Search results for "pubmed"

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