User: Paul Fisher

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

53 Friends

9 Groups (admin)

10 Groups (member)

145 Workflows

8 Packs

48 Files

2 Favourites

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 specified

Interests:

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

Organisation(s):

Not specified

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Contents (click to expand/contract)

Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v1) Created: 27/05/11 @ 11:06:11 \| Last updated: 27/05/11 @ 11:06:52 Credits: Paul Fisher 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 7 times Tags (15): chromosome \| entrez \| genes \| genotype \| kegg \| Kegg Pathways \| loci \| locus \| pathway \| pathways \| phenotype \| qtl \| quanitative \| rice \| trait	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Remove_Duplicates (v1) Created: 21/04/11 @ 12:36:37 \| Last updated: 21/04/11 @ 13:59:52 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 9 times Tags (4): duplicate \| remove \| remove duplicates \| remove nulls	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations forQTL region (v1) Created: 24/03/11 @ 15:14:48 \| Last updated: 24/03/11 @ 15:37:48 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 9 times Tags (12): data-driven \| entrez \| homo sapiens \| human \| kegg \| Kegg Pathways \| KeggID \| microarray \| pathway \| pathway-driven \| pathways \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	XPath Pubmed Ids (v2) Created: 23/03/11 @ 16:19:10 \| Last updated: 30/03/11 @ 09:28:13 Credits: Paul Fisher Attributions: XPath Pubmed Ids 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 21 times Tags (3): pubmed \| xml \| xpath	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	XPath Pubmed Ids (v1) Created: 23/03/11 @ 11:24:23 \| Last updated: 23/03/11 @ 11:24:58 Credits: Paul Fisher 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 16 times Tags (3): bonn \| pubmed \| xpath	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations forQTL region (v2) Created: 17/03/11 @ 11:10:28 \| Last updated: 30/08/11 @ 10:40:14 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 13 times Tags (26): bilateral perisylvian polymicrogyria \| chromosome \| data integration \| data-driven \| database \| disease \| ensembl \| entrez \| epilepsy \| gene \| gene identifier \| geneid \| genes \| genomic \| genotype \| homo sapiens \| human \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| uniprot	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathway and Gene to Pubmed (v2) Created: 10/02/11 @ 16:10:52 \| Last updated: 18/02/11 @ 13:47:08 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 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 57 times \| Downloaded: 18 times Tags (36): annotation \| concept \| concept profile \| controlled vocabulary \| cosine vector space \| data integration \| data-driven \| dresden \| efetch \| enrichment \| entity recognition \| esearch \| eutils \| gene \| gene identifier \| geneid \| genotype \| kegg \| Kegg Pathways \| KeggID \| literature \| loci \| locus \| medline \| mesh \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| text mining \| text mining; term extraction; entity recognition \| trait \| triat	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Gene to Pubmed (v4) Created: 08/02/11 @ 13:04:06 \| Last updated: 10/02/11 @ 16:01:41 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 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 38 times \| Downloaded: 22 times Tags (30): abstracts \| cosine vector space \| data-driven \| disease \| enrichment \| entity recognition \| evidence \| kegg \| Kegg Pathways \| literature \| loci \| locus \| medline \| microarray \| mining \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| ranking \| re-use \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| trichuris muris	View Download (v4)
Taverna 2 Original Uploader Paul Fisher	Read files from Directory (v1) Created: 03/02/11 @ 16:05:02 \| Last updated: 03/02/11 @ 16:05:52 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 7 times Tags (3): directory \| files \| read file	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Remove Non-ASCII (v1) Created: 03/02/11 @ 15:49:07 \| Last updated: 03/02/11 @ 15:59:08 Credits: Paul Fisher 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 5 times \| Downloaded: 9 times Tags (5): ascii \| entity recognition \| literature \| terms \| text	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	PubMed Search (v1) Created: 03/02/11 @ 15:24:57 \| Last updated: 03/02/11 @ 15:25:32 Credits: Paul Fisher 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 19 times Tags (4): literature \| medline \| pubmed \| term	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Rank Phenotype Terms (v1) Created: 01/02/11 @ 11:22:14 \| Last updated: 01/02/11 @ 11:24:42 Credits: Paul Fisher Attributions: Cosine vector space Rank Phenotype Terms 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 10 times Tags (26): concept \| concept profile \| cosine vector space \| data-driven \| enrichment \| entity recognition \| eutils \| evidence \| getconcepts \| literature \| mining \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| ranking \| significance \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations forQTL region (v1) Created: 21/01/11 @ 16:56:47 \| Last updated: 21/01/11 @ 16:58:50 Credits: Paul Fisher 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 10 times Tags (22): african trypanosomiasis \| bos taurus \| cattle \| chromosome \| cow \| ensembl \| entrez \| gene \| genes \| genotype \| kegg \| Kegg Pathways \| KeggID \| pathway \| pathways \| phenotype \| qtl \| quanitative \| re-use \| region \| sleeping sickness \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Extract Scientific Terms (v2) Created: 08/12/10 @ 11:50:01 \| Last updated: 11/01/11 @ 11:58:09 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 39 times \| Downloaded: 13 times Tags (13): abstracts \| ascii \| concept \| concept profile \| dresden \| entity recognition \| genotype \| phenotype \| term \| term extraction \| terms \| text \| text mining; term extraction; entity recognition	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathway to Pubmed (v2) Created: 08/12/10 @ 11:47:10 \| Last updated: 11/01/11 @ 12:00:16 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 19 times Tags (13): abstracts \| concept \| data-driven \| genotype \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| text \| text mining \| text mining; term extraction; entity recognition	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Rank Phenotype Terms (v2) Created: 08/12/10 @ 11:38:37 \| Last updated: 11/01/11 @ 12:02:30 Credits: Paul Fisher Attributions: Rank Phenotype Terms 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 21 times \| Downloaded: 9 times Tags (12): abstracts \| concept \| concept profile \| enrichment \| genotype \| phenotype \| pubmed \| ranking \| term \| text \| text mining \| text mining; term extraction; entity recognition	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Cosine vector space (v2) Created: 08/12/10 @ 11:35:18 \| Last updated: 11/01/11 @ 12:05:41 Credits: Paul Fisher Attributions: Cosine vector space 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 11 times Tags (14): abstracts \| concept \| concept profile \| cosine vector space \| genotype \| pathway \| phenotype \| space \| term \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| vector	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	KEGG pathways common to both QTL and microarray based investigations (v1) Created: 15/11/10 @ 12:30:21 \| Last updated: 15/11/10 @ 12:30:59 Credits: Paul Fisher 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 20 times \| Downloaded: 14 times Tags (21): affmetrix \| affymetrix \| binfo \| chromosome \| common \| data-driven \| gene expression \| gene identifier \| geneid \| genotype \| kegg \| Kegg Pathways \| KeggID \| microarray \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| trait	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for RefSeq ids (v1) Created: 15/11/10 @ 12:25:01 \| Last updated: 15/11/10 @ 12:28:12 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 62 times \| Downloaded: 35 times Tags (34): affmetrix \| affymetrix \| bconv \| binfo \| chromosome \| common \| data-driven \| database \| disease \| ensembl \| entrez \| expression \| gene \| gene expression \| gene identifier \| geneid \| genes \| genomic \| kegg \| Kegg Pathways \| KeggID \| microarray \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| species \| swissprot \| trait \| transcribe \| transcription \| trichuris muris \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v1) Created: 15/11/10 @ 12:08:18 \| Last updated: 16/11/10 @ 16:07:49 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 27 times \| Downloaded: 10 times Tags (33): african trypanosomiasis \| binfo \| chromosome \| common \| data-driven \| database \| disease \| ensembl \| entrez \| gene \| gene identifier \| geneid \| genes \| genomic \| genotype \| kegg \| Kegg Pathways \| KeggID \| loci \| locus \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| region \| sleeping sickness \| species \| trait \| trichuris muris \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Phenotype to pubmed (v3) Created: 05/07/10 @ 14:07:33 \| Last updated: 11/01/11 @ 12:07:22 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 107 times \| Downloaded: 24 times Tags (18): abstracts \| african trypanosomiasis \| disease \| efetch \| entrez \| esearch \| loci \| ncbi \| phenotype \| pubmed \| qtl \| quanitative \| sleeping sickness \| term \| text \| text mining \| text mining; term extraction; entity recognition \| trait	View Download (v3)
Taverna 2 Original Uploader Paul Fisher	Gene to Pubmed (v3) Created: 05/07/10 @ 13:14:36 \| Last updated: 26/01/11 @ 16:57:39 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 43 times \| Downloaded: 25 times Tags (12): abstracts \| efetch \| esearch \| gene \| gene identifier \| geneid \| genes \| literature \| medline \| pubmed \| text \| text mining	View Download (v3)
Taverna 2 Original Uploader Paul Fisher	Perfrom a text based search through PubMed (v1) Created: 05/07/10 @ 13:03:35 \| Last updated: 05/07/10 @ 13:03:37 Credits: Paul Fisher 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 16 times Tags (5): efetch \| eutils \| literature \| medline \| pubmed	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Entrez Gene to KEGG Pathway (v2) Created: 15/04/10 @ 12:22:12 \| Last updated: 15/04/10 @ 12:22:13 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 64 times \| Downloaded: 1 time Tags (7): entrez \| gene \| gene pattern \| geneid \| kegg \| pathway \| pathways	View
