About | Mailing List | Publications

Give us Feedback |

Invite

Home
»
Tags
»
annotation

Tag Results

Items tagged with "annotation" (11)

Note: some items may not be visible to you, due to viewing permissions.

Workflows (7)

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: 594 times \| Downloaded: 205 times Tags (6): affymetirx \| affymetrix \| annotation \| disease \| gene \| graves	View Download (v2)
Taverna 1 Original Uploader Alan Williams	Fetch Dragon images from BioMoby (v3) Created: 05/03/08 @ 14:09:35 \| Last updated: 14/07/10 @ 16:46:37 Credits: Tomoinn License: Creative Commons Attribution 3.0 Unported License Fetch images and annotations of snapdragons Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 305 times \| Downloaded: 108 times Tags (8): annotation \| bioinformatics \| biomoby \| example \| image \| mygrid \| snapdragon \| taverna	View Download (v3)
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: 25 times \| Downloaded: 1 time Tags (10): annotation \| filter \| graph \| ondex \| orthologue \| ovtk \| oxl \| pfam \| protein \| terms	View
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 1 Original Uploader EdwardK...	Fetch Dragon images from BioMoby (v1) Created: 14/07/10 @ 16:20:46 \| Last updated: 14/07/10 @ 16:20:48 Credits: EdwardKawas Tomoinn Attributions: Fetch Dragon images from BioMoby License: Creative Commons Attribution-Share Alike 3.0 Unported License Fetch images and annotations of snapdragons Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 11 times Tags (8): annotation \| bioinformatics \| biomoby \| example \| image \| mygrid \| snapdragon \| taverna 1	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: 64 times \| Downloaded: 19 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 Rafael C. Jimenez	DAS features retrieval (v2) Created: 01/06/11 @ 17:10:43 \| Last updated: 01/06/11 @ 17:57:45 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieve Protein or Genome features (annotations) using the Distributed Annotation System (DAS). Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 4 times Tags (3): annotation \| das \| sequence	View Download (v2)

Packs (1)

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

Comments: 0 | Viewed: 16 times | Downloaded: 2 times

Tags:

annotation
|
chromosome
|
controlled vocabulary
|
cosine vector space
|
data integration
|
data-driven
|
dresden
|
efetch
|
enrichment
|
ensembl
|
entity recognition
|
esearch
|
evidence
|
gene expression
|
gene identifier
|
genotype
|
kegg
|
Kegg Pathways
|
KeggID
|
literature
|
loci
|
locus
|
medline
|
microarray
|
mining
|
pathway
|
pathway-driven
|
phenotype
|
pubmed
|
qtl
|
quanitative
|
ranking
|
re-use
|
significance
|
term
|
term extraction
|
terms
|
text
|
text mining
|
text mining; term extraction; entity recognition
|
trait
|
trichuris muris

View

Download

Groups (1)

Administrator:

Tony Linde

SKUA

Unique name: skua Created: Wednesday 09 January 2008 @ 17:49:07 (GMT)

SKUA is a JISC-funded project (Jan'08-Jun'09) which intends the creation of a semantic infrastructure for astronomy based on the organisation of assertion services with relatively simple interfaces. As a testbed for these services, we propose a social application called Spacebook in which individuals will be able to create and share queries, workflows and assertions about VO resources, in addit...

0 shared items | 0 announcements

Members (1):

Tony Linde

Tags:

View

Files (2)

Uploader:

Paul Fisher

Ondex and Taverna Tutorial

Created: 22/10/09 @ 13:50:53 | Last updated: 22/10/09 @ 13:51:51

Credits: George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Biological Data Integration Using Ondex and Taverna: A Tutorial 25/26th November 2009 The University of Manchester The Ondex SABR project (http://ondex.org/sabr.html) invite you to a two-day tutorial that aims to show participants how to use Ondex and Taverna to perform common biological data collection, integration and visualisation tasks.

File type: Word document

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 30 times | Downloaded: 24 times

Tags: