Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes.
The last 20 years of advancement in DNA sequencing technologies have led to the sequencing of thousands of microbial genomes, creating mountains of genetic data. While our efficiency in generating the data improves almost daily, applying meaningful relationships between the taxonomic and genetic entities on this scale requires a structured and integrative approach. Currently, the knowledge is distributed across a fragmented landscape of resources from government-funded institutions such as NCBI and UniProt to topic-focused databases like the ODB3 database of prokaryotic operons, to the supplemental table of a primary publication. A major drawback to large scale, expert curated databases is the expense of maintaining and extending them over time. No entity apart from a major institution with stable long term funding can consider this, and their scope is limited considering the magnitude of microbial data being generated daily. Wikidata is an, openly editable, semantic web compatible framework for knowledge representation. It is a project of the Wikimedia Foundation and offers knowledge integration capabilities ideally suited to the challenge of representing the exploding body of information about microbial genomics. We are developing a microbial specific data model, based on Wikidata's semantic web compatibility, that represents bacterial species, strains and the gene and gene products that define them. Currently, we have loaded 1736 gene items and 1741 protein items for two strains of the human pathogenic bacteria Chlamydia trachomatis and used this subset of data as an example of the empowering utility of this model. In our next phase of development, we will expand by adding another 118 bacterial genomes and their gene and gene products, totaling over 900,000 additional entities. This aggregation of knowledge will be a platform for community-driven collaboration, allowing the networking of microbial genetic data through the sharing of knowledge by both the data and domain expert.
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- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!