doc(readme.md): add figure links and tutorial for run the app locally

bmascat · Mar 23, 2024 · 6fc329a · 6fc329a
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diff --git a/.gitignore b/.gitignore
@@ -28,8 +28,6 @@ Thumbs.db
 
 #Folders
 results/
-figures/
-
 #Files
 notebooks/crossref-api-review.ipynb
 notebooks/resultados.json

diff --git a/figures/adverse-effects-filtering.png b/figures/adverse-effects-filtering.png
diff --git a/figures/adverse-effects.png b/figures/adverse-effects.png
diff --git a/figures/pubmed_tipotumor_farmaco.png b/figures/pubmed_tipotumor_farmaco.png
diff --git a/readme.md b/readme.md
@@ -6,10 +6,17 @@ This application performs a co-occurrence analysis on PubMed of two lists of ter
 
 - **Co-occurrence Analysis**: The application uses PubMed data to perform a co-occurrence analysis of disease and drug terms.
 
+![Co-occurrence Analysis](figures/pubmed_tipotumor_farmaco.png)
+
+
 - **Adverse Effects Extraction**: In addition to the co-occurrence analysis, the application extracts adverse effects from the provided list of drugs.
 
+    ![Adverse Effects Extraction](figures/adverse-effects.png)
+
 - **Adverse Effects Filtering**: An optional third list can be used to filter adverse effects of interest, enabling a more specific and personalized analysis.
 
+    ![Adverse Effects Filtering](figures/adverse-effects-filtering.png)
+
 ## Usage
 
 1. **Data Loading**: Load the CSV files containing the lists of diseases and drugs. You can also load an additional file for the list of adverse effects, if necessary.
@@ -20,6 +27,21 @@ This application performs a co-occurrence analysis on PubMed of two lists of ter
 
 4. **Data Download**: You can download the analysis results for further analysis or reference.
 
+## Running Locally
+
+To run the application locally, follow these steps:
+
+1. Create a directory named `.streamlit` in the root directory of the project.
+2. Create a file named `secrets.toml` inside the `.streamlit` directory.
+3. Add your FAERS API key to the `secrets.toml` file with the following format:
+    ```toml
+    FAERS_API_KEY = "your_api_key_here"
+    ```
+You can obtain your FAERS API key <a href="https://open.fda.gov/apis/authentication/" target="_blank">here</a>.
+
+For more information on how secrets work in Streamlit, visit <a href="https://docs.streamlit.io/streamlit-community-cloud/deploy-your-app/secrets-management" target="_blank">this link</a>.
+
+
 ## Built With
 
 - Python