Software

ADOG - Anotating Data with Ontologies and Graphs

System that participated in the 2019 edition of the SemTab: Semantic Web Challenge on Tabular Data to Knowledge Graph Matching and obtained 3rd prize for the entity annotation task.

For more information see:
Oliveira, D., D’Aquin, M.: ADOG - Annotating Data with Ontologies and Graphs. In: Proceedings of the Semantic Web Challenge on Tabular Data to Knowledge Graph Matching co-located with the 18th International Semantic Web Conference. p. 6. CEUR-WS.org (2019). http://ceur-ws.org/Vol-2553/paper1.pdf

bioont-search-benchmark

Benchmark to compare the performance of different information retrieval methods in searching for ontology terms. This benchmark can be used for any ontology domain but this project focuses on biomedical ontologies and includes comparision with the biomedical ontology repositories BioPortal and OLS.

For more information see:
Oliveira, D., Butt, A.S., Haller, A., Rebholz-Schuhmann, D., Sahay, R.: Where to search top-K biomedical ontologies? Brief Bioinform. 20, 1477–1491 (2019). https://doi.org/10.1093/bib/bby015.

AML-Compound

Implementation of the novel compound matching algorithm developed as part of the research for my MSc thesis. The open source code allows the user to input three ontologies of the same domain and obtain alignments of the intersection between the concepts of these ontologies.

For more information see:
Oliveira, D., Pesquita, C.: Improving the interoperability of biomedical ontologies with compound alignments. Journal of Biomedical Semantics. 9, 1 (2018). https://doi.org/10.1186/s13326-017-0171-8.