39 lines
2.0 KiB
Markdown
39 lines
2.0 KiB
Markdown
## Biomedical Article Abstract Summariser using Europe PMC + Ollama
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This is a simple app that demonstrates an article abstract summariser leveraging Europe PMC’s API and Ollama LLMs to generate concise summaries of biomedical literature.
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## 🔍 About Europe PMC (EPMC)
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Europe PMC is a free, open-access database that provides access to millions of life sciences and biomedical articles, research papers, and preprints. It is part of the PubMed Central International (PMCI) network.
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## Features
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This solution presents 2 methods:
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1. A simple demo via a jupyter notebook
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2. An interactive demo via gradio, running on your local computer.
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**Core Features:**
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- Fetch an article’s metadata and abstract via Europe PMC’s API (using a provided PMCID).
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- Preprocess and clean the abstract text unnecessary tags e.g referenc tag or math formula.
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- Summarise abstracts into bullet points + a short paragraph using Ollama models.
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## 📌 How to Use
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- Go to [Europe PMC' website](https://europepmc.org/).
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- Use the search bar to find an open-access article by keywords, entity names, journal, or author. E.g Genes, Diseases, nutrition etc
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- Since the app currently only runs on open-access only articles, you'll need to restrict results to `open-access` only articles: add filters like `HAS_FT:Y` or `IN_EPMC:Y` to your search syntax. E.g .`"Genes: HAS_FT:Y"`
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- Select your article of interest and copy its PMCID (e.g., PMC1234567).
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- Run the summariser:
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- via notebook: Paste the `PMCID` as a string in the display_response func, after running all other cells.
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- via gradio:
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- run the python script via CLI:
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```python
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python article_summariser-gradio.py
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```
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- Paste the `PMCID` as you've copied it in the `Enter a **EuropePMC Article ID` textbox.
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- click on the `Fetch Article Abstract and generate Summary` button.
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**N.B**: I've observed that using `llama3.2` runs faster on my pc. You may experience some delays with all other models. Also make sure to already have ollama running via `ollama serve` on your terminal before running the script.
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