User: Paul Fisher

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Nested UnigeneID_to_KEGG in Import and Convert

Created: 2013-08-29 14:09:53

Credits: Katy Wolstencroft Alan Williams Paul Fisher

Attributions: UnigeneID to KEGG Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Trident (Package)

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Bonn Taverna Presentation - Case Studies

Created: 2012-09-04 10:17:41 | Last updated: 2012-09-04 13:45:55

Credits: Helen Hulme Katy Wolstencroft Paul Fisher Shoaib Sufi Mcornell Robert Haines

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint 2007 presentation

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Ondex Workflows

Created: 2011-09-01 17:17:57 | Last updated: 2011-09-01 17:18:05

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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Taverna XPath practical slides .

Created: 2011-03-30 09:17:52 | Last updated: 2011-03-30 09:17:55

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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Taverna Iteration training slides

Created: 2011-03-28 11:44:06 | Last updated: 2011-03-28 11:44:08

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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Bonn Taverna Training agenda March/April 2011

Created: 2011-03-28 11:31:38 | Last updated: 2011-03-28 11:31:39

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word document

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Taverna Introduction

Created: 2011-03-28 11:29:08 | Last updated: 2011-03-28 11:29:10

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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Example XML

Created: 2011-03-23 17:25:09 | Last updated: 2011-03-23 17:25:11

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

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Schema for flat file cross-referencing

Created: 2011-03-23 17:00:58 | Last updated: 2011-03-23 17:01:01

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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XML Result from Pubmed Search

Created: 2011-03-23 11:49:33 | Last updated: 2011-03-23 11:49:36

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

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Bilateral Perisylvian Polymicrogyria - Single Nucleo...

Created: 2011-03-17 11:21:06 | Last updated: 2011-03-17 11:21:12

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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Bilateral Perisylvian Polymicrogyria

Created: 2011-03-17 10:56:15 | Last updated: 2011-03-17 11:16:53

Credits: Paul Fisher

Attributions: Pathway and Gene to Pubmed Pathways and Gene annotations forQTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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Trichuriasis Induced Colitis

Created: 2011-02-16 15:16:17 | Last updated: 2011-02-16 15:16:24

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for RefSeq ids KEGG pathways common to both QTL and microarray based investigations Pathways and Gene annotations for QTL region Pathway and Gene to Pubmed

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Bilateral Perisylvian Polymicrogyria (Epilepsy)

Created: 2010-12-07 16:34:31 | Last updated: 2010-12-07 16:34:37

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/x-zip-compressed

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KEGG Compounds to Inchi strings

Created: 2009-11-02 16:15:39 | Last updated: 2009-11-02 16:15:57

Credits: Paul Fisher Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Chemistry Plan

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Pathway Term Enrichment Scores

Created: 2009-08-11 14:23:49

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Pathway Abstracts for Day7 Microarray Tir1 QTL

Created: 2009-08-11 14:08:41 | Last updated: 2009-08-11 14:15:58

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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PubMed Term Counts

Created: 2009-08-11 13:59:35

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Phenotype Term Counts (in Phenotype Corpus)

Created: 2009-08-11 13:34:42 | Last updated: 2009-08-11 13:58:28

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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PubMed Abstract Number

Created: 2009-08-11 13:54:45

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Phenotype Concept Profile - Terms

Created: 2009-08-11 13:05:07 | Last updated: 2009-08-11 13:06:51

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Phenotype Abstracts for Trypanosomiasis Resistance

Created: 2009-08-11 12:45:24

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Gene Cosine Scores

Created: 2009-08-10 16:00:45

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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Pathway Cosine Scores from Day7 and Tir1 QTL

Created: 2009-08-10 15:55:24

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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Authors table

Created: 2009-04-08 13:36:10 | Last updated: 2009-08-10 12:37:37

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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Re-sequenced Daxx gene info

Created: 2009-04-08 17:53:46 | Last updated: 2009-08-10 12:30:59

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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Ensembl database release

Created: 2009-04-08 18:00:35 | Last updated: 2009-08-10 12:12:09

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Kegg gene descriptions

Created: 2009-04-08 18:06:23 | Last updated: 2009-08-10 12:10:07

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Kegg-Uniprot-Entrez cross-references

