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User: Paul Fisher
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Name: Paul Fisher Joined: Thursday 26 July 2007 @ 16:46:52 (GMT) Last seen: Monday 30 January 2012 @ 09:16:48 (GMT) Email (public): Not specified Website: http://twitter.com/#!/paul_r_fisher Location: Manchester, United Kingdom |
Paul Fisher has been credited 267 times Paul Fisher has an average rating of: 4.6 / 5 (25 ratings in total) for their items |
I am currently employed by Astrazeneca. As a consequence, the workflows developed previously to this employment (before 5th September 2011) may no longer be supported.
Other contact details:
Not specifiedInterests:
Workflows
QTL analysis
Microarrays
Biological pathway analysis
In silico automation
Epilepsy
Alzheimers
Genome Sequencing
Disease gene identification
Field/Industry: Bioinformatics
Occupation/Role(s): Bioinformatics Scientist - Oncology
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Created: 01/09/11 @ 17:17:57 | Last updated: 01/09/11 @ 17:18:05
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This zip file contains a large number of Taverna 2 workflows that utilise the Ondex Web Service, for manipulating Ondex graphs.
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Created: 30/03/11 @ 09:17:52 | Last updated: 30/03/11 @ 09:17:55
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Taverna training material for using and configuring XPath queries using native XPath Java methods, and XPath Service templates.
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Created: 28/03/11 @ 11:44:06 | Last updated: 28/03/11 @ 11:44:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Training slides to outline how to use iterations and iteration strategies in Taverna
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Created: 28/03/11 @ 11:31:38 | Last updated: 28/03/11 @ 11:31:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Agenda of Taverna training
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Created: 28/03/11 @ 11:29:08 | Last updated: 28/03/11 @ 11:29:10
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This powerpoint presentation contains a set of starting exercises for begining your Taverna training.
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Created: 23/03/11 @ 17:25:09 | Last updated: 23/03/11 @ 17:25:11
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains some example XML to be used for teaching material and XPath queries
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Created: 23/03/11 @ 17:00:58 | Last updated: 23/03/11 @ 17:01:01
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This powerpoint slide shows the how data in each flat file can be cross-reference to other flat file data items.
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Created: 23/03/11 @ 11:49:33 | Last updated: 23/03/11 @ 11:49:36
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This xml file conatins results from a pubmed search for 'Blood Clotting'.
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Created: 17/03/11 @ 11:21:06 | Last updated: 17/03/11 @ 11:21:12
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of all the SNP found with the Villard et al., (2002) QTL for Bilateral Perisylvian Polymicrogyria.
Please download this data as you wish, and use in whatever study you like. The data is open access, and freely available for all to use to help undertand this condition.
Genes related to these SNP can be found in the file http://www.myexperiment.org/files/466.
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Created: 17/03/11 @ 10:56:15 | Last updated: 17/03/11 @ 11:16:53
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This zip file contains the results of running a QTL workflow for Bilateral Perisylvian Polymicrogyria in human (homo sapiens). Provided are a list of candidate QTL genes (QTg) and their corresponding KEGG pathways. Each gene and pathway have been subsequently run through a series of text mining workflows to determine the significance each may play in relation to Bilateral Perisylvian Polymicrogyria.
If you want to help me identify candidate genes for this disorder, please get i...
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Created: 16/02/11 @ 15:16:17 | Last updated: 16/02/11 @ 15:16:24
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This zip file contains the results of workflow runs for: identifying genes in each of the 7 QTL regions for Trichuris muris infection; identifying genes differentially expressed in mice challenged with Trichuris muris; and Text mining results (including cosine vector scores and Term Enrichment values).
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Created: 07/12/10 @ 16:34:31 | Last updated: 07/12/10 @ 16:34:37
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This zip file contains the results of running a QTL workflow for Bilateral Perisylvian Polymicrogyria in human (homo sapiens). Provided are a list of candidate QTL genes (QTg) and their corresponding KEGG pathways. Each gene and pathway have been subsequently run through a series of text mining workflows to determine the significance of each may play in relation to Bilateral Perisylvian Polymicrogyria AND/OR Epilepsy. Further to this, I have also collected the SNPs (single nucleotide...
