Community Bonding Period - Second Meeting and Weekly work update



Hi,

On the June 23th, I met with the mentors again for the second time on Zoom. It was great meeting after a long discussion on the slacks. Now, here's the summary of the meeting.

  • Topic 1 : ols

    • No need to update the current rule based system.

    • Local sbo table fields: no need to save the tree

    Topic 2:llm

    • Use rule based system first to set sbo 

    • Pseudo reaction ， transporter reaction and other element of reaction would totally rely on rule based system to set sbo

    • Biochemical reaction would get sbo first from the rule based system.  Then we should hard code to filter reactions that are assigned the parent level of sbo . LLM would be used to find suitable leave level  sbo for these reactions.

    • Only one type of prompt template here , since only one type of reaction would be assigned abo by llm

    • We would use Explore enz to fetch 6000+ ec numbers and turn them into vector.We would use ols to fetch 40+ sbo , and turn them into vectors. When we input a reaction with ec, we would parse the ec, and use cosine similarity to find the top k sbo.  

    Topic 3: brenda

    • We will not use Brenda .

    • Question:should we find one more database since we only have bigg and kegg?

    Communication:

    • Weekly meeting is on 9am  Wednesday, CEST


Work I have done:

Regards!

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