This is a repository with a set of sparql queries to answer questions posed in an ACS Synthetic Biology Paper titled: The Synthetic Biology Knowledge System Queries should be run in the sparql interface of synbioks.org.
Each query comes as a template where variables are indicated as and as an example query (fully functional). The different queries are described bellow.
Any line starting with # in SPARQL is a comment meaning it will not do anything but describes the code or can be removed to add an additional feature.
Any urls must be surrounded by < and > e.g. <https://synbioks.org/public/MoClo_Yeast_Toolkit_Dueber_Lab/KanR/1>
For more information on SPARQL see the SPARQL 1.1 W3 Overview.
Example queries:
- What are some papers about metabolic engineering?
- What are some papers about yeast?
- What are some papers about S. cerevisiae?
The example file and the template file. Remember to copy the PREFIX section too and to remove the prefilled PREFIX lines in the synbioks sparql interface.
Example query:
- Which papers use the KanR kanamycin resistance sequence?
The example file and the template file. Remember to copy the PREFIX section too and to remove the prefilled PREFIX lines in the synbioks sparql interface.
Example query:
- Which papers have keyword yeast or S. cerevisiae?
- Which papers about metabollic engineering use S. cerevisiae?
- Which papers using KanR kanamycin resistance also use S. cerevisiae?
The example file and the template file. Remember to copy the PREFIX section too and to remove the prefilled PREFIX lines in the synbioks sparql interface.
Example query:
- What are all the parts used in 'Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids'?
- What are all the parts used in https://pubs.acs.org/doi/10.1021/acssynbio.7b00399?
The example file and the template file. Remember to copy the PREFIX section too and to remove the prefilled PREFIX lines in the synbioks sparql interface.