[WIP] Biothings tools

[ahueb]

Note: updating branch with overlapping sources, work in progress

Summary

Biothings is an ecosystem of FAIR APIs containing gene, variant, chemical, disease, and taxon data (https://biothings.io/). This PR adds a tool wrapping the existing biothings-client Python library https://pypi.org/project/biothings-client/

Changes Made

Added a new tool, query_biothings, in tools/database.py and description in tool_description/database.py

Future improvements

I noticed other database tools have internal prompt structures to build API requests, I didn't include internal prompting as we aren't fetching directly from a REST API but rather using the existing biothings-client package. I'm unsure if internal prompting may be beneficial so this is a possible future improvement.

Testing

import sys

sys.path.append("../")

from biomni.agent import A1

agent = A1(path="<your_path>", llm="gpt-5.2")

log = agent.go("""please locate gene information for gene ID 1017 using the query_biothings tool""")
log = agent.go("""please locate disease information for alzheimer's disease using the query_biothings tool""")
log = agent.go("""please locate chemical information for dexamethasone using the query_biothings tool""")
log = agent.go("""please locate taxon information for Saccharomyces cerevisiae using the query_biothings tool""")
log = agent.go("""please create a temporary tab separated vcf file with the following contents then use that file to get all variant information from biothings:
##fileformat=VCFv4.2
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO
7\t140453136\t.\tA\tT\t.\tPASS\t.”""")

✅ all were sucessful