Hi,

Thank you for creating the library, it is very helpful. Have checked with downloaded data, it gives only the Back Ground or objective or whichever come first in Abstract. Is any possibility to get the entire Abstract(Back Ground, Objective, Methods, Results, Conclusion, Conclusion) as displayed when we search in the website.

happy to help you, if I can do something.

Hi, Is there a way to get count of the relevant results with respect to the query and \ or to paginate the results. E.g. read the first 500, then 500-1000, etc.?

Describe the bug

When importing pymed I get the following error:

$ python3 
Python 3.5.3 (default, Sep 27 2018, 17:25:39)  
[GCC 6.3.0 20170516] on linux 
Type "help", "copyright", "credits" or "license" for more information.
>>> from pymed import PubMed 
Traceback (most recent call last): 
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.5/dist-packages/pymed/__init__.py", line 1, in <module> 
    from .api import PubMed
  File "/usr/local/lib/python3.5/dist-packages/pymed/api.py", line 118
    response = requests.get(f"{BASE_URL}{url}", params=parameters)
                                             ^ 
SyntaxError: invalid syntax
>>> import pymed 
Traceback (most recent call last): 
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.5/dist-packages/pymed/__init__.py", line 1, in <module>
    from .api import PubMed
  File "/usr/local/lib/python3.5/dist-packages/pymed/api.py", line 118
    response = requests.get(f"{BASE_URL}{url}", params=parameters)
                                             ^
SyntaxError: invalid syntax `

To Reproduce Just try to import it in the interpreter.

Environment (please complete the following information):

• OS: Same error in WSL Ubuntu and Debian 9
• Version: Python 3.5.3

Is your feature request related to a problem? Please describe. It's important to me to see the affiliation information associated with an author if applicable. I can't see where this is being extracted from the returned XML.

Describe the solution you'd like Ideally, this would be an additional return in the form of .affiliation.

Describe alternatives you've considered

I created a "hack" by editing article.py def _extractAuthors(self: object, xml_element: TypeVar("Element")) -> list: return [ { "lastname": getContent(author, ".//LastName", None), "firstname": getContent(author, ".//ForeName", None), "initials": getContent(author, ".//Initials", None), "affiliation": getContent(author, ".//AffiliationInfo/Affiliation", None), } for author in xml_element.findall(".//Author") ]

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added support for conclusion, method and results fields within the AbstractText field via _attemptGrab function.

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fix article_id to be pulled from the new pubmed_id method

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I've found that I often need to get additional data from an article. For this it would be helpful to have access to the original xml.

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Is your feature request related to a problem? Please describe. Could you please add some filter features with Pubmed API

Additional context I'm facing problems passing filter queries to the API.

Hi Gjis,

I am using pymed package in one of my project. Everything is going well but some queries gives lots of articles. I want to give response in pagination, I have tried #1 but it takes lots of time. Can you help me out for solution.

Thank you

This will fix the PMID parsing issue in articles for which currently multiple PMID's are getting parsed. Resolves issue #22

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Thanks for the useful and well written library!

This minimal fix make the parser returning only the paper pubmed id. Before, also the ids of the citations papers were returned.(they are within the ReferenceList element of the xml).

Fixes #22

An alternative XPath to be used: path = ".//PubmedData/ArticleIdList/ArticleId[@IdType='pubmed']"

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Is your feature request related to a problem? Please describe. Currently one cannot enter the PubMed API key, so one cannot increase the rate limit to 10calls/sec

Describe the solution you'd like It would be great to add another param to the PubMed object.

Describe alternatives you've considered Writing my own code to handle the API :)

Additional context See here for info about the API key

THANKS!

Is there a way to fetch MESH terms of a publication from the API using the packadge?

This information is found under 'MeshHeadingList' of the xml returned using efetch.