pub-worm 0.3.3

Wormbase/PudMed API Access

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

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nlmcatalog&term=journalspmc[All%20Fields]

Search nlmcatalog only get pubmed journals

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nlmcatalog&term=nlmcatalog%20pubmed[subset]

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

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nlmcatalog&retmode=xml&id=101682128,101233170

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nlmcatalog&retmode=xml&id=297618,7505876

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=34577062,24475906&rettype=fasta&retmode=text

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=MCID_6570ac6193da3159df3e2274

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" }

Pytest

• Run a specific test from the command line

cd /Users/dan/Code/Python/pub_worm/tests export PYTHONPATH=..;python -m pytest ncbi/test_entreze_api.py::test_entreze_esearch