Box 2. Frequently asked questions about the MIMIx guidelines

To clarify when researchers should use MIMIx and some frequently asked questions about the guidelines, we provide select questions and answers below:

When should I use MIMIx?

• When describing any molecular interaction within a paper that you are writing
• When preparing your data for submission to any MIMIx-compliant database

How should I describe my experiment in a way that is clear to the reader?

• Use the appropriate terms from the PSI-MI controlled vocabulary; if you cannot find your technique listed, request a new term
• Add any additional detail to Materials and Methods as usual, or in a free-text description in a database submission

Why do I need to use accession numbers; surely a gene name is enough?

• Gene names often change with time, and their use may lead to ambiguities in the data
• Gene names give no indication as to originating species, and this important information is often missing from papers

What is meant by 'participant role'?

• In many experiments, a specific protein will be modified or specifically targeted by antibodies and then used to capture its interacting partners; this is a bait-prey relationship
• We can also infer that proteins are physically interacting if they have a biological relationship, such as enzyme–enzyme target
• In many cases, for example, cosedimentation, no such relationships can be assigned, and these interactions are described as 'neutral' in MIMIx terminology

Why should I submit my results to a MIMIx-compatible database; surely writing a paper is enough?

• Data deposition ensures that your data are available, in a downloadable format, to the entire interactome community
• It increases the visibility and readership (and thus potentially citations) of your paper
• It results in your data being available through many other routes, such as the UniProtKB database
• The database can help you provide data to the journal, give you accession numbers and ensure long-term storage of your data