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Items tagged with "concept" (27)

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Network-member 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.

3 shared items   |   3 announcements

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Files (2)
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Blob PubMed Term Counts

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

Credits: User 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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Blob Ondex and Taverna Tutorial

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

Credits: User 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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Workflows (23)
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Workflow Rank Phenotype Terms (1)

Created: 10/08/09 @ 15:43:48

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 139 times | Downloaded: 0 times

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Workflow Table Parser (1)

Created: 19/08/09 @ 16:04:12

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow parsers a table (specified by the user), into an Ondex Graph on the web server.

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Workflow Tab Parser (1)

Created: 19/08/09 @ 16:05:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow Concept Class Filter (1)

Created: 19/08/09 @ 16:10:36

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 14 times | Downloaded: 1 time

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Workflow Concept Class Neighbours Filter (1)

Created: 19/08/09 @ 16:11:56

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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Workflow Context Consensus Filter (1)

Created: 19/08/09 @ 16:13:11

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 ...

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Workflow SubGraph Filter (2)

Created: 19/08/09 @ 16:38:17

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow Cosine vector space (2)

Created: 08/12/10 @ 11:35:18 | Last updated: 11/01/11 @ 12:05:41

Credits: User Paul Fisher

Attributions: Workflow Cosine vector space

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Original Uploader

Workflow Rank Phenotype Terms (2)

Created: 08/12/10 @ 11:38:37 | Last updated: 11/01/11 @ 12:02:30

Credits: User Paul Fisher

Attributions: Workflow Rank Phenotype Terms

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 ...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 32 times | Downloaded: 15 times

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Workflow Pathway to Pubmed (2)

Created: 08/12/10 @ 11:47:10 | Last updated: 11/01/11 @ 12:00:16

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 46 times | Downloaded: 21 times

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Workflow Extract Scientific Terms (2)

Created: 08/12/10 @ 11:50:01 | Last updated: 11/01/11 @ 11:58:09

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Original Uploader

Workflow Rank Phenotype Terms (1)

Created: 01/02/11 @ 11:22:14 | Last updated: 01/02/11 @ 11:24:42

Credits: User Paul Fisher

Attributions: Workflow Cosine vector space Workflow Rank Phenotype Terms

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 34 times | Downloaded: 15 times

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Workflow Pathway and Gene to Pubmed (2)

Created: 10/02/11 @ 16:10:52 | Last updated: 18/02/11 @ 13:47:08

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Match concept profiles (4)

Created: 02/12/11 @ 09:07:34 | Last updated: 14/09/12 @ 09:57:48

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles. The result is a list of concepts ordered by their match to the query concept profiles. The workflow matches two sets of concept profiles. At the time of writing the concepts are derived from human, rat, and mouse terminologies, ontologies, and database identifiers. The profiles are lists of concepts ranked by their association with the identifying concept, as determined by c...

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Explain concept scores (5)

Created: 07/02/12 @ 11:05:50 | Last updated: 14/09/12 @ 10:01:37

Credits: User Reinout van Schouwen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 5 | Reviews: 0 | Comments: 0 | Citations: 0

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

Created: 17/04/12 @ 08:55:46 | Last updated: 25/04/12 @ 07:54:26

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow DatabaseID_to_ConceptID (4)

Created: 25/06/12 @ 20:48:28 | Last updated: 14/09/12 @ 10:03:01

Credits: User Marco Roos User Martijn Schuemie User Reinout van Schouwen Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Resources: Table of database identifiers and concept identifiers. Database identifiers from ... EMC ontology compiled from ... Comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Find Supporting Documents (2)

Created: 26/06/12 @ 10:21:17 | Last updated: 18/07/12 @ 14:00:02

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow finds documents that serve as evidence for the association between two concepts. Results: Document titles Document identifiers Author comment: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

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Workflow SNPs to Concept Set through Concept Profil... (5)

Created: 26/06/12 @ 10:27:33 | Last updated: 14/09/12 @ 10:10:23

Credits: User Kristina Hettne User Eleni User Harish Dharuri User Reinout van Schouwen User Marco Roos User Martijn Schuemie Network-member BioSemantics

Attributions: Workflow Find Supporting Documents Workflow SNP_ID2EntrezGene_ID Workflow DatabaseID_to_ConceptID Workflow Match gene lists based on information in literature Workflow Match concept profiles Workflow Explain concept scores

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose: Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www...

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Workflow Get Concept IDs (4)

Created: 06/07/12 @ 14:17:35 | Last updated: 14/09/12 @ 09:54:38

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose: The workflow retrieves the concepts within a concept set. Author comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

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Workflow Get concept information (3)

Created: 06/07/12 @ 14:20:40 | Last updated: 14/09/12 @ 09:56:11

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The workflow takes a concept ID as input and returns the ID, definition and name of the concept. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow List Concept Sets (2)

Created: 06/07/12 @ 14:25:52 | Last updated: 18/07/12 @ 13:53:33

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Pupose: The workflow returns a list of all Concept Set IDs currently available in the database. The Concept Sets have an hierarchical structure that can be inferred by referring to the parent Concept Set ID. Author comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Filter concepts with profiles (2)

Created: 14/09/12 @ 10:14:12 | Last updated: 14/09/12 @ 13:37:07

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose: This workflow can be used to check if a concept has a concept profile in the database. Author comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

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Packs (1)
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Pack Functional annotation of SNPs using next-generation ...


Created: 26/06/12 @ 10:41:38 | Last updated: 14/09/12 @ 10:53:41

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 ...

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