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Created: 02/11/09 @ 16:15:39 | Last updated: 02/11/09 @ 16:15:57
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of KEGG compounds which are reffered to by their Inchi strings.
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Created: 11/08/09 @ 14:23:49
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of each pathway identified from day 7 post infection and linked to the Tir1 QTL. With each pathway is a list of terms that are common to both pathway and phenotype corpora. These terms were ranked accoring to their enrichement scores. The higher the score, the more significant the term is in relation to correlating the pathway with the African trypanosomiasis resistance phenotype.
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Created: 11/08/09 @ 14:08:41 | Last updated: 11/08/09 @ 14:15:58
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains all the abstracts for pathways found to be differentially expressed at day 7 post infection and intersect the Tir1 QTL region, from the African Trypanosomiasis project.
Each pathway is listed as ">> [Pathway Name]", together with a PubMed identifier, date, and abstract for each article. Each pathway has been restricted to 500 abstracts, and is given in the date range 31/12/2007 to 01/01/2009. Note, some pathways do not have any abstracts available due to th...
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Created: 11/08/09 @ 13:59:35
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a count of each phenotype term extracted from corpus of phenotype abstracts. Each value represents the number of articles in MEDLINE the term appears. The use of this file is to calculate a cosine vector score for correlating a given concept (e.g. pathway or gene) with a phenotype.
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Created: 11/08/09 @ 13:34:42 | Last updated: 11/08/09 @ 13:58:28
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a count of each phenotype term extracted from corpus of phenotype abstracts. Each value represents the number of articles in the phenotype corpus the term appears. The use of this file is to calculate a cosine vector score for correlating a given concept (e.g. pathway or gene) with a phenotype.
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Created: 11/08/09 @ 13:54:45
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains the number of articles available in MEDLINE, through PubMed, at the time of performing these data analyses. The date of identifying these publications was 25/02/2009.
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Created: 11/08/09 @ 13:05:07 | Last updated: 11/08/09 @ 13:06:51
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of all terms extracted from the phenotype corpus, relating to African trypanosomiasis resistance in the mouse model.
These terms were extracted using the following service: http://gopubmed4.biotec.tu-dresden.de/GoPubMedTermGenerationService/services/GoPubMedTermGeneration?wsdl
These terms represent the concept profile for the phenotype.
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Created: 11/08/09 @ 12:45:24
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of published abstracts from MEDLINE, that are related to the African Trypanosomiasis resistance phentoype in the mouse. The term used in the PubMed search was: trypanosom* AND (tolerance OR resistance) .
The workflow limited the date of the search using PubMed between 31/12/2005 to 01/01/2009, and was restricted to 500 abstracts.
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Created: 10/08/09 @ 16:00:45
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This excel file contains a list of genes linked to the resistance to African trypanosomiasis in the mouse. Genes from the Tir1 QTL were used in a search through PubMed. The results were then correlated to the trypanosomiasis resistance phenotype. The higher the score (and ranking) the more related to the phenotype the gene is likely to be. This is based on the co-occurrence of terms within the gene and phentoype corpora.
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Created: 10/08/09 @ 15:55:24
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This excel file contains a list of all pathways found to be differentially expressed at day 7 post infection in the trypanosomiasis resistance phenotype, which contain genes in the Tir1 QTL.
The pathways in this file have been ranked according to the scores obtained after calculating a cosine vector value against the trypanosomiasis resistance phenotype. The higher the score, the more closely linked to a phentype a given pathway is.
This allows each pathway to be ranked giving biologists a ...
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Created: 08/04/09 @ 13:36:10 | Last updated: 10/08/09 @ 12:37:37
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This table contains a list of articles used to construct a list of issues with regards to the lack of systematic and explicit data analyses conducted in bioinformatcis. Each author list is linked directly to their publication within PubMed.
