User: Paul Fisher

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Paul Fisher

Get Gene Ids for Human (v1)

Created: 04/02/10 @ 12:47:17 | Last updated: 04/02/10 @ 12:48:12

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow gets a list of gene ids (number depending on Ret_Max_value variable) for Homo sapiens. The species may be changed according to that desired, by altering the term_value string constant

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Paul Fisher

Spreadsheet Importer (v1)

Created: 24/08/09 @ 14:11:52 | Last updated: 24/08/09 @ 14:11:53

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow is designed to import a spreadhseet from a local computer. The imported spreadsheet is parsed to extract the first two columns, A and B, for all rows in the spreadsheet. These are returned as two separate outputs.

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Paul Fisher

Tranitive Filter (v1)

Created: 19/08/09 @ 16:34:17 | Last updated: 19/08/09 @ 16:34:18

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Paul Fisher

Significance Filter (v1)

Created: 19/08/09 @ 16:31:25 | Last updated: 19/08/09 @ 16:31:26

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Paul Fisher

Relation Type Filter (v1)

Created: 19/08/09 @ 16:29:12 | Last updated: 19/08/09 @ 16:29:13

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Paul Fisher

Pfam Based Ortholog Filter (v1)

Created: 19/08/09 @ 16:26:56 | Last updated: 19/08/09 @ 16:26:58

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Paul Fisher

One Pair Shortest Path Filter (v1)

Created: 19/08/09 @ 16:24:42 | Last updated: 19/08/09 @ 16:24:44

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 -...

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Paul Fisher

Graph Cloner (v1)

Created: 19/08/09 @ 16:22:14 | Last updated: 19/08/09 @ 16:22:16

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Paul Fisher

GDS Value Filter (v1)

Created: 19/08/09 @ 16:17:28 | Last updated: 19/08/09 @ 16:17:30

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 ...

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Paul Fisher

CV Filter (v1)

Created: 19/08/09 @ 16:15:21 | Last updated: 19/08/09 @ 16:15:23

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

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Paul Fisher

Context Consensus Filter (v1)

Created: 19/08/09 @ 16:13:12 | Last updated: 19/08/09 @ 16:13:14

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 ...

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Paul Fisher

Concept Class Filter (v1)

Created: 19/08/09 @ 16:10:38 | Last updated: 19/08/09 @ 16:10:39

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...

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Paul Fisher

Clean GO Filter (v1)

Created: 19/08/09 @ 16:07:28 | Last updated: 19/08/09 @ 16:07:29

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

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Paul Fisher

Tab Parser (v1)

Created: 19/08/09 @ 16:05:21 | Last updated: 19/08/09 @ 16:05:22

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...

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Paul Fisher

KEGG Pasrer (v1)

Created: 19/08/09 @ 16:03:09 | Last updated: 19/08/09 @ 16:03:10

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow parses a KEGG species database into an Ondex Graph graphId - the ID of the Graph. inputDir - the plugin input directory Species - Use this parameter to specify the species to be loaded from the kegg database. Default value is all. ParseSequences - KEGG species code. Default value is false (boolean) ImportOrthologFillers - Import Ortholog Pathway Fillers. Default value is false (boolean)

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Paul Fisher

Phenotype to pubmed (v1)

Created: 10/08/09 @ 15:40:18 | Last updated: 10/08/09 @ 15:40:21

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

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Paul Fisher

Extract Scientific Terms (v1)

Created: 10/08/09 @ 13:31:07 | Last updated: 10/08/09 @ 13:32:22

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow takes in a document containg text and removes any non-ascii characters. The cleaned text is then sent to a service in Dresden, to extract all scientific terms. These terms represent a concept profile for the input concpet. Any null values are also removed.

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Paul Fisher

Arabidopsis thaliana Microarray Analysis (v1)

Created: 08/07/09 @ 16:28:35 | Last updated: 08/07/09 @ 16:28:38

Credits: Paul Fisher

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow searches for genes which are found to be differentially expressed in a microarray study using Arabidopsis thaliana. The workflow requires an input of a list of differentially expressed AffyMetrix Probeset identifiers. Data is then extracted from BioMart to annotate each of the genes. The 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 database.

