Subpar responses from AOP-related neuronal use case

[gingin77]

Hi, I'm sharing this output from my Translator A&C program project that I'm working on with Kara.

In the "Rating" column, "R" means rejected and "B" means borderline accept.

Rating	Input Phrase	Output Label	Output Curie	Comment
R	neuronal network	A0A8D0R8C7_PIG Leucine rich repeat neuronal 2 (trembl)	UniProtKB:A0A8D0R8C7	Wrong LoBO - protein name given for organ level attribure
R	Ca2+-calmodulin signal transduction	CA2	NCBIGene:100154873	Result is too simple for the complex input
R	Neurodegeneration	pantothenate kinase-associated neurodegeneration	MONDO:0009319	Result adds meaning not present in the input; HP_0002180 would be preferred
R	synaptic formation and plasticity	A0A4W2HWR1_BOBOX Synaptic plasticity regulator PANTS (trembl)	UniProtKB:A0A4W2HWR1	Process needed; Protein given
R	Hippocampal Physiology,	Abnormal respiratory system physiology	HP:0002795	poor match, "physiology" is shared but other terms don't match
R	Pro-Inflammatory Mediators	inflammatory myofibroblastic tumor	MONDO:0015798	A tumor type doesn't match input
R	Deposition of Energy	light chain deposition disease	MONDO:0019730	poor mathc, "deposition" is shared but other terms don't make sense
R	Neural Remodeling	F2Z3E4_HUMAN Nucleolus and neural progenitor protein (trembl)	UniProtKB:F2Z3E4	Wrong LoBO - protein name given for tissu/organ level process
R	Thyroid hormone synthesis,	Hypothyroidism due to defect in thyroid hormone synthesis	UMLS:C0271825	Disease phenotype returned instead of a process
R	Na+/I- symporter (NIS)	nis	NCBIGene:33337	A gene from flybase, no individualized sperm
R	neuronal network	A0A8D0R8C7_PIG Leucine rich repeat neuronal 2 (trembl)	UniProtKB:A0A8D0R8C7	poor match, "physiology" is shared but other terms don't match
B	Nicotinic acetylcholine receptor	F6ZNF4_CIOIN Nicotinic acetylcholine receptor subunit (trembl)	UniProtKB:F6ZNF4	Result protein name is correct, but includes species specificity, which is not included in the input
B	levels of BDNF	BDNF	NCBIGene:397495	Close; levels of BDNF implies a phenotype, not just the BDNF on its own
B	Na+/I- symporter	Slc5a5	NCBIGene:114613	Rat-specific gene but ok

[karafecho]

@gaurav : The above terms are from the AOP-wiki and related to KE 341: Impairment, Learning and memory. I think "neuronal network" may actually be "neuronal network function" or "neuronal network function, decreased", but @gingin77 can confirm.

[gingin77]

@karafecho and @gaurav - I can confirm, the input phrases are based on Key Event titles, but I stripped off action-like terms that describe the direction of perturbation for each event and a handful of terms like "function", which seemed to yield poor matches from Name Resolver.

[karafecho]

I see. Thanks for the clarification.

Rather than change the AOP-wiki terms and hence their semantic definitions, I'm wondering if it makes more sense to start with the AOP-wiki terms and determine how best to map them to terms that Name Resolver supports or should support.