Tag Results

Items tagged with "GO" (23)

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


Packs (2)
Creator

Pack wf4ever Deliverable 6.3 Pack


Created: 2011-12-02 09:31:26 | Last updated: 2011-12-02 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: 60 times | Downloaded: 0 times

Tags:

Creator

Pack Functional annotation of SNPs using next-generation ...


Created: 2012-06-26 10:41:38 | Last updated: 2015-09-01 14:31:18

This pack implements the concept profile matching pipeline in the knowledge discovery tool Anni (http://biosemantics.org/anni), and adapts it to interpret the top SNPs from a GWAS. The underlying literature and concept profile databases are the same as the for the current version of Anni (2.1). The pack consists of three main workflows (http://www.myexperiment.org/workflows/2999, http://www.myexperiment.org/workflows/2973, http://www.myexperiment.org/workflows/2972). Workflow 2999 returns a ...

12 items in this pack

Comments: 0 | Viewed: 163 times | Downloaded: 17 times

Tags:

Workflows (21)

Workflow EBI_OLS_TermInfo (1)

Thumb
Get details of an ontology term given its identifer. This workflow uses the EBI's Ontology Lookup Service (OLS) to get the details of the ontology term. The OLS suports a wide range of biological and bioinformatic ontologies. See http://www.ebi.ac.uk/ontology-lookup/ for more information.

Created: 2008-07-09

Credits: User Hamish McWilliam

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

Thumb
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 Load GO terms in the triplestore (1)

Thumb
No description

Created: 2009-05-01

Credits: User Francois Belleau

Workflow Clean GO Filter (1)

Thumb
This workflow filters an Ondex graph, by cleaning up any GO terms 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.

Created: 2009-08-19

Credits: User Paul Fisher

Workflow Triplify GO database external reference [... (1)

Thumb
Get GO external database list from http://www.geneontology.org/doc/GO.xrf_abbs 

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

Credits: User Francois Belleau

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

Thumb
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 Gene expression interpretation by the Glob... (1)

Thumb
This workflow adds meaning to gene expresion values by performing a standard and a literature weighted Global Test. Gene expression is expected to be from Affymetrix microarrays, for which an RMA normalization and entrez Gene ID mapping/summation is performed. Original workflow is by Dennis Leenheer, edits by Marco Roos. Scripts by Kristina Hettne, acknowledging Rob Jellier, Jelle Goeman, and Peter-Bram 't Hoen. The workflow was created for the LUMC BioSemantics group, part of the Human Gen...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: User Marco Roos

Workflow [untitled] (1)

Thumb
This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: User Dennis Leenheer

Uploader

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

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

Thumb
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 DatabaseID to ConceptID (7)

Thumb
Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Comments: Database: one of CAS, DRUG, etc. The supported databases are listed below (database, description, example). CAS, Chemical Abstracts Service registry number, 64-17-5. DRUG, Drug Bank, DB00316. AF, Affymetrix, 200007_at. CHEB, ChEBI, 16236. CHID, ChemIDplus, 0000050000. EG, Entrez-Gene, 3064. GO, Gene Ontol...

Created: 2012-06-25 | Last updated: 2014-07-14

Credits: User Marco Roos User Martijn Schuemie User Reinout van Schouwen Network-member BioSemantics

Workflow Get a list of proteins annotated with an O... (3)

Thumb
A service to look for models in BioModels using an Ontology Id as input. First the workflow will look in QuickGO for UniProt accessions annotated with the provided Ontology Id. Then it will look for models using the list of proteins. If one of the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.

Created: 2012-08-22 | Last updated: 2013-07-10

Credits: User Rafael C. Jimenez

Workflow SNPs to Concept Set through Concept Profil... (6)

Thumb
Purpose: Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www...

Created: 2012-06-26 | Last updated: 2013-02-05

Credits: User Kristina Hettne User Eleni User Harish Dharuri User Reinout van Schouwen User Marco Roos User Martijn Schuemie Network-member BioSemantics

Attributions: Workflow Find Supporting Documents Workflow SNP_ID2EntrezGene_ID Workflow DatabaseID to ConceptID Workflow Match gene lists based on information in literature Workflow Match concept profiles Workflow Explain concept scores

Workflow Match concept profiles with predefined set (2)

Thumb
Purpose of workflow: The workflow can be used to match a set of concept profiles with predefined set of concept profiles. Result: A list of concepts ordered by their match to the query concept profiles.

Created: 2013-02-05 | Last updated: 2014-07-14

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

Workflow GWAS to biomedical concept (3)

Thumb
Genome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow ...

Created: 2013-04-15 | Last updated: 2014-07-14

Credits: User Kristina Hettne User Harish Dharuri User Marco Roos User Reinout van Schouwen

Workflow Mapping to ontologies (Gene table) (1)

Thumb
This workflow is designed to classify an input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input file can be any gene or protein table.At the first step, the input table is converted into a table with Ensembl Gene IDs.This table with Ensembl Gene Ids is subjected to functional classification, which is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: User geneXplain

Workflow Use Case C, Worflow 4 (1)

Thumb
Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  Requirements:- Knime v2.9- Open PHACTS Knime nodes 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts.utils.json_1.0.0.zip" and unzip it in the plugins folder of your KNIME installation- Download ...

Created: 2014-05-27 | Last updated: 2014-11-25

Credits: User Emiliano Cuadrado User Joseline Ratnam User Daniela Digles Network-member Open PHACTS

Workflow FunctionalClusterDavid (1)

Thumb
This workflow takes a list of Entrez Gene IDs as input and submits them to the DAVID REST API for functional clustering using OG annotaiton, biological pathways and disease associations. Used for analysing a set of genes (i.e. those differentially expressed for a particular disease condition).

Created: 2014-09-05

Credits: User Katy Wolstencroft

Workflow SNP identification and evaluation for Diab... (1)

Thumb
This workflow gathers SNP information for a gene set of Diabetes Type II phenotype using BioMart queries. Furthermore, GO Terms and functional annotation clustering are defined for this gene set using FunctionalClusterDavid workflow. 

Created: 2015-06-23

Credits: User Nikolaos Bismpikos User Katy Wolstencroft

Attributions: Workflow FunctionalClusterDavid

Uploader

Workflow GOgetter (2)

Thumb
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

Uploader

Workflow GOgetter (no merge) (1)

Thumb
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

What is this?

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/221


Alternative Formats

HTML
RDF
XML