Pack: Genotype-phenotype knowledge discovery using the Concept Profile Analysis Web Services

Description:

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/5.pdf
Concept Profiles version: July 2012

Web service used: https://www.biocatalogue.org/services/3559

Description:

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

Description:

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.

Description:

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 of the ISMB’2014 SIG meeting “BioLINK.” Retrieved from http://phenoday2014.bio-lark.org/pdf/5.pdf
Concept Profiles version: July 2012

Web service used: https://www.biocatalogue.org/services/3559

Description:

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