myExperiment - Tags

Workflows (15)

Taverna 1 Original Uploader Paul Fisher	Rank Phenotype Terms (v1) Created: 10/08/09 @ 15:43:48 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 124 times \| Downloaded: 0 times Tags (24): abstracts \| append term \| authors \| concept \| cosine vector space \| data-driven \| enrichment \| gene identifier \| geneid \| genes \| genotype \| information \| mining \| ncbi \| pathways \| phenotype \| pubmed \| ranking \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Taverna 1 Original Uploader Paul Fisher	Table Parser (v1) Created: 19/08/09 @ 16:04:12 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow parsers a table (specified by the user), into an Ondex Graph on the web server. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 1 time Tags (7): concept \| ondex \| ovtk \| oxl \| parser \| table \| text	View
Taverna 1 Original Uploader Paul Fisher	Tab Parser (v1) Created: 19/08/09 @ 16:05:20 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a tab separated file, and then parses specific rows and columns from the file into an Ondex Graph. Additional prarameters are provided, though these are optional: graphId Long the ID of the Graph (REQUIRED) input String the plugin input (REQUIRED) skip Integer How many rows to skip at begin of document (Optional). Default value is 22. fromCol Integer Index of concept parser id for from concept. Default value is 0. (REQUIRED) toCol Integer Index of concept par... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 21 times \| Downloaded: 1 time Tags (12): concept \| file \| gene \| line \| ondex \| ovtk \| oxl \| parser \| protein \| tab \| table \| taxonomy	View
Taverna 1 Original Uploader Paul Fisher	Concept Class Filter (v1) Created: 19/08/09 @ 16:10:36 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters a Ondex graph based on a specific concept class. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. TargetConceptClass - Target Concept Class to filter out. RefactorTrinaries - Where the qualifier of a trinary relation is out of scope create a bina... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 1 time Tags (6): concept \| filter \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	Concept Class Neighbours Filter (v1) Created: 19/08/09 @ 16:11:56 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters a given Ondex graph based on a user defined concept class. The neighbours of the concept class are returned as a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. Depth - The Depth (distance from seed in relations) to apply the filter to. ConceptClass - The Conce... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 1 time Tags (7): concept \| distance \| filter \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	Context Consensus Filter (v1) Created: 19/08/09 @ 16:13:11 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters a given Ondex graph according to a consensus with regards to a specific context (concept list). The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. Threshold - Double value representing the share of contexts that qualify a graph element for ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 1 time Tags (7): concept \| consensus \| filter \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	SubGraph Filter (v2) Created: 19/08/09 @ 16:38:17 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters a given Ondex graph to return a new ondex sub-graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. ConceptID - The root concept to start at. Valid value range is 1 to 2147483647. FirstRelationType - RelationType limitation for depth 1 (Optional). FirstConceptClass - C... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 36 times \| Downloaded: 1 time Tags (7): concept \| filter \| graph \| ondex \| ovtk \| oxl \| sub-graph	View
Taverna 2 Original Uploader Paul Fisher	Cosine vector space (v2) Created: 08/12/10 @ 11:35:18 \| Last updated: 11/01/11 @ 12:05:41 Credits: Paul Fisher Attributions: Cosine vector space License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. this is some extra text vbeing added Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 12 times Tags (14): abstracts \| concept \| concept profile \| cosine vector space \| genotype \| pathway \| phenotype \| space \| term \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| vector	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Rank Phenotype Terms (v2) Created: 08/12/10 @ 11:38:37 \| Last updated: 11/01/11 @ 12:02:30 Credits: Paul Fisher Attributions: Rank Phenotype Terms License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 14 times Tags (12): abstracts \| concept \| concept profile \| enrichment \| genotype \| phenotype \| pubmed \| ranking \| term \| text \| text mining \| text mining; term extraction; entity recognition	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathway to Pubmed (v2) Created: 08/12/10 @ 11:47:10 \| Last updated: 11/01/11 @ 12:00:16 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 36 times \| Downloaded: 19 times Tags (13): abstracts \| concept \| data-driven \| genotype \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| text \| text mining \| text mining; term extraction; entity recognition	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Extract Scientific Terms (v2) Created: 08/12/10 @ 11:50:01 \| Last updated: 11/01/11 @ 11:58:09 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a document containg text and removes and non-ascii characters. The cleaned text is then sent to a service in dresden to extract all scientific terms. These terms represent a profile for the input document. Any null values are also removed. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 55 times \| Downloaded: 17 times Tags (13): abstracts \| ascii \| concept \| concept profile \| dresden \| entity recognition \| genotype \| phenotype \| term \| term extraction \| terms \| text \| text mining; term extraction; entity recognition	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Rank Phenotype Terms (v1) Created: 01/02/11 @ 11:22:14 \| Last updated: 01/02/11 @ 11:24:42 Credits: Paul Fisher Attributions: Cosine vector space Rank Phenotype Terms License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 14 times Tags (26): concept \| concept profile \| cosine vector space \| data-driven \| enrichment \| entity recognition \| eutils \| evidence \| getconcepts \| literature \| mining \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| ranking \| significance \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathway and Gene to Pubmed (v2) Created: 10/02/11 @ 16:10:52 \| Last updated: 18/02/11 @ 13:47:08 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 License: Creative Commons Attribution-Share Alike 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 64 times \| Downloaded: 19 times Tags (36): annotation \| concept \| concept profile \| controlled vocabulary \| cosine vector space \| data integration \| data-driven \| dresden \| efetch \| enrichment \| entity recognition \| esearch \| eutils \| gene \| gene identifier \| geneid \| genotype \| kegg \| Kegg Pathways \| KeggID \| literature \| loci \| locus \| medline \| mesh \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| text mining \| text mining; term extraction; entity recognition \| trait \| triat	View Download (v2)
Taverna 2 Original Uploader Reinout van Schouwen	ExplainScores demo (v2) Created: 07/02/12 @ 11:05:50 \| Last updated: 21/03/12 @ 15:10:04 Credits: Reinout van Schouwen License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow demonstrates the explainScores method from the Anni web services. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 11 times Tags (3): anni \| concept \| demo	View Download (v2)
Taverna 2 Original Uploader Marco Roos	Match gene lists based on information in literature (v7) Created: 17/04/12 @ 08:55:46 \| Last updated: 25/04/12 @ 07:54:26 Credits: Marco Roos Reinout van Schouwen Eleni Kristina Hettne BioSemantics Attributions: ExplainScores demo License: Creative Commons Attribution-Share Alike 3.0 Unported License [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... Rating: 0.0 / 5 (0 ratings) \| Versions: 7 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 27 times \| Downloaded: 6 times Tags (11): association \| bioinformatics \| biology \| concept \| concept mining \| concept web \| literature \| protein \| proteins \| semantic \| uniprot	View Download (v7)

