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Blob Ondex and Taverna Tutorial

Created: 2009-10-22 13:50:53 | Last updated: 2009-10-22 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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Pack Natural product likeness filter


Created: 2011-05-13 19:35:39 | Last updated: 2011-08-29 14:25:47

Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work...

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Workflows (38)

Workflow All Pairs Filter (1)

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This workflow filters a given Ondex graph based on the occurrence of directed edges within the graph. Only those concepts that have directional edges are returned to the user, in the form of a new 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. GdsWeight - The name of the GDS type to ...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Clean GO Filter (1)

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This workflow filters an Ondex graph, by cleaning up any GO terms within the Graph (?). 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.

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Clean UniProt Filter (1)

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This workflow filters a given Ondex graph, removing any erroneous UniProt data. The result is a new Ondex graph that conatains only connected UniProt data. 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.

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Concept Class Filter (1)

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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...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Concept Class Neighbours Filter (1)

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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...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Context Consensus Filter (1)

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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 ...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Context Filter (1)

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This workflow filters an Ondex graph according to a given context. The result is a new Ondex graph with only selected contexts. 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. ContextID - The Concept ID of the Context that starts the path. ContextBoolean - Defines two ContextIDs and a boolean operati...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow CV Filter (1)

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This workflow filters a given Ondex graph according to a controlled vocabulary specified by the user. The result is a new Ondex graph with only those concepts that passed the filter. The parameters that can be used with this service 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. CV - A CV to include/exclude Concepts and Relations of (see Exclude param). R...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Evidence Type Filter (1)

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This workflow filters a given Ondex graph according to some user defined evidence values. The result is a new Ondex graph. The parameters that can be used with this web service are given below: 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. EvidenceType - EvidenceType to be taken into consideration. RefactorTrinaries - Where the qualifier of a trinary rel...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow GDS Value Filter (1)

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This workflow filters a given Ondex graph based on a given GDS value supplied by the user. The result is a new Ondex graph with filtered content. 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. AttributeName - AttributeName to filter out. GDSValue - A value which will be matched against the ...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Genomic Filter (1)

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This workflow filters a given Ondex graph according to a chromosomal region, or QTL region. 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. ContextID - The Concept ID of the Context (Chromosome). From - The start position on the chromosome, e.g. 100. To - The stop pos...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Graph Cloner (1)

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This workflow clones a given Ondex Graph, based on an Ondex Graph identifier.

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Isolate Clusters Filter (1)

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This workflow filters a given Ondex graph, isolating clusters within the graph and returning only those clusters as a new 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 be contained in clusters.

Created: 2009-08-19

Credits: User Paul Fisher

Workflow One Pair Shortest Path Filter (1)

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This workflow filters a pre-existing Ondex graph using the shortest path algorithm on the graph. 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. StartConceptID - The Concept ID that starts the path EndConceptID - The Concept ID that ends the path UseWeights -...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Optimal Paths Filter (1)

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This workflow filters a given Ondex graph based on the optimal path between one or more concepts. The result is a new Ondex graph. The parameters that can be used with 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. PathwayDefinition - pathway definition file. StatisticsOutputDir - The directory to output statistics (Optional). Incl...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Pfam Based Ortholog Filter (1)

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This workflow filters an Ondex graph based on the occurrence of Pfam orthologs within the graph. 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. ConfidenceThreshold - Threshold value for inparanoid confidence. Default value is 100. AnnotationScoreThreshold - Threshold...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Relation Neighbours Filter (1)

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This workflow filters a given Ondex graph based on some neighbour parameters supplied by the user. 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. Depth - The Depth (distance from seed in relations) to apply the filter to ConceptID - The Concept ID to seed th...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Relation Type Filter (1)

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This workflow filters a pre-existing ONdex graph based on a some paramters provided by the user. 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. TargetRelationType - Target RelationType to filter out. ConceptClassRestriction - Concept Class Restriction as ordered pair representing from/to C...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Shortest Path (1)

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This workflow filters a given Ondex graph according to the shortest path (graph) algorithm. 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. StartConceptID - The Concept ID that starts the path. Valid value range is 1 to 2147483647. UseWeights - Use gds values as edge ...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Significance Filter (1)

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This workflow filters a given Ondex graph according to a level of significance set by the user. 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. TargetAttributeName - Target AttributeName to filter for significance. Significance - A significance value to filter relatio...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow SubGraph Filter (2)

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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...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Tranitive Filter (1)

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This workflow filters an Ondex graph to extract a sub-graph. The result is a new Ondex graph containing only the transitive 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). If no output graph is specified filtered items will be removed from the input graph. CV - Seed cv that will be used to extract the subgraph (Optional). AttributeName - Seed attribute name that will be us...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Unconnected Filter (1)

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This workflow removes any unconnected nodes from a given Ondex graph through filtering, and returns 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. RemoveContextDependencies - Set true to remove context dependencies, otherwise unconnected concepts will still remain in the ...

