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## Extending Knowledge Representation for current KG
**Current Release:** [v2.0.0](https://github.com/callahantiff/PheKnowLator/wiki/v2.0.0)
**Description**
Adding the following entities/data…
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Sorry again to bother!
Quick question - should molecules be rendered into a "canonical" SMILES format before training, or does the model learn the features regardless? My intuition is that yes, the…
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Example R-HSA-186797
It looks like some reactions e.g. R-HSA-9674095 have drugs in them as inputs/outputs but are not being removed. (As they should according to https://github.com/geneontology/…
goodb updated
3 years ago
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The (under development) OBO dashboard checks that each ontology describes itself with an annotation using the `http://purl.org/dc/elements/1.1/description` property. Can someone comment here with a co…
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**Is your feature request related to a problem? Please describe.**
Not really a problem, just the inconvenience of not being able to visualize molecules without converting to something external
**…
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The weight matrices `W_a` and `W_b` in the attention layer are not mentioned in the paper, but present in the code. I am not so familiar with attention layers, but I was wondering if I missed somethin…
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I haven't traced back the exact point when something changed on the NCBI side, however currently attempts to build new dbs using `taxit new_database` from the latest `taxdmp.zip` fail during node upd…
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Hi there,
Robert and I have written an OpenMM command line executable which is planned to be in the next release. It can be downloaded here:
https://github.com/rmcgibbo/openmm-cmd.git
I've also ma…
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Posting random ideas if we choose not to stick with `Topology` and `subtopology`
* Model/SubModel - in theory, this data structure includes all the information for how you want to model your system. …
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problem ones:
https://www.ebi.ac.uk/complexportal/complex/CPX-5684
https://www.ebi.ac.uk/complexportal/complex/CPX-5695
https://www.ebi.ac.uk/complexportal/complex/CPX-5696
haven't looked into t…