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Items tagged with "uniprot" (39)

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Workflows (35)

Taverna 1 Original Uploader Duncan Hull	getFragWithClosure (v2) Created: 03/10/07 @ 18:36:25 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License getFragment with closure "workflow", actually just one service, but need example inputs for smiles string, group and closure parameters. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 37 times \| Downloaded: 37 times Tags (4): tRNA \| ugi \| uniprot \| unitary matrix	View Download (v2)
Taverna 1 Original Uploader Duncan Hull	getFragWithClosure (v2) Created: 03/10/07 @ 18:36:26 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License Bit of a hack, but it works now, adds trailing "%90" to the output. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 42 times \| Downloaded: 31 times Tags (5): ugi \| uniprot \| unitary matrix \| up-and-down \| uracil	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: 118 times \| Downloaded: 82 times Tags (1): uniprot	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: 517 times \| Downloaded: 135 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 Sirisha Gollapudi	kegg_gene_to_swissprot_identifier (v1) Created: 27/11/07 @ 11:53:11 \| Last updated: 28/11/07 @ 12:58:38 Credits: Sirisha Gollapudi License: Creative Commons Attribution-Share Alike 3.0 Unported License Takes a KEGG gene identifier, e.g. sce:YAL038W (yeast pyruvate kinase) and converts to the corresponding Swissprot identifier. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 117 times \| Downloaded: 49 times Tags (5): gene identifier \| kegg \| pathways \| swissprot \| uniprot	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: 276 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 2 Original Uploader Francois Belleau	What is Paget's disease sparql query example (v3) Created: 20/01/09 @ 03:34:08 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License SELECT distinct ?s1 FROM <http://atlas.bio2rdf.org/sparql> WHERE { ?s1 ?p1 ?o1 . ?o1 bif:contains "paget" . FILTER( regex(?s1, "omim") OR regex(?s1, "geneid") OR regex(?s1, "uniprot")) } followed by SELECT ?type1, count() FROM <http://localhost:8890/sparql> WHERE { ?s1 ?p1 ?o1 . ?o1 bif:contains "paget" . ?s1 Rating:* 3.0 / 5 (1 rating) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 291 times \| Downloaded: 70 times Tags (8): bio2rdf \| example \| GO \| OMIM \| pubmed \| sparql \| text_mining \| uniprot	View Download (v3)
Taverna 2 Original Uploader Francois Belleau	What is known about HIV using Bio2RDF's SPARQL endpoints ? (v2) Created: 05/02/09 @ 06:13:53 \| Last updated: 05/02/09 @ 06:15:22 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched. The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert mode into the graph. Once the mashup is built, two SPARQL queries analyze the obtained graph. Finally you can submit queries to the RDF mashup about HIV as you like. Enjoy. This is the queries present in t... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 217 times \| Downloaded: 68 times Tags (8): bio2rdf \| geneid \| hiv \| OMIM \| pubmed \| sparql \| uniprot \| virtuoso	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: 224 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	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 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: 13 times \| Downloaded: 1 time Tags (6): filter \| graph \| ondex \| ovtk \| oxl \| uniprot	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 2 Original Uploader Francois Belleau	What is [query] from NCBI, EBI, UniProt and KEGG ? (v2) Created: 03/11/09 @ 04:29:15 \| Last updated: 03/11/09 @ 04:29:19 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License test values: query = paget disease query = pdb4 query = hk1 query = h1n1 This rdfiser query those four federated search services EB-Eye, KEGG LinkDB, NCBI Entrez and UniProt knowledgebase. RDF triples are returned for search statistics with Bio2RDF normalised URIs. This workflow should be used responsibly because it can generate high load at the provider resources. test values: query = paget disease query = pdb4 query = hk1 query = h1n1 query = paget disease query = pdb4 query = hk1 que... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 125 times \| Downloaded: 28 times Tags (8): bio2rdf \| cognoscope \| eb-eye \| kegg \| ncbi \| rdfiser \| search \| uniprot	View Download (v2)
Taverna 2 Original Uploader Francois Belleau	Triplify namespace list from global search services from EBI, KEGG, NCBI and UniProt [myexperiment:search_services_namespace2rdf] (v1) Created: 30/11/09 @ 21:38:23 \| Last updated: 30/11/09 @ 21:44:57 Credits: Francois Belleau 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: 22 times \| Downloaded: 13 times Tags (7): banff_manifesto \| bio2rdf \| cognoscope \| ebi \| kegg \| ncbi \| uniprot	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify UniProt database external reference [myexperiment:uniprot_xref_namespace2rdf] (v2) Created: 01/12/09 @ 04:08:08 \| Last updated: 01/12/09 @ 04:09:39 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License Get UniProt external database list from http://www.ncbi.nlm.nih.gov/projects/collab/db_xref.html Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 13 times Tags (4): banff_manifesto \| bio2rdf \| uniprot \| xref	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 David Withers	Uniprot Protein Visualization (v1) Created: 01/05/10 @ 20:29:37 \| Last updated: 01/05/10 @ 20:40:10 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License Jmol 3D visualization of a protein structure. Rating: 5.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 1 \| Comments: 1 \| Citations: 0 Viewed: 168 times \| Downloaded: 46 times Tags (3): pdb \| sadi \| 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: 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 Katy Wolstencroft	EBI_NCBI_BLAST (v1) Created: 17/01/11 @ 12:51:58 \| Last updated: 17/01/11 @ 12:52:03 Credits: Katy Wolstencroft Hamish McWilliam Attributions: EBI_NCBI_BLAST License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs an NCBI blast at the EBI. It uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 75 times \| Downloaded: 34 times Tags (13): async \| asynchronous services \| BLAST \| blastp \| database \| ebi \| example \| looping \| ncbi \| ncbi blast \| protein sequence \| sequence \| 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 (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: 23 times \| Downloaded: 12 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 Morgan Taschuk	KEGG Pathways and Additional Information from BLAST (v2) Created: 29/03/11 @ 11:16:17 \| Last updated: 30/03/11 @ 16:09:01 Credits: Morgan Taschuk Attributions: extract_uniprot_embl_gi.xml License: Creative Commons Attribution-Share Alike 3.0 Unported License Takes in a tab-delimited BLAST file and finds additional information about the target proteins from KEGG, Gene Ontology, Interpro and PubMed. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 45 times \| Downloaded: 20 times Tags (6): BLAST \| GO \| interpro \| medline \| pathway \| uniprot	View Download (v2)
