Annotation files related to the Telomere-to-Telomere genome assembly of the clubroot pathogen Plasmodiophora brassicae (GCA_036867785.1)
Bibliographic record
Abstract
This repository contains annotation files related to the T2T genome aseembly of Plasmodiophora brassicae. Link to the NCBI genome submission- https://www.ncbi.nlm.nih.gov/bioproject/1071157 Description of the files : GCA_036867785.1_ULAVAL_Pb3A_genomic.fna - Soft-masked genome sequence FASTA file representing 20 chromosomes. sequence_report.jsonl - Detailed information about individual chromosome seqeunce. PBTT_annotation.gtf - GTF file corresponding to the genomic FASTA file.The GTF file was generated by BRAKER3 and contains information about all possible transcripts. PBTT_CDS_longest_isoform.fasta - Contains 10521 FASTA sequences representing the CDS of only the longest isoform of the gene models. PBTT_protein_longest_isoform.fasta - Contains 10521 FASTA sequences representing the amino acid sequences of only the longest isoform of the gene models.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.003 |
| Meta-epidemiology (narrow) | 0.003 | 0.001 |
| Meta-epidemiology (broad) | 0.003 | 0.002 |
| Bibliometrics | 0.005 | 0.008 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.004 | 0.002 |
| Research integrity | 0.003 | 0.003 |
| Insufficient payload (model declined to judge) | 0.075 | 0.113 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".