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Review_paper
Ontologies in Support of Metagenomic Annotation and Analysis a Review
YES
The Global Genome Biodiversity Network (GGBN) Data Standard specification Ramona mentioned this in a comment and I should prob include GGBN.
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification definitely should cite this poster claiming GOLD5 to be mixs compliant cites this. GOLD is fully compliant with the GSC's MIxS standards in capturing metadata and provides a platform to query projects based on various metadata features.
Sequencing data discovery with MetaSeek Should probably add this.
Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records In January 2014, NCBI will cease assigning strain-level taxids. Instead, submitters are encouraged provide strain information and rich metadata with their submission to the sequence database, BioProject and BioSample. Might help to answer the questions of how NCBITaxon is used now in response to one of Chris' comments.
MAYBE
The Microbial Antarctic Resource System: Integrating discoverability and preservation of environmentally-annotated microbial 'omics data, mars site Follows MiMarks template maybe worth mentioning?
Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research FOG and Pelin on this, seems relevant (maybe more for paper2? or maybe for this...).
Standardized Metadata for Human Pathogen/Vector Genomic Sequences
Training Biomedical Researchers in Metadata with a MIBBI-Based Ontology generic lightweight ontology based on the Minimum Information for Biological and Biomedical Investigations (MIBBI) standard
Clarifying Concepts and Terms in Biodiversity Informatics2013 ramona and john
Genomes OnLineDatabase (GOLD) v.5: an improved metadata management system based on a four level (meta)genome project classification poster so might not be able to cite, but it claims GOLD is fully compliant with the Genomic Standards Consortium (GSC) Minimum Information about any (x) Sequence (MIxS) standards (see Reddy, T. B. K. et al.The Genomes OnLineDatabase (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res.1–6 (2014))
??
Measures for interoperability of phenotypic data: minimum information requirements and formatting Minimum Information About a Plant Phenotyping Experiment (MIAPPE) like MIxS maybe mention?
Minimum Information about an Uncultivated Virus Genome (MIUViG)
Minimum Information about a Biosynthetic Gene cluster
PlutoF: Biodiversity data management platform forthe complete data lifecycle
Ecobiomics: Environmental metagenomic biomonitoring Maybe try to follow up on this for the review paper??
The Earth Microbiome Project: Planetary-scale systems ecology.
Linking Biodiversity Data with the Biological Collections Ontology Ramona
Standards-based management of specimen-derived DNA sequences SeqDB
Genomic Biodiversity Working Interest Group (GBWG) John Deck
Genomic Biodiversity Working Interest Group (GBWG) Meeting John Deck
Using the Biological Collections Ontology to Advance Biodiversity Science Ramona