searchPublications_and_MapAffil

Created: 2017-04-19 09:31:22

Download Workflow

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 longitudes.

The workflow also outputs the total number of hits of the search query.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/4981/download?version=1
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
Query	Europe PMC query string

Processors (1)

Name	Type	Description
searchPublications_and_MapAffil	workflow

Beanshells (2)

Name	Description	Inputs	Outputs
Build_Query	This build_query BeanShell constructs the Europe PMC search query for a single protein in UniProt.	nextCursorMark Query Iteration	queryString cursorMark Iteration
Build_URL_for_MapAffil		PMIDs	url

Outputs (2)

Name	Description
Coordinates
hitCount

Datalinks (3)

Source	Sink
Query	searchPublications_and_MapAffil:Query
searchPublications_and_MapAffil:Coordinates	Coordinates
searchPublications_and_MapAffil:hitCount	hitCount

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Magnus Palmblad

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Magnus Palmblad

Information Attributions (0)

(Workflows/Files)

None

Information Tags (5)

Uploader tags

Log in to add Tags

Information Shared with Groups (1)

Bibliometrics and Scientometrics

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

1802 viewings

935 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

searchPublications_and_MapAffil

Created by Magnus Palmblad on Wednesday 19 April 2017 09:31:18 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (15)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 2

Uploader

Magnus Palmblad

Online PubMed author search and geographic... (2)

Download

This workflow retrieves bibliographic data for a single author using the PMC Europe RESTful Web service and visualizes the geographic distribution of this author's and their co-authors' geographic distribution using the rworldmap package. This is version 2.0 of this workflow, incorporating changes to the Web service allowing up to 1,000 records to be retrieved at once, using the pageSize parameter.

Created: 2015-08-19 | Last updated: 2015-09-07

Credits: Magnus Palmblad Arzu Tugce Guler

Taverna 2

Uploader

Magnus Palmblad

Get article titles from Europe PMC for sin... (2)

Download

This small workflow demonstrates how to connect to the new (August 2015) version of Europe PMC (http://europepmc.org/RestfulWebService). Changes from previous versions include the addition of a pageSize parameter, allowing the client to request up to 1,000 records at once. If this would still not be sufficient, the offSet paremeter can be used to retrieve data in chunks of 1,000 records and the Flatten List service used to concatenate the results.

Created: 2015-09-07 | Last updated: 2015-09-10

Credits: Magnus Palmblad