Taverna 2 Original Uploader Paul Fisher	microRNA to KEGG Pathways and Abstracts (v1) Created: 17/03/10 @ 10:53:02 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region 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 Rating: 5.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 128 times \| Downloaded: 2 times Tags (21): bconv \| beanshell \| elico \| ensembl \| esearch \| eutils \| gene identifier \| geneid \| genes \| homo sapiens \| kegg \| KeggID \| microrna \| ncbi \| pathway \| pathway-driven \| pathways \| pubmed \| swissprot \| text mining \| uniprot	View
Taverna 2 Original Uploader Paul Fisher	[untitled] (v1) Created: 16/03/10 @ 16:33:35 Credits: Paul Fisher 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: 16 times Tags (6): abstracts \| compound \| gene \| genes \| pathway \| pathways	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Get Kegg Pathway information (v1) Created: 10/03/10 @ 17:15:47 \| Last updated: 10/03/10 @ 17:18:47 Credits: Paul Fisher 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 84 times \| Downloaded: 36 times Tags (6): genes \| kegg \| Kegg Pathways \| KeggID \| pathway \| pathways	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Get Gene Ids for Human (v1) Created: 04/02/10 @ 12:47:16 \| Last updated: 04/02/10 @ 12:48:11 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow gets a list of gene ids (number depending on Ret_Max_value variable) for Homo sapiens. The species may be changed according to that desired, by altering the term_value string constant Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 67 times \| Downloaded: 18 times Tags (8): database \| esearch \| gene \| gene identifier \| homo sapiens \| human \| ncbi \| species	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Entrez Gene to KEGG Pathway (v5) Created: 04/12/09 @ 16:04:38 \| Last updated: 30/11/10 @ 12:18:53 Credits: Paul Fisher License: Creative Commons Attribution 3.0 Unported License This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned. Rating: 4.8 / 5 (4 ratings) \| Versions: 5 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 1029 times \| Downloaded: 442 times Tags (9): entrez \| genotype \| kegg \| ncbi \| pathway \| pathway-driven \| pathways \| phenotype \| shim	View Download (v5)
Taverna 1 Original Uploader Paul Fisher	Perform a search through NCBI eUtils eSearch (v3) Created: 27/11/09 @ 14:44:11 \| Last updated: 03/12/09 @ 16:32:26 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow takes in a search term and a database (e.g. snp, gene, protein) in which to perfom the search over. The result is an xml file containing summary information about the search term. Example input for this workflow are given below: database: pubmed terms: cancer AND diabetes Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 8 \| Citations: 0 Viewed: 368 times \| Downloaded: 192 times Tags (4): esearch \| eutils \| ncbi \| pubmed	View Download (v3)
Taverna 1 Original Uploader Paul Fisher	KEGG pathways common to both QTL and microarray based investigations (v3) Created: 24/11/09 @ 17:14:43 \| Last updated: 03/12/09 @ 15:28:49 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype. Example input for this workflow is given below (as newline separated values). qt... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 1 Viewed: 261 times \| Downloaded: 125 times Tags (11): common \| data-driven \| disease \| genotype \| kegg \| microarray \| pathway \| pathway-driven \| pathways \| phenotype \| similarity	View Download (v3)
Taverna 1 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v2) Created: 20/11/09 @ 14:04:37 \| Last updated: 20/11/09 @ 14:04:39 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 129 times \| Downloaded: 20 times Tags (28): annotation \| binfo \| chromosome \| data integration \| data-driven \| ensembl \| entrez \| gene \| gene identifier \| geneid \| genes \| kegg \| Kegg Pathways \| KeggID \| loci \| locus \| merge \| pathway \| pathway-driven \| pathways \| pig \| qtl \| quanitative \| species \| sus scrofa \| swissprot \| trait \| uniprot	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v7) Created: 19/11/09 @ 18:18:52 \| Last updated: 02/09/11 @ 11:44:57 Credits: Paul Fisher 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... Rating: 4.9 / 5 (8 ratings) \| Versions: 7 \| Reviews: 1 \| Comments: 7 \| Citations: 1 Viewed: 4177 times \| Downloaded: 714 times Tags (22): adasd \| chromosome \| data-driven \| disease \| ensembl \| entrez \| gene \| genes \| genotype \| kegg \| mouse \| nbiconworkflows \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| shim \| subworkflow \| uniprot	View Download (v7)