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Created: 08/04/09 @ 17:53:46 | Last updated: 10/08/09 @ 12:30:59
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This spreadsheet contains information about the re-sequencing of the daxx gene, identified as a candidate QTg for the African Trypanosomiasis resiatance phenotype. This file is related to the paper: http://www.ncbi.nlm.nih.gov/pubmed/17709344
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Created: 08/04/09 @ 18:00:35 | Last updated: 10/08/09 @ 12:12:09
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
The release of the Ensembl database used to identify genes in Tir1 QTL region.
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Created: 08/04/09 @ 18:06:23 | Last updated: 10/08/09 @ 12:10:07
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of KEGG gene descriptions, for each KEGG gene identified within the Tir1 QTL region.
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Created: 08/04/09 @ 19:23:53 | Last updated: 10/08/09 @ 12:08:00
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of KEGG gene identifiers, cross-referenced to UniProt and Entrez identifiers. The UniProt and Entrez ids were obtained from BioMart for genes located in the Tir1 QTL region.
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Created: 08/04/09 @ 19:25:05 | Last updated: 10/08/09 @ 12:06:18
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains the version of the KEGG pathway database used in the analysis of the Tir1 QTL region
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Created: 08/04/09 @ 19:26:26 | Last updated: 10/08/09 @ 11:41:55
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of all genes found within the Tir1 QTL region. These are represented as KEGG gene identifiers. Each gene is listed in tab deliminated format along with all KEGG pathway ids in which the gene is involved. These are given as KEGG pathway identifiers. Each gene may be included in zero or more pathways, with multiple instances of the same pathway being included in the file (due to multiple genes included in a single pathway).
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Created: 08/04/09 @ 19:27:55 | Last updated: 10/08/09 @ 11:29:34
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of KEGG pathway descriptions, identified from genes found within the Tir1 QTL region (for African Trypanosomiasis). Each pathway may contain multiple genes from within the QTL region.
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Created: 08/04/09 @ 19:30:15 | Last updated: 10/08/09 @ 11:05:59
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains all genes identified in the Tir1 QTL region.
Each gene is (if available) associated with an Entrez, UniProt, External Gene Id, Affymetrix probeset identifers (mouse_430_A chip), and Ensembl identifers for genes and their transcripts.
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Created: 08/04/09 @ 19:28:52 | Last updated: 10/08/09 @ 11:03:00
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains a list of KEGG pathway identifiers, derived from a list of Ensembl genes found to be located with a given QTL/chromosomal region in the mouse. These genes are located in the Tir1 QTL.
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Created: 08/04/09 @ 17:57:57
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 7 differentially expressed genes
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Created: 08/04/09 @ 17:56:10
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 3 differentially expressed genes
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Created: 08/04/09 @ 13:29:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This file contains the results of re-sequencing the Daxx gene
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Created: 08/04/09 @ 13:27:20
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This protocol provides details on how to identify candidate genes from the returned workflow results.
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Created: 08/04/09 @ 13:23:03
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This PDF is my personal copy of the NAR publication.
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Created: 04/08/08 @ 17:49:10
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 04/08/08 @ 17:40:21
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Created: 16/01/12 @ 10:54:39 | Last updated: 16/01/12 @ 11:14:44
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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, according to the KEGG database.
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Created: 12/01/12 @ 09:38:10 | Last updated: 12/01/12 @ 15:04:00
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database.
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Created: 27/05/11 @ 11:06:11 | Last updated: 27/05/11 @ 11:06:52
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in 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...
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Created: 21/04/11 @ 12:36:37 | Last updated: 21/04/11 @ 13:59:52
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow removes any duplicates from a list of inputs, merges the unique values, and then removes any null values.
