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Items tagged with "gene" (50)

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Workflows (36)

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 Katy Wolstencroft	Gene annotation pipeline for the Graves disease scenario (v2) Created: 03/10/07 @ 18:36:09 \| Last updated: 22/11/07 @ 16:03:15 Credits: Katy Wolstencroft Peter Li License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 562 times \| Downloaded: 195 times Tags (6): affymetirx \| affymetrix \| annotation \| disease \| gene \| graves	View Download (v2)
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	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	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 Katy Wolstencroft	omim and pathways (v2) Created: 03/03/09 @ 13:17:27 \| Last updated: 02/11/09 @ 10:13:38 Credits: Katy Wolstencroft Paul Fisher Attributions: Get Kegg Gene information 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 Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 84 times \| Downloaded: 32 times Tags (9): bconv \| disease \| disease-associated genes \| gene \| genes \| kegg \| Kegg Pathways \| OMIM \| pathways	View Download (v2)
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	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	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	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	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 2 Original Uploader Rory	chicken_ensembl_gene_id (v1) Created: 07/09/09 @ 15:00:01 \| Last updated: 09/09/09 @ 14:21:48 Credits: Rory License: Creative Commons Attribution-Share Alike 3.0 Unported License Accepts a chromosome eg. 1 and returns the ensembl gene ids for that chromosome Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 32 times \| Downloaded: 18 times Tags (5): chromosome \| ensembl \| example \| gene \| test	View Download (v1)
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 Wei Tan	caArray data retrieving (v1) Created: 23/11/09 @ 18:09:47 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They ca be later used as training and test data set in many classification algorithms.Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They can be later used as training and test data set in many classification algorithms. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 3 \| Citations: 0 Viewed: 47 times \| Downloaded: 17 times Tags (8): caarray \| cabig \| cagrid \| functional workflow \| gene \| globus \| grid service \| microarray	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 2 Original Uploader Jannetta	Kegg pathway diagrams (v1) Created: 13/03/10 @ 08:17:39 Credits: Jannetta License: Creative Commons Attribution-Share Alike 3.0 Unported License Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 16 times Tags (3): gene \| pathway \| visualise	View Download (v1)
Taverna 2 Original Uploader Peter Li	Calculating frequencies of gene expression levels using microarray data in MaxD (v1) Created: 15/03/10 @ 08:43:31 Credits: Peter Li License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 52 times \| Downloaded: 0 times Tags (9): beanshell \| database \| expression \| gene \| image \| maxd \| microarray \| r \| xpath	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	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 Nadia Cerezo	Get KEGG gene descriptions and pathways (v1) Created: 30/04/10 @ 16:09:29 \| Last updated: 30/04/10 @ 16:12:02 Credits: Nadia Cerezo Paul Fisher Attributions: Get Kegg Gene information 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 73 times \| Downloaded: 25 times Tags (11): gene \| gene identifier \| genes \| information \| kegg \| Kegg Pathways \| KeggID \| pathway \| pathways \| taverna \| workflow	View Download (v1)
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	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	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 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	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	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 Naser	gene subset extract (v1) Created: 29/03/11 @ 14:55:31 \| Last updated: 29/03/11 @ 15:00:22 Credits: Naser Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 7 times Tags (2): gene \| spread sheet	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	BiomartAndEMBOSSAnalysis (v4) Created: 27/01/11 @ 17:03:03 \| Last updated: 12/05/11 @ 13:31:41 Credits: Katy Wolstencroft Alan Williams Attributions: BiomartAndEMBOSSAnalysis License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 97 times \| Downloaded: 55 times Tags (16): alignment \| biomart \| biomart emboss \| bonn \| disease \| emboss \| emma \| ensembl \| gene \| genes \| homolog \| human \| mouse \| sequence \| sequence alignment \| soaplab	View Download (v4)
BioExtract Server Original Uploader Carol Lushbough	tblastx non-redundant alignment (v1) Created: 30/06/11 @ 15:26:13 \| Last updated: 04/07/11 @ 16:51:41 Credits: Carol Lushbough License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow carries out alignments using TCoffee and ClustalW2 for a set of non-redundant proteins where the starting point is a particular genomic coding sequence representing only one member of the gene family in a given species. For the BioExtract Server implementation, the necessary steps for accomplishing this task involve: 1. Selecting the NCBI tblastx tool and providing the accession number of the known nucleotide sequence record as input. 2. The output from ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 3 times Tags (7): alignment \| gene \| genomic \| proteins \| sequence \| species \| workflow	View Download (v1)
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: 6 \| Citations: 1 Viewed: 4207 times \| Downloaded: 718 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)
Kepler Original Uploader Wdsnellg	Extract Gene Sequence with Kepler (v1) Created: 05/10/11 @ 05:04:40 \| Last updated: 05/10/11 @ 05:04:42 Credits: Wdsnellg License: Creative Commons Attribution-Share Alike 3.0 Unported License This is a workflow which allows one to extract gene sequence information using the accession number as the input. Multiple outputs include a file output of sequence header information, as well as one output window of base pair count, ratios and gene sequence. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 11 times Tags (3): bioinformatics \| gene \| ist600	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	NCBI Gi to Kegg Pathway Descriptions (v2) Created: 12/01/12 @ 09:46:31 \| Last updated: 12/01/12 @ 14:54:37 Credits: Katy Wolstencroft Attributions: NCBI Gi to Kegg Pathways 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 3 times \| Downloaded: 2 times Tags (8): bconv \| genbank \| gene \| genes \| gi \| ncbi \| pathway \| pathways	View Download (v2)
Taverna 2 Original Uploader Katy Wolstencroft	Import and convert (v1) Created: 15/01/12 @ 10:23:33 \| Last updated: 17/01/12 @ 15:22:07 Credits: Katy Wolstencroft License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Unigene identifiers Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 6 times \| Downloaded: 21 times Tags (2): ensembl \| gene	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	Reactome pathways (v1) Created: 16/01/12 @ 15:31:40 Credits: Katy Wolstencroft License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow returns a list of pathways gene products are involved in, along with their descriptions and Gene Ontology annotations Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 0 times \| Downloaded: 1 time Tags (3): gene \| pathways \| reactome	View Download (v1)
Taverna 2 Original Uploader Paul martin	Define Associated Regions and Genes (v1) Created: 08/02/12 @ 16:08:08 \| Last updated: 08/02/12 @ 16:08:09 Credits: Paul martin License: Creative Commons Attribution-Share Alike 3.0 Unported License Defines regions and genes from associated SNPs Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 0 times \| Downloaded: 0 times Tags (14): association \| disease \| disease-associated genes \| ensembl \| gene \| genes \| genome wide association studies \| gwas \| mapping \| ncbi \| ngs \| sequencing \| snp \| ucsc	View Download (v1)
Taverna 2 Original Uploader Paul martin	Associated Region to Gene List (v1) Created: 08/02/12 @ 16:14:17 \| Last updated: 08/02/12 @ 16:14:47 Credits: Paul martin License: Creative Commons Attribution-Share Alike 3.0 Unported License Produces a gene list from the Associated Region XML file Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 2 times \| Downloaded: 0 times Tags (2): associated genes \| gene	View Download (v1)

