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Items tagged with "literature" (18)

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Blob Bilateral Perisylvian Polymicrogyria (Epilepsy)

Created: 2010-12-07 16:34:31 | Last updated: 2010-12-07 16:34:37

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains the results of running a QTL workflow for Bilateral Perisylvian Polymicrogyria in human (homo sapiens). Provided are a list of candidate QTL genes (QTg) and their corresponding KEGG pathways. Each gene and pathway have been subsequently run through a series of text mining workflows to determine the significance of each may play in relation to Bilateral Perisylvian Polymicrogyria AND/OR Epilepsy. Further to this, I have also collected the SNPs (single nucleotide...

File type: application/x-zip-compressed

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Groups (1)
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Network-member BioSemantics

Unique name: biosemantics
Created: Thursday 30 June 2011 13:06:48 (UTC)

Group for members of the BioSemantics group and their close collaborators.BiosemanticsWith the explosion of information in the biomolecular field, there is a dire need for information technology that assists in retrieving, extracting, and relating information and knowledge in the biomedical literature and databases. Biosemantics researchers and developers develop, evaluate, and apply such techn...

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Packs (4)
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Pack Text Mining Workflows


Created: 2010-12-08 11:55:03 | Last updated: 2011-02-01 11:33:11

This pack contains workflows to navigate from candidate Quantitative Trait genes and pathways to a given phenotype.

5 items in this pack

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Pack Trichuriasis induced Colitis


Created: 2011-02-16 12:49:21 | Last updated: 2011-02-16 15:26:36

This pack contains the workflows and data relating to Trichuriasis induced colitis.

5 items in this pack

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Pack Functional annotation of SNPs using next-generation ...


Created: 2012-06-26 10:41:38 | Last updated: 2015-09-01 14:31:18

This pack implements the concept profile matching pipeline in the knowledge discovery tool Anni (http://biosemantics.org/anni), and adapts it to interpret the top SNPs from a GWAS. The underlying literature and concept profile databases are the same as the for the current version of Anni (2.1). The pack consists of three main workflows (http://www.myexperiment.org/workflows/2999, http://www.myexperiment.org/workflows/2973, http://www.myexperiment.org/workflows/2972). Workflow 2999 returns a ...

12 items in this pack

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Pack Concept profile analysis using Anni Web services


Created: 2013-02-06 19:11:26 | Last updated: 2014-07-15 08:17:33

Concept profile analysis is a knowledge discovery method that proved successful in generating hypotheses about molecular mechanisms explaining the results from genotype-phenotype studies. This technology has been implemented in the Anni standalone application (http://biosemantics.org/anni). This pack contains a number of workflows that can be used together to configure and run typical user pipelines from Anni through the Anni Web services (http://www.biocatalogue.org/services/3559).

11 items in this pack

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Workflows (12)

Workflow 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: User Hamish McWilliam

Workflow 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: User Paul Fisher

Workflow 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: User Paul Fisher

Workflow 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: User Paul Fisher

Attributions: Workflow Cosine vector space Workflow Rank Phenotype Terms

Workflow 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: User Paul Fisher

Workflow Remove Non-ASCII (1)

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THis workflow removes any non-ascii characters from a segment of text. Any characters that are found are removed. Letters either side f the non-ASCII are concatenated - this may cause the loss of word meaning

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

Credits: User Paul Fisher

Workflow 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: User Paul Fisher

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

Workflow 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: User Paul Fisher

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

Workflow Match gene lists based on information in l... (7)

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[THIS WORKFLOW IS IN BETA STAGE] This workflow computes the match between two lists of Entrez Gene Identifiers by means of concept profile matching (Jelier et al., van Haagen et al.). The result of this is a list of concepts ordered by their matching score (the length of the list set by maxMatchNr). Of this list the summed scores are explained by computing the concepts that contribute most to the combination of the matching genes. Example to explain (by analogy): When a group of informatic...

Created: 2012-04-17 | Last updated: 2012-04-25

Credits: User Marco Roos User Reinout van Schouwen User Eleni User Kristina Hettne Network-member BioSemantics

Attributions: Workflow Match concept profiles Workflow Explain concept scores

Workflow 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: User Kristina Hettne User Reinout van Schouwen User Marco Roos User Martijn Schuemie Network-member BioSemantics

Workflow Filter concepts with profiles (4)

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Purpose: Filter a list of concept id(s) by returning only those with a concept profile in the database.

Created: 2012-09-14 | Last updated: 2014-07-14

Credits: User Kristina Hettne User Reinout van Schouwen User Martijn Schuemie Network-member BioSemantics

Workflow Explain concept scores (7)

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Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the pe...

Created: 2012-02-07 | Last updated: 2014-07-14

Credits: User Reinout van Schouwen

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Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/867


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