references_to_external_databases
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
references_to_external_databases [2024/09/02 11:07] – shankar | references_to_external_databases [2024/09/02 12:28] (current) – shankar | ||
---|---|---|---|
Line 1: | Line 1: | ||
====== References to External Databases ====== | ====== References to External Databases ====== | ||
- | Compounds and reactions in enviPath can be automatically linked to external databases.At the compound | + | |
+ | Compounds and reactions in enviPath can be automatically linked to external databases.At the Compound | ||
+ | |||
+ | ===== Algorithm logic ===== | ||
+ | |||
+ | ==== Updating references of a compound ==== | ||
+ | |||
+ | - Check if the compound is a labelled compound, i.e. 14C labelled compound. If so, we do not check for external references. | ||
+ | - Try to find a match< | ||
+ | * Use the isomeric SMILES to calculate the InChIkey (mild canonicalization) | ||
+ | * Neutralise the molecule and calculate its InChIkey (charge removal) | ||
+ | * Canonicalize the SMILES, removing stereochemical information and calculate its InChIkey (strong canonicalization) | ||
+ | - Use the SMILES obtained on the previous steps a, b, c and search on PubChem using them. | ||
+ | - If any PubChem identifier was obtained from the previous workflow, these are used to extract all the synonyms of each identifier and the corresponding ChEBI and KEGG identifiers are extracted by pattern matching. | ||
+ | - We expand the amount of ChEBI identifiers by using their REST API library [[https:// | ||
+ | |||
+ | ==== Updating references of a reaction ==== | ||
+ | |||
+ | - For each substrate and product, check if the references were updated at any point. If not, update their references. | ||
+ | - Check if all substrates and products have a ChEBI identifier. If so, use it to query Rhea identifiers available using the [[https:// | ||
+ | |||
+ | ---- | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | 1. We find matches by performing a request to [[https:// | ||
+ | |||
+ | |||
+ |
references_to_external_databases.1725275225.txt.gz · Last modified: 2024/09/02 11:07 by shankar