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Items tagged with "data integration" (22)
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Created: 27/02/09 @ 16:33:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow gets all the concepts in an Ondex graph, using a given graph id
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Created: 27/02/09 @ 16:38:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow lets users retrive all controlled vocabularies for a given Ondex graph
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Created: 27/02/09 @ 16:40:22
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow gets all the evidence types within a specified Ondex graph
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Created: 05/11/09 @ 12:38:22
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Thiw workflow simply returns all the Ondex graphs that are present on a given server (where the web service is)
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Created: 27/02/09 @ 16:42:35
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow gets the Ondex graphs relating to a specified name
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Created: 27/02/09 @ 16:45:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow gets all the realtions from a given Ondex graph
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Created: 20/11/09 @ 14:04:37 | Last updated: 20/11/09 @ 14:04:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the Pig, Sus scrofa. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway ...
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Created: 03/06/10 @ 11:26:48 | Last updated: 03/06/10 @ 11:30:10
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithms M1-M5 in one workflow, yielding a sparse matrix of matches annotated by match types.
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Created: 03/06/10 @ 11:32:02
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M1 which matches fully specified molecules on the basis of their canonical representations.
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Created: 03/06/10 @ 11:33:36
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M2 which reads molecules from two sources and produces clusters of highly similar molecules.
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Created: 03/06/10 @ 11:35:03
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M3 which strips stereochemical information from molecules, performs exact matching, and restores stereochemistry.
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Created: 03/06/10 @ 11:38:27
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M4 which generates canonical tautomers prior to matching, matches, then restores original structures.
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Created: 03/06/10 @ 11:39:28
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M5 which ionises molecules at pH 7 prior to matching, restores original structures.
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Created: 10/02/11 @ 16:10:52 | Last updated: 18/02/11 @ 13:47:08
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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...
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Created: 17/03/11 @ 11:10:28 | Last updated: 30/08/11 @ 10:40:14
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Human, Homo sapiens. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway ...
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Created: 03/06/10 @ 11:43:43 | Last updated: 03/06/10 @ 11:47:16
The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems.
These problems include finding identical structures across sources, which is trivial, but also structures that differ due to idiosyncrasies of the sources or annotators. This includes charge differences, varying stereochemistry, tautomers, and so forth. Workflows in this pack allow sets of ...
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Created: 16/02/11 @ 12:49:21 | Last updated: 16/02/11 @ 15:26:36
This pack contains the workflows and data relating to Trichuriasis induced colitis.
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Unique name: symba Created: Wednesday 12 September 2007 @ 11:30:41 (GMT)
SyMBA was originally developed to be a high-throughput data archive for the data created at CISBAN at Newcastle University, but is now a project applicable for many in the biology & bioinformatics community. New developers are always welcome. SyMBA is a data and metadata archive that is based on the Functional Genomics Object Model(FuGE) and which archives, stores, and retrieves raw high-t...
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Unique name: ONDEX Created: Tuesday 10 February 2009 @ 10:45:09 (GMT)
A group for sharing ONDEX graphs in oxl format
http://ondex.sourceforge.net/
http://www.ondex.org/
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Unique name: SabrOndex Created: Friday 27 February 2009 @ 15:42:55 (GMT)
This group is set up for the SABR Ondex-Taverna integration
http://www.ondex.org
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Created: 22/10/09 @ 13:50:53 | Last updated: 22/10/09 @ 13:51:51
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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 Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 28 times | Downloaded: 23 times Tags: |
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Created: 17/03/11 @ 10:56:15 | Last updated: 17/03/11 @ 11:16:53
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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 each may play in relation to Bilateral Perisylvian Polymicrogyria.
If you want to help me identify candidate genes for this disorder, please get i...
File type: ZIP archive Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 8 times | Downloaded: 5 times Tags: |
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