bibcodex 1.0.0

Access, analyze, and display bibliographic information

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.codex.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
• 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.