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add docstrings
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korikuzma committed Apr 2, 2024
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16 changes: 7 additions & 9 deletions README.md
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Expand Up @@ -72,9 +72,7 @@ Next, initialize the [Variation Normalizer](https://github.com/cancervariants/va
The MetaKB can acquire all other needed normalizer data, except for that of [OMIM](https://www.omim.org/downloads), which must be manually placed:

```sh
cd disease/ # starting from the site-packages dir of your virtual environment's Python instance
mkdir -p data/omim
cp ~/YOUR/PATH/TO/mimTitles.txt data/omim/omim_<date>.tsv # replace <date> with date of data acquisition formatted as YYYYMMDD
cp ~/YOUR/PATH/TO/mimTitles.txt ~/.local/share/wags_tails/omim/omim_<date>.tsv # replace <date> with date of data acquisition formatted as YYYYMMDD
```

### Environment Variables
Expand All @@ -94,24 +92,24 @@ MetaKB relies on environment variables to set in order to work.
```

* Required when using the `--load_normalizers_db` or `--force_load_normalizers_db` arguments in CLI commands
* `RXNORM_API_KEY`
* `UMLS_API_KEY`
* Used in Therapy Normalizer to retrieve RxNorm data
* RxNorm requires a UMLS license, which you can register for one [here](https://www.nlm.nih.gov/research/umls/index.html). You must set the `RxNORM_API_KEY` environment variable to your API key. This can be found in the [UTS 'My Profile' area](https://uts.nlm.nih.gov/uts/profile) after singing in.
* RxNorm requires a UMLS license, which you can register for one [here](https://www.nlm.nih.gov/research/umls/index.html). You must set the `UMLS_API_KEY` environment variable to your API key. This can be found in the [UTS 'My Profile' area](https://uts.nlm.nih.gov/uts/profile) after singing in.

Example:

```shell script
export RXNORM_API_KEY={rxnorm_api_key}
export UMLS_API_KEY={rxnorm_api_key}
```

* `DATAVERSE_API_KEY`
* `HARVARD_DATAVERSE_API_KEY`
* Used in Therapy Normalizer to retrieve HemOnc data
* HemOnc.org data requires a Harvard Dataverse API key. After creating a user account on the Harvard Dataverse website, you can follow [these instructions](https://guides.dataverse.org/en/latest/user/account.html) to generate a key. You will create or login to your account at [this](https://dataverse.harvard.edu/) site. You must set the `DATAVERSE_API_KEY` environment variable to your API key.
* HemOnc.org data requires a Harvard Dataverse API key. After creating a user account on the Harvard Dataverse website, you can follow [these instructions](https://guides.dataverse.org/en/latest/user/account.html) to generate a key. You will create or login to your account at [this](https://dataverse.harvard.edu/) site. You must set the `HARVARD_DATAVERSE_API_KEY` environment variable to your API key.

Example:

```shell script
export DATAVERSE_API_KEY={dataverse_api_key}
export HARVARD_DATAVERSE_API_KEY={dataverse_api_key}
```

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