Form Submission: Session, Poster, Demo Submission

Demo/Poster Number

Steel
13

Contact Information
First Name: 
Timothy
Last Name: 
Putman
Session Information
Presentation Title: 
Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes
Description: 
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 over 28000 gene and protein items for 16 bacterial genomes including two strains of the human pathogenic bacteria Chlamydia trachomatis. We 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 uniting the efforts of the entire microbial research community, data and domain experts alike.
Presenter Information
Same As Contact: 
Yes
Organization/Affiliation: 
The Scripps Research Institute
Contributors
First Name: 
Sebastian
Last Name: 
Burgstaller-Muehlbacher
Organization/Affiliation: 
The Scripps Research Institute
First Name: 
Andra
Last Name: 
Waagmeester
Organization/Affiliation: 
The Scripps Research Institute
First Name: 
Chunlei
Last Name: 
Wu
Organization/Affiliation: 
The Scripps Research Institute
First Name: 
Andrew I.
Last Name: 
Su
Organization/Affiliation: 
The Scripps Research Institute
First Name: 
Benjamin M.
Last Name: 
Goo
Organization/Affiliation: 
The Scripps Research Institute