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Tutorial: entry review
All submissions to the MITE Submission System are automatically submitted as pull requests (PRs) to the mite_data GitHub repository. The reviewer pool is notified by email, and any registered reviewer can claim the entry by assigning themself to the PR. The reviewer inspects the preview and reviews it following the Review Guidelines laid out below. Reviewers can modify the pending entry to fix small issues. By approving the entry, the reviewer signs it with their ORCID. The system automatically updates the PR on GitHub and adds the tag "Reviewed".
- Assign yourself to the PR (e.g. by answering the notification email you received)
- Open the preview link to inspect the entry
- Are the reaction(s) described as such in the linked literature reference(s)? If the reaction is abstract (i.e. not a specific substrate-product pair), does the reaction depict the minimal, experimentally verified common substructure the tailoring enzyme needs for the reaction?
- On the Reaction Information tab, does the Tailoring term accurately describe the reaction?
- On the Reaction Information tab, do the Evidence terms match the experimental data described in the reference(s)?
- In the reaction examples, is the Intermediate flag set correctly (i.e. Intermediate=True: product is not the end product of the pathway)
- Is the Enzyme Name correct? Multiple names should be separated by slashes ("/")
- Is the Enzyme Description concise?
- Are the Database References correct? Are they pointing to the correct organism as described in the literature reference(s)?
- Are the Cofactors correct? If they are missing, are there any cofactors known that can be added?
If all is correct, confirm the review by hitting Approve
Figure 1: The approval button that completes and signs the entry as reviewed.
- Q: How are tailoring enzymes defined in MITE? A: MITE takes its definition of "tailoring enzyme" from Walsh 2024. In a nutshell, any natural product-acting enzyme that is not shunting primary metabolite building blocks into the pathway is considered a tailoring enzyme. Please refer to the article for specific questions and feel free to discuss edge cases with other reviewers.
- Q: An enzyme was submitted that is not a tailoring enzyme per se, e.g. precursor synthesis. What do we do with that? A: Such enzymes are out of scope of MITE. We still review the entry and give it a MITE accession number, but the enzyme will be retired right away to not show up on the webpage. This way, the effort of the contributor is preserved. Please make sure to add a comment indicating that it is not a tailoring enzyme.
- Q: Can entries be rejected? A: Yes, but it should be only in exceptional cases as defined in the GOVERNANCE file. If necessary, corrections can also be discussed in the comments of the PR. Additional reviewers can be consulted by tagging them (e.g. @mmzdouc)
- Q: What is meant by the minimal common substructure? A: The minimal common substructure is the chemical substructure that is recognized by the enzyme. Some enzymes are very specific and only accept a specific substrate, others are promiscuous and recognize a broader range of substrates. This information is a key asset of MITE and very important to get right. For example, consider a promiscuous halogenase (Figure 2). This halogenase accepts a range of substrates containing phenol rings, and chlorinates the hydroxy group (Figure 1a). Therefore, it is legitimate to assume that the minimal common substructure the enzyme accepts is a phenol (Figure 1b). However, it is not legitimate to assume that the minimal common substructure is a methoxy group (Figure 2b), since this would also encompass substrates that are not covered by the experimental data, such as methanol.
Figure 2: Figure showing the relationship between experimentally verified substrates accepted by a putative promiscuous halogenase. In this example, the minimal common substrate substructure can be assumed to be a phenol, but not a methoxy group.
Author(s) of this page: Mitja M. Zdouc