enhancing the human phenotype ontology for use by the … · 2016. 4. 11. · enhancing the human...
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EnhancingtheHumanPhenotypeOntologyforusebytheLayperson
Introduction
Nicole Vasilevsky1, Mark Engelstad1, Erin Foster1, Chris Mungall3, Peter Robinson2, Sebastian Köhler2, Melissa Haendel1
1Ontology Development Group, Oregon Health & Science University, Portland, OR, USA 2Charité - Universitätsmedizin, Berlin, Germany, 3Lawrence Berkeley National Laboratory, Berkeley, CA, USA
Enhancing the Human Phenotype Ontology for Use by the Layperson
Human Phenotype Ontology
Workflow Outcomes
Many diseases present with distinct phenotypes, making computational description critical for diagnostics
Patients are a good source of phenotypic information and need to participate in their diagnostic odyssey
The Human Phenotype Ontology can be used to capture structured information about patient phenotypes
§ Contains over 12,000 classes describing human phenotypic features
§ Used for clinical “deep phenotyping” § HPO annotations utilized in semantic
similarity analysis within and across species for rare disease diagnostics 4 | Synonym classification
Exact synonyms: precise alternatives to the HPO term Broad synonyms: more general than the HPO term Narrow synonyms: more specific than HPO term Related synonyms: associated with the HPO term.
3 | Assign synonyms Assign synonyms to existing classes or mark existing synonyms as layperson
§ Wikipedia § MedlinePlus § Mayo Clinic § OMIM § Uberon
§ Elements of Morphology
§ SNOMED CT Browsers
§ Specialty texts
1 | Systematic review of HPO classes
Challenges
Use of HPO
The inclusion of plain language synonyms will support patient-driven applications for deep phenotyping, that can be utilized clinical and computationally
44% of synonyms in HPO are layperson
HPO can be integrated into patient registries and other platforms such as the following:
§ Recognizing when an HPO class did not have an equivalent layperson synonym
e.g., joint contracture
§ Aligning synonyms with definition of HPO classes
e.g., Neoplasm of breast ≠ Breast cancer
§ Applying synonyms consistently across HPO classes and subclasses
e.g., “Yellowing of skin” à Jaundice, Intermittent jaundice, Prolonged neonatal jaundice
§ Continuous review of HPO OWL file for quality assurance § Validcharacter-encoding§ Checkforduplicatedsynonyms§ Titlecaseforma?ng
§ Check annotation consistency between similar terms
§ Reviewed by 3 curators
6 | Quality Assurance
All synonyms
in HPO Synonyms
marked as lay
All synonyms 14,253 6,240
Exact 12,167 5,357
Broad 441 298
Related 1,236 419
Narrow 409 166
On the left is a mouse phenotypic profile using the Mammalian Phenotype Ontology; on the right, a disease profile using HPO. In the center are shown the phenotypes in common based semantic similarity matching.
Goal Add new layperson synonyms to terms to increase the usability of the HPO, and make it useful for data interoperability for patients, clinicians, and researchers
5 | Script in new synonyms to HPO OWL file
§ Initial review in HPO OWL files in the ontology editing tool, Protégé
§ HPO terms and synonyms were downloaded to a spreadsheet to allow sorting and grouping of terms
§ HPO curation team, with clinical and biocuration expertise, cross-reviewed each class
2 | Search for synonyms
Acknowledgements
This work is supported by NIH Office of Director grant: 1R24OD011883. Thank you to Tudor Groza and Julie McMurry for their help. Apert’s syndrome image credits available from monarchinitiative.org
Contact
Nicole Vasilevsky: [email protected], @N_Vasilevsky Sebastian Köhler: [email protected] Monarch Initiative: @MonarchInit
File available at: www.purl.obolibrary.org/obo/hp.owl
Community contributions welcome! https://github.com/obophenotype/human-
phenotype-ontology
@hp_ontology