Curation Guidelines for INDRA errors¶

This document outlines the most common type of errors identified in the BEL statements extracted from INDRA.

When they’re encountered:

Add a column with the label ‘Error Type’ to your document
Whenever you find a type of error mentioned in the table, please put the type of error in the column
If the error does not correspond to any of those categories, add a new error type to this table and give an example

Gene-centric¶

Knock Down. A knock down of the gene is not labelled as such.
Gene skipping. Exon/intron regulation is not labelled as such.
Promoter activity. Missing promotor activity labels.

Relationship¶

Target. Labelled as target but not clear from the evidence.
Modulate. Labelled as modulation but not clear from the evidence.
Regulate. Labelled as regulation but not clear from the evidence.
Mediate. Labelled as mediation but not clear from the evidence.

Identification¶

The Named-entity recognition system labels an entity wrong. For example, confusing an abbreviation with a different meaning (e.g., FIP means USF2 but is also a recombinant protein (FasL Interfering Protein))

Negation¶

But not. False positive negation.
Negative mediator.

Subject/object¶

Subject and object are correctly labelled but there is not relationship between them.

Not Evidence¶

The evidence information is not sufficient to code the BEL statement.

Site of Modification¶

The entity was labelled with the wrong modification site.

Physical Contact Missing¶

The relationship was labelled as directed but the evidence does not show that.