• shareshare
  • link
  • cite
  • add
auto_awesome_motion View all 4 versions
Other research product . Other ORP type . 2017

YAM-BIO – Results for OAEI 2017

Annane, Amina; Bellahsene, Zohra; Azouaou, Faiçal; Jonquet, Clement;
Published: 01 Nov 2017
Publisher: HAL CCSD
Country: France
System paper Ontology Alignment Evaluation Initiative 2017 Campaign; The YAM-BIO ontology alignment system is an extension of YAM++ but dedicated to aligning biomedical ontologies. YAM++ has successfully participated in several editions of the Ontology Alignment Evaluation Initiative (OAEI) between 2011 and 2013, but this is the first participation of YAM-BIO. The biomedical extension includes a new component that uses existing mappings between multiple biomedi-cal ontologies as background knowledge. In this short system paper, we present YAM-BIO's workflow and the results obtained in the Anatomy and Large Biomedical Ontologies tracks of the OAEI 2017 campaign. 1 Presentation of the YAM-BIO system 1.1 State, purpose, general statement YAM-BIO may be seen as an extension of YAM++ [5] that uses existing map-pings between multiple biomedical ontologies as background knowledge to enhance the matching results. The latest version of YAM++, which we reused in YAM-BIO, obtained excellent results in multiple Ontology Alignment Evaluation Initiative (OAEI) campaigns, especially in 2013 [11]. YAM++ did not participate more since then. Four years on from the last participation, our objective this year was to establish a comparison between the potential performance of a bio-customized YAM++, and state-of-the-art systems in matching biomedical ontologies. Over last OAEI campaigns, state-of-the-art systems such as AML [7] and LogMapBio [9] used specialized background knowledge to improve their results. More generally, the use of background knowledge –or indirect matching techniques– as recently allowed to obtain better results. YAM-BIO is an equivalent evolution of YAM++ in which we added a component that uses existing mappings as background knowledge. With YAM-BIO, we participated this year to the Anatomy and Large Biomedical Ontologies (Largebio) tracks.

[INFO.INFO-WB]Computer Science [cs]/Web

16 references, page 1 of 2

1. Annane Amina, Bellahsene Zohra, Azouaou Faical, and Jonquet Clement. Selection and combination of heterogeneous mappings to enhance biomedical ontology matching. In 20th International Conference on Knowledge Engineering and Knowledge Management, EKAW, Bologna, Italy, pages 19{33, 2016.

2. Faria Daniel, Pesquita Catia, Santos Emanuel, Cruz Isabel F, and Couto Francisco M. Automatic background knowledge selection for matching biomedical ontologies. PloS One, 9(11):e111226, 2014.

3. d'Aquin Mathieu, Gridinoc Laurian, Angeletou So a, Sabou Marta, and Motta Enrico. Watson: A Gateway for Next Generation Semantic Web Applications. In 6th International Semantic Web Conference, ISWC, Poster and Demonstration, Busan, Korea, pages 11{15, 2007.

4. Kevin Donnelly. SNOMED-CT: The advanced terminology and coding system for eHealth. Studies in health technology and informatics, 121:279, 2006.

5. Ngo DuyHoa and Bellahsene Zohra. Overview of YAM++:(not) yet another matcher for ontology alignment task. Journal of Web Semantics, 41:30 { 49, 2016.

6. Noy Natalya F, Shah Nigam H, Whetzel Patricia L, Dai Benjamin, Dorf Michael, Gri th Nicholas, Jonquet Clement, Rubin Daniel L, Storey Margaret-Anne, and Chute Christopher G. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research, 37:170{173, 2009. [OpenAIRE]

7. Daniel Faria, Catia Pesquita, Booma S Balasubramani, Catarina Martins, Joao Cardoso, Hugo Curado, Francisco M Couto, and Isabel F Cruz. Oaei 2016 results of AML. In 11th International Workshop on Ontology Matching, Kobe, Japan., pages 138{145, 2016.

8. Terry F. Hayamizu, Mary Mangan, John P. Corradi, James A. Kadin, and Martin Ringwald. The adult mouse anatomical dictionary: a tool for annotating and integrating data. Genome Biology, 6(3):R29, Feb 2005.

9. E Jimenez-Ruiz, B Cuenca Grau, and V Cross. Logmap family participation in the oaei 2016. In 11th International Workshop on Ontology Matching, Kobe, Japan., pages 185{189, 2016.

10. Christopher J. Mungall, Carlo Torniai, Georgios V. Gkoutos, Suzanna E. Lewis, and Melissa A. Haendel. Uberon, an integrative multi-species anatomy ontology. Genome Biology, 13(1):R5, Jan 2012.

Funded by
Semantic Indexing of French Biomedical Data Resources - mobility
  • Funder: European Commission (EC)
  • Project Code: 701771
  • Funding stream: H2020 | MSCA-IF-GF
ANR| PractiKPharma
Practice-based evidences for actioning Knowledge in Pharmacogenomics
  • Funder: French National Research Agency (ANR) (ANR)
  • Project Code: ANR-15-CE23-0028