Question: How to retrieve article ids list from pubmed
0
gravatar for aqsaawan.459
12 months ago by
aqsaawan.4590 wrote:

Hey, I'm doing a project which includes data mining but for that I want to build a crawler which extract pubmed articles ids using a single term like cancer or tumor? (semantics based ) I'm currently working in python. If someone is familiar with this issue kindly help me

pubmed python R pubmedlookup • 603 views
ADD COMMENTlink modified 11 months ago by Maria_Levchenko60 • written 12 months ago by aqsaawan.4590
1

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

New questions should be posted to a new thread.

ADD REPLYlink written 12 months ago by genomax62k

okay got it! thanks

ADD REPLYlink written 12 months ago by aqsaawan.4590

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

ADD REPLYlink written 12 months ago by WouterDeCoster37k

now I want to upload these ids to mysql database, But I do't know hoe to connect python to mysql?

ADD REPLYlink written 12 months ago by aqsaawan.4590
1

This tutorial will help, https://www.tutorialspoint.com/python/python_database_access.htm . Please mark the answer as accepted.

ADD REPLYlink written 12 months ago by arup850
1
gravatar for arup
12 months ago by
arup850
India
arup850 wrote:

Use Biopython.

An example, cancer as a search term.

from Bio import Entrez
Entrez.email = "yourmail@gmail.com"
handle = Entrez.esearch(db="pubmed", term="cancer", retmax="10", sort="relevance", retmode="xml")
records = Entrez.read(handle)
print(records["IdList"])
ADD COMMENTlink modified 12 months ago • written 12 months ago by arup850
1

I would like to suggest that you write Python3 in your examples (using print as a function) to make this code snippet valid on all python versions. Python2 will only be around for limited time, so better bite the bullet now and get used to Python3 syntax.

ADD REPLYlink written 12 months ago by WouterDeCoster37k

thanks for the suggestion.

ADD REPLYlink written 12 months ago by arup850

What if I want urls of a specific word instead of ids?

ADD REPLYlink written 12 months ago by aqsaawan.4590
1

Sorry, what do you mean by "urls of specific word"? If you are talking about article URLs, use https://www.ncbi.nlm.nih.gov/pubmed/ as base URL and add the fetched PMIDs after it.

ADD REPLYlink written 12 months ago by arup850

Hlo sir. I want to extract specific gene articles. for every gene I have number of articles so how can I extract pubmed id and abstract of the article alone. could you please suggest how to extract id and abstract of the article alone. thanking you sir

ADD REPLYlink written 10 days ago by venkatarao1421520
0
gravatar for Maria_Levchenko
11 months ago by
EMBL-EBI
Maria_Levchenko60 wrote:

You can also try out Annotations API from Europe PMC. It allows you to retrieve a list of PMIDs for artciles that contain text-mined terms. Diseases (including cancer or tumor) is one of the annotation types. So for retrieving article iDs for cancer you could use the following response URL: https://www.ebi.ac.uk/europepmc/annotations_api/annotationsByEntity?entity=cancer&filter=1&format=ID_LIST&pageSize=4

ADD COMMENTlink written 11 months ago by Maria_Levchenko60
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