Library to access, analyze, and display bibliographic information.
pip install bibcodex
Import the pandas and bibcodex together and load a dataframe:
import bibcodex
import pandas as pd
# You should always cast your search variables (pmid, doi) to str.
df = pd.read_csv("data/sample_data.csv", dtype={'pmid':str})Valid download methods are: icite, doi2pmid, semanticScholar, or pubmed:
# Set the index to search query
df = df.set_index("doi")
# Download the information, and combine it with the original dataframe:
info = df.bibcodex.download('semanticScholar')
print(df.combine_first(info[["title"]]))
"""
doi title
10.1001/jama.2017.18444 Progressive Massive Fibrosis in Coal Miners Fr...
10.1001/jama.2018.0126 Birth Defects Potentially Related to Zika Viru...
10.1001/jama.2018.0708 Association Between Estimated Cumulative Vacci...
10.1001/jama.2018.10488 Electronic Cigarette Sales in the United State...
"""All search queries are cached locally in ./cache. To clear the cache use:
df.codex.clear()| API | Returned fields |
|---|---|
pubmed |
title, issue, pages, abstract, journal, authors, pubdate, mesh_terms, publication_types, chemical_list, keywords, doi, references, delete, languages, vernacular_title, affiliations, pmc, other_id, medline_ta, nlm_unique_id, issn_linking, country |
semanticScholar |
abstract, arxivId, authors, citationVelocity, citations, corpusId, fieldsOfStudy, influentialCitationCount, isOpenAccess, isPublisherLicensed, is_open_access, is_publisher_licensed, numCitedBy, numCiting, paperId, references, s2FieldsOfStudy, title, topics, url, venue, year |
icite |
year, title, authors, journal, is_research_article, relative_citation_ratio, nih_percentile, human, animal, molecular_cellular, apt, is_clinical, citation_count, citations_per_year, expected_citations_per_year, field_citation_rate, provisional, x_coord, y_coord, cited_by_clin, cited_by, references, doi |
doi2pmid |
live, status, errmsg, pmcid, pmid, versions |
- API access: Pubmed (Parsed MEDLINE data)
- API access: Semantic Scholar (PMID)
- API access: iCite
- API access: Semantic Scholar (DOI)
- API access: DOI to PMID NLM www.ncbi.nlm.nih.gov/pmc/tools/idconv/
- API access: Pubmed (XML)
- API access: arXiv
- API access: CoLIL
- API access, validation of input
- API access, multi item requests
- API access, chunking
- API access, include status_code in download results
- API access, better error handling
- API caching, clearing
- Codex, validate PMID
- Codex, validate DOI
- Codex, build dataframe from items
- Testing harness
- Full testing coverage
- Code linting
- pypi library
- README with examples
- Status bar for long downloads
- Embedding functions (SPECTER)
- Clustering
- Visualization (streamlit)
Built with ❤ ️by @metasemantic. Package is linted by black and conforms to standards by flake8. Pull requests accepted, but please provide tests with full coverage for new code.