Taverna 1 Original Uploader Paul Fisher	Get graphs (v2) Created: 05/11/09 @ 12:38:22 Credits: Paul Fisher 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) Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 39 times \| Downloaded: 18 times Tags (3): data integration \| graph \| ondex	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Spreadsheet Importer (v1) Created: 24/08/09 @ 14:11:52 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow is designed to import a spreadhseet from a local computer. The imported spreadsheet is parsed to extract the first two columns, A and B, for all rows in the spreadsheet. These are returned as two separate outputs. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 94 times \| Downloaded: 31 times Tags (5): column \| excel \| row \| spreadsheet \| table	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	SubGraph Filter (v2) Created: 19/08/09 @ 16:38:17 Credits: Paul Fisher 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 34 times \| Downloaded: 1 time Tags (7): concept \| filter \| graph \| ondex \| ovtk \| oxl \| sub-graph	View
Taverna 1 Original Uploader Paul Fisher	Unconnected Filter (v1) Created: 19/08/09 @ 16:35:08 Credits: Paul Fisher 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 29 times \| Downloaded: 1 time Tags (6): filter \| graph \| ondex \| ovtk \| oxl \| unconnected	View
Taverna 1 Original Uploader Paul Fisher	Tranitive Filter (v1) Created: 19/08/09 @ 16:34:16 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters an Ondex graph to extract a sub-graph. The result is a new Ondex graph containing only the transitive sub-graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. CV - Seed cv that will be used to extract the subgraph (Optional). AttributeName - Seed attribute name that will be us... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 1 time Tags (7): cv \| filter \| graph \| ondex \| ovtk \| oxl \| transitive	View
Taverna 1 Original Uploader Paul Fisher	Significance Filter (v1) Created: 19/08/09 @ 16:31:24 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters a given Ondex graph according to a level of significance set by the user. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. TargetAttributeName - Target AttributeName to filter for significance. Significance - A significance value to filter relatio... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 1 time Tags (6): filter \| graph \| ondex \| ovtk \| oxl \| significance	View
Taverna 1 Original Uploader Paul Fisher	Shortest Path (v1) Created: 19/08/09 @ 16:30:35 Credits: Paul Fisher 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 1 time Tags (7): filter \| gds \| graph \| ondex \| ovtk \| oxl \| shortest path	View
Taverna 1 Original Uploader Paul Fisher	Relation Type Filter (v1) Created: 19/08/09 @ 16:29:10 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters a pre-existing ONdex graph based on a some paramters provided by the user. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional) parameter. If no output graph is specified filtered items will be removed from the input graph. TargetRelationType - Target RelationType to filter out. ConceptClassRestriction - Concept Class Restriction as ordered pair representing from/to C... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 14 times \| Downloaded: 1 time Tags (6): filter \| graph \| ondex \| ovtk \| oxl \| relation type	View
Taverna 1 Original Uploader Paul Fisher	Relation Neighbours Filter (v1) Created: 19/08/09 @ 16:28:09 Credits: Paul Fisher 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 1 time Tags (6): filter \| graph \| ondex \| ovtk \| oxl \| relation nieghbour	View
Taverna 1 Original Uploader Paul Fisher	Pfam Based Ortholog Filter (v1) Created: 19/08/09 @ 16:26:55 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters an Ondex graph based on the occurrence of Pfam orthologs within the graph. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ConfidenceThreshold - Threshold value for inparanoid confidence. Default value is 100. AnnotationScoreThreshold - Threshold... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 24 times \| Downloaded: 1 time Tags (10): annotation \| filter \| graph \| ondex \| orthologue \| ovtk \| oxl \| pfam \| protein \| terms	View
Taverna 1 Original Uploader Paul Fisher	Optimal Paths Filter (v1) Created: 19/08/09 @ 16:25:49 Credits: Paul Fisher 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 1 time Tags (9): filter \| gds \| graph \| ondex \| optimal path \| ovtk \| oxl \| pathway \| statistics	View
Taverna 1 Original Uploader Paul Fisher	One Pair Shortest Path Filter (v1) Created: 19/08/09 @ 16:24:41 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters a pre-existing Ondex graph using the shortest path algorithm on the graph. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. StartConceptID - The Concept ID that starts the path EndConceptID - The Concept ID that ends the path UseWeights -... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 1 time Tags (7): filter \| gds \| graph \| ondex \| ovtk \| oxl \| shortest path	View
Taverna 1 Original Uploader Paul Fisher	Isolate Clusters Filter (v1) Created: 19/08/09 @ 16:23:45 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 1 time Tags (7): clusters \| filter \| graph \| isolate \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	Graph Cloner (v1) Created: 19/08/09 @ 16:22:13 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow clones a given Ondex Graph, based on an Ondex Graph identifier. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 1 time Tags (6): cloner \| filter \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	Genomic Filter (v1) Created: 19/08/09 @ 16:19:01 Credits: Paul Fisher 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 20 times \| Downloaded: 1 time Tags (12): chromosome \| filter \| genomic \| graph \| loci \| ondex \| ovtk \| oxl \| qtl \| quanitative \| region \| triat	View
