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Supplementary file 5: Percentile scores

Created: 2016-10-25 15:05:47

Credits: Eleni

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Supplementary file 4: Decision about the promoter re...

Created: 2016-10-25 15:05:15

Credits: Eleni

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Supplementary file 3: Gene prioritization

Created: 2016-10-25 15:04:40

Credits: Eleni

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Supplementary file 2: Annotations of CpG containing ...

Created: 2016-10-25 15:03:45

Credits: Eleni

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Supplementary file 1: Unique annotations of genes in...

Created: 2016-10-25 15:01:52

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converter_nanopublications

Created: 2015-04-03 21:08:40

Credits: Eleni BioSemantics

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create nanopublications

Created: 2015-04-03 21:05:56

Credits: Eleni BioSemantics

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workflow sketch Hd chromatin analysis

Created: 2013-08-30 12:01:45 | Last updated: 2013-11-04 19:18:11

Credits: Eleni

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Supplementary information for paper submission @ F10...

Created: 2016-10-25 14:57:58 | Last updated: 2016-10-25 15:06:18

5 items in this pack

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PW2ENS (2)

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This workflow uses the WikiPathways Webservice/API to query to retrieve all ENSEMBL identifers for the given pathway.

Created: 2015-10-02 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

PW2CHEBI (2)

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This workflow uses the WikiPathways Webservice/API to query to retrieve all Chemical Entities of Biological Interest (ChEBI) identifers for the given pathway.

Created: 2015-09-01 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

ListAllWikiPathways (2)

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This workflow retrieves all pathways currently in the WikiPathways database, using the WikiPathways REST API.

Created: 2015-09-01 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

GetWikiPWByENS (2)

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This workflow uses the WikiPathways Webservice/API to query for pathways containing a specific ENSEMBL identifier. The mapping service behind WikiPathways takes care of the identifier mapping, making sure that all relevant results are found even if they were originally reported using a different identifier scheme.

Created: 2015-10-02 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

GetWikiPWByCHEBI (2)

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This workflow uses the WikiPathways Webservice/API to query for pathways containing a specific Chemical Entities of Biological Interest (ChEBI) identifier. The mapping service behind WikiPathways takes care of the identifier mapping, making sure that all relevant results are found even if they were originally reported using a different identifier scheme.

Created: 2015-09-01 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

AllPW2ENS (2)

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This workflow uses the WikiPathways Webservice/API to query to retrieve all ENSEMBL identifers for all pathways and merge them into one, unique list.

Created: 2015-10-02 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

AllPW2CHEBI (2)

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This workflow uses the WikiPathways Webservice/API to query to retrieve all Chemical Entities of Biological Interest (ChEBI) identifers for all pathways and merge them to one, unique list.

Created: 2015-09-01 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

Get properties of drugs for genes by Entre... (3)

Given a Entrez gene_id the workflow extracts features of its protein (e.g. function, cellular localization and name) and properties of specific drugs for this protein (including activity, PSA, RO5, Smiles and molweight). This workflow uses 3 different services of OpenPHACTS (Target Pharmacology, Compound Information, Target Information).

Created: 2015-07-24 | Last updated: 2015-07-28

Credits: Katerina Nosikova Marco Roos Eleni Eelke van der Horst Elizaveta Besedina

Prioritize gene list for the Cure game (1)

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This workflow prioritizes a gene list according to its association with the 'concept_id'. Here we are prioritizing a gene list against breast cancer, in order to try to beat Barney in the game The Cure (http://genegames.org/cure/). Note: Before running this workflow the gene names supplied in the game first needs to be mapped to Entrez gene identifiers. This can be done using either this workflow http://www.myexperiment.org/workflows/3722 or a by performing a search in the NCBI Entrez gene d...

Created: 2015-04-29

Credits: Kristina Hettne Eleni

Attributions: Prioritize gene list

Create nanopublications (1)

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This workflow creates nanopublications for a gene list that is associated to Huntington's Disease

Created: 2015-04-03

Credits: Eleni BioSemantics

Attributions: create nanopublications converter_nanopublications

Prioritize gene list (1)

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This workflow prioritizes a gene list according to its association with the 'concept_id'. In our example here we are prioritizing a gene list to obtain genes that are more closely associated to huntingtin, the cause of huntington's disease

Created: 2015-04-03

Credits: Eleni BioSemantics

List Concept Sets (1)

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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: 2015-04-03

Credits: Eleni BioSemantics

Explain score between two concepts (1)

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Purpose of workflow: This workflow takes two ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage...

Created: 2015-04-03

Credits: Eleni BioSemantics

Get concept suggestions from term (1)

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This workflow suggests concept ids that match the query term. The user can run this workflow with any term of interest as for example "human", "htt", "Transcription" etc, and will get suggestions for concept ids together with descriptions. Then can choose the concept id that matches the best to her/his needs and use it to the rest of the CPA workflows.

Created: 2015-02-18

Credits: Eelke van der Horst Kristina Hettne Marco Roos Eleni

Attributions: Get concept suggestions from term

Map genes to chromosomal location (1)

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This workflow maps a gene list to the genome using the biomart service, and afterwards computes a promoter region for each gene. The user needs to define the promoter region to be computed. The direction that a gene is transcribed is being taken into account in the "compute_promoter_region_with_strand" component. The variable "strand" is responsible for that. NOTE: The library(biomaRt) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

get promoter region + operate on genomic i... (1)

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Finds the overlap between two datasets which contain genomic information (e.g. [gene id], chromosome name, gene start, gene end), plus some statistics. Returns rows of file_1 which overlap with the second file. A kolmogorov smirnov test is applied between the list that overlaps and the one that does not. NOTE: The library(GenomicRanges) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

Get differentially expressed genes for Arr... (1)

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****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133b.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow. Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for ...

Created: 2013-11-04

Credits: Eleni

Get differentially expressed genes for Arr... (1)

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****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133a.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow. Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for ...

Created: 2013-11-04

Credits: Eleni

Download data from array express + create ... (1)

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This workflow uses the array express library to download data from the array express repository and creates two separate files. The gene expression and the phenotype files. The files are saved in the directory that the user has to specify in the input. NOTE: The library(ArrayExpress) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

get promoter region + operate on genomic i... (5)

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This workflow computes a promoter region for each gene that we provide as input carrying the genomic information. Then it computes the overlap between the two datasets that contain genomic information plus some statistics. Returns rows of file_1 which overlap with the second file. A kolmogorov smirnov test is applied between the list that overlaps and the one that does not. Uses the R package GenomicRanges.

Created: 2013-10-04 | Last updated: 2013-11-04

Credits: Eleni

Map genes to chromosomal location for T2WEB (1)

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This workflow maps a gene list on the genome using the biomart service. IMPORTANT NOTE: Keep in mind that for uploading files on t2web, you need to wait few minutes before executing the workflow. That's essential because the file needs first to be uploaded on the server.

Created: 2013-11-04

Credits: Eleni

Annotate gene list with top ranking concepts (4)

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This workflow annotates a comma separated gene list with a predefined concept set as for example Biological processes or Disease/syndrome. To obtain the particular id for each concept set (e.g. "5" for Biological processes), the workflow listPredefinedConceptSets needs to run first. The output provides us with the top (cutoff) concepts that describe our gene list of interest The workflow is using the anni web services .

Created: 2013-12-03 | Last updated: 2015-04-03

Credits: Eleni

Get concept suggestions from term (1)

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This workflow suggests concept ids that match the query term. The user can run this workflow with any term of interest as for example "human", "htt", "Transcription" etc, and will get suggestions for concept ids together with descriptions. Then can choose the concept id that matches the best to her/his needs and use it to the rest of the CPA workflows.

Created: 2013-08-31

Credits: Eleni BioSemantics

Test RShell (1)

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workflow hacked to include empty username and password elements

Created: 2013-02-27

Credits: Reinout van Schouwen Eleni

Attributions: workflow to test Rshell (for internal purposes)

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

workflow to test Rshell (for internal purp... (1)

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 This is a workflow to test if Rserve is working properly, for internal purposes.  Takes as input two integers. output is the sum of integer 1 and integer 2  

Created: 2013-01-21 | Last updated: 2013-03-11

Credits: Eleni

Retention Time Prediction with X!Tandem (1)

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This workflow identifies peptides from tandem mass spectra using X!Tandem as in a standard installation of the Trans-Proteomic Pipeline (TPP, version 4.6, but earlier versions should also work). The peptide-spectrum matches are validates using PeptideProphet (also from a standard installation of TPP) and peptides with at least a probability 0.95 are used to train a linear retention time predictor (Palmblad et al., 2002), whereby retention coefficients are also derived. These indirectly provid...

Created: 2012-09-03 | Last updated: 2012-09-03

Credits: Magnus Palmblad Yassene Eleni

Attributions: rt3.c

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: Marco Roos Reinout van Schouwen Eleni Kristina Hettne BioSemantics

Attributions: Match concept profiles Explain concept scores

Get Pathway-Genes and gene description by ... (2)

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Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes (including their description) are associated with.

Created: 2012-03-27 | Last updated: 2012-04-03

Credits: Eleni

Get Pathway-Genes by Entrez gene id (4)

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Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes are associated with. The workflow outputs also a KEGG pathway map and the objects are colored according to the input color values.

Created: 2012-03-08 | Last updated: 2012-04-14

Credits: Eleni