myExperiment - Tags

Workflows (19)

Taverna 1 Original Uploader Wassinki	Mapping OligoNucleotides to an assembly (v7) Created: 13/02/09 @ 09:05:35 \| Last updated: 13/02/09 @ 09:08:20 Credits: Wassinki Pieter Neerincx Attributions: Blat against ENSEMBLE Danio_rerio_Genome BlatBlastCombi Blast against ENSEMBLE Danio_rerio_Genome AppendToFile Test Input for Mapping oligonucleotides to an assembly Input for Mapping oligonucleotides to an assembly License: Creative Commons Attribution-Share Alike 3.0 Unported License Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ... Rating: 0.0 / 5 (0 ratings) \| Versions: 7 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 554 times \| Downloaded: 105 times Tags (7): biomart \| BLAST \| blat \| ensembl \| microarray \| r \| rshell	View Download (v7)
Taverna 1 Original Uploader Kieren Lythgow	Biomart Protein Sequence Retrieval (v1) Created: 09/03/09 @ 11:38:10 Credits: Kieren Lythgow License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow queries Biomart to retrieve the Ensembl gene id, protein id, gene name, description and amino acid sequence from the Ensembl Homo sapiens dataset. The user needs to specify a defined chromosomal region i.e. Chromo = 1, Start = 100000000, End = 250000000. This returns all unique entries in FASTA format. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 176 times \| Downloaded: 46 times Tags (5): biomart \| ensembl \| FASTA \| protein \| sequence	View Download (v1)
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: 145 times \| Downloaded: 30 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: 63 times \| Downloaded: 30 times Tags (15): arabidopsis \| chromosome \| crop \| ensembl \| kegg \| loci \| locus \| nucleotide \| pathway \| pathways \| plants \| qtl \| thaliana \| trait \| uniprot	View Download (v1)
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: 34 times \| Downloaded: 20 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: 134 times \| Downloaded: 21 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	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: 150 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	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: 33 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: 72 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: 19 times \| Downloaded: 13 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	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: 25 times \| Downloaded: 14 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 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: 102 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)
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: 4941 times \| Downloaded: 839 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 2 Original Uploader Rafael C. Jimenez	Biomart datasets for the Ensembl Genes mart service (v1) Created: 03/10/11 @ 10:17:40 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieve Biomart datasets for the Ensembl Genes mart service (one dataset per specie). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 6 times \| Downloaded: 5 times Tags (3): biomart \| datasets \| ensembl	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Find Orthologs for proteins in Ensembl (v1) Created: 03/10/11 @ 14:33:04 \| Last updated: 03/10/11 @ 14:33:07 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Find Orthologs for proteins in Ensembl using biomart. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 5 times \| Downloaded: 7 times Tags (4): biomart \| ensembl \| orthologous \| protein	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Find orthologs using a uniprot accession (v1) Created: 14/10/11 @ 13:07:41 \| Last updated: 14/10/11 @ 13:07:44 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Find orthologs based on ensembl information using as input/output uniprot accession Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 7 times Tags (3): ensembl \| orthologous \| uniprot	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Find orthologs using a list of uniprot accessions (v1) Created: 14/10/11 @ 13:12:36 \| Last updated: 14/10/11 @ 13:12:39 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Find orthologs based on ensembl information using as input/output uniprot accessions Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 6 times \| Downloaded: 4 times Tags (3): ensembl \| orthologous \| uniprot	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	Import and convert gene list (v1) Created: 15/01/12 @ 10:23:33 \| Last updated: 12/03/12 @ 11:59:15 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: 14 times \| Downloaded: 35 times Tags (2): ensembl \| gene	View Download (v1)
Taverna 2 Original Uploader Paul martin	Define Associated Regions and Genes (v2) Created: 08/02/12 @ 16:08:08 \| Last updated: 09/05/12 @ 09:52:18 Credits: Paul martin License: Creative Commons Attribution-Share Alike 3.0 Unported License Defines regions and genes from associated SNPs A JAVA MySQL connector is required to run the workflow and must be placed in the $TAVERNA_HOME/lib directory. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 13 times Tags (14): association \| disease \| disease-associated genes \| ensembl \| gene \| genes \| genome wide association studies \| gwas \| mapping \| ncbi \| ngs \| sequencing \| snp \| ucsc	View Download (v2)

Packs (3)

Creator:

Wassinki

Package: mapping oligonucleotides to an assembly

Created: 11/12/08 @ 12:02:47 | Last updated: 22/01/09 @ 09:06:26

This package contains all elements required to run the RShell use case "Mapping oligonucleotides to an assembly"

5 items in this pack

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Creator:

Paul Fisher

Trichuriasis induced Colitis

Created: 16/02/11 @ 12:49:21 | Last updated: 16/02/11 @ 15:26:36

This pack contains the workflows and data relating to Trichuriasis induced colitis.

5 items in this pack

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Tags:

annotation
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chromosome
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controlled vocabulary
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cosine vector space
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data integration
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data-driven
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dresden
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efetch
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enrichment
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ensembl
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entity recognition
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esearch
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evidence
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gene expression
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gene identifier
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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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medline
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microarray
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mining
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pathway
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pathway-driven
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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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re-use
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significance
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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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trichuris muris

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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

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Files (2)

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: 18 times | Downloaded: 13 times

Tags:

ensembl
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gene
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geneid
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qtl

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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

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Tag Results

Items tagged with "ensembl" (24)