Taverna 1 Original Uploader Paul Fisher	GDS Value Filter (v1) Created: 19/08/09 @ 16:17:27 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters a given Ondex graph based on a given GDS value supplied by the user. The result is a new Ondex graph with filtered content. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. AttributeName - AttributeName to filter out. GDSValue - A value which will be matched against the ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 1 time Tags (8): comparison \| filter \| gds \| general data store \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	Evidence Type Filter (v1) Created: 19/08/09 @ 16:16:15 Credits: Paul Fisher 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 7 times \| Downloaded: 1 time Tags (6): evidence \| filter \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	CV Filter (v1) Created: 19/08/09 @ 16:15:20 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters a given Ondex graph according to a controlled vocabulary specified by the user. The result is a new Ondex graph with only those concepts that passed the filter. The parameters that can be used with this service graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. CV - A CV to include/exclude Concepts and Relations of (see Exclude param). R... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 20 times \| Downloaded: 1 time Tags (7): controlled vocabulary \| cv \| filter \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	Context Filter (v1) Created: 19/08/09 @ 16:14:13 Credits: Paul Fisher 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 14 times \| Downloaded: 1 time Tags (6): context \| filter \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	Context Consensus Filter (v1) Created: 19/08/09 @ 16:13:11 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters a given Ondex graph according to a consensus with regards to a specific context (concept list). The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. Threshold - Double value representing the share of contexts that qualify a graph element for ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 1 time Tags (7): concept \| consensus \| filter \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	Concept Class Neighbours Filter (v1) Created: 19/08/09 @ 16:11:56 Credits: Paul Fisher 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 1 time Tags (7): concept \| distance \| filter \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	Concept Class Filter (v1) Created: 19/08/09 @ 16:10:36 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters a Ondex graph based on a specific concept class. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. TargetConceptClass - Target Concept Class to filter out. RefactorTrinaries - Where the qualifier of a trinary relation is out of scope create a bina... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 1 time Tags (6): concept \| filter \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	Clean UniProt Filter (v1) Created: 19/08/09 @ 16:08:48 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 1 time Tags (6): filter \| graph \| ondex \| ovtk \| oxl \| uniprot	View
Taverna 1 Original Uploader Paul Fisher	Clean GO Filter (v1) Created: 19/08/09 @ 16:07:27 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters an Ondex graph, by cleaning up any GO terms within the Graph (?). The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 23 times \| Downloaded: 1 time Tags (8): filter \| GO \| go terms \| graph \| ondex \| ovtk \| oxl \| terms	View
Taverna 1 Original Uploader Paul Fisher	All Pairs Filter (v1) Created: 19/08/09 @ 16:06:29 Credits: Paul Fisher 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 1 time Tags (5): filter \| graph \| ondex \| ovtk \| oxl	View
Taverna 1 Original Uploader Paul Fisher	Tab Parser (v1) Created: 19/08/09 @ 16:05:20 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a tab separated file, and then parses specific rows and columns from the file into an Ondex Graph. Additional prarameters are provided, though these are optional: graphId Long the ID of the Graph (REQUIRED) input String the plugin input (REQUIRED) skip Integer How many rows to skip at begin of document (Optional). Default value is 22. fromCol Integer Index of concept parser id for from concept. Default value is 0. (REQUIRED) toCol Integer Index of concept par... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 1 time Tags (12): concept \| file \| gene \| line \| ondex \| ovtk \| oxl \| parser \| protein \| tab \| table \| taxonomy	View
Taverna 1 Original Uploader Paul Fisher	Table Parser (v1) Created: 19/08/09 @ 16:04:12 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 1 time Tags (7): concept \| ondex \| ovtk \| oxl \| parser \| table \| text	View
