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biocypher/biochatter
Add liteLLM for LLM requests

https://docs.litellm.ai/docs/
  • slobentanzer
  • Opened 
    13 days ago
  • #264

biocypher/biocypher
Upgrade CI components to Python 3.11 default

Currently has 3.9 for setup and install, leading to errors in BioChatter publish step.
  • slobentanzer
  • Opened 
    13 days ago
  • #404

biocypher/DFG528753569
Add "User Story" template

Create a Custom GitHub Issues template with the following information: Template name: User Story About: This template is for creating user stories Template content: add the following Markdown code **As ...
  • ecarrenolozano
  • Opened 
    16 days ago
  • #15

biocypher/biocypher
Umbrella package to unify access to raw biocypher adapters, ontoweaver adapters, and pipeline functions

Resulting from discussions with ontoweaver developers, it would probably be the most user-friendly solution to have an umbrella package that can execute pipelines composed of raw biocypher adapters, ontoweaver ...
  • slobentanzer
  • Opened 
    19 days ago
  • #400

biocypher/open-targets
Proposing a new design to replace the existing unclear and unconfigurable API with hidden nodes and edges production logic

Currently the API of the adapter is as follows: open_targets_adapter= OpenTargetsAdapter( datasets=target_disease_datasets, node_fields=target_disease_node_fields, target_disease_edge_fields=target_disease_edge_fields, ...
enhancement
refactoring
  • kpto
  • 1
  • Opened 
    20 days ago
  • #36

biocypher/metalinks
Version of the neo4j.dump

Despite my efforts I did not manage to make the python create_knowledge_graph.py runnable. Instead I just wanted to use the neo4j.dump but it is not clear to me which version has been used here (of Neo4j). ...
  • gl-007
  • 2
  • Opened 
    22 days ago
  • #13

biocypher/biochatter-next
Separate embedding and runtime settings for RAG

Current RAG settings mix embedding-time (fragment length, overlap) and retrieval-time (number of chunks to inject) settings; would be more intuitive to show them in separation. Show retrieval-time settings ...
  • slobentanzer
  • Opened 
    26 days ago
  • #76

biocypher/biochatter-light
Add KG configuration tab

Add a tab to configure a BioCypher KG, also including OntoWeaver setup, which then yields a YAML schema configuration to be used in the project. - [ ] Drop-down menu for selecting entity and relation ...
  • slobentanzer
  • Opened 
    26 days ago
  • #60

biocypher/biochatter
Project management: Automated curation of issues and milestones

Managing issues and milestones of complex long-term projects is difficult with a high risk of falling into disrepair. An automated process that can review milestones and individual issues of a project ...
  • slobentanzer
  • Opened 
    26 days ago
  • #260

biocypher/biochatter
Find a generic way to let a tool using LLM agent know which module a function is from

When passing tools to bind_tools() with pydantic classes, the method name can be included as title , which is ensured by using pydantics create_model method to build the pydantic class (See https://github.com/biocypher/biochatter/issues/245). ...
  • mengerj
  • Opened 
    on Dec 13, 2024
  • #258
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Learn how you can use GitHub Issues to plan and track your work.

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