Table 2.

Technical gaps and weaknesses identified as part of the translator QotM challenge series

Issue Type	Number of Issues	Example of a Specific Issue
Bugs	6	Translator service issue. β-sitosterol is incompletely mapped in the Node Normalization [29] and Name Resolver [30] services. UMLS identifier for β-sitosterol is C0106127, but it is not mapped by Node Normalizer to CHEMBL.COMPOUND:CHEMBL:221542.
UI features	6	“Compare” and “exclude” lists. Compare lists of genes, e.g., extract those that are up/down regulated. Translator cannot directly compare two answer sets to identify overlap and distinction, e.g., “in PsA gene set but not in PsO gene set.”
Data/attribute gaps	19	WikiPathways [31] and BioPlanet [32]. Considered “trusted” by toxicologists but are not Translator knowledge sources.
Biolink Model/TRAPI	6	Drug classes and side effects. Drug classes and side effects are not supported in Translator. Biolink Model [11] “has_chemical_role” attribute was added to “ChemicalEntity” class. Plan is to tag ChemicalEntity with ChEBI roles as Biolink class, with role related to a ChemicalEntity via an edge property “has_chemical_ role.”
Answer ordering/ organizing	5	Grouping. SMEs expressed a desire to group answers by, e.g., phenotypes or chemicals. Translator does not currently support this.
Answer quality	6	SemMedDB [33]: incomplete, incorrect, or missing annotation; liberal or incorrect predicate assertions. SemMedDB sometimes provides incomplete or incorrect annotation and predicate assertions, e.g., the predicate treat is sometimes used too liberally for assertions that are more accurately captured with predicates such as affects.

ChEBI = chemical entities of biological interest; PsA = psoriatic arthritis; PsO = psoriasis; QotM = question-of-the-month; SemMedDB = semantic medline database; SME = subject matter expert; UI = user interface; UMLS = unified medical language system.