User: Maria_Levchenko

Reputation:
70
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@EuropePMC_news
Last seen:
2 months, 1 week ago
Joined:
1 year, 6 months ago
Email:
l*******@ebi.ac.uk

Community Manager for Europe PMC. Will gladly help with any literature-related issues.

Posts by Maria_Levchenko

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Retrieve PubMed records based on some genes
... Oh, great point. I have not thought about it. ...
written 3 months ago by Maria_Levchenko70
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Answer: A: Retrieve PubMed records based on some genes
... If you would like to retrieve PubMed records containing a certain gene name and its aliases/synonyms you can use Europe PMC RESTful API search module with synonym parameter set to true. This will expand your query to include synonyms found in MeSH vocabulary and the UniProt synonyms list. Meaning th ...
written 3 months ago by Maria_Levchenko70
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Answer: A: How to get publications associated with list of genes
... Europe PMC Annotations API can be useful: https://europepmc.org/AnnotationsApi. It is based on public text-mining data provided by the research community and made available by Europe PMC programmatically. In your case you can retrieve all text-mined annotations (including gene names) for a list of ...
written 3 months ago by Maria_Levchenko70
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Answer: A: How to get the corresponding PMCID from PMID with python?
... In case this is useful, Europe PMC (PubMed Central partner) provides a file with PMID-PMCID-DOI mappings that you can download via FTP: ftp://ftp.ebi.ac.uk/pub/databases/pmc/DOI/ Disclaimer: I work for Europe PMC ...
written 3 months ago by Maria_Levchenko70
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Tutorial: Webinar: Extracting research evidence from publications
... Want to know which potential treatment targets have been linked to a specific syndrome in the literature? Want to check which components of a signalling pathway already have a protein structure available? Interested if a particular chemical is reported in the methods section of particular papers? Ex ...
tutorial ontology pubmed text mining mining written 8 months ago by Maria_Levchenko70
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Answer: A: How to retrieve article ids list from pubmed
... You can also try out [Annotations API][1] 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: htt ...
written 8 months ago by Maria_Levchenko70
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Comment: C: Associations between biological terms and gene names in the literature
... If you'd like to learn more about the annotations API, and what it offers you can join an upcoming webinar: https://www.ebi.ac.uk/training/events/2018/extracting-research-evidence-publications ...
written 8 months ago by Maria_Levchenko70
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Comment: C: Associations between biological terms and gene names in the literature
... For annotations in Europe PMC there is no information on association scores. For named entity annotations (genes, GO, diseases, organisms...) you can only infer co-occurence in a specific section of the article. Annotations reporting relationships, e.g. gene-disease relationships, are supplied by ex ...
written 8 months ago by Maria_Levchenko70
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Answer: A: python module to download any paper by DOI
... You could try [Europe PMC API][1] to retrieve publication full text via DOI. You would need to first map the DOI to the corresponding PMCID using the search module, and then use the PMCID to retrieve full text XML from the open access subset. Here is an example: [search module][2] for the following ...
written 9 months ago by Maria_Levchenko70
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Answer: A: Associations between biological terms and gene names in the literature
... Europe PMC offers an open RESTful annotations API. You can access text mined annotations contained in PubMed abstracts and open access full text articles, and find co-occurences between different text-mined entities: e.g. gene names and GO terms that appear in the same paper. The list of text-mined ...
written 9 months ago by Maria_Levchenko70

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