologies in JBMS: challenges and new directions.
PMID:24602198
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.
PMID:24595056