Search results for "pubmed"

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PubMed Abstract Number

Created: 2009-08-11 13:54:45

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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PubMed Term Counts

Created: 2009-08-11 13:59:35

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Pubmed Identifiers

Created: 2009-11-14 16:23:47

Credits: George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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XML Result from Pubmed Search

Created: 2011-03-23 11:49:33 | Last updated: 2011-03-23 11:49:36

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

Comments: 0 | Viewed: 47 times | Downloaded: 31 times

PubMed Search and Solr storage (5)

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Based on the work of Fisher: This workflow takes in a search term, are passed to the eSearch function and searched for in PubMed. I extended by removing outputs and text extraction and addded an automatic Solr storage process using a post.jar, specified by the user. Before running this workflow, make sure that a solr server is up and running and the variable attached to the SolrImport process contains the correct path. Dependencies: - Solr

Created: 2013-07-25 | Last updated: 2013-08-26

Credits: Sander van boom

Attributions: PubMed Search

Pubmed mashup demo in a Virtuoso triplestore (1)

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This workflow build a mashup in your local virtuoso server (available at http://localhost:8890/sparql) by downloading the needed pubmed documents from NCBI and by converting them into N3 format.  Once all documents loaded into the triplestore you can query them with SPARQL. For example try those queries : SELECT count(*) WHERE {?s ?p ?o} SELECT ?o, count(*) WHERE {?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?o} Dr Labrie's MeSH subject of interest : SELECT ?o, count...

Created: 2009-02-11

Credits: Francois Belleau

PubMed Search (1)

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This workflow takes in a search term, are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

Created: 2011-02-03 | Last updated: 2011-02-03

Credits: Paul Fisher

pubmed abstracts from pathways (1)

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Extraction of the abstracts from pubmed pubblications related to the pathways involving the input genes

Created: 2014-02-28

Credits: Massimo La Rosa Antonino Fiannaca

Attributions: NCBI Gi to Kegg Pathway Descriptions Pathway to Pubmed

Pubmed -Google Tag Cloud (1)

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A simple workflow to query PubMed, Google and build a Tag Cloud after some preprocessing.

Created: 2015-11-01

Credits: Insilicoconsulting

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Pubmed rdfiser from Bio2RDF project

Created: 2009-02-11 06:00:37 | Last updated: 2009-02-11 06:32:03

Credits: Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

Comments: 0 | Viewed: 82 times | Downloaded: 34 times

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

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ONDEX Graph from the Yeast Jamboree SBML

Created: 2009-02-10 10:51:58 | Last updated: 2009-02-10 12:48:52

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: GNU Zip Archive

Comments: 0 | Viewed: 623 times | Downloaded: 60 times

Rank Phenotype Terms (1)

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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: 2011-02-01 | Last updated: 2011-02-01

Credits: Paul Fisher

Attributions: Cosine vector space Rank Phenotype Terms

Gene to Pubmed (3)

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This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2010-07-05 | Last updated: 2011-01-26

Credits: Paul Fisher

Phenotype to pubmed (3)

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This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

Created: 2010-07-05 | Last updated: 2011-01-11

Credits: Paul Fisher

Phenotype to pubmed (1)

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This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

Created: 2015-09-01

Credits: Heiko Schoof Paul Fisher

Attributions: Phenotype to pubmed

Pathway to Pubmed (1)

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This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2008-09-02 | Last updated: 2008-09-08

Credits: Stian Soiland-Reyes Paul Fisher

Attributions: ProteinSynonymsToQuery

Gene to Pubmed (4)

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This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2011-02-08 | Last updated: 2011-02-10

Credits: Paul Fisher

Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms

XPath Pubmed Ids (1)

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml

Created: 2011-03-23 | Last updated: 2011-03-23

Credits: Paul Fisher

XPath Pubmed Ids (2)

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml. The xml is then parsed to retrieve a list of PubMed ids

Created: 2011-03-23 | Last updated: 2011-03-30

Credits: Paul Fisher

Attributions: XPath Pubmed Ids

Pathway to Pubmed (2)

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This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Pathway to Pubmed (1)

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This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2013-09-03

Credits: Alan Williams Paul Fisher

Attributions: Pathway to Pubmed

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

Rank Phenotype Terms (2)

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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: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Attributions: Rank Phenotype Terms

Pathway and Gene to Pubmed (2)

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This workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype). The 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 PubMe...