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Created: 23/03/11 @ 11:24:23 | Last updated: 23/03/11 @ 11:24:58
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml
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Created: 29/03/11 @ 14:55:31 | Last updated: 29/03/11 @ 15:00:22
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 24/03/11 @ 15:14:48 | Last updated: 24/03/11 @ 15:37:48
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 23/03/11 @ 16:19:10 | Last updated: 30/03/11 @ 09:28:13
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
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Created: 17/03/11 @ 11:10:28 | Last updated: 30/08/11 @ 10:40:14
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Human, Homo sapiens. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway ...
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Created: 10/02/11 @ 16:10:52 | Last updated: 18/02/11 @ 13:47:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype). The workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMe...
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Created: 08/02/11 @ 13:04:06 | Last updated: 10/02/11 @ 16:01:41
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Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 03/02/11 @ 16:05:02 | Last updated: 03/02/11 @ 16:05:52
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 03/02/11 @ 15:49:07 | Last updated: 03/02/11 @ 15:59:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
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Created: 03/02/11 @ 15:24:57 | Last updated: 03/02/11 @ 15:25:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
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Created: 01/02/11 @ 11:22:14 | Last updated: 01/02/11 @ 11:24:42
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Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
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 ...
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Created: 21/01/11 @ 16:56:47 | Last updated: 21/01/11 @ 16:58:50
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in 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...
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Created: 02/09/08 @ 20:53:53 | Last updated: 08/09/08 @ 15:35:53
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Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 08/12/10 @ 11:50:01 | Last updated: 11/01/11 @ 11:58:09
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 08/12/10 @ 11:47:10 | Last updated: 11/01/11 @ 12:00:16
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 05/07/10 @ 13:14:36 | Last updated: 26/01/11 @ 16:57:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 08/12/10 @ 11:38:37 | Last updated: 11/01/11 @ 12:02:30
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Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
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 ...
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Created: 08/12/10 @ 11:35:18 | Last updated: 11/01/11 @ 12:05:41
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
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Created: 15/11/10 @ 12:30:21 | Last updated: 15/11/10 @ 12:30:59
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License: Creative Commons Attribution-Share Alike 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
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Created: 15/11/10 @ 12:25:01 | Last updated: 15/11/10 @ 12:28:12
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 15/11/10 @ 12:08:18 | Last updated: 16/11/10 @ 16:07:49
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Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the 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...
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Created: 03/03/09 @ 13:17:27 | Last updated: 02/11/09 @ 10:13:38
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Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
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Created: 05/07/10 @ 14:07:33 | Last updated: 11/01/11 @ 12:07:22
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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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Created: 05/07/10 @ 13:03:35 | Last updated: 05/07/10 @ 13:03:37
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
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Created: 30/04/10 @ 16:09:29 | Last updated: 30/04/10 @ 16:12:02
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Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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Created: 15/04/10 @ 12:22:12 | Last updated: 15/04/10 @ 12:22:13
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License: Creative Commons Attribution-Share Alike 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.
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Workflow
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Created: 17/03/10 @ 10:53:02
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
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Created: 16/03/10 @ 16:33:35
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 10/03/10 @ 17:15:47 | Last updated: 10/03/10 @ 17:18:47
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
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Created: 04/02/10 @ 12:47:16 | Last updated: 04/02/10 @ 12:48:11
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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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Created: 20/11/09 @ 14:04:37 | Last updated: 20/11/09 @ 14:04:39
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Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the Pig, Sus scrofa. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway ...
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Created: 24/08/09 @ 14:11:52
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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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Workflow
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Created: 19/08/09 @ 16:35:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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 ...
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Workflow
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Created: 19/08/09 @ 16:34:16
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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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Workflow
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Created: 19/08/09 @ 16:38:17
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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Workflow
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Created: 19/08/09 @ 16:31:24
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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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Workflow
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Created: 19/08/09 @ 16:30:35
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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 ...
