The Environment Ontology: Linking Environmental Data

submitted by: dougramsey
Norman Morrison, University of Manchester Every biological specimen that is collected or sampled — whether for a museum collection, for epidemiological studies, for population studies, for ecological research, for research into evolution, biodiversity or sustainability, indeed any biological research — comes from a particular habitat where particular physical conditions prevail. How ever, at present there is no accepted semantic standard for describing the environment from which these...

Metadata Capture in the IMG/IMGm: Getting Scientists to Contribute

submitted by: dougramsey

Metadata Capture in the IMG/IMGm: Getting Scientists to Contribute - Victor Markowitz, Lawrence Berkeley National Lab

The Genomes Online Database (GOLD): The Value of a Comprehensive Metadata Collection

submitted by: dougramsey

The Genomes Online Database (GOLD): The Value of a Comprehensive Metadata Collection - Nikos Kyrpides, Joint Genome Institute

Efficient Metagenomics Data Processing: Pitfalls and Solutions

submitted by: dougramsey
Nikos Kyrpides, Joint Genome Institute Co-authors: Kostas Mavrommatis, Natalia Ivanova Metagenomics has emerged as a powerful tool for exploration of the functional capabilities of microbial communities regardless of the ability of their members to grow in pure culture. However, little is known for the efficacy of the methods used to process these datasets. Further more, sequencing of environmental genomic DNA usually results in large, highly fragmented datasets representing a significant...

Implementing MIGS/MIMS: The Genomic Contextual

submitted by: dougramsey
The MIGS/MIMS checklist developed by the Genomic Standards Consortium (GSC) aims to enrich our ever growing data collection of genomic and metagenomic sequences. Therefore, the checklist defines what minimal list of contextual data attributes has to be added to the sequences in order to conform to the MIGS/MIMS specification. However, MIGS/MIMS itself does not specify how the contextual data should be documented; thus the GSC is developing the Genomic Contextual Data Markup Language (GCDML),...

Targeted Gene Identification from Short Gene Fragments in Metagenome and their Use in Biogeochemical Studies

submitted by: dougramsey
Metagenomics allows for a new approach to studying biogeochemical processes in an environment, by giving an approximation of a community’s biogeochemical potential through the genes involved in a given process. Lipid biomarkers are well suited to this kind of approach because they are important for a number of biogeochemical questions and some have well studied biosynthetic pathways. One important class of lipid biomarkers, triterpenoids, were investigated in a new metagenomic sample that...