Created: 2011-02-10 | Last updated: 2011-02-18

Credits: Paul Fisher

Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms Gene to Pubmed

Perfrom a text based search through PubMed (1)

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This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format

Created: 2010-07-05 | Last updated: 2010-07-05

Credits: Paul Fisher

Parsed UniProt to PubMed (1)

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Uses the parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve information from PubMed.

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Morgan Taschuk

GeneIlluminator_GetPubMedQuery (2)

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Example workflow demonstrating how to use GeneIlluminator_GetPubMedQuery, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service uses GeneIlluminator to create clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. GeneIlluminator provides also aliases associated to the input gene symbol. Finally, using the cluster characteristics it creates a boolean PubMed query that could be used to...

Created: 2008-02-27 | Last updated: 2008-03-03

Credits: Pieter Neerincx Alako

compare_pubmed_results_geographically (1)

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This workflow analyzes the scientific output, as documented by PubMed, geographically. The workflow takes as input the PubMed data in XML and the ISO 3166-1 and ISO 3166-3 country lists. The XML file can contain any subset from a specific PubMed search. The XPath components extract author affiliations, and feed these to a series of Beanshell components that match these with countries in the ISO standard. This data is then fed to an Rshell using the rworldmap R package to map the affiliation ...

Created: 2015-05-05 | Last updated: 2015-05-05

Credits: Magnus Palmblad Arzu Tugce Guler Bibliometrics and Scientometrics

Attributions: ISO 3166-1 and ISO 3166-3 Former countries

Author's collaborators according to pubmed (1)

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SELECT distinct ?s2 FROM <http://atlas.bio2rdf.org/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "author" .   ?s2 ?p2 ?s1 .   FILTER( regex(?s1, "pubmed") ) } followed by SELECT ?creator, count() FROM <http://localhost:8890/sparql> WHERE {   ?s1 ?p1 .   ?s1 ?p2 ?o2 .   FILTER( regex(?o2, "author"))   ?s1 ?creator . } ORDER BY DESC(count())

Created: 2009-01-20 | Last updated: 2009-01-20

Credits: Francois Belleau

Visualize Geographical Bias between PubMed... (3)

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This workflow analyzes the scientific output, as documented by PubMed, geographically. The workflow takes as input the PubMed data in XML and the ISO 3166-1 and ISO 3166-3 country lists. The XML files can contain any subset from two specific PubMed searches. for example for two different journals in the same field. The XPath components extract author affiliations, and feed these to a series of Beanshell components that match these with countries in the ISO standard. This data is then fed to ...

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

Credits: Magnus Palmblad Arzu Tugce Guler

Create Local Citation Graph (1)

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This workflow demonstrates how to build a local citation/reference graph for a single pubilcation in PubMed. The id input is the PubMed id (pmid) for any publication in the PubMed or PMC Europe. The workflow then queries the PMC Europe Web services to get the citations and references for this publication. Two XPath parsers are used to extract the citation and reference ids, which are then combined and passed on to an Rshell that draws a Sugiyama style layered graph using the igraph package. T...

Created: 2015-10-11

Credits: Magnus Palmblad

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

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Phenotype Abstracts for Trypanosomiasis Resistance

Created: 2009-08-11 12:45:24

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

Comments: 0 | Viewed: 69 times | Downloaded: 0 times

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

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

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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

A template example workflow using U-Compar... (2)

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An example workflow using the U-Compare text mining system inside embedded. Users can easily make their own workflow with U-Compare reusing this workflow. This workflow retrieves abstract texts from Pubmed with user specified query, inputs the texts to U-Compare, interprets the output of U-Compare. You have to download and store the UIMA CPE XML descriptor file (StdinPPIExtraction-CPE-EventMine.xml) to run the default setting, which runs a event extraction text mining workflow by U-Compare. S...

