Data

Pretrained Weights

You can download the pre-trained weights used in the INTREPPPID manuscript from the GitHub releases page.

Precomputed Datasets

You can download precomputed datasets from the sources below:

1. Zenodo (DOI: 10.5281/zenodo.10594149)

2. Internet Archive

All datasets are made available under the Creative Commons Attribution-ShareAlike 4.0 International license.

Dataset Format

INTREPPPID requires that datasets be prepared specifically in HDF5 files.

Each INTREPPPID dataset must have the following hierarchical structure

intrepppid.h5
├── orthologs
├── sequences
│
├── splits
│   ├── test
│   ├── train
│   └── val
│
└── interactions
    ├── c1
    │    ├── c1_train
    │    ├── c1_val
    │    └── c1_test
    │
    ├── c2
    │    ├── c2_train
    │    ├── c2_val
    │    └── c2_test
    │
    └── c3
         ├── c2_train
         ├── c2_val
         └── c2_test

All but one of the “c” folders under “interactions” need be present, so long as that is the dataset you specify in the train step with the --c_type flag.

Here is the schema for the tables:

orthologs schema

Field Name	Type	Example	Description
ortholog_group_id	Int64	1048576	The OMA Group ID of the protein in the protein_id column
protein_id	String	M7ZLH0	The UniProt accession of a protein with OMA Group ID ortholog_group_id

sequences schema

Field Name	Type	Example	Description
name	String	Q9NZE8	The UniProt accession that corresponds to the amino acid sequence in the sequence column.
sequence	String	MAASAFAGAVRAASGILRPLNI…	The amino acid sequence indicated by the name column.

Schema for all tables under interactions

Field Name	Type	Example	Description
protein_id1	String	Q9BQB4	The UniProt accession of the first protein in the interaction pair.
protein_id2	String	Q9NYF0	The UniProt accession of the second protein in the interaction pair.
omid_protein_id	String	C1MTX6	The UniProt accession of the anchor protein for the orthologous locality loss.
omid_id	Int64	737336	The OMA Group ID of the anchor protein, from which a positive protein can be chose for the orthologous locality loss.
label	Bool	False	Label indicating whether protein_id1 and protein_id2 interact with one another.