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Kegg Pathway release

Created: 2009-04-08 19:25:05 | Last updated: 2009-08-10 12:06:18

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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fits/votable to SQL converter

Created: 2013-12-05 11:53:20 | Last updated: 2013-12-19 10:24:00

Credits: Alexey Mints

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: text/x-python

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SyMBA: Systems and Molecular Biology Data ...

Unique name: symba
Created: Wednesday 12 September 2007 11:30:41 (UTC)

0 shared items   |   0 announcements

Bio2RDF: Rdfiser for Bind protein interact... (1)

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CONSTRUCT{ <bmuri>, ?p, ?o . } FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE { <bmuri>, ?p, ?o . }

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

fetch_fasta (1)

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This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain. Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree. The output is prese...

Created: 2009-03-20 | Last updated: 2009-03-20

Credits: Jumblejumble

Identify_strain_and_phylogenetic_tree (1)

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No description

Created: 2009-03-20 | Last updated: 2009-03-20

Credits: Aailyso Hamish McWilliam AID

Search InChI in NCBI eSearch (pccompound) (1)

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This workflow takes in a search term (e.g. InChI) for search in PubChem pccompound database. The result is an xml file containing summary information about the search term and also a compound image and the compound webpage fetched from Pubchem.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

MassBank to KEGG (1)

Workflow that queries MassBank DB to retrieve database identifiers (KEGG, PubChem, InChI) and continue search with them to retrieve pathways from KEGG for given compound identifier,searches PubChem via eutils and PUG, queries ChemSpider for compound information and image. Note: Usage of ChemSpider web services requires a valid security token - receive one by registering at ChemSpider (look at your profile to see your token)

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

DOI Files (1)

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This workflow generates additional files required for handling DOI creation: the DOI URL mapping required for the DOI deposit, and a set of sql update statements to insert the DOIs into an eprints database. Note that it is extremely important for this workflow to use the same CSV file as was used with the DOI record generator, as well as the same seed number.

Created: 2009-06-05

Credits: Andrea Wiggins

Attributions: DOI Record Generator

Example 3 (1)

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Search in the Datenbank SWISS the Sequence 1220173

Created: 2009-10-20

Credits: Ruben

Get Gene Ids for Human (1)

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This workflow gets a list of gene ids (number depending on Ret_Max_value variable) for Homo sapiens. The species may be changed according to that desired, by altering the term_value string constant

Created: 2010-02-04 | Last updated: 2010-02-04

Credits: Paul Fisher

Tutorial Taverna (1)

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No description

Created: 2010-02-26 | Last updated: 2010-02-26

Credits: Rodriguez

Taverna Tutorial2 (1)

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No description

Created: 2010-02-26 | Last updated: 2010-02-26

Credits: Rodriguez

Attributions: EBI_InterProScan for Taverna 2

Calculating frequencies of gene expression... (1)

This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script

Created: 2010-03-15

Credits: Peter Li

blastp of target vs source database (1)

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This worlflow allows the user to input two sets of proteins in fasta format. One file is converted to a database using formatdb, the set is blasted against this database to test for Blast hits. Users is able to set eValue and destination of files for database and blast file. Arguments can be added to either formatdb or blast in beanshell supplied. Blast and formatdb must be installed locally and the correct filepaths for these applications must entered into the workflow accordingly.

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Ian Laycock nclteamc

Attributions: fetchEnsemblSeqsAndBlast

Get list of chemspider databases (1)

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Returns a list of databases catalogedReturns a list of databases cataloged by ChemSpider

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Create an OpenTox API dataset and add mole... (2)

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 Bioclipse script that creates a data set  at an OpenTox API capable server, and adds molecules to it.

Created: 2010-08-04 | Last updated: 2010-11-13

Credits: Egon Willighagen

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: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

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: Paul Fisher

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: Katy Wolstencroft Hamish McWilliam

Attributions: EBI_NCBI_BLAST

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: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

Example of Execute_SQL_Query with parameters (1)

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This workflow connects to a mysql on localhost, queries the "world" database which is one of the test databases on MySQL 5.5, queries it about which countries have Dutch as a language, and emits answers in both Lists and in xml. This workflow is intended as an example to help you see the syntax for the various inputs to this local service beanshell. see: http://www.mygrid.org.uk/dev/wiki/display/taverna/Execute+SQL+Query for instructions on jars, dependencies etc. The jar used he...

