Ontology Alignment Evaluation Initiative - OAEI-2016 Campaign

Disease and Phenotype Track

OAEI 2016::Disease and Phenotype Track (phenotype)

NEWS:

• 2016 results available now!

General description

There will be two tasks for this track which will comprise of pairwise alignment of:

1. Human Phenotype Ontology (HPO) to Mammalian Phenotype Ontology (MP), and
2. Human Disease Ontology (DOID) to the Orphanet and Rare Diseases Ontology (ORDO).

The first task is important for translational science where human phenotype includes inherited diseases and mammalian phenotype ontology which is based on roadents as a model mammalian organism for many laboratory studies, including gene knock out. The second task includes representation of rare human diseases in both ontologies which are of fundamental importance for understanding how genetic variation can cause disease. Currently, such mappings are mostly curated by bioinformatics and disease experts who would benefit from automation supported by implementation of ontology matching algorithms into their workflows.

We have extracted a "baseline" reference alignments for the track based on the available BioPortal mappings. Most of the BioPortal mappings are automatically generated by the LOOM system; therefore this BioPortal-based reference alignment should only be considered as a baseline since it is incomplete or may contain erroneous mappings.

The complete datasets for the OAEI 2016 campaign can be downloaded as a zip file (OAEI_phenotype_dataset_baseline.zip [7Mb]) or accessed via the SEALS platform (see dataset identifiers below).

The Pistoia Alliance will sponsor a prize of $7,500 for the winner of this track as an incentive for participation.

Evaluation process

• Precision and Recall with respect to a voted reference alignment that will be automatically built by merging/voting the outputs of the participating systems. We will probably use vote=2 or vote=3.
• Recall with respect to manually generated mappings for three areas (carbohydrate, obesity and breast cancer).
• Manual assessment of a subset of the generated mappings, specially the ones that are not suggested by other systems.
• Performance in other tracks will also be taken into account (especially in the Interactive track wrt the Phenotype-Disease dataset).

SEALS support

The evaluation of the Disease and Phenotype Track will be run with support of the SEALS infrastructure. This requires that you wrap your matching system in a way that allows us to execute it using the SEALS client (see OAEI 2016 evaluation details).

HP-MP matching problem

This task consists of matching the HP (11,828 entities) and MP (11,752 entities) ontologies. The BioPortal-based alignment contains 639 mappings.

DOID-ORDO matching problem

This task consists of matching the DOID (9,301 entities) and ORDO (12,974) ontologies. The BioPortal-based alignment contains 1,018 mappings.