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Paul Fisher

NCBI Gi to Kegg Pathways (v1)

Created: 08/06/09 @ 18:39:38 | Last updated: 14/12/09 @ 11:51:22

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow converts a list of NCBI gi numbers and  converts them to a list of KEGG genes. Those KEGG gene ids are subsequently turned into KEGG pathway identifiers and descriptions. It also removes any null values from a list of strings. Example input for this workflow is as follows (new line separated): gi:215422388 gi:120407068

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Paul Fisher

Pathways and Gene annotations for Arabidopsis affy data (v2)

Created: 05/03/09 @ 15:15:59 | Last updated: 03/12/09 @ 16:59:13

Credits: Paul Fisher Peter Li

Attributions: Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow searches for genes obtained from affy_ath1 affymetrix probeset identifiers. 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 database.

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Paul Fisher

Get Graphs of Name (v1)

Created: 27/02/09 @ 16:42:36 | Last updated: 27/02/09 @ 16:42:37

Credits: Paul Fisher

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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Paul Fisher

Get Evidence Types (v1)

Created: 27/02/09 @ 16:40:23 | Last updated: 27/02/09 @ 16:40:24

Credits: Paul Fisher

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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Paul Fisher

Get Concepts (v1)

Created: 27/02/09 @ 16:33:40

Credits: Paul Fisher

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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Paul Fisher

Retrieve Protein Sequence (v1)

Created: 30/07/08 @ 16:36:56 | Last updated: 03/12/09 @ 16:54:03

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1

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Paul Fisher

Human Microarray Analysis (v1)

Created: 08/02/08 @ 14:30:18 | Last updated: 03/12/09 @ 16:50:30

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow takes in probesets from and AffyMetrix  Affy HG U133A micorarray experiment and returns: genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data.   Example input for this workflow is: 212283_at 221634_at 220399_at

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Paul Fisher

Add Mesh String to Biological Process (v2)

Created: 03/10/07 @ 18:36:28 | Last updated: 03/12/09 @ 16:42:49

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow is designed to add the following MeSH term to the end of a KEGG pathway name: AND "Metabolic Networks and Pathways" [MeSH Terms]   Example input for this service is as follows:   VEGF signaling pathway Hematopoietic cell lineage GnRH signaling pathway Type II diabetes mellitus

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Paul Fisher

Parse UniProt text file (v2)

Created: 03/10/07 @ 18:36:08 | Last updated: 03/12/09 @ 16:36:55

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow performs a search through the SRS linking system to find the text files for a particular UniProt identifier. This UniProt text file is then parsed to extract a small list to summarise the file, primarily consisting of external identifiers. Example input for this workflow is: O35613

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Paul Fisher

BLAST using DDBJ service (v2)

Created: 03/10/07 @ 18:36:06 | Last updated: 03/12/09 @ 16:31:21

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Perform a sequence similarity search using the BLAST algorithm through the DDBJ web service.   Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNIL SRVLARSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLT NTENTASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEAR LKRKLIRLFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDY GDVLRAVEKAATRHSLGLP...

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Paul Fisher

BLASTP with simplified results returned (v2)

Created: 03/10/07 @ 18:36:06 | Last updated: 03/12/09 @ 16:28:51

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output.   Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSV...

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Paul Fisher

Remove null values (v2)

Created: 03/10/07 @ 18:36:05 | Last updated: 13/11/07 @ 16:20:42

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow removes any null values from a list of strings

Rating: 4.0 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 46 times | Downloaded: 35 times

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Paul Fisher

Remove duplicate strings (v2)

Created: 03/10/07 @ 18:36:03 | Last updated: 13/11/07 @ 16:25:42

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow takes in two list of strings and then concatenates them together. Any duplicates that are present are then removed, and the resulting file is returned back to the user.

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Paul Fisher

Entrez Gene to KEGG Pathway (v4)

Created: 03/10/07 @ 18:36:00 | Last updated: 04/12/09 @ 16:04:39

Credits: Paul Fisher

License: Creative Commons Attribution 3.0 Unported License

This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Rating: 4.7 / 5 (3 ratings) | Versions: 4 | Reviews: 0 | Comments: 2 | Citations: 0

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Paul Fisher

KEGG pathways common to both QTL and microarray based investigations (v3)

Created: 03/10/07 @ 18:35:58 | Last updated: 03/12/09 @ 15:28:50

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype.   Example input for this workflow is given below (as newline separated values). qt...

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Paul Fisher

HUMAN Microarray CEL file to candidate pathways (v4)

Created: 03/10/07 @ 18:35:55 | Last updated: 26/11/09 @ 17:34:25

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also returned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

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