Abstract
We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.
Highlights
The engineering of new biological systems has begun to demonstrate the advantages of leveraging living cells as machines for the production of medicine [1], nutrients [2], biofuels [3,4], and as biosensors [5,6]
We asked the knowledge base to answer the following question, ‘‘Which promoters can I use for a design?’’ Because ‘‘promoter’’ is a class in our controlled vocabulary, this is a straightforward SPARQL query to ask of our Standard Biological Parts knowledge base (SBPkb), and it returns 538 parts that are annotated as promoters
This query seems simple, we must compare the capabilities of SBPkb to current technology: How would one answer this question, with current technology, i.e., directly of the Parts Registry? the only way to retrieve this set of parts is by manual browsing of web pages, and manual compilation and analysis of the results listed on these web pages
Summary
The engineering of new biological systems has begun to demonstrate the advantages of leveraging living cells as machines for the production of medicine [1], nutrients [2], biofuels [3,4], and as biosensors [5,6]. Synthetic biologists need software tools that support the engineering process of biological systems [13] Several such software tools are currently in development and aim to aid the design of new systems by predicting their behavior, TinkerCell [14], BioNetCAD [15], SynBioSS [16,17], and BioJADE [18] planning the assembly process [19], and validating the design GenoCAD [20,21,22,23]. Such design tools require computational access to a library of parts, the ability to query such a library
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