Table 7

Gene Entity Recognition errors and potential solutions

Error Class


Example (PMCID)

Potential Solution

Synonym Not Found

New synonym is not found in databases

AtHscB (PMC2764847)

Increase breadth of databases searched by tool

Species prefix obfuscates synonym

AtHscB (PMC2764847)

Ability to add synonym or species-specific rules for string matching


Synonym is a common English word


Ability to add or remove a synonym and reprocess highlighting

Synonym maps to more than one identifier


Present matches simultaneously with clues like other synonyms and interacting partners

Species not clearly specified

Reference 5 in PMC2680910

Be able to navigate to other sections of the paper, other papers; be able to curate to orthologous cluster of proteins

Synonym refers to a protein family or an enzymatic activity

Ability to curate to protein family or orthologous cluster of proteins

Arighi et al. BMC Bioinformatics 2011 12(Suppl 8):S4   doi:10.1186/1471-2105-12-S8-S4

Open Data