Packs (3)

Creator:

Paul Fisher

Text Mining Workflows

Created: 08/12/10 @ 11:55:03 | Last updated: 01/02/11 @ 11:33:11

This pack contains workflows to navigate from candidate Quantitative Trait genes and pathways to a given phenotype.

5 items in this pack

Comments: 0 | Viewed: 75 times | Downloaded: 12 times

Tags:

concept profile
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cosine vector space
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data-driven
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efetch
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entity recognition
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esearch
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gene
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gene identifier
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geneid
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genes
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genotype
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kegg
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Kegg Pathways
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KeggID
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literature
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loci
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locus
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ncbi
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pathway
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pathway-driven
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pathways
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phenotype
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pubmed
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qtl
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quanitative
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ranking
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space
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term
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term extraction
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terms
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text
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text mining
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text mining; term extraction; entity recognition
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trait
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vector

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Creator:

Wdsnellg

Extract Gene Sequence Information with Kepler

Created: 05/10/11 @ 04:58:33 | Last updated: 05/10/11 @ 06:11:56

This workflow and pack were designed for a class project. The Kepler based workflow allows one to extract specific information from a gene sequence by using the accession ID as input. By using two web services created for the DNA Data Bank of Japan (DDBJ, http://www.xml.nig.ac.jp/wabi/Method?serviceName=DDBJ&mode=methodList&lang=en), one can extract the sequence header information as an output file, as well as retrieve the sequence, base pair count, and base pair ratios in...

5 items in this pack

Comments: 0 | Viewed: 1 time | Downloaded: 0 times

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Creator:

Marco Roos

wf4ever Deliverable 6.3 Pack

Created: 02/12/11 @ 09:31:26 | Last updated: 02/12/11 @ 10:21:03

This pack contains (references to) the workflows for GWAS analysis by workflows that perform pathway and GO analysis and biosemantics data interpretation (a special form of text mining). This pack aggregates the deliverable materials for month 8 for Work Package 6. The workflows have not been published in the scientific domain yet, so its content cannot yet be made public. They are available upon request, in particular for reviewers. Please contact Kristina Hettne or Marco Roos (see credit...

