Bioscape Result Assessment

The suggestions produced by Bioscape's search activities can be assessed subject to the availability of "gold standard" data which confirms whether each particular result can be regarded as genuine.

BioCreative 2 Gene Normalisation

In the bsindex distribution, a script is available to export filtered results from Bioscape for assessment against the BioCreative gold standard:

python scripts/bsindex_export_bc2gn_results.py --bionames <generation> --results <generation> --methods human_gene --min-score 1 --output <output>

Once result data is available, this data can be scored through comparison to the gold standard file:

python scripts/bsindex_score_bc2gn_results.py gold <output>

A number of options to the scoring script help compare different sets of results:

python scripts/bsindex_score_bc2gn_results.py gold <output files> --pretty

The --pretty option provides a table with the following columns:

1. Output filename
2. Number of true positive results
3. Number of false positive results
4. Number of false negative results
5. Precision
6. Recall

Combining the output of this script with other Unix commands can be convenient:

python scripts/bsindex_score_bc2gn_results.py gold <output files> --pretty | sort -n -k 5

The above combination should sort the entries on the precision column in order of increasing precision.