pub-worm 0.3.14

Wormbase/PudMed API Access

pub_worm

Wormbase

• http://rest.wormbase.org/index.html

API integration of Wormbase and NCBI Utils

• Call from the commandline
• $PYTHONPATH="./src" python -m pub_worm.wormbase.WormbaseREST

Helpful Sites

• https://researchguides.library.wisc.edu/c.php?g=1144260&p=8349872

ncbi_utils

• https://www.ncbi.nlm.nih.gov/books/NBK25501/

• https://www.ncbi.nlm.nih.gov/books/NBK25497/table/chapter2.T._entrez_unique_identifiers_ui/?report=objectonly

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]%20CellMetabolism[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