Ontology Alignment Evaluation Initiative - OAEI-2020 Campaign

Disease and Phenotype Track

OAEI 2020::Disease and Phenotype Track (phenotype)

NEWS:

• 2020 results available now!

General description

The 2020 edition is composed by two tasks requiring the pairwise alignment of:

1. Human Phenotype Ontology (HP) to Mammalian Phenotype Ontology (MP);
2. Human Disease Ontology (DOID) to the Orphanet Rare Disease Ontology (ORDO);

Currently, mappings between these ontologies are mostly curated by bioinformatics and disease experts who would benefit from automation of their workflows supported by implementation of ontology matching algorithms.

Table 1 summarizes the ontology versions and sources of the ontologies used in the OAEI 2020 (same as 2017-2019). Note that the version and source of HP, MP, DOID and ORDO are different from the ones used in 2016.

We have extracted "baseline" reference alignments based on the available BioPortal mappings (July 8, 2017). Most of the BioPortal mappings are generated automatically by the LOOM system; which should only be considered as a baseline since it is incomplete or may contain erroneous mappings.

The ontologies and baseline mappings for the OAEI 2020 campaign can be downloaded as zip files: Ontologies [25Mb] and BioPortal mappings [0.6Mb]. The OAEI 2020 campaign datasets can also be accessed via the SEALS client (see dataset identifiers below).

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 use vote=2 and vote=3.

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 2020 evaluation details).

HP-MP matching problem

This task consists of matching the HP (31,034 classes) and MP (30,273 entities) ontologies. The BioPortal-based alignment contains 696 mappings.

DOID-ORDO matching problem

This task consists of matching the DOID (38,240 classes) and ORDO (13,504) ontologies. The BioPortal-based alignment contains 1,237 mappings.