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There is a PUBMED API, as detailed [here](https://www.ncbi.nlm.nih.gov/books/NBK25499/) (with a weird syntax, but why not), so searching through it is possible, and its free. The list of journal would…
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I recently received a question about search and realized that the user would have to learn about more advanced arguments like `pages` and `options` to do a simple search. A helper functions would make…
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This issue highlights a need to provide description and provenance for a file used to run the full RTX-KG2 pipeline, `SMPDB_pubmed_IDs.csv`. This file appears to be required for a full workflow run of…
d33bs updated
8 months ago
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Probably using continuous -> quintiles approach rather than finding a third example. Good chance to discuss https://pubmed.ncbi.nlm.nih.gov/24487212/
- [ ] ATO: https://arxiv.org/pdf/1808.05339.pdf…
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Due to various issues with using the NCBI Entrez API (e.g, #257 ) we could explore using pubmed dumps instead of calling their API.
- the ftp dump page https://www.ncbi.nlm.nih.gov/pmc/tools/ftp/ …
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The Europe PubMed Central seems out of sync with NCBI PubMed.
_Example_
Take the PMID `26672148`. This was published in April of 2015.
- The Europe PubMed Central link is [here](http://www.ebi.ac.uk…
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PubMed Central provides JATS XML for 4.4 million articles. Not all of these are OpenAccess, so we will start with the ones that are definitely OK to distribute.
I propose to create a live-updating …
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Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations - Nhan T Ho – Nature Communications
https://pubmed.ncbi.nlm.nih.gov/30301893/
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
import sys; print(sys.version)
import platform; print(platform.python_imp…
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Another category, besides data integrity (#4), should be file retrieval. One current request in particular is to add documents by Pubmed ID. The code would go from Pubmed ID to file, download the file…