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Workflow
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Created: 19/08/09 @ 16:29:10
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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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Workflow
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Original Uploader |
Created: 19/08/09 @ 16:28:09
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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Workflow
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Created: 19/08/09 @ 16:26:55
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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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Workflow
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Original Uploader |
Created: 19/08/09 @ 16:25:49
Credits:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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Workflow
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Original Uploader |
Created: 19/08/09 @ 16:24:41
Credits:
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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Workflow
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Created: 19/08/09 @ 16:23:45
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Workflow
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Created: 19/08/09 @ 16:22:13
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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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Workflow
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Created: 19/08/09 @ 16:19:01
Credits:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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Workflow
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Original Uploader |
Created: 19/08/09 @ 16:17:27
Credits:
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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Workflow
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Created: 19/08/09 @ 16:16:15
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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Created: 19/08/09 @ 16:15:20
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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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Created: 19/08/09 @ 16:14:13
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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Workflow
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Created: 19/08/09 @ 16:13:11
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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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Workflow
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Created: 19/08/09 @ 16:11:56
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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Workflow
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Created: 19/08/09 @ 16:10:36
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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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Workflow
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Created: 19/08/09 @ 16:08:48
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 19/08/09 @ 16:07:27
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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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Workflow
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Created: 19/08/09 @ 16:06:29
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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 ...
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Created: 19/08/09 @ 16:05:20
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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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Created: 19/08/09 @ 16:04:12
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow parsers a table (specified by the user), into an Ondex Graph on the web server.
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Created: 19/08/09 @ 16:03:07
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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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Created: 10/08/09 @ 15:43:48
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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 ...
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Created: 10/08/09 @ 13:31:07 | Last updated: 10/08/09 @ 13:32:21
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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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Created: 10/08/09 @ 13:19:36 | Last updated: 10/08/09 @ 13:24:28
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 08/06/09 @ 18:39:38 | Last updated: 14/12/09 @ 11:51:20
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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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Created: 22/05/09 @ 16:07:50
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow converts an inchi string to a chebi id.
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Created: 06/03/09 @ 17:18:13 | Last updated: 03/12/09 @ 16:59:11
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Attributions:
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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Created: 12/07/08 @ 09:11:08 | Last updated: 12/07/08 @ 20:21:50
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 09:14:19 | Last updated: 12/07/08 @ 20:21:22
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 09:15:13 | Last updated: 12/07/08 @ 20:20:52
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 09:17:40 | Last updated: 12/07/08 @ 20:20:20
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 12/07/08 @ 09:41:31 | Last updated: 12/07/08 @ 20:19:45
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 12/07/08 @ 10:03:35 | Last updated: 12/07/08 @ 20:19:04
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 12/07/08 @ 09:20:04 | Last updated: 12/07/08 @ 20:07:57
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 09:16:00 | Last updated: 12/07/08 @ 11:48:03
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 12/07/08 @ 10:59:33 | Last updated: 12/07/08 @ 11:00:38
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 12/07/08 @ 10:56:39 | Last updated: 12/07/08 @ 10:56:54
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 10:55:37 | Last updated: 12/07/08 @ 10:55:52
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 10:54:27 | Last updated: 12/07/08 @ 10:54:44
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 10:53:12 | Last updated: 12/07/08 @ 10:53:27
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow links between a specified EMBL accesion number to corresponding identifiers in the MEDLINE database.
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Created: 12/07/08 @ 10:52:14 | Last updated: 12/07/08 @ 10:52:34
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 12/07/08 @ 10:51:05 | Last updated: 12/07/08 @ 10:51:21
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 12/07/08 @ 10:48:08 | Last updated: 12/07/08 @ 10:48:29
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 12/07/08 @ 10:44:19 | Last updated: 12/07/08 @ 10:45:22
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 12/07/08 @ 10:42:42 | Last updated: 12/07/08 @ 10:42:56
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 12/07/08 @ 10:41:23 | Last updated: 12/07/08 @ 10:41:40
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 10:40:21 | Last updated: 12/07/08 @ 10:40:43
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 10:39:09 | Last updated: 12/07/08 @ 10:39:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 12/07/08 @ 10:37:57 | Last updated: 12/07/08 @ 10:38:21
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 12/07/08 @ 10:35:17 | Last updated: 12/07/08 @ 10:36:46
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 10:33:04 | Last updated: 12/07/08 @ 10:33:27
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 10:30:46 | Last updated: 12/07/08 @ 10:32:11
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License: Creative Commons Attribution-Share Alike 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.
