ArticlePloS one2011
Standard biological parts knowledgebase.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
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- Designing a synthetic moss genome using GenoDesigner.Nature plants · 2024Review
- Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems.BMC bioinformatics · 2024Article
- Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology.bioRxiv : the preprint server for biology · 2024Article
- A new era of synthetic biology-microbial community design.Synthetic biology (Oxford, England) · 2024Review
- Bypassing the Restriction System To Improve Transformation of Staphylococcus epidermidis.Journal of bacteriology · 2017Article
- Engineering biological systems using automated biofoundries.Metabolic engineering · 2017Review
- A computational method for the investigation of multistable systems and its application to genetic switches.BMC systems biology · 2016Article
- Synbiological systems for complex natural products biosynthesis.Synthetic and systems biotechnology · 2016Review
- Improving transformation of Staphylococcus aureus belonging to the CC1, CC5 and CC8 clonal complexes.PloS one · 2015Article
- Next-Generation Sequencing for Binary Protein-Protein Interactions.Frontiers in genetics · 2015Article
- GeneGenie: optimized oligomer design for directed evolution.Nucleic acids research · 2014Article
- The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.Nature biotechnology · 2014Article
- A brief history of synthetic biology.Nature reviews. Microbiology · 2014Review
- In silico design and in vivo implementation of yeast gene Boolean gates.Journal of biological engineering · 2014Article
- High-throughput, cost-effective verification of structural DNA assembly.Nucleic acids research · 2014Article
- One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy.Nucleic acids research · 2014Article
- Developments in the tools and methodologies of synthetic biology.Frontiers in bioengineering and biotechnology · 2014Review
- Improving collaboration by standardization efforts in systems biology.Frontiers in bioengineering and biotechnology · 2014Review
- Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits.BMC systems biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
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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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.