Comments (3)
titipata
commented on June 11, 2024
Hi @shrimonmuke0202, so the simple way is to download the MEDLINE dump and then use the MEDLINE parser (parse_medline_xml) to parse MeSH tags. The tags are separated by ; which you can get Mesh IDs and terms to use later on.
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shrimonmuke0202
commented on June 11, 2024
Thanks for your quick reply @titipata,
Are the tokens of text contained in the abstract of any paper exactly matching the MeSH tags?
From where can I download the MEDLINE dump?
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titipata
commented on June 11, 2024
- Are the tokens of text contained in the abstract of any paper exactly matching the MeSH tags? I think MeSH tags are kinda high-level concepts of the given abstract. It may match or not match the abstract.
- From where can I download the MEDLINE dump? https://www.nlm.nih.gov/databases/download/pubmed_medline.html (there are multiple ways to download API or bulk download)
from pubmed_parser.
Related Issues (20)
- Is there a reason why PubMed/MEDLINE extracted list elements are joined with ";" instead of keeping them as lists ? HOT 2
- All of PubMed XML was updated to follow the MEDLINE XML format.
- PMC OA: tags in the <journal-title> field break parse_pubmed_xml HOT 2
- parse_pubmed_paragraph() function seems to miss some paragraphs sometimes.
- physical & electronic publication dates can be mixed into erroneous dates HOT 1
- Error: parse_medline_xml() is unable to parse the file even though the provided path is correct HOT 11
- AttributeError: 'NoneType' object has no attribute 'find' HOT 2
- Table parsing issues with parse_pubmed_table HOT 2
- parse_pubmed_table() and parse_pubmed_references() returning None HOT 1
- Question for extracting text HOT 1
- question using pp.parese_medline HOT 2
- Question: parsing error first line expecting '<' not found
- parse_pubmed_caption() failing on some papers
- ValueError when attempting to parse OA XML HOT 3
- Bug report - XML citations from website HOT 1
- CALL FOR MAINTAINER/CONTRIBUTOR FOR PUBMED_PARSER HOT 7
- Parse language in `parse_xml_web()` HOT 1
- Update tests: Use current data
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