User: Maria_Levchenko

Reputation:
40
Status:
New User
Location:
EMBL-EBI
Twitter:
@EuropePMC_news
Last seen:
6 days, 4 hours ago
Joined:
1 year, 1 month ago
Email:
l*******@ebi.ac.uk

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

Posts by Maria_Levchenko

<prev • 11 results • page 1 of 2 • next >
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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 3 months ago by Maria_Levchenko40
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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 3 months ago by Maria_Levchenko40
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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 3 months ago by Maria_Levchenko40
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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 3 months ago by Maria_Levchenko40
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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 4 months ago by Maria_Levchenko40
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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 4 months ago by Maria_Levchenko40
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Answer: A: The first article about identifying lncRNAs using H3K4me3 and H3K36me3 markers
... You can try composing your search as: lncRNA AND H3K4me3 AND H3K36me3, and then sorting results by date in ascending order, e.g.: https://europepmc.org/search?query=lncRNA+AND+H3K4me3+AND+H3K36me3&page=1&sortby=Date%2BASC. The first paper is then from 2010: Long noncoding RNAs in neuronal-gl ...
written 12 months ago by Maria_Levchenko40
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Answer: A: What information about VARIANTS are found in biomedical literature rather than d
... Perhaps The European Variation Archive ([EVA][1]), the EMBL-EBI’s open-access genetic variation archive could be helpful as a resource. They do link to publications for the studies were a variant was mentioned [1]: http://www.ebi.ac.uk/eva/ ...
written 13 months ago by Maria_Levchenko40
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Answer: A: Index MEDLINE/PubMed with Apache Solr
... Europe PMC indexes PubMed and PMC articles using Apache Solr: http://blog.europepmc.org/2016/08/search-improvements.html You can always contact them to ask more about technical details ...
written 13 months ago by Maria_Levchenko40
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Answer: A: Programmatically Retrieve Info About Articles Citing My Article
... You can use Europe PMC (former UKPMC) [API][1] to retrieve a list of publications which cite a given paper. For a RESTful request you can construct the URL using the PMID of the paper you want retrieve citations for: http://www.ebi.ac.uk/europepmc/webservices/rest/MED/[PMID]/citations. You can also ...
written 13 months ago by Maria_Levchenko40

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