API Card Library

Welcome to the API Card Library!

Application Programming Interfaces (APIs) are software intermediaries that enable two applications to communicate. Many biomedical knowledge bases and software tools support API access.

These API Cards were developed as part of the class projects from UCLA Bioinformatics 201 2022-2023 and as hands-on projects from Bridge2AI ENABLE Scholar Program.

The goal of this project is to: - Learn which APIs are available for biomedical knowledge, software tools, or datasets, and how they can be accessed. - Describe how these APIs can be leveraged for omics-related data analysis workflows.

Each API card document is prepared by a group of students which includes: - Title - Description - Use Cases - Tutorials

A Sample API Card

Following is a sample API card prepared by instructors on Uniprot API. To create your own API Card, please follow the similar pattern below with additional information (e.g., cheat sheet, citations, supporting papers) if applicable.

Title: UniProt Web API

Description:

UniProt is a protein knowledge base which provides information on proteins, including their sequences, their biological function, and other properties, curated from their references in the biomedical literature. UniProt can be accessed directly at uniprot.org and instructions to the API are detailed at online API document.

Use cases:

  • Retrieve individual or batch entries of proteins of interest (e.g., the text representation of a protein entry, parsable by a custom script, given at a text file

  • Convert database identifiers (e.g., If a collaborator gave you protein IDs from another knowledgebase such as STRING DB but your software uses UniProt IDs. You want your software to convert these to UniProt so you can run your analysis properly. You can use UniProt’s web API described here to convert these IDs.)

Tutorial:

We encourage participants to create a Google Colab jupyter notebook as a tutorial with necessary code to illustrate the use of API with some tasks. Here we provide a sample tutorial for Uniprot API.

Tutorial on Uniprot API in Google Colab is available here

Brought to you by Ping Lab Utils (GitHub), UCLA, 2023