Workflows

Search for citations and related article i... (1)

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graph = http://nur77 bmuri = http://bio2rdf.org/pubmed:18843482 http://bio2rdf.org/pubmed:18466322 http://bio2rdf.org/pubmed:17201484 http://bio2rdf.org/pubmed:14603264 http://bio2rdf.org/pubmed:12629527

Created: 2009-11-17

Credits: Francois Belleau

Rank Phenotype Terms (1)

This workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ...

Created: 2009-08-10

Credits: Paul Fisher

Cosine vector space (1)

This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. The result is a cosine vector score between 0 and 1, showing the significance of any links between one concept (e.g. pathway) to another (e.g. phenotype). A score of 0 means there is no or an undetermined correlation between the two concepts. A score approaching 1 represents positive correlation.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: Paul Fisher

EBI_CiteXplore (1)

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Perform a literature search using the EBI's CiteXplore service (http://www.ebi.ac.uk/citexplore/), and get the results in a minimal XML format containing the citation information (i.e. title, author, journal, etc.), the identifier of the citation in the source database (PubMed/Medline, Agricola, Patent Abstracts, CBA, CiteSeer, etc.) and information about abstract and full article availablity including URLs.

Created: 2008-07-09

Credits: Hamish McWilliam

Search for BMURI in PubMed [myexperiment:p... (1)

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test values: subkecttest values: query = bio2rdf graph = http://bio2rdf query = nur77 AND Rouillard,C graph = http://nur77 test values: query = bio2rdf graph = http://bio2rdf query = nur77 AND Rouillard,C graph = http://nur77 query = labrie graph = http://labrie

Created: 2009-11-17

Credits: Francois Belleau

Deriving factual information from WHO COVI... (1)

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 WHO has posted a CSV that's frequently updated with COVID abstracts. A simple PubMed search reveals thousands of abstracts too. So here's an NLP pipeline to mine these and extract meaningful sentences/facts using Stanford Open Information Extractor and Biological entity tagging. #knime #naturallanguageprocessing #textanalytics #textmining #covid19 #nlp #datascience #WHO 

Created: 2020-04-12

Credits: Insilicoconsulting

searchPublications_and_MapAffil (1)

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This is a workflow for spatiotemporal analysis of literature indexed in PubMed. The workflow takes an arbitrary Europe PMC search query, calls the Europe PMC Web service searchPublications and extracts the publication year and PubMed ID from the results. The first author affiliation is then geoparsed by the MapAffil Web server to get latitude and longitudes. The coordinates are then concatenated together with the publication year, to produce a single list of publication years, latitudes and ...

Created: 2017-04-19

Credits: Magnus Palmblad

profilePublications_over_time (1)

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This workflow takes a list of arbitrary Europe PMC search queries and generates the corresponding profiles of the number of matching publications per publication year.

Created: 2017-04-19

Credits: Magnus Palmblad

Author Publications and Citations by Year ... (1)

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This workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService) to count the number of publications and citations per year for one author. Two Web service calls are made. First, we searchPublications to retrieve the bibliographic records for all published work of a single author. Then, we getCitations to extract the year of all articles citing the work of this author. The pubYear fields is extracted from the raw Web service results and fed to an Rshel...

Created: 2015-12-04

Credits: Magnus Palmblad

SImple Europe PMC Search (1)

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This very simple workflow searches Europe PMC using the searchPublications Web Service and a conditional XPath to retrieve the article titles for all cited work matching the search query.

Created: 2015-12-04

Credits: Magnus Palmblad