Taverna 1 Original Uploader Paul Fisher	KEGG Pasrer (v1) Created: 19/08/09 @ 16:03:07 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow parses a KEGG species database into an Ondex Graph graphId - the ID of the Graph. inputDir - the plugin input directory Species - Use this parameter to specify the species to be loaded from the kegg database. Default value is all. ParseSequences - KEGG species code. Default value is false (boolean) ImportOrthologFillers - Import Ortholog Pathway Fillers. Default value is false (boolean) Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 2 times Tags (7): kegg \| Kegg Pathways \| KeggID \| ondex \| ovtk \| oxl \| species	View
Taverna 1 Original Uploader Paul Fisher	Rank Phenotype Terms (v1) Created: 10/08/09 @ 15:43:48 Credits: Paul Fisher 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 119 times \| Downloaded: 0 times Tags (24): abstracts \| append term \| authors \| concept \| cosine vector space \| data-driven \| enrichment \| gene identifier \| geneid \| genes \| genotype \| information \| mining \| ncbi \| pathways \| phenotype \| pubmed \| ranking \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Taverna 1 Original Uploader Paul Fisher	Extract Scientific Terms (v1) Created: 10/08/09 @ 13:31:07 \| Last updated: 10/08/09 @ 13:32:21 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a document containg text and removes any non-ascii characters. The cleaned text is then sent to a service in Dresden, to extract all scientific terms. These terms represent a concept profile for the input concpet. Any null values are also removed. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 119 times \| Downloaded: 0 times Tags (18): abstracts \| authors \| data-driven \| entity recognition \| gene \| getconcepts \| kegg \| Kegg Pathways \| mining \| mouse \| pathway-driven \| pathways \| phenotype \| sleeping sickness \| term extraction \| text \| text mining \| text mining; term extraction; entity recognition	View
Taverna 1 Original Uploader Paul Fisher	Cosine vector space (v1) Created: 10/08/09 @ 13:19:36 \| Last updated: 10/08/09 @ 13:24:28 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 48 times \| Downloaded: 0 times Tags (14): abstracts \| cosine vector space \| gene \| information \| Kegg Pathways \| pathway \| phenotype \| pubmed \| qtl \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| vector	View
Taverna 1 Original Uploader Paul Fisher	Arabidopsis thaliana Microarray Analysis (v1) Created: 08/07/09 @ 16:28:34 Credits: Paul Fisher License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow searches for genes which are found to be differentially expressed in a microarray study using Arabidopsis thaliana. The workflow requires an input of a list of differentially expressed AffyMetrix Probeset identifiers. Data is then extracted from BioMart to annotate each of the genes. The UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 142 times \| Downloaded: 28 times Tags (19): affmetrix \| affymetrix \| arabidopsis \| bconv \| data-driven \| ensembl \| gene \| gene expression \| geneid \| genes \| genotype \| kegg \| Kegg Pathways \| microarray \| pathway \| pathways \| phenotype \| thaliana \| uniprot	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Arabidopsis thaliana QTL Analysis (v1) Created: 08/07/09 @ 16:26:13 \| Last updated: 14/12/09 @ 11:59:14 Credits: Paul Fisher 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. ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 60 times \| Downloaded: 26 times Tags (15): arabidopsis \| chromosome \| crop \| ensembl \| kegg \| loci \| locus \| nucleotide \| pathway \| pathways \| plants \| qtl \| thaliana \| trait \| uniprot	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	NCBI Gi to Kegg Pathways (v1) Created: 08/06/09 @ 18:39:38 \| Last updated: 14/12/09 @ 11:51:20 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow converts a list of NCBI gi numbers and converts them to a list of KEGG genes. Those KEGG gene ids are subsequently turned into KEGG pathway identifiers and descriptions. It also removes any null values from a list of strings. Example input for this workflow is as follows (new line separated): gi:215422388 gi:120407068 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 220 times \| Downloaded: 144 times Tags (6): bconv \| gene \| genes \| ncbi \| pathway \| pathways	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	inchi to Chebi (v1) Created: 22/05/09 @ 16:07:50 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow converts an inchi string to a chebi id. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 24 times \| Downloaded: 2 times Tags (3): chebi \| compound \| inchi	View
Taverna 1 Original Uploader Paul Fisher	Pathways and Gene annotations for Arabidopsis affy data (v2) Created: 06/03/09 @ 17:18:13 \| Last updated: 03/12/09 @ 16:59:11 Credits: Paul Fisher Peter Li Attributions: Pathways and Gene annotations for QTL region License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow searches for genes obtained from affy_ath1 affymetrix probeset identifiers. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 216 times \| Downloaded: 1 time Tags (12): affymetrix \| arabidopsis \| binfo \| entrez \| gene \| kegg \| Kegg Pathways \| ncbi \| pathway \| pathways \| swissprot \| uniprot	View
