bibcodex 1.1.7

Description:

bibcodex 1.1.7

bibcodex
Library to access, analyze, and display bibliographic information.

Installation
pip install bibcodex

Examples
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



Roadmap

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)

Development
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.