- It helps you to get information about genes of Human, Mouse, and Arabidopsis for version 1
- Gene Information
- Gene Description
- Gene Function
- Cell related to Gene
- Pathway
- Subcellular Location
- Protein-Protein Interaction
- Using the official api of various websites and preloaded datasets downloaded from them, it extracts information about the target gene.
- It uses LLM for organizing the retrieved contents. (You should use your own OpenAI API key)
- NCBI
- Uniprot
- MyGene.info
- STRING
You should check the file names and download them. Insert them into main.py
- Cell_marker_Seq.xlsx (http://www.bio-bigdata.center/CellMarker_download.html)
- PanglaoDB_markers_27_Mar_2020.tsv (https://panglaodb.se/markers.html?cell_type=%27choose%27)
- singleCellBase_dataset.txt (http://cloud.capitalbiotech.com/SingleCellBase/download.jsp)
- proteinatlas.tsv (https://www.proteinatlas.org/about/download)
- interaction_consensus.tsv (https://www.proteinatlas.org/humanproteome/structure+interaction/interaction/data#protein_interaction_data)
- cl.obo (https://github.com/obophenotype/cell-ontology/releases)
- cl-basic.obo (https://github.com/obophenotype/cell-ontology/releases)
- PCMDB_Download_20250909177169.csv (https://www.tobaccodb.org/pcmdb/download)
- arabidopsis_thaliana.marker_fd.csv (https://biobigdata.nju.edu.cn/scplantdb/marker)
- You should get an OpenAI API key first and make
.env.
OPENAI_API_KEY=
- git clone
git clone https://github.com/hyun-jin891/GeneTriever.git
- Install the required packages
pip install -r requirements.txt
- Download the required data and insert the file path into
main.py - Run
main.py(Genes input should be able to be split by ", "): species(human, mouse, arabidopsis)
python main.py --genes "gene1, gene2, gene3" --species "human"
- Check the result file
GeneRetriever_result.txt
- It is used to design CellTyper, which is an LLM-based cell annotation tool.