Wormbase/PudMed API Access
Project description
pub_worm
API integration of Wormbase and NCBI Utils
Call from the commandline $PYTHONPATH="./src" python -m pub_worm.wormbase.WormbaseREST
Deploy
- Advance the version number in setup.py
conda deactivate # twine is installed in base env
cd <project directory>
rm -rf ./dist
rm -rf ./pub_worm.egg-info
python setup.py sdist
twine check dist/*
twine upload --repository pypi dist/*
git add .
git commit -m "some comment"
git push
Helpful Sites
https://researchguides.library.wisc.edu/c.php?g=1144260&p=8349872
ncbi_utils
ncbi_utils https://www.ncbi.nlm.nih.gov/books/NBK25501/
eInfo
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pmc
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=nlmcatalog
eSearch
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=20&term=Dennis+Voelker
Search nlmcatalog only get pubmed journals
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nlmcatalog&term=nlmcatalog%20pubmed[subset]%20Cell Metabolism[All%20Fields]
eSummary
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=37144896
eFetch
Pull Article
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8322431/pdf/41598_2021_Article_94902.pdf
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi" efetch_params = { "db": "pubmed", "id": ",".join(papers), # Join IDs with comma "retmode": "json", "rettype": "abstract" }
Project details
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