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Experiences from the anatomy track in the ontology alignment evaluation initiative

Zlatan Dragisic, Valentina Ivanova, Huanyu Li, Patrick Lambrix
2017 Journal of Biomedical Semantics  
This paper improves on the "Preliminary results" initially published in the on-site proceedings of the ISWC workshop on Ontology Matching (OM-2014).  ...  These test cases can use ontologies of different nature (from simple thesauri to expressive OWL ontologies) and use different modalities, e.g., blind evaluation, open evaluation and consensus.  ...  We also thank for their support the other members of the Ontology Alignment Evaluation Initiative steering committee:  ... 
doi:10.1186/s13326-017-0166-5 pmid:29202830 pmcid:PMC5715990 fatcat:zvet5vb6zncxnlgd225ndhcik4

Creating mappings for ontologies in biomedicine: simple methods work

Amir Ghazvinian, Natalya F Noy, Mark A Musen
2009 AMIA Annual Symposium Proceedings  
Our evaluation has shown that (1) most of the advanced algorithms are either not publicly available or do not scale to the size of biomedical ontologies today, and (2) for many biomedical ontologies, simple  ...  Our results have practical implications for biomedical researchers who need to create alignments for their ontologies.  ...  Acknowledgments This work was supported by the National Center for Biomedical Ontology, under roadmap-initiative grant U54 HG004028 from the National Institutes of Health.  ... 
pmid:20351849 pmcid:PMC2815474 fatcat:q62bsfye2bawzh33aao3pd735q

Ontology Alignment Evaluation Initiative: Six Years of Experience [chapter]

Jérôme Euzenat, Christian Meilicke, Heiner Stuckenschmidt, Pavel Shvaiko, Cássia Trojahn
2011 Lecture Notes in Computer Science  
In this paper, we report results and lessons learned from the Ontology Alignment Evaluation Initiative (OAEI), a benchmarking initiative for ontology matching.  ...  The goal of this work is twofold: on the one hand, we document the state of the art in evaluating ontology matching methods and provide potential participants of the initiative with a better understanding  ...  From 2005 on, joint activities are carried out under the heading of the Ontology Alignment Evaluation Initiative.  ... 
doi:10.1007/978-3-642-22630-4_6 fatcat:hefawjfxvvdz7pd7zzmzjpxw6a

Experiments Varying Semantic Similarity Measures and Reference Ontologies for Ontology Alignment [chapter]

Valerie Cross, Pramit Silwal, Xi Chen
2013 Lecture Notes in Computer Science  
The results of experiments using the MMSS on the anatomy track of the Ontology Alignment Evaluation Initiative (OAEI) are reported.  ...  Semantic similarity measures within a reference ontology have been used in a few ontology alignment (OA) systems.  ...  In [2] the MMSS replaces the MM in its OAEI 2011 configuration. Their performances are compared on the anatomy track running both on the same cluster computer.  ... 
doi:10.1007/978-3-642-41242-4_42 fatcat:5cvsbr5fyrbxdkqlgfx6zzktse

SANOM-HOBBIT: simulated annealing-based ontology matching on HOBBIT platform

Majid Mohammadi, Wout Hofman, Yao-Hua Tan
2020 Knowledge engineering review (Print)  
Ontology alignment evaluation initiative (OAEI) has been taken place for more than a decade to monitor and help the progress of the field and to compare systematically existing alignment systems.  ...  The outcomes of SANOM on the HOBBIT for several OAEI tracks are reported, and the results are compared with other competing systems in the corresponding tracks.  ...  Anatomy track The anatomy track is one of the earliest benchmarks in the OAEI.  ... 
doi:10.1017/s026988892000017x fatcat:ckqrn5n5nraxxb7jvijn7k4y5u

A Method for Recommending Ontology Alignment Strategies [chapter]

He Tan, Patrick Lambrix
2007 Lecture Notes in Computer Science  
The method is based on the evaluation of the different available alignment strategies on several small selected pieces from the ontologies, and uses the evaluation results to provide recommendations.  ...  We also experiment with different implementations of the steps in the method.  ...  We acknowledge the financial support of the Swedish Research Council, the Center for Industrial Information Technology , the Swedish national graduate school in computer science, and the EU NoE REWERSE  ... 
doi:10.1007/978-3-540-76298-0_36 fatcat:qxcitojlorfuxfq6p77mt5hi6y

Selecting Optimal Background Knowledge Sources for the Ontology Matching Task [chapter]

Abdel Nasser Tigrine, Zohra Bellahsene, Konstantin Todorov
2016 Lecture Notes in Computer Science  
We evaluate our system in a series of experiments in both general-purpose and domain-specific matching scenarios.  ...  It is a common practice to rely on background knowledge (BK) in order to assist and improve the ontology matching process.  ...  pair of ontologies to be matched, the selection process is a result of querying the indexed corpus for semantically similar BK sources from the indexed data.  ... 
doi:10.1007/978-3-319-49004-5_42 fatcat:cs6rrkjm6bb3de7g7zy7mzaate

Towards valid and reusable reference alignments — ten basic quality checks for ontology alignments and their application to three different reference data sets

Elena Beisswanger, Udo Hahn
2012 Journal of Biomedical Semantics  
In this article, these quality checks are applied to a standard reference alignment in the biomedical domain, the Ontology Alignment Evaluation Initiative Anatomy track reference alignment, and two more  ...  The usefulness of a manually created or curated alignment as reference for the evaluation of ontology  ...  Acknowledgements We gratefully thank Terry Hayamizu (curator of the anatomy alignment), Angela Locoro (curator of the Mascardi data set) and Christian Meilicke (OAEI Anatomy track organizing committee)  ... 
doi:10.1186/2041-1480-3-s1-s4 pmid:22541595 pmcid:PMC3337267 fatcat:7agc5knlp5dufn3lnw2tcvkzde

