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Method Article
Matthew Oberhardt
Ruppin Lab, University of Maryland
Corresponding Author
Uri Gophna
Tel Aviv University
Corresponding Author
Eytan Ruppin
University of Maryland
Corresponding Author
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
This protocol describes the process used to convert >1300 microbial media recipes, listed on the website of the Leibniz Institute DSMZ (see: https://www.dsmz.de/?id=441), into a machine readable format, and then to read them into a SQL database. In the process, we combine compounds with degenerate names and include concentrations of all compounds in standard units. The protocol includes steps for error-checking, as well as a process to recursively add media when they cross-reference each other. The protocol might be useful in other, similar database building tasks, and especially might help in efforts to incorporate other microbial media recipes from literature into this or another database.
Keywords
systems biology, bacterial culturing, microbial database, microbial media
Figure 1
The authors declare no competing financial interests
This is a list of supplementary files associated with this preprint. Click to download.
- supplement0.xlsx
Table 1 Concentration conversions This shows how we converted any concentration, mass, or volume unit into a set of 5 standard units (see Step 9 of the protocol).
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Posted 03 Sep, 2015
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An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Matthew Oberhardt
Ruppin Lab, University of Maryland
Corresponding Author
Uri Gophna
Tel Aviv University
Corresponding Author
Eytan Ruppin
University of Maryland
Corresponding Author
Version History
CURRENT STATUS: Posted
Version 1
Posted 03 Sep, 2015
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
This protocol describes the process used to convert >1300 microbial media recipes, listed on the website of the Leibniz Institute DSMZ (see: https://www.dsmz.de/?id=441), into a machine readable format, and then to read them into a SQL database. In the process, we combine compounds with degenerate names and include concentrations of all compounds in standard units. The protocol includes steps for error-checking, as well as a process to recursively add media when they cross-reference each other. The protocol might be useful in other, similar database building tasks, and especially might help in efforts to incorporate other microbial media recipes from literature into this or another database.
Figure 1
The authors declare no competing financial interests
This is a list of supplementary files associated with this preprint. Click to download.
- supplement0.xlsx
Table 1 Concentration conversions This shows how we converted any concentration, mass, or volume unit into a set of 5 standard units (see Step 9 of the protocol).
Loading...