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Items tagged with "data integration" (18)

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Pack Mapping Metabolites for Metabolic Network Reconstructions

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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Network-member SyMBA: Systems and Molecular Biology Data and Metadata Archive

Unique name: symba Created: Wednesday 12 September 2007 @ 11:30:41 (BST)

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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Network-member ONDEX Graphs

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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Network-member SabrOndexProject

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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Files (1)

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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 (13)
Taverna 1

Original Uploader

Workflow Get Concepts (v1)

Created: 27/02/09 @ 16:33:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_concepts
This workflow gets all the concepts in an Ondex graph, using a given graph id

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

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Taverna 1

Original Uploader

Workflow Get CVs (v1)

Created: 27/02/09 @ 16:38:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_cvs
This workflow lets users retrive all controlled vocabularies for a given Ondex graph

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

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Taverna 1

Original Uploader

Workflow Get Evidence Types (v1)

Created: 27/02/09 @ 16:40:22

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_evidence_types
This workflow gets all the evidence types within a specified Ondex graph

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Taverna 1

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Workflow Get graphs (v2)

Created: 05/11/09 @ 12:38:22

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_graphs
Thiw workflow simply returns all the Ondex graphs that are present on a given server (where the web service is)

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

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Taverna 1

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Workflow Get Graphs of Name (v1)

Created: 27/02/09 @ 16:42:35

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_graphs_of_name
This workflow gets the Ondex graphs relating to a specified name

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

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Taverna 1

Original Uploader

Workflow Get relations (v1)

Created: 27/02/09 @ 16:45:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_relations
This workflow gets all the realtions from a given Ondex graph

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Taverna 1

Original Uploader

Workflow Pathways and Gene annotations for QTL region (v2)

Created: 20/11/09 @ 14:04:37 | Last updated: 20/11/09 @ 14:04:39

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pathways_and_gene_annotations_for_qtl_region
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 ...

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

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Pipeline Pilot

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Workflow C1 Combined Workflow (v1)

Created: 03/06/10 @ 11:26:48 | Last updated: 03/06/10 @ 11:30:10

Credits: User Paul Dobson

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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Pipeline Pilot

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Workflow M1 Exact Matching (v1)

Created: 03/06/10 @ 11:32:02

Credits: User Paul Dobson

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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Pipeline Pilot

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Workflow M2 Similarity Matching (v1)

Created: 03/06/10 @ 11:33:36

Credits: User Paul Dobson

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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Pipeline Pilot

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Workflow M3 Non-stereo Matching (v1)

Created: 03/06/10 @ 11:35:03

Credits: User Paul Dobson

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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Pipeline Pilot

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Workflow M4 Tautomer Matching (v1)

Created: 03/06/10 @ 11:38:27

Credits: User Paul Dobson

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.

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

Viewed: 4 times | Downloaded: 2 times

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Pipeline Pilot

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Workflow M5 Charge Matching (v1)

Created: 03/06/10 @ 11:39:28

Credits: User Paul Dobson

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.

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

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