Group: BioSemantics

Overview

Group for members of the BioSemantics group and their close collaborators.

Biosemantics

With the explosion of information in the biomolecular field, there is a dire need for information technology that assists in retrieving, extracting, and relating information and knowledge in the biomedical literature and databases. Biosemantics researchers and developers develop, evaluate, and apply such technology, focusing on elucidation of hidden or implicit knowledge and resolution of mechanisms behind rare and common diseases.

Biosemantics groups in the Netherlands form the core of the Netherlands' activities towards interoperability and preservation of methods and data, for which they participate in the Data Integration and Stewardship Centre (DISC), the Dutch node in Elixir.

Created at: Thursday 30 June 2011 13:06:48 (UTC)

Unique name: biosemantics

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  1. 3772?size=48x48
    Kristina Hettne shared KEGG:Get PW for met
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    The purpose of the workflow is to retrieve all the pathways that the input metabolite(s) participates in.
    Tuesday 21 June 2016 19:06:49 (UTC)
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    Kristina Hettne shared chebi2keggID
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    This workflow converts a (list of) chebi identifiers to kegg compound identifiers.
    Tuesday 21 June 2016 17:35:46 (UTC)
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    Kristina Hettne shared Get targets for compound
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    This workflow retrieves single protein targets for a compound from open PHACTS.
    Monday 22 February 2016 20:01:21 (UTC)
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    Kristina Hettne shared Get similar phenotypes for a disease and a gene
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    This workflow retrieves the similar phenotypes between a disease and a gene based on the Monarch services at http://monarchinitiative.org/page/services . Phenotype similarity is calculated based on OwlSim, see http://owlsim.org .
    Monday 22 February 2016 19:50:02 (UTC)
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    Kristina Hettne shared Pathway analysis with WikiPathways
    This pack contains workflows needed to perform pathway overrepresentation analysis based on the WikiPathways Web services.
    Monday 16 November 2015 09:58:55 (UTC)
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    Kristina Hettne shared Get ontology parents
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    Retrieves the ontology parents of an entity including the relationship type, using the ChEBI identifier.
    Monday 16 November 2015 09:56:19 (UTC)
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    Kristina Hettne shared PW2ENS
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    This workflow uses the WikiPathways Webservice/API to query to retrieve all ENSEMBL identifers for the given pathway.
    Monday 12 October 2015 12:43:16 (UTC)
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    Kristina Hettne shared GetWikiPWByENS
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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 iden …
    Monday 12 October 2015 12:42:14 (UTC)
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    Kristina Hettne shared AllPW2ENS
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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.
    Monday 12 October 2015 12:41:21 (UTC)
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    Kristina Hettne shared AllPW2CHEBI
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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.
    Monday 12 October 2015 12:39:38 (UTC)
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    Kristina Hettne shared GetWikiPWByCHEBI
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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 o …
    Monday 12 October 2015 12:38:04 (UTC)
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    Kristina Hettne shared ListAllWikiPathways
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    This workflow retrieves all pathways currently in the WikiPathways database, using the WikiPathways REST API.
    Monday 12 October 2015 12:36:39 (UTC)

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14 members

70 shared items

This group has been credited 24 times

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Blob converter_nanopublications

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

Credits: User Eleni Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

this script is part of the nanopublication workflow from pack http://www.myexperiment.org/packs/486.html

File type: application/x-ruby

Comments: 0 | Viewed: 2 times | Downloaded: 2 times

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Blob create nanopublications

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

Credits: User Eleni Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This ruby script creates nanopublications for the results of the prioritized gene list from pack : http://www.myexperiment.org/packs/486.html 

File type: application/x-ruby

Comments: 0 | Viewed: 8 times | Downloaded: 4 times

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Blob HTT-HPO concept profile match result

Created: 2014-10-20 08:26:32 | Last updated: 2014-10-20 08:35:28

Credits: User Marco Roos User Rajireturn Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example Concept Profile of the Human Phenotype named 'Chorea' also referred to by as Human Phenotype Ontology concept HP_0002072.This file contains a list of concepts from the Human Phenotype Ontology, ranked according to Concept Profile Matching with the profile of huntingtin, the protein whose aberrant form is the cause of Huntington's Disease.Versions:HPO-UMLS mapping: Winnenburg, R., & Bodenreider, O. (2014). Coverage of Phenotypes in Standard Terminologies. In Proceedings...