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Created: 12/07/08 @ 10:29:41 | Last updated: 12/07/08 @ 10:29:58
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 10:28:19 | Last updated: 12/07/08 @ 10:28:52
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 10:27:05 | Last updated: 12/07/08 @ 10:27:18
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
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Created: 12/07/08 @ 10:26:05 | Last updated: 12/07/08 @ 10:26:25
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 29 times | Downloaded: 24 times Tags (1): |
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Created: 12/07/08 @ 10:25:08 | Last updated: 12/07/08 @ 10:25:22
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 24 times | Downloaded: 23 times Tags (1): |
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Created: 12/07/08 @ 10:24:11 | Last updated: 12/07/08 @ 10:24:26
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 31 times | Downloaded: 26 times Tags (1): |
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Created: 12/07/08 @ 10:23:10 | Last updated: 12/07/08 @ 10:23:23
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
No description
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 35 times | Downloaded: 24 times Tags (1): |
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Created: 12/07/08 @ 10:22:13 | Last updated: 12/07/08 @ 10:22:29
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Created: 12/07/08 @ 10:20:46 | Last updated: 12/07/08 @ 10:21:18
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Created: 12/07/08 @ 10:19:16 | Last updated: 12/07/08 @ 10:19:48
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Created: 12/07/08 @ 10:17:40 | Last updated: 12/07/08 @ 10:18:27
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Created: 12/07/08 @ 10:16:31 | Last updated: 12/07/08 @ 10:16:48
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Created: 12/07/08 @ 10:14:43 | Last updated: 12/07/08 @ 10:15:28
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Created: 12/07/08 @ 10:13:37 | Last updated: 12/07/08 @ 10:13:50
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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]
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Created: 12/07/08 @ 10:12:36 | Last updated: 12/07/08 @ 10:12:55
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Created: 12/07/08 @ 10:11:18 | Last updated: 12/07/08 @ 10:11:38
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Created: 12/07/08 @ 10:10:10 | Last updated: 12/07/08 @ 10:10:34
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Created: 12/07/08 @ 10:07:42 | Last updated: 12/07/08 @ 10:07:57
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Created: 12/07/08 @ 10:05:17 | Last updated: 12/07/08 @ 10:05:32
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Created: 12/07/08 @ 10:02:03 | Last updated: 12/07/08 @ 10:02:17
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Created: 12/07/08 @ 10:00:53 | Last updated: 12/07/08 @ 10:01:18
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Created: 12/07/08 @ 09:59:53 | Last updated: 12/07/08 @ 10:00:11
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Created: 12/07/08 @ 09:58:25 | Last updated: 12/07/08 @ 09:58:43
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Created: 12/07/08 @ 09:56:46 | Last updated: 12/07/08 @ 09:57:40
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Created: 12/07/08 @ 09:55:38 | Last updated: 12/07/08 @ 09:55:52
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Created: 12/07/08 @ 09:53:37 | Last updated: 12/07/08 @ 09:54:51
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Created: 12/07/08 @ 09:52:27 | Last updated: 12/07/08 @ 09:52:42
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Created: 12/07/08 @ 09:51:09 | Last updated: 12/07/08 @ 09:51:36
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Created: 12/07/08 @ 09:49:45 | Last updated: 12/07/08 @ 09:50:26
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Created: 12/07/08 @ 09:48:28 | Last updated: 12/07/08 @ 09:48:42
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Created: 12/07/08 @ 09:46:59 | Last updated: 12/07/08 @ 09:47:42
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Created: 12/07/08 @ 09:45:59 | Last updated: 12/07/08 @ 09:46:13
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Created: 12/07/08 @ 09:45:02 | Last updated: 12/07/08 @ 09:45:21
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Created: 12/07/08 @ 09:44:05 | Last updated: 12/07/08 @ 09:44:22
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Created: 12/07/08 @ 09:42:44 | Last updated: 12/07/08 @ 09:43:00
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Created: 12/07/08 @ 09:40:38 | Last updated: 12/07/08 @ 09:40:52
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Created: 12/07/08 @ 09:38:57 | Last updated: 12/07/08 @ 09:39:12
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Created: 12/07/08 @ 09:37:32 | Last updated: 12/07/08 @ 09:38:10
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Created: 12/07/08 @ 09:36:15 | Last updated: 12/07/08 @ 09:36:33
