Gsoc2025: Enhancing SBOannotator with LLM Integration & Dynamic Term Retrieval

Hi, As discussed in the last blog, I started working on my first milestone of fetching SBO table from OLS to SBO annotator. This blog contains a summary of the meeting with the new features I added and the issues I worked on and fixed this week to add SBML L3V2 support. So, let's quickly dive in summary: 1. Change Detection Mechanism for SBO Terms ❓ Issue : OLS API’s updated field changed, but no observable differences in content. ✅ Observation : Compared OLS (API) and GitHub .owl versions – content is identical . Latest update timestamp on OLS is 2025, but GitHub file was last modified in 2023. New terms are already included in the GitHub version. ✅ Decision : We can rely on GitHub .owl file for consistency and reduced request time. 2. Fetching ‘is_a’ / Parent Info Performance Issue ⏱️ Fetching subclass_of (parent info) via OLS takes ~10 minutes. ⚡ Other fields can be fetched in <1 minute. ✅ Optimization : Parent info should be pulled from ...

Hi,   On the May 15, 2025 (23:00–24:00 PDT 14 th of May (which is 08:00–09:00 CEST 15 th of May), I had my first online meeting with my mentors on Zoom meeting. It was a fantastic experience meeting them. We discussed how to start with the project. Here’s the summary of the meeting   Introduction   Established Slack as communication channel Half of my time will be for GSoC, half of the time will be preparing for interviews in job hunting market Discussed and filled out the Contributor-Mentor Agreement Create Shared Google Drive Discussed about proposed timeline and next steps By Friday 23 rd , we will have a fixes schedule Use blogpost.com to document brief weekly updates: https://gsoc2025jiahui.blogspot.com/ Use GitHub issues with comments to document updates on code The weekly work I have done: Play with the current Web application hosted at  TueVis  . Read the article of sbo Read the code in the repository line by line Regards!

  Hi, I am Jiahui Hu, 2nd year CSE student at the Northeastern University, Roorkee, India. I am incredibly excited to share that I was selected in the Google Summer of Code (GSoC) this year with the National Resource for Network Biology (NRNB) as a mentoring organization. I will be working on the project "Optimization of SBOannotator for Dynamic Term Integration and AI Enhancement" in this program. I am incredibly thankful to the wonderful mentors, namely Dr Nantia Leonidou，Dr. Andreas Dräger, who helped me to get selected and will guide me throughout this project. This blog series is dedicated mainly to share my progress for the project. The official coding period started from 23nd June, and the community bonding period begun from 8th May. In this period, I will be exploring the codebase with solving some small issues and will discuss the implementation details with the mentors and finalize them. What is NRNB? The National Resource for Network Biology (NRNB, https://www.nrnb...