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PSI-MI Feature TAB Format

Introduction

PSI-MI FeatureTab is a new format, it takes inspiration from the existing PSI-MI TAB 2,8 (1), which is actively supported by the MI worktrack. Most users will continue to use PSI-MI MITAB or PSI-MI XML2.5/3.0 to exchange experimental-based interaction data, the PSI-MI FeatureTab will be required only for specialist use cases, as for example, parsing all the molecular interaction data where mutations have been shown to affect a protein interaction.

(1) https://europepmc.org/article/MED/30793173

Column definitions

The column contents should be as follows:

  1. Feature AC, is designed to report the accession number for a feature such as mutations, binding sites, PTMs, etc. (ex. EBI-489661; EBI-1000504; EBI-1234567).
  2. Feature short label, contains human-readable short label summarizing the amino acid changes and their positions. In the case of sequence mutation features these are compliant with the Human Genome Variation Society recommendations (see https://hgvs-nomenclature.org/stable/recommendations/general/).
  3. Feature range(s), contains position(s) in the molecule sequence involved in that specific feature (Ex: mutation (ex. 255-255), binding sites (ex. 12-153), PTMs (ex. 15-15), etc).
  4. Original sequence, contains the wild type molecule residue(s) affected, in one letter amino acid or nucleotide code.
  5. Resulting sequence, contains the replacement sequence (or deletion) in one letter amino acid or nucleotide code.
  6. Feature type, contains the feature type, following the PSI-MI controlled vocabularies (EX: mutation (MI:0118); mutation decreasing (MI:0119); mutation disrupting strength (MI:1128); Necessary binding region (MI:0429), etc.)
  7. Feature annotation, contains specific comments, in free text, about the annotated feature that can be of interest.
  8. Affected molecule identifier, contains affected molecule identifier (for proteins, preferably UniProtKB accession, if available, Ex: UniProtKB:P12346. ChEBI identifiers are recommended for small molecules and RNACentral identifiers for noncoding RNAs). It is represented as databaseName:identifier, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and identifier is the unique primary identifier of the molecule in the database.
  9. Affected molecule symbol, contains, for example, the gene name of the protein affected by a specific feature, as given by UniProtKB (EX. Gene name, DLG4).
  10. Affected molecule full name, contains, for example, the full name of the protein affected by a specific feature, as given by UniProtKB (EX. DLG4, Disks large homolog 4).
  11. Affected molecule organism, contains the TaxID and species name when the molecule is genome encoded as given by the NCBI taxonomy database. It is represented as taxid:identifier(organism name) where the identifier is the taxon id of the organism and organism name can either be the common name or scientific name (EX. 9606 – Homo sapiens).The use of the term ‘Chemical synthesis’ is acceptable for small molecules.
  12. Interaction participants, contains information about the identifiers for all participants in the affected interaction, along with their species and molecule type between brackets. Ex.: (UniprotKB:P15153(protein(MI:0326), 9606 – Homo sapiens)|ensembl:ENSP00000356505(protein(MI:0326), 9606 – Homo sapiens)).
  13. PubMed ID, contains the reference to the publication where the interaction evidence was reported. It is recommended to give one PubMed ID per MITAB line and IMEx IDs can be added. Ex: PubMed:16980971|IMEx:IM-1
  14. Figure legend, contains the reference to the specific figures or tables in the paper where the interaction evidence was reported.
  15. Interaction AC, describes the interaction accession within our databases. This can be used to obtain further information about the interaction (EX.: EBI-489644; EBI-8285478).
  16. Xref ID, contains whenever is available the Xref Identifier associated to a feature. It is represented as databaseName:ac(text), where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the primary accession in the database. For example, the InterPro cross references associated to a protein binding domain ((EX. Feature AC=EBI-7665833; INTERPRO_ID=IPR001478)). Multiple cross references are separated by “|”.

Empty columns should be represented with '-' to keep track of the columns.

Syntax

Columns are normally formed by fields delimited by "|", with a structure like this one:

<XREF>:<VALUE>(<DESCRIPTION>)

Due to the unsafe use of reserved characters in the values, we have recently added the possibility to surround <XREF>, <VALUE> or <DESCRIPTION> with quotes if they contain a special symbol.

In MI-TAB, the reserved characters are:

|
(
)
:
\t (tabulation)

Whenever this happen in your data, surround the value with double quotes:

"<XREF_WITH_RESERVED_CHARS>":"<VALUE_WITH_RESERVED_CHARS>"("<DESCRIPTION>")

Note that the quotes are before and after each part. The escaped data should look like in the following examples:

psi-mi:"MI:0000"(a cv term)
psi-mi:"MI:0000"("I can now use braces ()()() or pipes ||| here and ::colons::")

If you want to use a quote within a quote, escape it:

uniprotkb:P12345("a \"nice\" protein")