titipata / pubmed_parser

:clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset

http://titipata.github.io/pubmed_parser/

titipata/pubmed_parser Issues

Missing paragraphs from parse_pubmed_paragraph output
Updated 22 days ago
physical & electronic publication dates can be mixed into erroneous dates
Closed 23 days ago1
Fix GitHub workflows
Updated 2 months ago3
PMC OA: tags in the <journal-title> field break parse_pubmed_xml
Closed 2 months ago2
parse_pubmed_table() and parse_pubmed_references() returning None
Closed 2 months ago1
ModuleNotFoundError: No module named 'pubmed_parser'
Closed 3 months ago3
Question about Original XML
Closed 3 months ago3
Is there a reason why PubMed/MEDLINE extracted list elements are joined with ";" instead of keeping them as lists ?
Closed 3 months ago2
All of PubMed XML was updated to follow the MEDLINE XML format.
Updated 3 months ago
Table parsing issues with parse_pubmed_table
Closed 3 months ago2
question using pp.parese_medline
Closed 3 months ago2
Handling of non-ASCII / unicode characters
Updated 3 months ago
Question: Abstract with Mesh Tag
Closed 3 months ago3
parse_pubmed_caption() failing on some papers
Closed 3 months ago
Inconsistent PMID and DOI when using parse_xml_web for an XML file.
Closed 3 months ago1
Parse VersionID and VersionDate
Updated 4 months ago
Fix Medline parser tests
Updated 5 months ago
Update tests: Use current data
Updated 5 months ago
Parse language in `parse_xml_web()`
Closed 5 months ago1
ValueError when attempting to parse OA XML
Closed 6 months ago3
Question for extracting text
Closed 6 months ago1
CALL FOR MAINTAINER/CONTRIBUTOR FOR PUBMED_PARSER
Updated 6 months ago7
Bug report - XML citations from website
Updated 10 months ago1
Question: parsing error first line expecting '<' not found
Closed a year ago
AttributeError: 'NoneType' object has no attribute 'find'
Closed 2 years ago2
Error: parse_medline_xml() is unable to parse the file even though the provided path is correct
Closed 2 years ago11
parse_pubmed_paragraph() function seems to miss some paragraphs sometimes.
Updated 3 years ago
medline_parser has syntax error: `"is not" with a literal`
Closed 3 years ago1
Example of processing in dask rather than pyspark
Closed 3 years ago2
Upload package on PyPI
Closed 3 years ago3
Error using parse_pubmed_xml
Updated 3 years ago5
Extracting sections at a time rather than paragraphs
Closed 3 years ago1
parse_pubmed_xml does not return "subjects"
Closed 4 years ago
Missing details in API docs
Closed 5 years ago1
SyntaxWarning raised during import
Closed 5 years ago2
Fix online parser to parse given PMID
Closed 5 years ago1
JOSS paper text
Closed 5 years ago2
Contributing guidelines are missing
Closed 5 years ago3
Create test function for Pubmed Parser
Closed 5 years ago3
Parse Pubmed OA Paragraph
Closed 5 years ago9
Question about downloading PubMed OA figures
Closed 5 years ago6
Missing dependencies
Closed 5 years ago1
Add community guideline
Closed 5 years ago1
ImportError: libicui18n.so.56: cannot open shared object file: No such file or directory
Closed 5 years ago3
Pubdate not returning correct year
Closed 5 years ago4
Parsing DOI Medline XML
Closed 5 years ago7
medline xml equivalent for "parse_pubmed_references"?
Closed 5 years ago10
pip3 install wget
Closed 5 years ago2
XMLSyntaxError
Closed 5 years ago
XMLSyntaxError
Closed 6 years ago4