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Split text/string into its lines and filte... (2)

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When retrieving a URL or soemthing alike, one can often identify the region of interest as a single line. Besides the expected output, also some interim values, like the lines split are forwarded, to allow some straight-forward cascading of filters with reduced redundancy.

Created: 2009-08-19

Credits: User Steffen Möller

Workflow find events in xray and radio (7)

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instruments: hessiEC, phoenix2 attention: hessi name has changed!

Created: 2010-03-16 | Last updated: 2010-03-16

Credits: User Anja Le Blanc

Workflow Extracting data from VOTable format by usi... (1)

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Input VOTable and 'name' of a Output corrosponding data of that field in an arrayInput VOTable and 'name' of a Field

Created: 2010-07-01 | Last updated: 2010-07-01

Credits: User Anja Le Blanc User Donal Fellows

Workflow Change Class Distribution of Your Training... (1)

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This example process shows how to change the class distribution of your training data set (in this case the training data is what ever comes out of the "myData reader"). The given training set has a distribution of 10 "Iris-setosa" examples, 40 "Iris-versicolor" examples and 50 "Iris-virginica" examples. The aim is to get a data set which has the class distribution for the label, lets say 10 "Iris-setosa", 20 "Iris-versicolor" and 20 "Iris-virginica. Beware that this may change some propert...

Created: 2011-01-21 | Last updated: 2011-01-21

Workflow Extract content of columns from VOTables (3)

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Extracts all values from all columns which are passed from the input ColumnNames

Created: 2011-02-24 | Last updated: 2012-08-20

Credits: User Anja Le Blanc

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Workflow Generate Atom Signatures of molecules give... (1)

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Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: User Kalai

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Workflow Scoring small molecules for metabolite lik... (2)

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 Prerequisite:   - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1   Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu...

Created: 2011-05-13 | Last updated: 2012-03-18

Credits: User Kalai

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Workflow Plotting distribution of natural product l... (1)

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 Prerequisite:  CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file.  - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1   Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: User Kalai

Workflow date filter for ice Class Map service (NERSC) (1)

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Workflow to filter available dates with ice classification images. Service provided by NERCS. Dates are filtered using a simple regular expression

Created: 2011-11-02 | Last updated: 2011-11-04

Credits: User Jorgejesus

Workflow Find periods of time where two ILS objects... (2)

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Inputs: name of target_obj of ILS of two objects and a number of degrees which these obejcts are allowed to be appart in hci longitude coordinates. Output VOTable of time periods where these two objects are closer than +/- input angle together.

Created: 2011-11-04 | Last updated: 2011-11-18

Credits: User Anja Le Blanc

Workflow Available instruments through DPAS which a... (1)

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This workflow uses a DPAS servlet to obtain all available intrument keys in the DPAS (Data Provider Access Service) and formats the return as VOTable.

Created: 2012-03-16 | Last updated: 2012-03-16

Credits: User Anja Le Blanc

Attributions: Workflow Available instruments through DPAS Workflow Split VOTable into its values

Workflow EBI NCBI BLAST filter e-value and length (1)

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The workflow queries the NCBI BLAST web service and extracts the e-values and length of the results. One of the sub-workflows filters the length first and afterwards the e-value and the other sub-workflow filters first the e-value and then the length. As the result may be different, this workflow was used for optimization purposes to find the sub-workflow performing best.

Created: 2013-08-23 | Last updated: 2014-02-06

Credits: User Sonja Holl

Attributions: Workflow EBI_NCBI_BLAST

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Project Biovel

Workflow Bioclim workflow (6)

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This workflow takes as input a file containing species occurrence points to create a model with the openModeller Web Service using the Bioclim algorithm. Environmental layers and mask are selected during the workflow. Points are filtered so that only environmentally unique points are used to create the model. You can use this workflow to either filter a set of species occurrence points excluding redundant points with the same environmental conditions (you can get the result in the output "se...

Created: 2013-09-02 | Last updated: 2015-04-04

Credits: User Renato De Giovanni Network-member BioVeL

Workflow FInd/filter idA and idB from MITAB (1)

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A workflow to filter idA and idB out of a MITAB file.

Created: 2015-11-05 | Last updated: 2015-11-05

Workflow Get targets for compound (1)

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This workflow retrieves single protein targets for a compound from open PHACTS.

Created: 2016-02-22

Credits: User Kristina Hettne User Eelke van der Horst User Aylin Metzner

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Non-Information Resource URI: http://www.myexperiment.org/tags/1551


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