Interactive biomedical ontology matching

Xingsi Xue, Zhi Hang, Zhengyi Tang, Xiangtao Li
2019 PLoS ONE  
The experiment is conducted on the Anatomy track and Large Biomedic track that are provided by the Ontology Alignment Evaluation Initiative (OAEI), and the experimental results show that our approach is  ...  On this basis, we further make the ETS-based ontology matching technique cooperate with the user in a reasonable amount of time to efficiently create high quality alignments, and make use of EA's survival  ...  Although this challenge has attracted the interest of the community such as Ontology Alignment Evaluation Initiative (OAEI) which includes specific tracks on matching biomedical ontologies, the research  ... 
doi:10.1371/journal.pone.0215147 pmid:30995257 pmcid:PMC6469807 fatcat:higy2xxmcrb3zbxf6hi6ohtifu

Fuzzy set and semantic similarity in ontology alignment

Valerie Cross, Xueheng Hu
2012 2012 IEEE International Conference on Fuzzy Systems  
A general semantic alignment quality (SAQ) measure is developed and used on the alignment results of 10 different OA systems produced on the anatomy track of the 2010 OA evaluation initiative.  ...  Ontology alignment (OA) addresses this challenge by identifying correspondences between entities in different ontologies.  ...  EXPERIMENTS USING THE OAEI ANATOMY TRACK Current OA systems typically compete in the ontology alignment evaluation initiative (OAEI) which has been conducted annually since 2004 [2] .  ... 
doi:10.1109/fuzz-ieee.2012.6251265 dblp:conf/fuzzIEEE/CrossH12 fatcat:j5gyuzim7zbrnnle4sm4rezrbm

Evaluating Ontology Matching Systems on Large, Multilingual and Real-world Test Cases [article]

Christian Meilicke, Cássia Trojahn, Heiner Stuckenschmidt University of Economics Prague, University of Oxford)
2012 arXiv   pre-print
In the field of ontology matching, the most systematic evaluation of matching systems is established by the Ontology Alignment Evaluation Initiative (OAEI), which is an annual campaign for evaluating ontology  ...  In this paper, we report on the results of an intermediary OAEI campaign called OAEI 2011.5. The evaluations of this campaign are divided in five tracks.  ...  Acknowledgements Some of the authors are partially supported by the EU FP7 project SEALS (IST-2009-238975). OndřejŠváb-Zamazal has been partially supported by the CSF grant no. P202/10/0761.  ... 
arXiv:1208.3148v1 fatcat:4mksls4knncbjc6tytslifmuym

Selection and Combination of Heterogeneous Mappings to Enhance Biomedical Ontology Matching [chapter]

Amina Annane, Zohra Bellahsene, Faiçal Azouaou, Clement Jonquet
2016 Lecture Notes in Computer Science  
We have implemented and evaluated our approach using the content of the NCBO BioPortal repository and the Anatomy benchmark from the Ontology Alignment Evaluation Initiative.  ...  This paper presents a novel background knowledge approach which selects and combines existing mappings from a given biomedical ontology repository to improve ontology alignment.  ...  Acknowledgment This work was achieved during a LIRMM-ESI collaboration within the SIFR project funded in part by the French National Research Agency (grant ANR-12-JS02-01001), as well as by University  ... 
doi:10.1007/978-3-319-49004-5_2 fatcat:a6ja52bygfg4ngmqj4hvgfzpzi

POMap: An Effective Pairwise Ontology Matching System

A. Laadhar, F. Ghozzi, I. Megdiche, F. Ravat, O. Teste, F. Gargouri
2017 Proceedings of the 9th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management  
The employed tracks in our testing process are: the Anatomy track and the Large Biomedical track.  ...  We choose to perform the experiment process analysis through two biomedical tracks of the OAEI benchmark as well as the conference track in order to show the efficiency of POMap in various matching tasks  ... 
doi:10.5220/0006492201610168 dblp:conf/ic3k/LaadharGMRTG17 fatcat:efod4exfsncffb2h62mricm73i

Enhanced Ontology Matching for Big Data Integration

Nesma Mahmoud, Hatem M Abdlkader
2020 Journal of Physics, Conference Series  
The applicability of the proposed semantic matcher is evaluated through an experiment. The conference and anatomy gold standard datasets are evaluating the experimental results.  ...  Based on the experimental results evaluation, the proposed semantic matcher is promising and efficient in the semantic OM for BDI.  ...  In the evaluation, the gold standard datasets and reference alignments from the Ontology Alignment Evaluation Initiative (OAEI) contest are exploited. The rest of the paper is organized as follows.  ... 
doi:10.1088/1742-6596/1447/1/012028 fatcat:ltonhtmpdvfalcf5aeairdxqpa

Using Partial Reference Alignments to Align Ontologies [chapter]

Patrick Lambrix, Qiang Liu
2009 Lecture Notes in Computer Science  
In these systems an alignment is computed from scratch.  ...  To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there already exist a number of ontology alignment systems.  ...  We are indebted to Christian Meilicke for running our algorithms on the Anatomy track test case of the OAEI.  ... 
doi:10.1007/978-3-642-02121-3_17 fatcat:wp3ppe4zcrelfemvm7pd4iit7y
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