Question

How to retrieve article ids list from pubmed

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6.8 years ago

aqsaawan.459 • 0

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

R python pubmed pubmedlookup • 4.4k views

ADD COMMENT • link updated 6.7 years ago by Maria_Levchenko ▴ 60 • written 6.8 years ago by aqsaawan.459 • 0

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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 REPLY • link 6.8 years ago by GenoMax 147k

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okay got it! thanks

ADD REPLY • link 6.8 years ago by aqsaawan.459 • 0

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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 REPLY • link 6.8 years ago by WouterDeCoster 47k

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

ADD REPLY • link 6.8 years ago by aqsaawan.459 • 0

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

ADD REPLY • link 6.8 years ago by Arup Ghosh 3.2k

score 1 · Answer 1 · 2018-02-21

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6.8 years ago

Arup Ghosh 3.2k

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 COMMENT • link 6.8 years ago by Arup Ghosh 3.2k

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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 REPLY • link 6.8 years ago by WouterDeCoster 47k

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thanks for the suggestion.

ADD REPLY • link 6.8 years ago by Arup Ghosh 3.2k

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

ADD REPLY • link 6.8 years ago by aqsaawan.459 • 0

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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 REPLY • link 6.8 years ago by Arup Ghosh 3.2k

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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 REPLY • link 5.8 years ago by venkatarao142152 • 0

score 0 · Answer 2 · 2018-03-02

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6.7 years ago

Maria_Levchenko ▴ 60

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