Taverna 1 Original Uploader Paul Fisher	Get relations (v1) Created: 27/02/09 @ 16:45:39 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow gets all the realtions from a given Ondex graph Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 11 times Tags (3): data integration \| graph \| ondex	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Get Graphs of Name (v1) Created: 27/02/09 @ 16:42:35 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow gets the Ondex graphs relating to a specified name Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 11 times Tags (3): data integration \| graph \| ondex	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Get Evidence Types (v1) Created: 27/02/09 @ 16:40:22 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow gets all the evidence types within a specified Ondex graph Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 21 times \| Downloaded: 12 times Tags (3): data integration \| graph \| ondex	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Get CVs (v1) Created: 27/02/09 @ 16:38:39 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow lets users retrive all controlled vocabularies for a given Ondex graph Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 15 times Tags (3): data integration \| graph \| ondex	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Get Concepts (v1) Created: 27/02/09 @ 16:33:39 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow gets all the concepts in an Ondex graph, using a given graph id Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 60 times \| Downloaded: 19 times Tags (3): data integration \| graph \| ondex	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Get Kegg Gene information (v2) Created: 26/01/09 @ 18:06:12 \| Last updated: 14/12/09 @ 12:05:21 Credits: Paul Fisher 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 Rating: 5.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 300 times \| Downloaded: 112 times Tags (6): gene \| gene identifier \| information \| kegg \| Kegg Pathways \| KeggID	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Retrieve Protein Sequence (v1) Created: 30/07/08 @ 16:36:55 \| Last updated: 03/12/09 @ 16:54:02 Credits: Katy Wolstencroft License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 377 times \| Downloaded: 125 times Tags (5): bioinformatics \| neuroscience \| newcastle \| protein \| sequence	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Human Microarray Analysis (v1) Created: 08/02/08 @ 14:30:17 \| Last updated: 03/12/09 @ 16:50:29 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in probesets from and AffyMetrix Affy HG U133A micorarray experiment and returns: genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data. Example input for this workflow is: 212283_at 221634_at 220399_at Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 268 times \| Downloaded: 4 times Tags (17): affymetrix \| cel \| data-driven \| disease \| expression \| gene \| gene identifier \| genotype \| kegg \| microarray \| pathway \| pathway-driven \| pathways \| shim \| transcribe \| transcription \| uniprot	View
Taverna 1 Original Uploader Paul Fisher	Microarray CEL file to candidate pathways (v2) Created: 08/02/08 @ 14:17:23 \| Last updated: 13/02/09 @ 11:29:52 Credits: Paul Fisher Saeedeh 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 263 times \| Downloaded: 5 times Tags (17): affymetrix \| cel \| data-driven \| ddbj \| disease \| entrez \| gene identifier \| genotype \| kegg \| microarray \| mouse \| pathway \| pathway-driven \| pathways \| shim \| transcribe \| transcription	View
Taverna 1 Original Uploader Paul Fisher	Add Mesh String to Biological Process (v2) Created: 03/10/07 @ 18:36:28 \| Last updated: 03/12/09 @ 16:42:48 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow is designed to add the following MeSH term to the end of a KEGG pathway name: AND "Metabolic Networks and Pathways" [MeSH Terms] Example input for this service is as follows: VEGF signaling pathway Hematopoietic cell lineage GnRH signaling pathway Type II diabetes mellitus Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 384 times \| Downloaded: 80 times Tags (2): append term \| mesh	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Parse UniProt text file (v2) Created: 03/10/07 @ 18:36:08 \| Last updated: 03/12/09 @ 16:36:54 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow performs a search through the SRS linking system to find the text files for a particular UniProt identifier. This UniProt text file is then parsed to extract a small list to summarise the file, primarily consisting of external identifiers. Example input for this workflow is: O35613 Rating: 3.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 102 times \| Downloaded: 78 times Tags (1): uniprot	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	BLASTP with simplified results returned (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 03/12/09 @ 16:28:50 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output. Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSV... Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 309 times \| Downloaded: 102 times Tags (6): bioinformatics \| BLAST \| ddbj \| sequence \| similarity \| simplifier	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Simplify a BLAST text file (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 28/07/09 @ 13:01:45 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simply pass in the string the SAME as the port name, e.g. seq_id, p, per etc. Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 335 times \| Downloaded: 137 times Tags (11): bioinformatics \| BLAST \| gene identifier \| gi \| matrix \| sequence \| similarity \| simple \| simplifier \| substitution \| summary	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	BLAST using DDBJ service (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 03/12/09 @ 16:31:20 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License Perform a sequence similarity search using the BLAST algorithm through the DDBJ web service. Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNIL SRVLARSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLT NTENTASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEAR LKRKLIRLFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDY GDVLRAVEKAATRHSLGLP... Rating: 4.5 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 541 times \| Downloaded: 199 times Tags (5): bioinformatics \| BLAST \| ddbj \| sequence \| similarity	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Mouse Microarray Analysis (v3) Created: 03/10/07 @ 18:36:05 \| Last updated: 03/12/09 @ 16:20:33 License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2. Example ids from the Mouse430_2 affymetrix array are as follows (newline separated): 1447227_at 1440624_at 1436240_at 1454904_at 1435665_at 1418148_at 1429831_at Rating: 5.0 / 5 (1 rating) \| Versions: 3 \| Reviews: 0 \| Comments: 1 \| Citations: 1 Viewed: 490 times \| Downloaded: 127 times Tags (18): affmetrix \| cel \| data-driven \| disease \| expression \| file \| gene \| genotype \| kegg \| microarray \| mouse \| nbiconworkflows \| pathway-driven \| phenotype \| RNA \| shim \| uniprot	View Download (v3)
Taverna 1 Original Uploader Paul Fisher	Remove null values (v2) Created: 03/10/07 @ 18:36:05 \| Last updated: 13/11/07 @ 16:20:42 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow removes any null values from a list of strings Rating: 4.0 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 64 times \| Downloaded: 50 times Tags (4): design pattern \| nulls \| remove \| shim	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Remove duplicate strings (v2) Created: 03/10/07 @ 18:36:03 \| Last updated: 13/11/07 @ 16:25:42 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow takes in two list of strings and then concatenates them together. Any duplicates that are present are then removed, and the resulting file is returned back to the user. Rating: 5.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 65 times \| Downloaded: 40 times Tags (5): design pattern \| duplicate \| remove \| string \| strings	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Back translate a protein sequence into a dna sequence (v2) Created: 03/10/07 @ 18:36:03 \| Last updated: 03/12/09 @ 16:18:43 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow back translates a protein sequence into a DNA sequence. Example input for this workflow is: MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSSNSG SRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNILSRVLA RSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLTNTENT ASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEARLKRKLIR LFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDYGDVLRAVE KAATRHSLGLPRQQLQLLAQDAFRDVGVRLQERRHLDLIYNFGCHLTDDYRPGVDPALSD PTLARRLRENRTLAM... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 90 times \| Downloaded: 59 times This Workflow has no tags!	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Cow-Human Ortholog Pathways and Gene annotations for QTL Phenotype (v2) Created: 03/10/07 @ 18:36:00 \| Last updated: 03/12/09 @ 16:16:31 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 the 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. As the Cow genome is currently unfinished, the workflow subsequently maps the cow ensembl gene ids to human orthologues. Entrez and UniProt identifiers are then identified... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 98 times \| Downloaded: 46 times Tags (1): nbiconworkflows	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Transcribe a DNA sequence into an RNA sequence (v2) Created: 03/10/07 @ 18:35:58 \| Last updated: 13/11/07 @ 16:16:54 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow transcribes a DNA sequence into an RNA sequence Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 82 times \| Downloaded: 72 times Tags (4): DNA \| RNA \| transcribe \| transcription	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	HUMAN Microarray CEL file to candidate pathways (v4) Created: 03/10/07 @ 18:35:55 \| Last updated: 26/11/09 @ 17:34:24 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also returned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ... Rating: 5.0 / 5 (2 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 1208 times \| Downloaded: 358 times Tags (12): affymetrix \| cel \| file \| genotype \| kegg \| microarray \| nbiconworkflows \| pathway-driven \| pathways \| phenotype \| shim	View Download (v4)