KGDataset.from_dataframe + custom data notebook #25
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AlCatt91
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I added to this PR with a few updates:
The updates to the notebook are from black formatting (can disregard). |
danjust
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Sep 27, 2023
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| This repository provides dataloaders for third party datasets. The use of these datasets is at own risk and Graphcore offers no warranties of any kind. It is the user's responsibility to comply with all license requirements for datasets downloaded with dataloaders in this repository. | ||
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| The tutorial notebooks make use of the following datasets: |
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If we keep the OpenBioLink nb we should include that here
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Thanks! I changed the dataset in the new notebook to biokg, please have a final look when you can :) |
danjust
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Sep 27, 2023
notebooks/0_custom_KG_dataset.ipynb
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| "We download the directed, high-quality version of [OpenBioLink2020](https://github.com/openbiolink/openbiolink#benchmark-dataset) directly from the link provided by the authors. This shouldn't take more than a minute.\n", | ||
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| "Notice that OpenBioLink2020 integrates data from other sources, whose licensing terms are detailed in [this table](https://openbiolink.readthedocs.io/en/latest/sources.html) and should be minded when utilizing or redistributing the dataset files." | ||
| "We download the OGBL-BioKG Knoweldge Graph using the `ogb` package (see [here](https://ogb.stanford.edu/docs/linkprop/#data-loader) for details on how to use it). This shouldn't take more than a couple of minutes." |
danjust
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Sep 27, 2023
…otebook Tech Docs Review of "Using BESS-KGE with your Own Data" notebook
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Added an ease-of-use method to build a
KGDatasettaking in directly labelled triples (organized in a pandas dataframe), performing the label -> ID conversion behind the curtain and re-ordering, if needed, to cluster entities of the same type. It is meant to be even higher-level than thefrom_triplesmethod.Using this, I also wrote up a notebook, as we were planning to do, to show how to build a custom dataset, using as example the OpenBioLink dataset (there are the usual concerns about licensing of data sources, but I hope that, if we use it just for this small demo notebook, it shouldn't be a problem?) Any feedback is welcome!