Index of /monthly_releases/2026/pombase-2026-08-01/training_data_for_ML_and_AI

 Name                                                              Last modified      Size  Description
 Parent Directory                                                                       -   
 alleles.tsv                                                       2026-08-01 02:00  936K  
 canto_go_annotations_with_comments.parquet                        2026-08-01 02:00  401K  
 canto_go_annotations_with_comments.tsv                            2026-08-01 02:00  5.5M  
 canto_publication_classification.tsv                              2026-08-01 02:00  624K  
 canto_single_locus_diploid_fypo_annotations_with_comments.tsv     2026-08-01 02:00  518K  
 canto_single_locus_haploid_fypo_annotations_with_comments.parquet 2026-08-01 02:00  1.5M  
 canto_single_locus_haploid_fypo_annotations_with_comments.tsv     2026-08-01 02:00   32M  
 curated_publications.tsv                                          2026-08-01 02:00  594K  
 gene_IDs_names_products.tsv                                       2026-08-01 02:00  1.2M  
 interactions_with_comments.tsv                                    2026-08-01 02:00  8.9M  
 protein_modification_annotations_with_comments.tsv                2026-08-01 02:00  9.9M  
 publications_with_annotations.txt                                 2026-08-01 02:00   78K  
 qualitative_gene_expression_with_comments.tsv                     2026-08-01 02:00  1.8M  

This directory contains files compiling data destined to train
Language Models and Artificial Intelligence models for curation
purposes.

 - alleles.tsv
   Information about curated alleles:
    - gene_systematic_id
    - gene_name
    - allele_current_internal_id - the internal PomBase ID for the allele,
                                   which changes each release
    - allele_name
    - allele_type
    - allele_description
    - allele_synonyms
   See this recent PomBase publication for details about allele
   nomenclature:
     https://doi.org/10.1093/genetics/iyad143

 - canto_publication_classification.tsv
   A TSV file of PubMed ID vs Canto publication triage status

 - canto_go_annotations_with_comments.tsv
   Manual GO annotations with comments, GAF 2.2 TSV format with a
   "comments" column
 - canto_go_annotations_with_comments.parquet
   The same information in Parquet format

 - canto_single_locus_haploid_fypo_annotations_with_comments.tsv
   Manual haploid single locus phenotype annotations with curator comments.
   PHAF TSV format with a "comments" column.
   Format documentation: https://www.pombase.org/downloads/phenotype-annotations
 - canto_single_locus_haploid_fypo_annotations_with_comments.parquet
   The same information in Parquet format
 - canto_single_locus_diploid_fypo_annotations_with_comments.tsv
   Manual single locus diploid phenotype annotations with curator comments.
   Diploid PHAF TSV format with a "comments" column.
   Format documentation: https://www.pombase.org/downloads/phenotype-annotations
 - curated_publications.tsv
   PubMed ID and title of publications that have been curated by PomBase

 - publications_with_annotations.txt is a list of the PubMed
   identifiers (PMID) of all publications with annotations in PomBase.

 - protein_modification_annotations_with_comments.tsv
   All protein modifications annotations currently featured in PomBase, with
   the curator comment (if any)
   See https://www.pombase.org/documentation/modification-data-bulk-upload-format
   for a description of the column contents

 - qualitative_gene_expression_with_comments.tsv
   This file has the same format as the bulk upload file documented here:
   https://www.pombase.org/documentation/qualitative-gene-expression-data-bulk-upload-format
   with an extra curator comment column.

 - interactions_with_comments.tsv
   This file has the same format as the interactions file:
   https://www.pombase.org/latest_release/interactions/
   with an extra curator comment column.

 - gene_IDs_names_products.tsv - see here for documentation:
     https://www.pombase.org/latest_release/gene_names_and_identifiers/


These files are part of PomBase release 2026-08-01

For use of this dataset please cite:
  Pascal Carme, Kim Rutherford, Jürg Bähler, Juan Mata, Valerie Wood
  PomBase in 2026: Expanding Knowledge, Modelling Connections
  Genetics, January 2026
  https://doi.org/10.1093/genetics/iyag001