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Items tagged with "uniprot" (44)

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Blob Kegg-Uniprot-Entrez cross-references

Created: 2009-04-08 19:23:53 | Last updated: 2009-08-10 12:08:00

Credits: User 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.

File type: Plain text

Comments: 0 | Viewed: 62 times | Downloaded: 76 times

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Blob Ensembl gene report

Created: 2009-04-08 19:30:15 | Last updated: 2009-08-10 11:05:59

Credits: User 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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Blob Ondex and Taverna Tutorial

Created: 2009-10-22 13:50:53 | Last updated: 2009-10-22 13:51:51

Credits: User 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

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Packs (1)
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Pack Towards Genotype-Phenotype Correlations


Created: 2009-04-08 13:14:54 | Last updated: 2009-08-11 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...

20 items in this pack

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Workflows (40)

Workflow getFragWithClosure (2)

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getFragment with closure "workflow", actually just one service, but need example inputs for smiles string, group and closure parameters.

Created: 2007-10-03

Workflow getFragWithClosure (2)

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Bit of a hack, but it works now, adds trailing "%90" to the output.

Created: 2007-10-03

Workflow Parse UniProt text file (2)

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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

Created: 2007-10-03 | Last updated: 2009-12-03

Workflow Mouse Microarray Analysis (3)

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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

Created: 2007-10-03 | Last updated: 2009-12-03

Workflow kegg_gene_to_swissprot_identifier (1)

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Takes a KEGG gene identifier, e.g. sce:YAL038W (yeast pyruvate kinase) and converts to the corresponding Swissprot identifier.

Created: 2007-11-27 | Last updated: 2007-11-28

Credits: User Sirisha Gollapudi

Workflow Human Microarray Analysis (1)

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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  

Created: 2008-02-08 | Last updated: 2009-12-03

Credits: User Paul Fisher

Workflow What is Paget's disease sparql query example (3)

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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  

Created: 2009-01-20

Credits: User Francois Belleau

Workflow What is known about HIV using Bio2RDF's SP... (2)

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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...

Created: 2009-02-05 | Last updated: 2009-02-05

Credits: User Francois Belleau

Workflow Pathways and Gene annotations for Arabidop... (2)

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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.

Created: 2009-03-06 | Last updated: 2009-12-03

Credits: User Paul Fisher User Peter Li

Attributions: Workflow Pathways and Gene annotations for QTL region

Workflow Arabidopsis thaliana Microarray Analysis (1)

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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.

Created: 2009-07-08

Credits: User Paul Fisher

Workflow Arabidopsis thaliana QTL Analysis (1)

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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. ...

Created: 2009-07-08 | Last updated: 2009-12-14

Credits: User Paul Fisher

Workflow Clean UniProt Filter (1)

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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.

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Pathways and Gene annotations for QTL region (2)

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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 ...

Created: 2009-11-20 | Last updated: 2009-11-20

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

Workflow What is [query] from NCBI, EBI, UniProt an... (2)

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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...

Created: 2009-11-03 | Last updated: 2009-11-03

Credits: User Francois Belleau

Workflow Triplify namespace list from global search... (1)

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No description

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Workflow Triplify UniProt database external referen... (2)

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Get UniProt external database list from http://www.ncbi.nlm.nih.gov/projects/collab/db_xref.html 

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: User Francois Belleau

Workflow microRNA to KEGG Pathways and Abstracts (1)

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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

Created: 2010-03-17

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

Workflow Uniprot Protein Visualization (1)

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Jmol 3D visualization of a protein structure.

Created: 2010-05-01 | Last updated: 2010-05-01

Workflow Pathways and Gene annotations for QTL region (1)

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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...

Created: 2010-11-15 | Last updated: 2010-11-16

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

Workflow Pathways and Gene annotations for RefSeq ids (1)

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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.

Created: 2010-11-15 | Last updated: 2010-11-15

Credits: User Paul Fisher

Workflow EBI_NCBI_BLAST (4)

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This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. This workflow uses the new EBI services. They are asynchronous and so require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now wo...

Created: 2011-01-17 | Last updated: 2013-05-30

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

Workflow Pathways and Gene annotations forQTL region (1)

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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...

Created: 2011-01-21 | Last updated: 2011-01-21

Credits: User Paul Fisher

Workflow Pathways and Gene annotations forQTL region (1)

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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.

Created: 2011-03-24 | Last updated: 2011-03-24

Credits: User Paul Fisher

Workflow KEGG Pathways and Additional Information f... (2)

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Takes in a tab-delimited BLAST file and finds additional information about the target proteins from KEGG, Gene Ontology, Interpro and PubMed.

