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| import streamlit as st | |
| st.sidebar.markdown(''' | |
| # Sections | |
| - [How to use](#how-to-use) | |
| ''', unsafe_allow_html=True) | |
| st.markdown(''' | |
| # ProtHGT User Guide | |
| ''') | |
| import streamlit as st | |
| st.markdown(""" | |
| ProtHGT is a web-based tool for **automated protein function prediction** using heterogeneous graph transformers and knowledge graphs. Follow the steps below to generate predictions for your proteins. | |
| """) | |
| st.subheader("1. Select Proteins") | |
| st.markdown(""" | |
| In the **sidebar**, choose how to input your proteins: | |
| - **Search Proteins**: Select or search UniProt IDs from the available dataset. | |
| - **Upload a File**: Upload a text file (.txt) containing UniProt IDs (one per line, max 100). | |
| """) | |
| st.warning("⚠️ Currently, our system can only generate predictions for proteins that are already included in our knowledge graph. Real-time retrieval of relationship data from external source databases is not yet supported. We are actively working on integrating this capability in future updates. Stay tuned!") | |
| st.info("📥 Selected proteins can be downloaded as a txt file.") | |
| st.subheader("2. Choose Gene Ontology (GO) Category") | |
| st.markdown(""" | |
| Select which **Gene Ontology (GO) sub-ontology** to use for function prediction: | |
| - **Molecular Function (MF)** – Biochemical activity of the protein | |
| - **Biological Process (BP)** – Biological roles and pathways | |
| - **Cellular Component (CC)** – Location within the cell | |
| - **All Categories** – Runs predictions for all three categories | |
| """) | |
| st.subheader("3. Generate Predictions") | |
| st.markdown(""" | |
| Click **"Generate Predictions"** to start the analysis. The model will process the selected proteins and return predicted functional annotations. | |
| 🔄 **Processing time**: A few minutes (depending on input size). | |
| """) | |
| st.subheader("4. View and Filter Results") | |
| st.markdown(""" | |
| Once predictions are generated, use the filter options to refine the output: | |
| - **Filter by Protein** (UniProt ID) | |
| - **Filter by GO Category** | |
| - **Set Probability Range** (Adjust prediction confidence thresholds) | |
| Results are displayed in a sortable table, with **probabilities** indicating prediction confidence. | |
| """) | |
| st.info("📥 Filtered predictions can be downloaded as a CSV file.") | |
| st.subheader("5. Start a New Query") | |
| st.markdown(""" | |
| After generating predictions, you can start a new query by selecting different options from the sidebar. | |
| """) | |
| st.subheader("🚀 Running Locally?") | |
| st.markdown(""" | |
| For **larger datasets** or **custom analyses**, you can run ProtHGT locally using our [**GitHub repository**](https://github.com/HUBioDataLab/ProtHGT). | |
| """) | |