6 items in this pack

Comments: 0 | Viewed: 3 times | Downloaded: 0 times

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Files (11)

Uploader: Paul Fisher	Candidate Gene protocol Created: 08/04/09 @ 13:27:20 Credits: Paul Fisher 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. File type: Word document Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 33 times \| Downloaded: 38 times Tags: affymetrix \| african trypanosomiasis \| gene \| gene identifier \| geneid \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| sleeping sickness	View Download
Uploader: Paul Fisher	Re-sequenced Daxx gene info Created: 08/04/09 @ 17:53:46 \| Last updated: 10/08/09 @ 12:30:59 Credits: Paul Fisher 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 File type: Excel workbook Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 25 times \| Downloaded: 19 times Tags: deletion \| gene \| mutation \| sequence \| snp	View Download
Uploader: Paul Fisher	Tir1 QTL - Day 3 Microarray intersecting pathways Created: 08/04/09 @ 17:56:10 Credits: Paul Fisher 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 File type: Excel workbook Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 17 times \| Downloaded: 19 times Tags: african trypanosomiasis \| expression \| gene \| microarray \| qtl \| sleeping sickness	View Download
Uploader: Paul Fisher	Tir1 QTL - microarray day 7 intersecting pathways Created: 08/04/09 @ 17:57:57 Credits: Paul Fisher 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 File type: Excel workbook Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 21 times \| Downloaded: 23 times Tags: affymetrix \| african trypanosomiasis \| gene \| microarray \| pathway \| qtl \| sleeping sickness	View Download
Uploader: Paul Fisher	Ensembl database release Created: 08/04/09 @ 18:00:35 \| Last updated: 10/08/09 @ 12:12:09 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License The release of the Ensembl database used to identify genes in Tir1 QTL region. File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 15 times \| Downloaded: 11 times Tags: ensembl \| gene \| geneid \| qtl	View Download
Uploader: Paul Fisher	Kegg gene descriptions Created: 08/04/09 @ 18:06:23 \| Last updated: 10/08/09 @ 12:10:07 Credits: Paul Fisher 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. File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 1 \| Viewed: 23 times \| Downloaded: 21 times Tags: gene \| kegg \| KeggID \| mouse	View Download
Uploader: Paul Fisher	Ensembl gene report Created: 08/04/09 @ 19:30:15 \| Last updated: 10/08/09 @ 11:05:59 Credits: Paul Fisher 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. File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 37 times \| Downloaded: 27 times Tags: affymetrix \| base pair \| chromosome \| ensembl \| entrez \| gene \| uniprot	View Download
Uploader: Paul Fisher	Gene Cosine Scores Created: 10/08/09 @ 16:00:45 Credits: Paul Fisher 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. File type: Excel workbook Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 13 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| authors \| cosine vector space \| data-driven \| enrichment \| entity recognition \| gene \| geneid \| genes \| mouse \| ncbi \| phenotype \| pubmed \| ranking \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Uploader: Paul Fisher	Phenotype Concept Profile - Terms Created: 11/08/09 @ 13:05:07 \| Last updated: 11/08/09 @ 13:06:51 Credits: Paul Fisher 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. File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 17 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| authors \| concept profile \| cosine vector space \| dresden \| enrichment \| entity recognition \| gene \| mining \| mouse \| protein \| pubmed \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Uploader: Paul Fisher	Bilateral Perisylvian Polymicrogyria Created: 17/03/11 @ 10:56:15 \| Last updated: 17/03/11 @ 11:16:53 Credits: Paul Fisher Attributions: Pathway and Gene to Pubmed Pathways and Gene annotations forQTL region License: Creative Commons Attribution-Share Alike 3.0 Unported License 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... File type: ZIP archive Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 8 times \| Downloaded: 5 times Tags: bilateral perisylvian polymicrogyria \| cosine vector space \| data integration \| data-driven \| enrichment \| entity recognition \| epilepsy \| gene \| homo sapiens \| human \| Kegg Pathways \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| region \| text mining \| text mining; term extraction; entity recognition	View Download
Uploader: Paul Fisher	Human Probeset data from Affymetrix Created: 01/04/11 @ 09:08:45 \| Last updated: 01/04/11 @ 09:08:51 License: Creative Commons Attribution-Share Alike 3.0 Unported License This file contains a list or affymetrix probest identifiers for Human gene expression data relating to the: Impact of NRSF variant over-expression in SK-N-AS human neuroblastoma cells (http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-GEOD-22467&expandefo=on) File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 5 times \| Downloaded: 4 times Tags: affymetrix \| arrayexpress \| expression \| gene \| gene expression \| madat \| probeset	View Download