pubmed | An API for querying Pubmed | REST library

my dataframe looks like this:

I have a dataset with articles from pubmed. DataFrame looks like this:

I'm trying to parse this .txt file in R: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt

It's essentially a single column data frame of some ~2 million rows, with each entity being described by multiple rows and bookended by rows containing the string "//".

Ideally, I could capture each entity, made up of multiple rows, as a list element by splitting at "//", but I'm not sure of the most efficient way to go about this.

Any help is much appreciated.

EDIT:

Here's a snippet of what I'm working with:

I am a beginner at Twitter Development and Python programming in general, but recently I have been trying to build a bot that, when tagged in reply to a Tweet, finds keywords and uses Google to deliver some info from reliable sources regarding the topic of the original Tweet. However, I have encountered one major problem while programming: API doesn't get created since the code triggers the error "only unicode objects are escapable". I have used module Config to set my Twitter API credentials as environmental variables and that seems to work fine on its own. Before trying to run the bot, I activate my virtual environment and export the env variables, so I do not think this issue has to do with incorrectly setting those variables, but I would not say I am certain about that either! The code goes this way:

I have

I'm trying to access Pubmed results via R using their API, but I consistently get fewer results than what the same query achieves when used with the web interface. By digging in the output I noticed that the problem lays in a different query translation between the two access methods.

I am using the rentrez package, but the results I get are the same also with other related rpackages, so I guess it's related to the API itself.

here's the code to reproduce the results:

I'm currently stuck to generate a specific kind of nested piechart. I would like to do something near of this figure I found in the following article : https://pubmed.ncbi.nlm.nih.gov/32271901/

Plot i would like to generate

I found something near of what I would like to do in this post : ggplot2 pie and donut chart on same plot

I applied the code to my data and obtain this : My current plot

It's not bad but not exactly what I want.

If anyone has an idea to improve the current code or a new one maybe ?

Here is the data :

I'm currently working on extracting specific data from a table in this website: http://bioinfo.life.hust.edu.cn/lncRNASNP/#!/lnc_disease . For this, I'm using Python and selenium.

My problem is that when I try to search for the table using read_html() from pandas, only the headers of the table are found, this is the output I get:

I'm working with a project where we are web-scraping PubMed research abstracts and detecting if any researchers from our organization have authorship on any new publications. When we detect a match, we want to add a bold HTML tag. For example, you might see something like this is PubMed: Sanjay Gupta 1 2 3, Mehmot Oz 3 4, Terry Smith 2 4 (the numbers denote their academic affiliation, which corresponds to a different field, but I've left this out for simplicity. If Mehmot Oz and Sanjay Gupta were in my list, I would add a bold tag before their first name and a tag to end the bold at the end of their name.

One of my challenges with PubMed is the authors sometimes only show their first and last name, other times it includes a middle initial (e.g., Sanjay K Gupta versus just Sanjay Gupta). In my list of people, I only have first and last name. What I tried to do is import my list of names, split first and last name, and then bold them in the list of authors. The problem is that my code will bold anyone with the first name or anyone with the last name (example: Sanjay Smith 1 2 3, Sanjay Gupta 1 3 4, Wendy Gupta 4 5 6, Linda Oz 4, Mehmet Jones 5, Mehmet Oz 1 4 6.) gets bolded. I realize the flaw in my code, but I'm struggling for how to get around this. Any help is appreciated.

Bottom Line: I have a list of people by first name and last name, I want to find their publications in PubMed and bold their name in the author credits. PubMed sometimes has their first and last name, but sometimes their middle initial.

To make things easier, I denoted the section in all caps for the part in my code where I need help.