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New Feature: Knowledge Engine Version 1.0 Online
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We are excited to announce that the first generation of KBase's Knowledge Engine is online! This feature allows you to explore and discover all the data KBase has related to your organism. The Knowledge Engine builds relationships between all data in the system using both biological information, such as taxonomy, and data provenance to find and return the reference data, shared user data and Narratives on system related to your organism. The graphic shows above demonstrates the many data types found to be linked to a particular genome: related genomes, expression sets, models, alignments, and reads. Check out this feature on your own data by expanding the view on some data in the Data Panel of a Narrative, clicking the
Explore data binoculars icon, and viewing the
Similar Data panel in the Data Viewer.
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New Feature: Organizations and Feeds
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Another new feature in KBase is the ability to create
Organizations for shared research, projects, and institutions. This allows collaborators to see each others Narratives and be notified when members of an organization add data or Narratives to the system. It also allows managers to track and maintain their project’s resources. Notifications for updates in your organizations and Narratives appear in the
Feeds menu. You can track system updates, requests from other users, and more with this feature.
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New Feature: Narrative Access Request
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Users often find links to Narratives in publications, or search and locate one of interest, but they don't have permission to access it. You can now request access to private Narratives when you locate them. The Narrative owner is informed of the request via
Feeds.
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Recent Publications Using KBase |
Several new publications have been released that showcase the diversity of applications for KBase in 'omics research. Check out how scientists are using KBase to explore data, run analyses, and discover new findings:
- Kothari A, Wu Y-W, Chandonia J-M, Charrier M, Rajeev L, Rocha AM, et al. Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes.
mBio
- Gao H, Mao Y, Zhao X, Liu W-T, Zhang T, Wells G. Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess.
Water Research
- Lewis RW, Islam A, Opdahl L, Davenport JR, Sullivan TS. Comparative Genomics, Siderophore Production, and Iron Scavenging Potential of Root Zone Soil Bacteria Isolated from ‘Concord’ Grape Vineyards.
Microbial Ecology
- Dobritsa AP, Kutumbaka KK, Samadpour M. Reclassification of Eubacterium combesii and discrepancies in the nomenclature of botulinum neurotoxin-producing clostridia: Challenging Opinion 69. Request for an Opinion.
International Journal of Systematic and Evolutionary Microbiology
- Contador CA, Rodríguez V, Andrews BA, Asenjo JA. Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora.
BMC Systems Biology
- Lima ARJ, Siqueira AS, Vasconcelos JM de, Pereira JS, Azevedo JSN de, Moraes PHG, et al. Insights Into Limnothrix sp. Metabolism Based on Comparative Genomics.
Frontiers in Microbiology
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Newsletter #10 |
March 18, 2019 |
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