Create README.md
Browse files
README.md
ADDED
|
@@ -0,0 +1,38 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
license: mit
|
| 3 |
+
tags:
|
| 4 |
+
- genomics
|
| 5 |
+
- bioinformatics
|
| 6 |
+
- benchmark
|
| 7 |
+
- grading
|
| 8 |
+
- synonyms
|
| 9 |
+
- databases
|
| 10 |
+
- ncbi-gene
|
| 11 |
+
- ncbi-taxonomy
|
| 12 |
+
- mirbase
|
| 13 |
+
- hmdb
|
| 14 |
+
- card
|
| 15 |
+
pretty_name: GenomicsBench Grader Databases
|
| 16 |
+
size_categories:
|
| 17 |
+
- 100M<n<1B
|
| 18 |
+
---
|
| 19 |
+
|
| 20 |
+
# GenomicsBench Grader Databases
|
| 21 |
+
|
| 22 |
+
Synonym databases for deterministic grading in [GenomicsBench](https://github.com/AfterQuery/GenomicsBench), a realism-first benchmark for AI coding agents in computational biology.
|
| 23 |
+
|
| 24 |
+
GenomicsBench ships with hundreds of prebuilt graders for highly specific biological outputs. These databases power the synonym-aware matching behind those graders, so that *TP53* and *tumor protein p53* are recognized as the same gene, *hsa-miR-21-5p* and *MIMAT0000076* as the same miRNA, and *E. coli* and *Escherichia coli* as the same organism.
|
| 25 |
+
|
| 26 |
+
## Contents
|
| 27 |
+
|
| 28 |
+
Five tab-separated files, one per biological database. Each is a flat lookup table mapping canonical identifiers to all known names and synonyms.
|
| 29 |
+
|
| 30 |
+
| File | Columns | Rows | Source | Description |
|
| 31 |
+
|---|---|---|---|---|
|
| 32 |
+
| `ncbi_gene_grader_db.tsv` | `organism gene_id name` | 218M | [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/) | Gene symbol, synonym, description, Entrez GeneID, and Ensembl ID resolution scoped by organism |
|
| 33 |
+
| `ncbi_taxonomy_grader_db.tsv` | `canonical_name name` | 3.2M | [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy) | Scientific name, common name, abbreviation, and synonym resolution for all taxa |
|
| 34 |
+
| `hmdb_grader_db.tsv` | `accession name` | 2.0M | [HMDB](https://hmdb.ca/) | Metabolite name, synonym, IUPAC name, and accession resolution |
|
| 35 |
+
| `mirbase_grader_db.tsv` | `accession name` | 185K | [miRBase](https://mirbase.org/) | miRNA precursor and mature name/accession resolution, including deprecated entries |
|
| 36 |
+
| `card_grader_db.tsv` | `aro_accession name` | 19K | [CARD](https://card.mcmaster.ca/) | Antimicrobial resistance gene name, synonym, and ARO accession resolution |
|
| 37 |
+
|
| 38 |
+
For information on the provenance, licensing, or the ETL process generating this dataset, you should visit the [GenomicsBench GitHub repository](https://github.com/AfterQuery/GenomicsBench).
|