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User: Magnus Palmblad

Workflow Search Europe PMC and get ChEBI annotations (3)

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This workflow first conducts a search and downloads the PMIDs for all publications in PubMed and PMC that match a particular query using the Europe PMC Articles API. In a second phase, the workflow fetches the ChEBI annotations for all these publications using the Europe PMC Annotations API.

Created: 2018-02-09 | Last updated: 2018-02-12

Credits: User Magnus Palmblad

Workflow 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: User Magnus Palmblad

Workflow 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: User Magnus Palmblad

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

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This small 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 REST 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. A conditional JSONPath is here used to only look up citing articles for cited work...

Created: 2016-05-09

Credits: User Magnus Palmblad

Workflow Author Publications and Citations by Year ... (2)

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This small 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 REST 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. A conditional XPath is here used to only look up citing articles for cited work, i...

Created: 2016-05-09 | Last updated: 2016-05-09

Credits: User Magnus Palmblad

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Blob Long list of stopwords

Created: 2015-12-07 14:46:51

Credits: User Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a longer list of unspecific stopwords frequently appearing in scientific abstracts. This is an extended version of the "Long Stopword List" on the Ranks NL Website (http://www.ranks.nl/stopwords). 

File type: Excel workbook

Comments: 0 | Viewed: 52 times | Downloaded: 11 times

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Blob Example results from the UniProt Protein Protein Net...

Created: 2015-12-04 14:50:06

Credits: User Magnus Palmblad User Yassene

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example results from the UniProt Protein Protein Network workflow (http://www.myexperiment.org/workflows/4778.html) on Apolipoprotein A-I (P02647). The purpose of the igraph graph is to check that the workflow ran OK. For further exploration and visualization of the network, one of the output files can be opened in Cytoscape or similar tool.

File type: PNG image

Comments: 0 | Viewed: 66 times | Downloaded: 6 times

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Workflow 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: User Magnus Palmblad

Workflow Connecting to Europe PMC (1)

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This very simple workflow connects to Europe PMC using the searchPublications Web Service.

Created: 2015-12-04

Credits: User Magnus Palmblad

Workflow 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: User Magnus Palmblad

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