Validate OGER/Ontorunner split_11 output

RENCI-NER / oger-benchmarks

An instance of OGER that we can benchmark

MIT License

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Open gaurav opened 2 years ago

gaurav commented 2 years ago

We now have Ontorunner output for split_11 available on Hatteras at /projects/ner/split_11_results/ontorunner/split_11-results.jsonl.

Number of results: 488,850 (the same number of results as split_11.txt)
Range: 0-34640 denotations per abstract (only one abstract has zero denotations)
Median: 207, mean: 225.62
25th percentile: 139, 75th percentile: 287

gaurav commented 2 years ago

Total number of denotations with IDs: 110,292,363

Top denotation sources:

1,023,728 OBO
1,346,978 PR
1,563,252 UO
2,513,530 BFO
2,851,868 CL
2,891,758 CHR
3,247,137 ENVO
3,466,881 HP
3,847,455 RO
5,436,511 SO
7,703,939 MONDO
8,178,312 GO
8,719,733 PATO
9,749,977 http (largely EFO and hgnc)
- most frequent: EFO:0001461 "control" (https://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0001461)
11,795,090 NCBITaxon
15,885,081 UBERON
16,261,706 CHEBI