Taverna 2 Original Uploader Morgan Taschuk	Compile Protein FASTA from Target to Drug file (v1) Created: 30/03/11 @ 10:34:37 \| Last updated: 30/03/11 @ 10:34:40 Credits: Morgan Taschuk Andrewsmeaton License: Creative Commons Attribution-Share Alike 3.0 Unported License Uses a tab-delimited file with protein target and drug information (created in Ondex) to compile a protein FASTA file including each target. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 9 times Tags (3): FASTA \| tab-delimited \| uniprot	View Download (v1)
Taverna 2 Original Uploader hindlem	Get names of proteins similar to RNA binding proteins (Simple example SADI workflow) (v1) Created: 18/05/11 @ 15:24:56 \| Last updated: 18/05/11 @ 15:39:02 Credits: hindlem License: Creative Commons Attribution-Share Alike 3.0 Unported License A very simple demo workflow using some existing SADI services. It finds UniProt proteins of GO function "RNA Binding", it then runs a BLAST service to find similar UniProt proteins and then outputs their names. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 11 times Tags (5): bioinformatics \| BLAST \| GO \| sadi \| 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 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: 4944 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	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 Rafael C. Jimenez	Get homologous from NCBI homoloGene using one UniProt accession (v1) Created: 14/10/11 @ 17:26:32 \| Last updated: 14/10/11 @ 17:26:28 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Get homologous from NCBI homoloGene for one UniProt protein accession. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 4 times Tags (3): homologene \| orthologous \| uniprot	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Get homologous from NCBI homoloGene using a list of UniProt accessions (v1) Created: 14/10/11 @ 17:45:28 \| Last updated: 27/10/11 @ 10:39:21 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Get homologous from NCBI homoloGene for a lsit of UniProt protein accession. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 4 times Tags (3): homologene \| orthologous \| uniprot	View Download (v1)
Taverna 2 Original Uploader Marco Roos	BioAID_ProteinDiscovery (v7) Created: 10/05/10 @ 16:21:09 \| Last updated: 20/03/12 @ 17:16:11 Credits: Marco Roos AID License: Creative Commons Attribution-Share Alike 3.0 Unported License This protein discovery workflow extracts protein names from documents retrieved from MedLine based on a user Query (cf Apache Lucene syntax). The protein names are filtered by checking if there exists a valid UniProt ID for the given protein name. Rating: 0.0 / 5 (0 ratings) \| Versions: 7 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 292 times \| Downloaded: 131 times Tags (12): AIDA \| BioAID \| biorange_nl \| lucene \| protein \| proteins \| pubmed \| search \| text_mining \| text_mining_network \| uniprot \| VL-e	View Download (v7)
Taverna 2 Original Uploader Rafael C. Jimenez	Get a list of proteins from a Gene Ontology (GO) term (v1) Created: 20/02/12 @ 23:00:06 \| Last updated: 22/02/12 @ 21:08:54 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Get a list of UniProt proteins that have been annotated with the same Gene Ontology (GO) term. This workflow uses the the QuickGO service Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 7 times \| Downloaded: 3 times Tags (4): gene ontology \| GO \| quickgo \| uniprot	View Download (v1)
Taverna 2 Original Uploader Marco Roos	Match gene lists based on information in literature (v7) Created: 17/04/12 @ 08:55:46 \| Last updated: 25/04/12 @ 07:54:26 Credits: Marco Roos Reinout van Schouwen Eleni Kristina Hettne BioSemantics Attributions: ExplainScores demo License: Creative Commons Attribution-Share Alike 3.0 Unported License [THIS WORKFLOW IS IN BETA STAGE] This workflow computes the match between two lists of Entrez Gene Identifiers by means of concept profile matching (Jelier et al., van Haagen et al.). The result of this is a list of concepts ordered by their matching score (the length of the list set by maxMatchNr). Of this list the summed scores are explained by computing the concepts that contribute most to the combination of the matching genes. Example to explain (by analogy): When a group of informatic... Rating: 0.0 / 5 (0 ratings) \| Versions: 7 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 27 times \| Downloaded: 6 times Tags (11): association \| bioinformatics \| biology \| concept \| concept mining \| concept web \| literature \| protein \| proteins \| semantic \| uniprot	View Download (v7)

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Paul Fisher

Towards Genotype-Phenotype Correlations

Created: 08/04/09 @ 13:14:54 | Last updated: 11/08/09 @ 14:50:01

It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing large datasets, and represent a framework for the re-use and the explicit declaration of experimental methods. In this pack is a paper which describes the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes.&n...

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Paul Fisher

Kegg-Uniprot-Entrez cross-references

Created: 08/04/09 @ 19:23:53 | Last updated: 10/08/09 @ 12:08:00

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of KEGG gene identifiers, cross-referenced to UniProt and Entrez identifiers. The UniProt and Entrez ids were obtained from BioMart for genes located in the Tir1 QTL region.

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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.

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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.

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