Zero-Shot Protein Segmentation (ZPS) Data and Embeddings

uniprotkb_Human.txt

• this is a raw text file that contains a downloaded copy of UniProtKB
• this inlcudes all reviewed human protein sequences 
• we used annotations from this file to copmare to ZPS predictions

uniprotkb_Human_Sequences.fasta

• this is a fasta file that contains reviewed human protein sequences
• these are the sequences we used as input to ProtT5 to generate protein embeddings

ZPS_Boundaries.tsv

• this is a tab separated file that contains the boundaries of protein segments defined by ZPS for reviewed human protein sequences
• we used zero-based indexing for the protein boundaries

ZPS_Segment_Embeddings.hdf5

• this is a hdf5 file that contains segment embeddings for the human proteome
• see "Zero-shot segmentation using embeddings from a language model identifies functional regions in the human proteome" A. G. Sangster 2025 for definition of segment embeddings
• segment boundaries in this file are also in zero-based indexing

evaluation_data.zip includes:

disprot_functional_annotations.tsv

• this conatins DisProt annotations that are labeled as "molecular_function" or "disorder_function" for the human proteome
• this is from the 2025-06 DisProt release

disprot_functional_annotations_per_segment.tsv

• this is a parsed version of disprot_functional_annotations.tsv 
• this includes protein segment keys and their corresponding disprot functional annotations
• these labels were used for multi-label evaluations

protGPS_dataset.csv

• this is a copy of the dataset provided on DOI 10.5281/zenodo.14795444 in notebook/dataset.csv

ProtGPS_idmapping_2025_08_13.tsv

• this is the ID mapping data downloaded from UniProt to map gene names and UniProt IDs found in protGPS_dataset.csv to UniProt IDs used in ZPS 

protGPS_data_only_disordered_segments.tsv

• this is the parsed version of protGPS_dataset.csv 
• this includes protein IDs, train/dev/test split, a list of labels attributed to the protein, and a list of segment keys that over-lap with MobiDB disorder annotations
• these labels were used for multi-label evaluations

uniprot_annotations_per_segment_multi-class.tsv

• this is a parsed version of uniprotkb_Human.txt
• this includes protein segment keys, protein IDs, gene IDs, and labels used in multi-class evaluations
• multi-class labels include:
• PROSITE_LABELS: labels of the top ~20 most commonly occuring protein domains as annotated by ProRule on UniProt
• IDR_VS_DOMAIN_LABELS: labels include Disordered (as annotated by MobiDB via UniProt), ProRule (as annotated by ProRule via UniProt, indicating domain), and Background (does not overlap with a MobiDB disorder annotation or a ProRule domain annotation)
• COMP_BIAS_LABLES: labels for compositional bias annotation (as annotated by MobiDB via UniProt)
• DISORDER_LABELS: for segments that overlap with a MobiDB disordered annotation (via UniProt), take the name of the other overlapping annotation with the highest IoU

uniprot_annotations_per_segment_multi-label.tsv

• this is a parsed version of uniprotkb_Human.txt
• this includes protein segment keys and labels used in multi-label evaluations

Protein segment keys: are formatted as "UniProtID start-stop", where start and stop positions reference the canonical protein sequence on UniProt and use zero-based indexing.

*see "Zero-shot segmentation using embeddings from a language model identifies functional regions in the human proteome" (A. G. Sangster 2025) on how annotations were transfered to protein segments