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In the original algorithm the identifiers of the alpha atoms of a center atom are used to calculate an updated identifier for the center atom.
This iterative procedure implicitly grows a circular substructure around the center atom because with an increasing number of iterations the updated identifier of a center atom contains information from further and further away.
This protocol uses the hash of its identifier as a response to a reader query to maintain scalability at the server, and the back-end server sends a message using the updated identifier to the tag after getting the tag response.
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A random sample of 100 automatically updated identifiers were also checked manually.
In addition to updating identifier types that were already present in Recon 2, we added identifiers for the LIPID MAPS Structure Database (LMSD) [32] which were previously missing.
All three applications enabled partially automatic updating of metabolite identifiers, but significant manual effort was still required to fully update identifiers.
We applied the best suited application to updating identifiers in Recon 2, the latest reconstruction of human metabolism.
A name search is the best option available for updating identifiers for metabolites that are only annotated with a name.
To speed up the process of updating identifiers, we took advantage of the extensive metabolite annotations that are available in HMDB [14, 15].
For example, old gene identifier 'TGME49_043440' gets automatically converted into the updated gene identifier 'TGME49_243440' during the upload process.
We updated metabolite identifiers in Recon 2 using additive mapping with CTS as described in the previous section.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com