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Standard biological parts knowledgebase.

Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH - PLoS ONE (2011)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Biomedical & Health Informatics, University of Washington, Seattle, Washington, United States of America.

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.

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SPARQL query of SBPkb for dual-regulated promoter parts and their descriptions.
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pone-0017005-g004: SPARQL query of SBPkb for dual-regulated promoter parts and their descriptions.

Mentions: Not only were we able to retrieve promoter parts based on specific factors (σ), but available to us as selection criteria were also Registry categories which specify the expected mode of regulation. For example, during the design of a new genetic Barkai-Leibler oscillator [46], [47] the synthetic biologist may want to find all pre-existing promoters that can be both ‘positively regulated’ AND ‘negatively regulated’, i.e., dual-regulated promoters (query #7 in File S2). Our query returned just 36 unique promoter parts meeting these criteria (note that this query result is not necessarily a subset of the 367 “Eσ70” promoters). The Barkai-Leibler oscillator relies heavily on the availability of such dual-regulated promoters, therefore having knowledge of all dual-regulated promoters available in the Registry is highly advantageous to the synthetic biologist. Since a sufficient number of dual-regulated promoters are available, the search can be further limited to promoters for known specific inducers and repressors that are appropriate for the new design. The SBPkb includes information from the Registry Features table, therefore, for our final refinement, we further restricted our query to return promoters that have sequence annotations of known transcription factor binding sites, i.e., operator sites. This example query (Figure 4) returns just six parts and their known binding sites (Table 2). A selection of these six candidates provides a list small enough that each one can be examined in greater detail for relevance to a specific design.


Standard biological parts knowledgebase.

Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH - PLoS ONE (2011)

SPARQL query of SBPkb for dual-regulated promoter parts and their descriptions.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3044748&req=5

pone-0017005-g004: SPARQL query of SBPkb for dual-regulated promoter parts and their descriptions.
Mentions: Not only were we able to retrieve promoter parts based on specific factors (σ), but available to us as selection criteria were also Registry categories which specify the expected mode of regulation. For example, during the design of a new genetic Barkai-Leibler oscillator [46], [47] the synthetic biologist may want to find all pre-existing promoters that can be both ‘positively regulated’ AND ‘negatively regulated’, i.e., dual-regulated promoters (query #7 in File S2). Our query returned just 36 unique promoter parts meeting these criteria (note that this query result is not necessarily a subset of the 367 “Eσ70” promoters). The Barkai-Leibler oscillator relies heavily on the availability of such dual-regulated promoters, therefore having knowledge of all dual-regulated promoters available in the Registry is highly advantageous to the synthetic biologist. Since a sufficient number of dual-regulated promoters are available, the search can be further limited to promoters for known specific inducers and repressors that are appropriate for the new design. The SBPkb includes information from the Registry Features table, therefore, for our final refinement, we further restricted our query to return promoters that have sequence annotations of known transcription factor binding sites, i.e., operator sites. This example query (Figure 4) returns just six parts and their known binding sites (Table 2). A selection of these six candidates provides a list small enough that each one can be examined in greater detail for relevance to a specific design.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Biomedical & Health Informatics, University of Washington, Seattle, Washington, United States of America.

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.

Show MeSH
Related in: MedlinePlus