Groups (1)

Administrator:

Jan Velterop

CWA-Working Group 3.2 ConceptWiki

Unique name: ConceptWiki Created: Wednesday 29 July 2009 @ 16:03:54 (GMT)

This CWA Working Group is concerned with the CWA ConceptWiki and its relationship to other scientific Wikis. This place on MyExperiment will serve as a common forum for the Working Group.

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Files (2)

Uploader:

Paul Fisher

PubMed Term Counts

Created: 11/08/09 @ 13:59:35

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a count of each phenotype term extracted from corpus of phenotype abstracts. Each value represents the number of articles in MEDLINE the term appears. The use of this file is to calculate a cosine vector score for correlating a given concept (e.g. pathway or gene) with a phenotype.

File type: Plain text

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Uploader:

Paul Fisher

Ondex and Taverna Tutorial

Created: 22/10/09 @ 13:50:53 | Last updated: 22/10/09 @ 13:51:51

Credits: George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Biological Data Integration Using Ondex and Taverna: A Tutorial 25/26th November 2009 The University of Manchester The Ondex SABR project (http://ondex.org/sabr.html) invite you to a two-day tutorial that aims to show participants how to use Ondex and Taverna to perform common biological data collection, integration and visualisation tasks.

File type: Word document

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Items tagged with "concept" (18)