Table 7.

Gene Entity Recognition errors and potential solutions

Error Class	Error	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
Ambiguity	Synonym is a common English word	WASp	Ability to add or remove a synonym and reprocess highlighting
	Synonym maps to more than one identifier	AIP1	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