Charles Tapley Hoyt

MeSH terms for protein families incorrectly output by PybelProcessor

1

Example from EMMAA covid model: WARNING: [2021-08-17 14:29:41] indra.assemblers.pybel.assembler - Node should not have variants: bp(MESH:D019895 ! Transposases), [{'kind': 'hgvs', 'hgvs': 'p.?'}]

https://drugtargetcommons.fimm.fi

http://drugcentral.org/download

Highlight phosphorylations and include information about site mapping in HTML assembler

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Statements like *MAPT is phosphorylated on S579* don't have mechanistic information, but are definitely interesting and informative. However, when they go through the HTML assembler, they are more difficult to...

Thanks for the nice work on this package. We made an [awesome list of KGEM packages](https://github.com/pykeen/kgem-software-review) and this one seems to be the only one without a logo. It would...

Include models from PyKEEN

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There are several KGE models implemented in https://github.com/smartDataAnalytics/PyKEEN from @mali-git that cover translational distance models (e.g., TransE, TransH, TransR, TransD, UM, SE) and semantic matching models (e.g., RESCAL, DistMult, ERMLP,...

Reproduction question: how were the datasets generated?

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This repository includes five nice datasets which makes reproduction much easier, but it's missing whatever scripts (or instructions if manually done) were used to generate them. This would be helpful...

Package code, make pip installable, and add CLI

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Closes #1 This is a really big PR, so very quickly it does a few things: - Reorganizes repository to follow python community standard - Adds `setup.cfg` and `setup.py` and...

Package code and make pip installable

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It would be nice to make this code pip installable and to use entrypoints to make a vanity script through which the scripts can be run. I'd be happy to...