Created: 2009-04-08 19:23:53 | Last updated: 2009-08-10 12:08:00

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Kegg Pathway release

Created: 2009-04-08 19:25:05 | Last updated: 2009-08-10 12:06:18

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Kegg pathways and genes

Created: 2009-04-08 19:26:26 | Last updated: 2009-08-10 11:41:55

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Kegg pathway descriptions

Created: 2009-04-08 19:27:55 | Last updated: 2009-08-10 11:29:34

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Ensembl gene report

Created: 2009-04-08 19:30:15 | Last updated: 2009-08-10 11:05:59

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Kegg pathway identifiers

Created: 2009-04-08 19:28:52 | Last updated: 2009-08-10 11:03:00

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Tir1 QTL - microarray day 7 intersecting pathways

Created: 2009-04-08 17:57:57

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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Tir1 QTL - Day 3 Microarray intersecting pathways

Created: 2009-04-08 17:56:10

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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Table of SNP sequenceing results

Created: 2009-04-08 13:29:32

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word document

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Candidate Gene protocol

Created: 2009-04-08 13:27:20

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word document

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A Systematic Strategy for Large-Scale Analysis of Ge...

Created: 2009-04-08 13:23:03

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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An Introduction to Taverna and myExperiment - Backgr...

Created: 2008-08-04 17:49:10

Credits: Paul Fisher Franck Tanoh Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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A Taverna Users Guide

Created: 2008-08-04 17:40:21

Credits: Paul Fisher Katy Wolstencroft Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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Phenotype to pubmed (1)

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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

Created: 2015-09-01

Credits: Heiko Schoof Paul Fisher

Attributions: Phenotype to pubmed

Pathway to Pubmed (1)

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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.

Created: 2013-09-03

Credits: Alan Williams Paul Fisher

Attributions: Pathway to Pubmed

UnigeneID to KEGG Pathways (1)

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This workflow accepts a list of Unigene gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2013-09-03

Credits: Katy Wolstencroft Alan Williams Paul Fisher

Attributions: NCBI Gi to Kegg Pathways

UnigeneID to KEGG Pathways (3)

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This workflow accepts a list of Unigene gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2012-01-16 | Last updated: 2012-12-17

Credits: Katy Wolstencroft Paul Fisher

Attributions: NCBI Gi to Kegg Pathways

Pathways and Gene annotations for QTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in rice, Oryza sativa. 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 UniGene 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 d...

Created: 2011-05-27 | Last updated: 2011-05-27

Credits: Paul Fisher

Remove_Duplicates (1)

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This workflow removes any duplicates from a list of inputs, merges the unique values, and then removes any null values.

Created: 2011-04-21 | Last updated: 2011-04-21

Credits: Paul Fisher

XPath Pubmed Ids (1)

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml

Created: 2011-03-23 | Last updated: 2011-03-23

Credits: Paul Fisher

gene subset extract (1)

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This workflow functions for matching a set of genes as a part of whole gene data set and aim to extract the subset as a separate list.

Created: 2011-03-29 | Last updated: 2011-03-29

Credits: Naser Paul Fisher

Pathways and Gene annotations forQTL region (1)

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This workflow searches for genes found from a set of differentially expressed probestes, in Human, Homo sapiens. The workflow requires an input human affymetrix probeset identifiers. 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 database.

Created: 2011-03-24 | Last updated: 2011-03-24

Credits: Paul Fisher

XPath Pubmed Ids (2)

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml. The xml is then parsed to retrieve a list of PubMed ids

Created: 2011-03-23 | Last updated: 2011-03-30

Credits: Paul Fisher

Attributions: XPath Pubmed Ids

Pathways and Gene annotations forQTL region (2)

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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 ...

Created: 2011-03-17 | Last updated: 2011-08-30

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

Pathway and Gene to Pubmed (2)

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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...

Created: 2011-02-10 | Last updated: 2011-02-18

Credits: Paul Fisher

Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms Gene to Pubmed

Gene to Pubmed (4)

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This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2011-02-08 | Last updated: 2011-02-10

Credits: Paul Fisher

Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms

Read files from Directory (1)

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This workflow reads files from a given directory, based on a known file extension (e.g. .txt), and then outputs the contents of each file in a single value/single list.

Created: 2011-02-03 | Last updated: 2011-02-03

Credits: Paul Fisher

Remove Non-ASCII (1)

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THis workflow removes any non-ascii characters from a segment of text. Any characters that are found are removed. Letters either side f the non-ASCII are concatenated - this may cause the loss of word meaning

Created: 2011-02-03 | Last updated: 2011-02-03

Credits: Paul Fisher

PubMed Search (1)

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

Created: 2011-02-03 | Last updated: 2011-02-03

Credits: Paul Fisher

Rank Phenotype Terms (1)

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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 ...

