Content from the BioSemantics group

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User: Marco Roos

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 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 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 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 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

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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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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

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Pack RD-Connect D4.03 Deliverable Pack


Created: 2014-10-19 21:05:07 | Last updated: 2014-10-20 16:34:40

This pack compiles workflows and workflow results for Deliverable D4.03 for RD-Connect (http://rd-connect.eu).

5 items in this pack

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Pack BioSemantics Concept Profile Generation Workflows


Created: 2014-06-04 12:31:09 | Last updated: 2014-06-04 13:01:44

This pack compiles concept profile-generation workflows by the LUMC/EMC Biosemantics groups.This work is made possible by EU projects 'Workflow Forever' (www.wf4ever-project.org) and RD-Connect (www.rd-connect.eu), and contribution from bioinformatics students from the Hogeschool Leiden.

9 items in this pack

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Workflow OPS_FreetextToTargetInfo (1)

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Workflow to retrieve target information for the concepts as refered to by humans (the input). Known issues: It produces error values for the concepts returned by ConceptWiki that are apparently not present in OPS (e.g. for "ezh2" and limit=10, it gives 7/10 error values vs "ezh2 (homo sapiens)" giving 2 valid values).

Created: 2013-06-18

Credits: User Marco Roos User Katy Wolstencroft User paul groth

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