# pubmed-zenbu
1. This tool collects literature data (title_only or title_and_abstract) of your interest.
2. 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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"description": "# pubmed-zenbu\n1. This tool collects literature data (title_only or title_and_abstract) of your interest.\n2. This tool also extracts metadata from literature data using ChatGPT if you set the parameters.\n\n## How to use \n- `conda create -n pubmedzenbu python=3.9`\n- Create a `config.yml` \n```\n# Sample config.yml\n\npubmed_search:\n # (Required) NCBI API Key\n ncbi_api_key: YOUR_NCBI_API_KEY\n # (Required) Search query to obtain the PubMed articles of your interest\n search_query: prime editing pig\n # (Required) How far back in time you want to search. \n search_oldest_year: 2010\n # (Required) `title` or `abstract`. If choose `abstract`, it means you get the joined string of title and abstract.\n which_text_to_use: title\nopenai:\n # (Required) if use, add 'yes'. If not, keep it empty.\n use_openai: yes\n # (Optional) if use_openai is true, add your openai_api_key. Otherwise, keep it empty.\n openai_api_key: YOUR_OPENAI_API_KEY\n # (Optional) Prompt to ask ChatGPT. If you don't use it, keep it empty.\n prompt: \"extract gene and species from the following text \\n\"\n # (Required) Set the output path. If use_openai is false, literature data will be written out.\n output_path: ./extract_result_20231004.csv\n```\n\n- `pubmedzenbu PATH_TO_YOUR_config.yml_FILE`\n",
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