Created: 2010-07-05 | Last updated: 2010-09-02

Credits: Yoshinobu Kano

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Pathway Abstracts for Day7 Microarray Tir1 QTL

Created: 2009-08-11 14:08:41 | Last updated: 2009-08-11 14:15:58

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

Comments: 0 | Viewed: 101 times | Downloaded: 0 times

Escherichia coli : From cDNA Microarray Ra... (1)

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This workflow takes in a CDNA raw file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the R and bioconductor. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed changes in the microarray data. By identifying the candidate pathways, more detailed...

Created: 2008-05-08 | Last updated: 2008-05-12

Credits: Saeedeh Paul Fisher

Attributions: HUMAN Microarray CEL file to candidate pathways

What is known about HIV using Bio2RDF's SP... (2)

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To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched.  The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert mode into the graph. Once the mashup is built, two SPARQL queries analyze the obtained graph.  Finally you can submit queries to the RDF mashup about HIV as you like.  Enjoy. This is the queries present in t...

Created: 2009-02-05 | Last updated: 2009-02-05

Credits: Francois Belleau

Sponge into Virtuoso triplestore the neede... (2)

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query = labrie,f query = labrie query = labrie,f query = labrie query = h1n1 query = morissette,j query = labrie,f query = labrie query = h1n1 Get a list of paper from pubmed.

Created: 2009-11-17 | Last updated: 2009-11-27

Credits: Francois Belleau

Find Supporting Documents (6)

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This workflow finds documents that serve as evidence for the association between two concepts. Results: Document titles Document identifiers There seems to be a bug at the moment, since it returns empty values.

Created: 2012-06-26 | Last updated: 2014-07-14

Credits: Kristina Hettne Marco Roos Reinout van Schouwen Martijn Schuemie BioSemantics

Author Citation Network (1)

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Map citation/reference network for one author using Europe PMC Web services. This workflow is intended to show the integration of several Web services, XPath XML parsing and use of the igraph package in R. Although the workflow is functional, the information in PubMed is incomplete. This means the results may be a subset of the correct citation graph.

Created: 2015-12-04 | Last updated: 2015-12-04

Credits: Magnus Palmblad Yassene

Retrieve_Pubmed_Publication_by_kegg_pathwa... (1)

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This workflow shows in your browser pubmed articles related to input pathway

Created: 2012-10-18

Credits: Massimo La Rosa Antonino Fiannaca

DOI2PMID (2)

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Converts Digital Object Identifiers into their corresponding PubMed identifiers, if they exist.

Created: 2007-10-03

Author Citation Network (1)

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Map citation/reference network for one author using Europe PMC Web services. This workflow was created during the Tavernathon exercise held at the LUMC on October 14, 2015 and is intended to show the integration of several Web services, XPath XML parsing and use of the igraph package in R. Although the workflow is functional, the information in PubMed is incomplete, resulting in the workflow producing a subset of the correct citation graph.

Created: 2015-10-20

Credits: Magnus Palmblad

Triplify NCBI databases list [myexperiment... (1)

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List NCBI's database name. Using this URL service: http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? This is NCBI's namespace list supported by Bio2RDF : pubmed protein nucleotide gene=geneid homologene mesh omim pccompound=cid pcsubstance=sid taxonomy unigene unists

Created: 2009-11-30 | Last updated: 2009-12-01

Credits: Francois Belleau

wf4ever_document_extraction_and_storage (1)

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The workflow uses parts of the existing BioAid workflow by Marco Roos (http://www.myexperiment.org/workflows/74.html) The workflow stores found articles in a Solr database. Make sure that Solr is running in the correct directory (stored in the Solr_directory value).

Created: 2013-07-24 | Last updated: 2013-08-29

Find co-occurring documents (6)

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Purpose: This workflow search an indexed literature database for documents mentioning both of the input concepts. Author comments: Currently, PubMed is the underlying data source.

Created: 2012-07-13 | Last updated: 2014-07-14

Credits: Kristina Hettne Reinout van Schouwen Marco Roos Martijn Schuemie BioSemantics

DataBiNS with Kegg ID (3)

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Consumes a KEGG gene id and mines for pathway, GO, PubMed and SNP information about that gene

Created: 2009-07-09 | Last updated: 2010-11-22

Credits: Mark Wilkinson Fong Chun Chan