Created: 2011-02-01 | Last updated: 2011-02-01

Credits: Paul Fisher

Attributions: Cosine vector space Rank Phenotype Terms

Pathways and Gene annotations forQTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Cow, Bos taurus. 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 data...

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

Credits: Paul Fisher

Pathway to Pubmed (1)

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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.

Created: 2008-09-02 | Last updated: 2008-09-08

Credits: Stian Soiland-Reyes Paul Fisher

Attributions: ProteinSynonymsToQuery

Extract Scientific Terms (2)

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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.

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Pathway to Pubmed (2)

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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.

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Gene to Pubmed (3)

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This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2010-07-05 | Last updated: 2011-01-26

Credits: Paul Fisher

Rank Phenotype Terms (2)

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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 ...

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Attributions: Rank Phenotype Terms

Cosine vector space (2)

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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

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Attributions: Cosine vector space

KEGG pathways common to both QTL and micro... (1)

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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

Created: 2010-11-15 | Last updated: 2010-11-15

Credits: Paul Fisher

Pathways and Gene annotations for RefSeq ids (1)

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This workflow searches for genes which were found to be differentially expressed from a microarray study in the mouse, Mus musculus. The workflow requires an input of gene ref_seq identifiers. Data is then extracted from BioMart to annotate each of the genes found for each ref_seq id. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to search for pathways in the KEGG pathway database.

Created: 2010-11-15 | Last updated: 2010-11-15

Credits: Paul Fisher

Pathways and Gene annotations for QTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. 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 path...

Created: 2010-11-15 | Last updated: 2010-11-16

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

omim and pathways (2)

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This workflow searches OMIM for entries associated with a particular disease in OMIM, returns the IDs and maps them to Kegg Gene IDs. For each gene, it then gets the description and any corresponding pathways those genes are involved with

Created: 2009-03-03 | Last updated: 2009-11-02

Credits: Katy Wolstencroft Paul Fisher

Attributions: Get Kegg Gene information

Phenotype to pubmed (3)

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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

Created: 2010-07-05 | Last updated: 2011-01-11

Credits: Paul Fisher

Perfrom a text based search through PubMed (1)

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This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format

Created: 2010-07-05 | Last updated: 2010-07-05

Credits: Paul Fisher

Get KEGG gene descriptions and pathways (1)

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This workflow takes a list of KEGG gene identifiers and supplies descriptions associated to said genes + pathways including all genes and the descriptions associated to said pathways. The list_to_string local beanshell scripts merely transform a given list into a string of unique not-null elements separated by new lines (for batch btit use). Note that the input is a real taverna list : multiple values must be declared as multiple values instead of a single string value with distinct identif...

Created: 2010-04-30 | Last updated: 2010-04-30

Credits: Nadia Cerezo Paul Fisher

Attributions: Get Kegg Gene information

Entrez Gene to KEGG Pathway (2)

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.

Created: 2010-04-15 | Last updated: 2010-04-15

Credits: Paul Fisher

microRNA to KEGG Pathways and Abstracts (1)

Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs

Created: 2010-03-17

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

[untitled] (1)

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No description

Created: 2010-03-16

Credits: Paul Fisher

Get Kegg Pathway information (1)

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This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: path:mmu04010 path:mmu05014

Created: 2010-03-10 | Last updated: 2010-03-10

Credits: Paul Fisher

Get Gene Ids for Human (1)

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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

Created: 2010-02-04 | Last updated: 2010-02-04

Credits: Paul Fisher

Pathways and Gene annotations for QTL region (2)

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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 ...

Created: 2009-11-20 | Last updated: 2009-11-20

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

Spreadsheet Importer (1)

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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.

Created: 2009-08-24

Credits: Paul Fisher

Unconnected Filter (1)

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: Paul Fisher

Tranitive Filter (1)

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: Paul Fisher

SubGraph Filter (2)

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: Paul Fisher

Significance Filter (1)

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: Paul Fisher

Shortest Path (1)

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: Paul Fisher

Relation Type Filter (1)

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: Paul Fisher

Relation Neighbours Filter (1)

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: Paul Fisher

Pfam Based Ortholog Filter (1)

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: Paul Fisher

Optimal Paths Filter (1)

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: Paul Fisher

One Pair Shortest Path Filter (1)

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: Paul Fisher

Isolate Clusters Filter (1)

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: Paul Fisher

Graph Cloner (1)

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

Created: 2009-08-19

Credits: Paul Fisher

Genomic Filter (1)

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: Paul Fisher

GDS Value Filter (1)

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: Paul Fisher

Evidence Type Filter (1)

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: Paul Fisher

CV Filter (1)

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: Paul Fisher

Context Filter (1)

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: Paul Fisher

Context Consensus Filter (1)

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: Paul Fisher

Concept Class Neighbours Filter (1)

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: Paul Fisher

Concept Class Filter (1)

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: Paul Fisher

Clean UniProt Filter (1)

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: Paul Fisher

Clean GO Filter (1)

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: Paul Fisher

All Pairs Filter (1)

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: Paul Fisher

Tab Parser (1)

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...