Created: 2012-03-16 | Last updated: 2012-03-16

Credits: Helen Hulme

Example of jdbc (1)

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No description

Created: 2012-05-24 | Last updated: 2012-05-24

List Concept Sets (3)

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Pupose: The workflow returns a list of all Concept Set IDs currently available in the database. The Concept Sets have an hierarchical structure that can be inferred by referring to the parent Concept Set ID.

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

Credits: Kristina Hettne Marco Roos Reinout van Schouwen Martijn Schuemie BioSemantics

Intialize Sample (2)

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This workflow saves a tabular *.pckl Python pickle dataset in the local file system, containing values calculated on physical parameters associated to potential companions of a sample of target galaxies. These original physical parameters are extracted from a postgreSQL database, containing information of all galaxies covered by the SDSS spectroscopic survey. The workflow first access the external database located in the AMIGA server and selects the target galaxies from the sample (those havi...

Created: 2013-01-04 | Last updated: 2013-01-05

Credits: Juandesant Jsm

Environment (2)

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From a previously selected cube of galaxies residing in a remote database, we provide extragalactic environment parameters for all galaxies sample. This workflow takes as input the path of the tabular *.pckl Python pickle dataset created in the previous workflow, as well as the database connection settings and several criteria on how to filter the potential companions of the target galaxies. It provides a file with the SDSS identifiers of each target galaxy of the sample, environmental estim...

Created: 2013-01-04 | Last updated: 2013-01-14

Credits: Juandesant Jsm

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

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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: Kristina Hettne Eleni Harish Dharuri Reinout van Schouwen Marco Roos Martijn Schuemie BioSemantics

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

Match concept profiles (6)

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

Created: 2011-12-02 | Last updated: 2014-07-14

Credits: Marco Roos Kristina Hettne Martijn Schuemie Reinout van Schouwen

Match concept profiles with predefined set (2)

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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: Kristina Hettne Marco Roos Reinout van Schouwen BioSemantics

GWAS to biomedical concept (3)

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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: Kristina Hettne Harish Dharuri Marco Roos Reinout van Schouwen

plotGenomic (1)

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This workflow returns a graphical representation of selected Nencki Genomics Database (www.nencki-genomics.org) content in the ± 10 kb flank of the transcription start site of a chosen gene. More precisely, it returns instances of selected area types, and instances of selected motif types that intersect any of the returned area instances. The results are returned as three files: a pdf file with the plot, and two tab-separated files with the details of areas and motifs shown in the plot. P...

Created: 2013-10-07

Credits: mdabr

showDatasetsGenomic (1)

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Shows all the datasets available in the Nencki Genomics Database (www.nencki-genomics.org). Click 'Use examples' to see all the datasets, separated into datasets of TFBS motifs, and all the remaining datasets (areas), the latter including data from Ensembl funcgen and (thus) Encode. Publication doi: 10.1093/database/bat069

Created: 2013-10-07

Credits: mdabr

PostgresSQL/PostGIS Database for Historians (1)

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This diagram depicts the steps that the 'Mapping the Jewish Communities of the Byzantine Empire' project took to populate the project's PostgreSQL/PostGIS database. 

Created: 2013-11-27 | Last updated: 2013-11-27

Credits: Gethin Rees

DatabaseID to ConceptID (7)

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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: Marco Roos Martijn Schuemie Reinout van Schouwen BioSemantics

Filter concepts with profiles (4)

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Purpose: Filter a list of concept id(s) by returning only those with a concept profile in the database.

Created: 2012-09-14 | Last updated: 2014-07-14

Credits: Kristina Hettne Reinout van Schouwen Martijn Schuemie BioSemantics

All-vs-All blastP commands (1)

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Creates all the necessary command-line commands to execute all-vs-all blastP from the given FASTA files. Includes making the necessary database. Does not execute the commands.  For OSX and UNIX/Linux only (due to path separator).

Created: 2015-04-17

Credits: Aurora Cain