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* Add CURIE parse benchmark * Update pages * Add more epochs to benchmark * Update README.md * Pass mypy
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# CURIE Parsing Benchmark | ||
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This benchmark checks the `bioregistry.parse_curie` function. | ||
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## Dataset | ||
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The benchmarking dataset is available in [`data.tsv`](data.tsv). It contains | ||
5 columns: | ||
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1. `prefix` - a canonical Bioregistry prefix | ||
2. `identifier` - a local unique identifier in the prefix's semantic space | ||
3. `prefix_synonym` - the synonym of the canonical prefix being used | ||
4. `banana` - the banana being used (i.e., redundant prefix in local identifier) | ||
5. `curie` - the CURIE for the prefix_synonym-banana-identifier triple | ||
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Example data: | ||
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| prefix | identifier | prefix_synonym | banana | curie | | ||
|---------------|--------------|----------------|--------|----------------------------| | ||
| 3dmet | B00162 | 3dmet | | 3dmet:B00162 | | ||
| 4dn.biosource | 4DNSR73BT2A2 | 4DN | | 4DN:4DNSR73BT2A2 | | ||
| 4dn.biosource | 4DNSR73BT2A2 | 4dn.biosource | | 4dn.biosource:4DNSR73BT2A2 | | ||
| 4dn.replicate | 4DNESWX1J3QU | 4dn.replicate | | 4dn.replicate:4DNESWX1J3QU | | ||
| abcd | AD834 | abcd | | abcd:AD834 | | ||
| cco | 0000003 | cco | | cco:0000003 | | ||
| cco | 0000003 | cco | CCO: | cco:CCO:0000003 | | ||
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## Results | ||
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Most parsing goes pretty fast (average around 4,000 CURIE/second). | ||
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![](results.svg) |
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