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Method Article
Building the KOMODO media database
Matthew Oberhardt
Ruppin Lab, University of Maryland
Corresponding Author
Uri Gophna
Tel Aviv University
Corresponding Author
Eytan Ruppin
University of Maryland
Corresponding Author
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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
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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This is a preprint. It has not completed peer review.
Method Article
Building the KOMODO media database
Matthew Oberhardt
Ruppin Lab, University of Maryland
Corresponding Author
Uri Gophna
Tel Aviv University
Corresponding Author
Eytan Ruppin
University of Maryland
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
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