Created: 2011-03-29 | Last updated: 2011-03-30

Credits: User Morgan Taschuk

Attributions: Workflow extract_uniprot_embl_gi.xml

Workflow Compile Protein FASTA from Target to Drug ... (1)

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Uses a tab-delimited file with protein target and drug information (created in Ondex) to compile a protein FASTA file including each target.

Created: 2011-03-30 | Last updated: 2011-03-30

Credits: User Morgan Taschuk User Andrewsmeaton

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Workflow Get names of proteins similar to RNA bindi... (1)

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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.

Created: 2011-05-18 | Last updated: 2011-05-18

Credits: User hindlem

Workflow Pathways and Gene annotations forQTL region (2)

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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 ...

Created: 2011-03-17 | Last updated: 2011-08-30

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

Workflow Pathways and Gene annotations for QTL region (7)

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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...

Created: 2009-11-19 | Last updated: 2012-09-07

Credits: User Paul Fisher

Workflow Find orthologs using a uniprot accession (1)

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Find orthologs based on ensembl information using as input/output uniprot accession

Created: 2011-10-14 | Last updated: 2011-10-14

Credits: User Rafael C. Jimenez

Workflow Find orthologs using a list of uniprot acc... (2)

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Find orthologs based on ensembl information using as input/output uniprot accessions

Created: 2011-10-14 | Last updated: 2014-06-03

Credits: User Rafael C. Jimenez

Workflow Get homologous from NCBI homoloGene using ... (1)

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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

Created: 2011-10-14 | Last updated: 2011-10-14

Credits: User Rafael C. Jimenez

Workflow Get homologous from NCBI homoloGene using ... (1)

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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

Created: 2011-10-14 | Last updated: 2011-10-27

Credits: User Rafael C. Jimenez

Workflow BioAID_ProteinDiscovery (8)

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The 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.

Created: 2010-05-10 | Last updated: 2013-08-16

Credits: User Marco Roos Network-member AID

Workflow Get a list of proteins from a Gene Ontolog... (1)

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Get a list of UniProt proteins that have been annotated with the same Gene Ontology (GO) term. This workflow uses the the QuickGO service

Created: 2012-02-20 | Last updated: 2012-02-22

Credits: User Rafael C. Jimenez

Workflow Match gene lists based on information in l... (7)

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[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...

Created: 2012-04-17 | Last updated: 2012-04-25

Credits: User Marco Roos User Reinout van Schouwen User Eleni User Kristina Hettne Network-member BioSemantics

Attributions: Workflow Match concept profiles Workflow Explain concept scores

Workflow Blast_and_Interproscan (5)

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This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. The sequences for the top 10 hits are retrieved from the UniProt database and analysed using InterproScan (also from the EBI) to determine functional domains and motifs in each sequenc...

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: User Katy Wolstencroft

Workflow Get ENSEMBL cross-references for UniProt IDs (1)

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This small workflow uses the PICR (http://www.ebi.ac.uk/Tools/picr/) WDSL Web Service to look up ENSEMBL (ENSP) cross-references for UniProt IDs. The input is a list of UniProt IDs and the output a corresponding list of ENSEMBL IDs. This instance of the workflow specifically uses the ENSEMBL_HUMAN database and taxonID 9606 (Homo sapiens).

Created: 2015-11-16

Credits: User Magnus Palmblad

Workflow UniProt Protein Protein Network (1)

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This workflow uses the Europe PMC Web Services searchPublications and getDatabaseLinks to reconstruct a protein-protein network based on co-occurence in the scientific literature, arbitrary filtered by a PubMed query, e.g. the word "complex" appearing in the title or abstract. The workflow also looks up the second degree connections, i.e. proteins co-occuring with proteins co-occuring with the protein given as input, but not with this protein itself. The output is a (1) Pajek graph file, a GM...

Created: 2015-12-04

Credits: User Magnus Palmblad User Yassene

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Workflow GOgetter (2)

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Retrieves all GO terms with experimental evidence associated with the given genelist. A GO term may apear multiple times in the resulting list if it is associated with multiple genes.

Created: 2016-06-10 | Last updated: 2016-06-10

Credits: User Davy Cats User Tom Rosman

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Workflow GOgetter (no merge) (1)

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Retrieves all GO terms (with experimental evidence) associated with the given genelist. The GO terms are returned in a list per gene.

Created: 2016-06-10

Credits: User Davy Cats User Tom Rosman

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Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/516


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