File type: Excel workbook

Comments: 0 | Viewed: 7 times | Downloaded: 0 times

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Blob Concept Profile of phenotype Chorea

Created: 2014-10-20 08:34:10

Credits: User Marco Roos Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concept Profile generated from HPO term 'Chorea' via mapping to the corresponding UMLS phenotype concept.The profile contains ranked associations with Chorea conform mutual information content derived from co-occurrence in MedLine abstracts.Versions:HPO-UMLS mapping: Winnenburg, R., & Bodenreider, O. (2014). Coverage of Phenotypes in Standard Terminologies. In Proceedings of the ISMB’2014 SIG meeting “BioLINK.” Retrieved from http://phenoday2014.bio-lark.org/pdf/...

File type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

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Workflow

Workflow Chemical2URIs (1)

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This workflow will map a chemical name or identifier to uniform resource identifiers (URIs). First the ChemSpider web service is used to map the chemical name to a ChemSpider identifier, then the ChemSpider identifier is mapped to URIs via the Open PHACTS platform.

Created: 2015-08-18

Credits: User Kristina Hettne User Eelke van der Horst Network-member BioSemantics

Workflow

Workflow Get HPO concept label and synonym (1)

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This workflow queries bioportal for label and synonyms of Human Phenotype Ontology concepts.Note: this workflow requires a BioPortal API key to work. It can be requested from bioportal.bioontology.org

Created: 2014-10-20 | Last updated: 2014-10-20

Credits: User Rajireturn Network-member BioSemantics

Workflow

Workflow Match concept to HPO profiles (1)

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This workflow matches a query concept to the list of Human Phenotypes. The Human Phenotypes are the subset of the Human Phenotype Ontology for which we have a mapped UMLS concept available and a concept profile. HPO-UMLS mapping: Winnenburg, R., & Bodenreider, O. (2014). Coverage of Phenotypes in Standard Terminologies. In Proceedings of the ISMB’2014 SIG meeting “BioLINK.” Retrieved from http://phenoday2014.bio-lark.org/pdf/5.pdf Concept Profile Database: July 2012

Created: 2014-10-20

Credits: User Marco Roos Network-member BioSemantics

Attributions: Workflow Match concept profiles Workflow Get concept information

Workflow

Workflow HPO-UMLS-ConceptID mapping (1)

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Generate HPO-Concept profiles via HPO-UMLS mappings. The result is a list of Concept IDs corresponding to Concept profiles for UMLS concepts that approximate HPO concepts. The output is a table of UMLS-ID, HPO- ID, COncept-ID rows.

Created: 2014-10-20

Credits: User Marco Roos Network-member BioSemantics

Workflow

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Workflow 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: User Eleni Network-member BioSemantics

Attributions: Blob create nanopublications Blob converter_nanopublications

Workflow

Uploader

Workflow 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: User Eleni Network-member BioSemantics

Workflow

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Workflow 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: User Eleni Network-member BioSemantics

Workflow

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Workflow 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: User Eleni Network-member BioSemantics

Workflow

Uploader

Workflow 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: User Eleni Network-member BioSemantics

Workflow

Workflow Annotate a gene list with disease concepts (1)

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Purpose: Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match. 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.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery.

Created: 2013-02-06

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

Attributions: Workflow SNPs to Concept Set through Concept Profile Matching v2

Workflow

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

Workflow

Workflow Find Supporting Documents (6)

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This workflow finds documents that serve as evidence for the association between two concepts. Results: Document titles Document identifiers There seems to be a bug at the moment, since it returns empty values.

Created: 2012-06-26 | Last updated: 2014-07-14

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

Workflow

Workflow 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: 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

Workflow Get Concept IDs (5)

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Purpose: The workflow retrieves the concepts within a concept set. The Web service/workflow currently returns no values (bug).

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

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

Workflow

Workflow Find co-occurring documents (6)

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Purpose: This workflow search an indexed literature database for documents mentioning both of the input concepts. Author comments: Currently, PubMed is the underlying data source.

Created: 2012-07-13 | Last updated: 2014-07-14

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

Workflow

Workflow 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: User Kristina Hettne User Reinout van Schouwen User Martijn Schuemie Network-member BioSemantics

Workflow

Workflow 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: User Kristina Hettne User Marco Roos User Reinout van Schouwen User Martijn Schuemie Network-member BioSemantics

Workflow

Workflow Get concept information (5)

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The workflow takes a (list of) concept ID(s) as input and returns the profile, ID, definition and name of the concept.

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

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

Workflow

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

Workflow

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


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