PMID Checker for PHI-base

A lightweight Streamlit web application to check whether PubMed IDs (PMIDs) have been curated in PHI-base 4 and/or PHI-Canto.

This tool helps prevent duplicate curation and supports efficient literature triage.

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Overview

The app compares user-entered PMIDs against two internal datasets:

• phibase_4.csv
• phibase_5.csv

It reports whether each PMID is:

• Curated in PHI-base4\
• Curated in PHI-Canto\
• Curated in BOTH\
• Not curated

The results can be viewed interactively and downloaded as a CSV file.

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Features

• Accepts up to 1000 PMIDs at once\
• Supports comma, space, or newline separation\
• Automatically ignores non-numeric input\
• Removes duplicate PMIDs\
• Interactive summary counts\
• Optional full results table\
• Downloadable CSV output\
• Fast membership checking using Python sets

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Requirements

• Python 3.9+
• Streamlit
• pandas

Install dependencies:

pip install streamlit pandas

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File Structure

project_folder/
│
├── app.py
├── phibase_4.csv
├── phibase_5.csv
└── README.md

phibase_4.csv and phibase_5.csv must:

• Be located in the same directory as the app
• Contain PMIDs in the first column
• Have one PMID per row

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Running the App

From the project directory:

streamlit run app.py

The application will open automatically in your browser.

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How It Works

1. CSV files are loaded into Python sets for fast lookup.
2. User input is cleaned and validated.
3. PMIDs are checked for membership in each dataset.
4. Status is assigned based on presence in one or both datasets.
5. Results are displayed and can be exported.

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Input Rules

• Maximum: 1000 PMIDs per submission
• Only numeric PMIDs are accepted
• Duplicate entries are automatically removed
• Non-numeric values are ignored

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Example Input

12345678
23456789, 34567890
45678901 56789012

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Output Example

PMID Status

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12345678 Curated in PHI-base4 23456789 Curated in BOTH PHI-base4 and PHI-Canto 34567890 Not curated

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Use Case

This tool is designed to support:

• Literature triage
• Pre-curation checks
• Internal database maintenance
• Avoiding duplicate curation
• Rapid reporting during meetings or conferences

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Maintainer

Developed for PHI-base curation workflow.