mikebada

It's certainly a useful term, though some complicating factors to consider: (1) Many (but not all) sources classify small molecules as organic compounds, though I'm guessing Translator folks would want...

Perhaps has_positive_correlation_with_condition_upon_exposure and has_negative_correlation_with_condition_upon_exposure as subpredicates of positively_correlated_with and negatively_correlated_with, respectively? Also, should ameliorates and exacerbates be subpredicates of the former and latter, respectively?

This is a position statement arguing for the possibility of defining KP-specific confidence/provenance/epistemic parameters/metadata as opposed to only those standardized across Translator and common to multiple KPs. Speaking for the...

In the CRAFT Corpus, which is the basis for our training, nearly all of the gene/gene-product (GGP) mentions are annotated with species-nonspecific PRO classes. (The one minor exception are tokens...

I forgot that the one other type of mention for which species-specific PRO classes are used are those for which the GGP name is specific to a species or relatively...

Finally, the CRAFT GGP annotations are not only almost entirely species-nonspecific but also entirely nonspecific as to gene/transcript/protein. For CRAFT we've actually created a parallel hierarchy of the PRO classes...

@bill-baumgartner Is this from checking via the assertion annotations? There could be more that would be relationally linked but not directly preceding, e.g., CLN2 from control mice. Additionally, there are...

@cmungall: We allow you to conflate GP but not T: https://biolink.github.io/biolink-model/docs/GeneOrGeneProduct It looks like GeneProduct includes transcripts (which I think is correct): GeneProduct - The functional molecular product of a...

I believe the only relations that are being used for both SO and MSO classes are mereotopological ones, particularly 'part of'. I would think that this these would hold for...

Hi Paola, Our plan is for an ontology named the MSO (Molecular Sequence Ontology) composed of analogs of the large majority of current SO classes; this ontology is a representation...