OWLSim Ontology Based Profile Matching
OWLSim is ontology-based profile matching software for calculating semantic similarity between ontology classes and individuals. The tool was used by the Monarch Initiative and related phenotype-comparison projects, and has since been replaced by Semsimian.
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{"activity_status": "inactive", "category": "DataSource", "creation_date": "2025-11-19T00:00:00Z", "description": "OWLSim is ontology-based profile matching software for calculating semantic similarity between ontology classes and individuals. The tool was used by the Monarch Initiative and related phenotype-comparison projects, and has since been replaced by Semsimian.", "domains": ["biomedical", "information technology", "phenotype", "genomics", "systems biology"], "homepage_url": "https://berkeleybop.org/software/owlsim/", "id": "owlsim", "infores_id": "owlsim", "last_modified_date": "2026-06-02T00:00:00Z", "layout": "resource_detail", "name": "OWLSim Ontology Based Profile Matching", "products": [{"category": "ProcessProduct", "description": "Java source repository for OWLSim v3 ontology-based profile matching and semantic similarity services", "format": "http", "id": "owlsim.v3", "name": "OWLSim v3 Source Repository", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "owlsim"}], "product_url": "https://github.com/monarch-initiative/owlsim-v3"}, {"category": "ProcessProduct", "description": "OWLTools Java library and command-line tools historically associated with OWLSim workflows", "format": "http", "id": "owlsim.owltools", "name": "OWLTools Source Repository", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "owlsim"}], "product_url": "https://github.com/owlcollab/owltools"}, {"category": "ProgrammingInterface", "description": "Local Dropwizard REST service documented by OWLSim v3 for ontology profile matching and matcher discovery", "format": "http", "id": "owlsim.rest", "name": "OWLSim v3 REST Service", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "owlsim"}], "product_url": "https://github.com/monarch-initiative/owlsim-v3", "warnings": ["The OWLSim v3 README documents a locally run REST service; no maintained public production endpoint was identified during 2026-06-02 curation."]}], "publications": [{"authors": ["Robinson PN", "K\u00f6hler S", "Oellrich A", "Wang K", "Mungall CJ", "Lewis SE", "Washington N", "Bauer S", "Seelow D", "Krawitz P", "Gilissen C", "Haendel M", "Smedley D"], "doi": "10.1101/gr.160325.113", "id": "PMID:24281164", "journal": "Genome Research", "preferred": true, "title": "Improved exome prioritization of disease genes through cross-species phenotype comparison", "year": "2014"}], "repository": "https://github.com/monarch-initiative/owlsim-v3", "synonyms": ["OWLSim"], "taxon": ["NCBITaxon:9606"], "warnings": ["BBOP documents OWLSim as replaced by Semsimian; this entry describes the legacy OWLSim resource and its historical products."]}