PubmedZenbu
Project description
pubmed-zenbu
- This tool collects literature data (title_only or title_and_abstract) of your interest.
- This tool also extracts metadata from literature data using ChatGPT if you set the parameters.
How to use
conda create -n pubmedzenbu python=3.9
- Create a
config.yml
# Sample config.yml
pubmed_search:
# (Required) NCBI API Key
ncbi_api_key: YOUR_NCBI_API_KEY
# (Required) Search query to obtain the PubMed articles of your interest
search_query: prime editing pig
# (Required) How far back in time you want to search.
search_oldest_year: 2010
# (Required) `title` or `abstract`. If choose `abstract`, it means you get the joined string of title and abstract.
which_text_to_use: title
openai:
# (Required) if use, add 'yes'. If not, keep it empty.
use_openai: yes
# (Optional) if use_openai is true, add your openai_api_key. Otherwise, keep it empty.
openai_api_key: YOUR_OPENAI_API_KEY
# (Optional) Prompt to ask ChatGPT. If you don't use it, keep it empty.
prompt: "extract gene and species from the following text \n"
# (Required) Set the output path. If use_openai is false, literature data will be written out.
output_path: ./extract_result_20231004.csv
pubmedzenbu PATH_TO_YOUR_config.yml_FILE
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