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drivendataorg / snomed-ct-entity-linking-runtime

Runtime repository for the SNOMED CT Entity Linking challenge on DrivenData
MIT License
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Add SciSpacy to runtime #8

Closed profliuhao closed 9 months ago

profliuhao commented 9 months ago

Can you consider adding scispacy==0.5.3 to the run time? ScispaCy is a Python package containing spaCy models for processing biomedical, scientific or clinical text. It is a better fit for this task than spaCy.

chrisjkuch commented 9 months ago

@profliuhao scispacy has been added and the images are building now, will be pushed and available via the container registry shortly.

If you have additional packages you would like to have available, please consider submitting a pull request to add them - it will be faster and easier, as we cannot guarantee that we can quickly respond to or fulfill all requests.

profliuhao commented 9 months ago

Dear Chris,

Thanks for the quick response and action. I have a quick question: For pre-trained embedding or BERT models, such as en_core_sci_lg from Scispacy or BioBERT variants, do you recommend just including the downloaded models in the submission, since the runtime will not provide internet access?

On Thu, Feb 8, 2024 at 9:31 AM Chris Kucharczyk @.***> wrote:

@profliuhao https://github.com/profliuhao scispacy has been added and the images are building now, will be pushed and available via the container registry shortly.

If you have additional packages you would like to have available, please consider submitting a pull request to add them - it will be faster and easier, as we cannot guarantee that we can quickly respond to or fulfill all requests.

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chrisjkuch commented 9 months ago

Yes, you should include such models in your submission.