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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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Example of Registry Categories to SBOL class structure conversion.These autogenerated classes are assigned to the partsregistry.org namespace to attribute them to the source and allow differentiation from SBOL-semantic classes, see the OWL implementation of SBOL-semantic File S1.
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pone-0017005-g003: Example of Registry Categories to SBOL class structure conversion.These autogenerated classes are assigned to the partsregistry.org namespace to attribute them to the source and allow differentiation from SBOL-semantic classes, see the OWL implementation of SBOL-semantic File S1.

Mentions: As part of the transformation of Registry data we used the categories attribute of the Registry parts table to provide a richer description of parts. The Registry includes a total of 346 categories organized as a hierarchy of 28 top level categories (e.g. chassis, classic, dna, function, plasmid, plasmidbackbone, primer, promoter, proteindomain, proteintag, rbs, regulation, ribosome, rnap, terminator, etc. For full listing see Supporting Information Table S1, which contains the list of terms extracted from the Registry data, and File S1., which contains the generated OWL encoded semi-structured controlled vocabulary used throughout this work). These categories are a rich vocabulary used to describe parts and constitute a controlled vocabulary, created and maintained by the Registry staff, while its use is enforced by the Registry website software application. The categories form the basis of organization for the Registry Catalog website. Thus, to provide a good structure for querying the Registry information, we needed to augment our core SBOL-semantic ontology with this terminology. To do so, we auto-generated a class structure within SBOL-semantic that mimics the registry category structure. For an example, see Figure 3. Finally, we loaded the SBOL-semantic data into a framework for querying RDF data, creating the Standard Biological Parts knowledgebase resource (SBPkb) (see Implementation and Availability for details). As we show in our results section, we can use these categories to directly query the SBPkb for specific features of parts.


Standard biological parts knowledgebase.

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

Example of Registry Categories to SBOL class structure conversion.These autogenerated classes are assigned to the partsregistry.org namespace to attribute them to the source and allow differentiation from SBOL-semantic classes, see the OWL implementation of SBOL-semantic File S1.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0017005-g003: Example of Registry Categories to SBOL class structure conversion.These autogenerated classes are assigned to the partsregistry.org namespace to attribute them to the source and allow differentiation from SBOL-semantic classes, see the OWL implementation of SBOL-semantic File S1.
Mentions: As part of the transformation of Registry data we used the categories attribute of the Registry parts table to provide a richer description of parts. The Registry includes a total of 346 categories organized as a hierarchy of 28 top level categories (e.g. chassis, classic, dna, function, plasmid, plasmidbackbone, primer, promoter, proteindomain, proteintag, rbs, regulation, ribosome, rnap, terminator, etc. For full listing see Supporting Information Table S1, which contains the list of terms extracted from the Registry data, and File S1., which contains the generated OWL encoded semi-structured controlled vocabulary used throughout this work). These categories are a rich vocabulary used to describe parts and constitute a controlled vocabulary, created and maintained by the Registry staff, while its use is enforced by the Registry website software application. The categories form the basis of organization for the Registry Catalog website. Thus, to provide a good structure for querying the Registry information, we needed to augment our core SBOL-semantic ontology with this terminology. To do so, we auto-generated a class structure within SBOL-semantic that mimics the registry category structure. For an example, see Figure 3. Finally, we loaded the SBOL-semantic data into a framework for querying RDF data, creating the Standard Biological Parts knowledgebase resource (SBPkb) (see Implementation and Availability for details). As we show in our results section, we can use these categories to directly query the SBPkb for specific features of parts.

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