Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

By Shulei Sun, Jing Chen, Weizhong Li, I. Altintas, A. Lin, S. Peltier, K. Stocks, Eric E. Allen, Mark Ellisman, J. Grethe and 1 more. Nucleic Acids Res., 2010

336 citations recorded by the source corpus.

The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.

Subfields: Ecology, Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/729a6c08629fee311e239954ffcf487dc3b6812a

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Citations in the corpus

Metagenomics - a guide from sampling to data analysis (2012, methodology): “MG-RAST, IMG/M, and CAMERA are three prominent systems [43,50,74].”
Ultrafast clustering algorithms for metagenomic sequence analysis (2012, methodology): “cd-hit web server [28], the CAMERA web portal [42] and the WebMGA server [43] for metagenomic”
MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences (2014, methodology): “Publicly available tools (NBC, MEGAN4, RAIPhy) were also trained on the same reference database as MyTaxa (1480 completed genomes) before applied to the (same) query datasets, using recommended or default settings.”
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing (2014, methodology): “For the MMETSP data to achieve maximum impact, the transcriptomes have been made readily available through the CAMERA [17] Data Distribution Center (http://camera.”
CD-HIT: accelerated for clustering the next-generation sequencing data (2012, background): “…non-redundant dataset creation (Suzek, et al., 2007), protein family classifications (Yooseph, et al., 2008), artifact identification (Niu, et al., 2010), metagenomics annotation (Sun, et al., 2011), RNA analysis (Loong and Mishra, 2007), to various prediction studies (Rubinstein and Fiser, 2008).”
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes (2013, methodology): “, 2007) were downloaded from CAMERA (Sun et al., 2011).”
New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data (2014, background): “Previous analyses recovered Tetraselmis, together with Scherffelia (not included in our analyses), as sister to all members of the UTC classes (which include Oltmannsiellopsis; e.g., Steinkötter et al., 1994; Nakayama et al., 1998).”