Tops в‚№ 35
Refreshed 2 years ago
Suggestion:
Minor Revision
Review Comment:

This manuscript was submitted as 'Tools and Systems Report' and should be reviewed along the following dimensions: (1) Quality, importance, and impact of the described tool or system (convincing evidence must be provided). (2) Clarity, illustration, and readability of the describing paper, which shall convey to the reader both the capabilities and the limitations of the tool.

This paper presents the OWL explanation workbench, an API, reference implementation and ProtГ©gГ© Plugin distributed together with ProtГ©gГ© 5.
The tool is grounded in years of research on computing justifications, and uses techniques making the computation efficient. The user interface in ProtГ©gГ© also uses techniques to improve the presentation of justification. This results in a mature, usable tool, that ontology engineers will certainly (are already) welcome.

The paper is well written, with a good backround introcution and a detailed, illustrated presentation of the tool and user interface.

The tool is however presented as a finished product. It would be helpful to give limitations, and to give plans for future releases or improvements.

The historical presentation of research on justifications is subjectively presenting two pieces of work. The amount of attention given to other (cited) works seems unbalanced. In particular, it would be good to compare to other tools for justification/debugging.

Minor:
- section 1. A user
is faced ... They need

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%
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