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...

Integrated Information System for Genomic and Metagenomic Data Analysis at National Center for Biotechnology Information (NCBI)

submitted by: dougramsey
Recent advances in biotechnology and bioinformatics has provided a flood of genomic data and tremendous growth in the number of associated data sets. Sequencing projects now include draft assemblies, complete genomes, comparative genomics, and metagenomics where genetic material is sequenced directly from environmental samples. The NCBI provides integrated systems for data storage, retrieval, and analysis. GenBank, an archival database of DNA sequences, contains consensus sequences assembled...

Exploring Next Generation Sequencing Today

submitted by: dougramsey

Exploring Next Generation Sequencing Today, Thomas Jarvie, 454 Life Sciences

Computational Aspects of Metagenome Analysis

submitted by: dougramsey

Computational Aspects of Metagenome Analysis
Daniel Huson, Tuebingen University

Towards Computer Assisted Markup of Data: Habitat-Lite

submitted by: dougramsey
Lynette Hirschman, The MITRE Corporation Co-authors: Scott Mardis, Cheryl Clark, Kevin Cohen Habitat-Lite (aka EnvO-Lite) is a set of structured terms designed to facilitate capture of high-level information about habitat and sample source metadata for genomics and metagenomics samples. It is designed to be light-weight and compact. Habitat-Lite terms are drawn from the full EnvO ontology and are made avail able by the EnvO Consortium in the EnvO-Lite-GSC OBO file. Habitat-Lite terms include...