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Created: 12/07/08 @ 09:33:56 | Last updated: 12/07/08 @ 09:35:15
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Created: 12/07/08 @ 09:31:13 | Last updated: 12/07/08 @ 09:32:55
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Created: 12/07/08 @ 09:30:11 | Last updated: 12/07/08 @ 09:30:26
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Created: 12/07/08 @ 09:29:12 | Last updated: 12/07/08 @ 09:29:26
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Created: 12/07/08 @ 09:27:59 | Last updated: 12/07/08 @ 09:28:18
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Created: 12/07/08 @ 09:27:06 | Last updated: 12/07/08 @ 09:27:22
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Created: 12/07/08 @ 09:25:59 | Last updated: 12/07/08 @ 09:26:15
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Created: 12/07/08 @ 09:22:10 | Last updated: 12/07/08 @ 20:14:04
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Created: 12/07/08 @ 09:21:29 | Last updated: 12/07/08 @ 11:54:06
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Created: 12/07/08 @ 09:18:36 | Last updated: 12/07/08 @ 11:49:23
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Created: 12/07/08 @ 09:12:44 | Last updated: 12/07/08 @ 11:45:59
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Created: 12/07/08 @ 09:10:15 | Last updated: 12/07/08 @ 11:44:53
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Created: 12/07/08 @ 09:08:24 | Last updated: 12/07/08 @ 11:44:21
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Created: 08/05/08 @ 15:25:29 | Last updated: 12/05/08 @ 09:01:37
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Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes in a CDNA raw file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the R and bioconductor. Also retruned 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 changes in the microarray data. By identifying the candidate pathways, more detailed...
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Created: 08/07/09 @ 16:26:13 | Last updated: 14/12/09 @ 11:59:14
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License: Creative Commons Attribution-No Derivative Works 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Arabidopsis thaliana. 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 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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Created: 04/12/09 @ 16:04:38 | Last updated: 30/11/10 @ 12:18:53
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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.
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Created: 08/07/09 @ 16:28:34
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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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Created: 19/11/09 @ 18:18:52 | Last updated: 02/09/11 @ 11:44:57
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the 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...
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Created: 27/02/09 @ 16:45:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow gets all the realtions from a given Ondex graph
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Created: 27/02/09 @ 16:42:35
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow gets the Ondex graphs relating to a specified name
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Created: 05/11/09 @ 12:38:22
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Thiw workflow simply returns all the Ondex graphs that are present on a given server (where the web service is)
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Created: 27/02/09 @ 16:40:22
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow gets all the evidence types within a specified Ondex graph
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Created: 27/02/09 @ 16:38:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow lets users retrive all controlled vocabularies for a given Ondex graph
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Created: 27/02/09 @ 16:33:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow gets all the concepts in an Ondex graph, using a given graph id
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Created: 08/02/08 @ 14:30:17 | Last updated: 03/12/09 @ 16:50:29
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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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Created: 08/02/08 @ 14:17:23 | Last updated: 13/02/09 @ 11:29:52
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License: Creative Commons Attribution-Share Alike 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 retruned 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 ch...
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Created: 26/01/09 @ 18:06:12 | Last updated: 14/12/09 @ 12:05:21
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.
Example input for this workflow is given below (new line separated):
mmu:13163
hsa:1616
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