Created: 2009-08-19

Credits: Paul Fisher

Table Parser (1)

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

Created: 2009-08-19

Credits: Paul Fisher

KEGG Pasrer (1)

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)

Created: 2009-08-19

Credits: Paul Fisher

Rank Phenotype Terms (1)

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 ...

Created: 2009-08-10

Credits: Paul Fisher

Extract Scientific Terms (1)

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.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: Paul Fisher

Cosine vector space (1)

This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. The result is a cosine vector score between 0 and 1, showing the significance of any links between one concept (e.g. pathway) to another (e.g. phenotype). A score of 0 means there is no or an undetermined correlation between the two concepts. A score approaching 1 represents positive correlation.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: Paul Fisher

NCBI Gi to Kegg Pathways (1)

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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

Created: 2009-06-08 | Last updated: 2009-12-14

Credits: Paul Fisher

inchi to Chebi (1)

This workflow converts an inchi string to a chebi id.

Created: 2009-05-22

Credits: Paul Fisher

Pathways and Gene annotations for Arabidop... (2)

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.

Created: 2009-03-06 | Last updated: 2009-12-03

Credits: Paul Fisher Peter Li

Attributions: Pathways and Gene annotations for QTL region

unnested_qtl_pathway_4.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

unnested_qtl_pathway_3.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

unnested_qtl_pathway_2.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

blast_simplifier.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Probeset_id_2_Swissport_id.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

interpro_url.xml (1)

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An example of how a more complex workflow can federate multiple resources to perform data mining. In this case a single input data item in the form of a probe set identifier is cross referenced to data sets in multiple locations to answer a kind of 'show me everything about this data' question.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Gi_to_pathway.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

geneId_to_pathway.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

DDBJ_BLAST.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

blast.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

blast_to_fasta.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

protein2dna.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

linking3.xml (1)

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This workflow links between a specified EMBL accesion number to corresponding identifiers in the MEDLINE database.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

genomic_sequence.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

linking1.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

interpro_scan_2.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

interpro_scan_3.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

metabolic.xml (1)

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An example of how a more complex workflow can federate multiple resources to perform data mining. In this case a single input data item in the form of a probe set identifier is cross referenced to data sets in multiple locations to answer a kind of 'show me everything about this data' question.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

example.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

affy_ids.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_ontology_diagram.xml (1)

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This workflow builds up a subgraph of the Gene Ontology (http://www.geneontology.org) to show the context for a supplied term or terms. It shows this context by colouring all ancestors of the term, all children and all siblings. By default, ancestors of the supplied term or terms are coloured orange, siblings purple and direct children teal. Other terms appear in the default wheat colour.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

getgenesbyspecies.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

maxdBrowse_strings.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

stringList.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

BlastComparer.xml (1)

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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.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

blast_GO.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_by_species.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

protein_protein_interactions.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

database_and_genes.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

probeset_in_qtl.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

genes_from_probesets.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

bind-text.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

bind-idsearch.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

SUB_genes_info_names.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_info_to_gene_name.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

string_complete.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Ensembl_genes_to_swiss_id.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

ACC_to_GI.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

metabolic_pathway.xml (1)

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A list of Kegg entires are supplied to the Kegg database which then retrieves the associated metabolic pathways for each entry supplied. e.g. Ids takes in a value of 351, whilst abbr takes in a value of hsa. Thus hsa:351 corresponds to neurodegenerative disorders and alzheimers disease pathways. [fisherp@cs.man.ac.uk]

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

parse_gene_name.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

expression_values.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

swiss_and_name.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

swiss_and_name_seq.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

parse_sequence.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

interpro_scan.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

uniprot_search.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

qtl_analysis.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

complete_test.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

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remove_duplicates.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

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remove_duplicates_full.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

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maxdBrowse.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

complete_deleted.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

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complete.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

parse_uniprot.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Ensembl_id_2_Swissport_id.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

lister.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

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linking.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

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remove_nulls.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

complete_2.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher