LogMap: An Ontology Alignment and Alignment Repair System

Highlights (Updated November 2024):

1. LogMap was awarded the SWSA Ten-Year Award that recognizes the highest impact papers from the International Semantic Web Conference (ISWC) proceedings ten years prior. LogMap reached >700 citations according to Google Scholar!
2. Check out...
   • OWL2Vec4OA embedings for Ontology Alignment (PDF) (Slides) (GitHub)
   • The new extension based on OWL2Vec* to integrate machine leaning techniques within the ontology alignment task here.
   • The new material about the division of the ontology alignment task here.
   • A proof-of-concept interface to offer LogMap as a service: KGAS documentation and codes (old web-interface is not functional but we are trying to build a new one).
   • The new interface with the MELT platform here.

About

LogMap is a highly scalable ontology matching system with ‘built-in’ reasoning and inconsistency repair capabilities. LogMap extract mappings between classes, properties and instances.

To the best of our knowledge, LogMap is one of the few matching systems that:

1. can efficiently match semantically rich ontologies containing tens (and even hundreds) of thousands of classes,

2. incorporates sophisticated reasoning and repair techniques to minimise the number of logical inconsistencies, and

3. provides support for user intervention during the matching process (see Web interface).

Please refer to the Ontology Alignment Evaluation Initiative (OAEI) for official results about LogMap.

Downloading and Development

Development requires a clone of this git repository. You can use the pre-configured Eclipse (Maven) project. Dependencies are automatically downloaded with the exception of google translate which needs to be manually added to the maven local repository (see lib/readme_mvn_install_google_translate.txt).

LogMap relies on the OWL API 4. There is a (non-maintained) branch that uses the OWL API 3

To generate a JAR file for LogMap from the command line using Maven, run: mvn package or mvn clean install. This will also generate a folder java-dependencies with all the necessary libraries. This folder together with the parameters.txt file should be placed in the same path as the generated "logmap-matcher.jar" file.

Releases and packages:

• Latest standalone release available here
• OAEI:
  • Latest LogMap's OAEI package available here.
  • Public OAEI packages available here (using MELT since OAEI 2021, SEALS packages in OAEI 2020 and earlier).
• HOBBIT:
  • LogMap also implemented support to be run in the HOBBIT platform. See details here.
• Old packages can also be downloaded from SourceForge.

Using LogMap

LogMap accepts the same ontology formats as the OWL API: e.g., RDF/XML, OWL/XML, OWL Functional, OBO, KRSS, and Turtle (n3).

As an Ontology Matching System

LogMap can be used from the command line with the standalone distribution or directly from its Web interface.

LogMap can also be easily integrated in other Java applications. See wiki for additional information.

OAEI: For the OAEI campaign, since 2021, LogMap implements an interface to communicate with the MELT platform. See wrapping here.

LogMap-ML: Recent research to augment LogMap with semantic embeddings and distant supervision. See details here (under development).

As a Mapping Debugging System

LogMap can also be used as a mapping debugging system from the command line (standalone distribution) or integrated in a Java application. See wiki for additional information.

We have also implemented a variant of LogMap to minimize the violations of the conservativity principle. Check details here.

Division of the Ontology Alignment Task

LogMap also includes a novel module to divide the ontology alignment task into manageable subtasks.

Resources: source classes, test classes, neural embeddings, datasets, paper, slides, video slides

Contact

Ernesto Jiménez-Ruiz (ernesto [.] jimenez [.] ruiz [at] gmail.com)

Follow us in twitter.

Please report any issue related to LogMap in our discussion group or in our issue tracker.

Main Publications

Matching System

• Ernesto Jiménez Ruiz‚ Bernardo Cuenca Grau‚ Yujiao Zhou and Ian Horrocks. Large−scale Interactive Ontology Matching: Algorithms and Implementation. In the 20th European Conference on Artificial Intelligence (ECAI 2012). (PDF)(Slides)

• Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau. LogMap: Logic-based and Scalable Ontology Matching. In the 10th International Semantic Web Confernece (ISWC 2011). (PDF)(Slides)

• Ernesto Jiménez-Ruiz et al. LogMap family results for OAEI 2014. 9th International Workshop on Ontology Matching (OM 2014). (PDF)

Combination with Machine Learning

• Jiaoyan Chen, Ernesto Jimenez-Ruiz, Ian Horrocks, Denvar Antonyrajah, Ali Hadian, Jaehun Lee. Augmenting Ontology Alignment by Semantic Embedding and Distant Supervision. European Semantic Web Conference, ESWC 2021. (PDF) (Slides) (OWL2Vec* work)

• Sevinj Teymurova, Ernesto Jiménez-Ruiz, Tillman Weyde, Jiaoyan Chen. OWL2Vec4OA: Tailoring Knowledge Graph Embeddings for Ontology Alignment. In 6th Knowledge Graph and Semantic Web Conference (long paper) & 19th Ontology Matching Workshop (poster paper). (PDF) (Slides) (GitHub)

Repair

• Alessandro Solimando, Ernesto Jiménez-Ruiz, Giovanna Guerrini: Minimizing conservativity violations in ontology alignments: algorithms and evaluation. Knowl. Inf. Syst. 51(3): 775-819 (2017). (PDF)

• Ernesto Jiménez-Ruiz, Terry R. Payne, Alessandro Solimando, Valentina A. M. Tamma: Limiting Logical Violations in Ontology Alignnment Through Negotiation. KR 2016: 217-226. (PDF)(Slides)

• Daniel Faria, Ernesto Jiménez-Ruiz, Catia Pesquita, Emanuel Santos and Francisco M. Couto. Towards annotating potential incoherences in BioPortal mappings. 13th International Semantic Web Confernece (ISWC 2014). (PDF)(Slides)

• Ernesto Jiménez-Ruiz, Christian Meilicke, Bernardo Cuenca Grau and Ian Horrocks. Evaluating Mapping Repair Systems with Large Biomedical Ontologies. In 26th International Workshop on Description Logics (DL 2013). (PDF)(Slides)

• Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau, Ian Horrocks and Rafael Berlanga. Logic-based assessment of the compatibility of UMLS ontology sources. Journal of Biomedical Semantics, volume 2, 2011 (PDF) (HTML). Preliminary repair work that led to LogMap's repair.

Division Matching Task

• Ernesto Jiménez-Ruiz, Asan Agibetov, Jiaoyan Chen, Matthias Samwald, Valerie Cross. Dividing the Ontology Alignment Task with Semantic Embeddings and Logic-based Modules. In the 24th European Conference on Artificial Intelligence (ECAI 2020). (PDF) (Slides) (Slides with Video)

• Ernesto Jiménez-Ruiz, Asan Agibetov, Matthias Samwald, Valerie Cross. Breaking-down the Ontology Alignment Task with a Lexical Index and Neural Embeddings. arXiv:1805.12402. (PDF)

Evaluation

• Yuan He, Jiaoyan Chen, Hang Dong, Ernesto Jiménez-Ruiz, Ali Hadian, Ian Horrocks. Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching. International Semantic Web Conference (ISWC) 2022, Resource paper. (PDF) (Video) (OAEI track)

• Huanyu Li, Zlatan Dragisic, Daniel Faria, Valentina Ivanova, Ernesto Jiménez-Ruiz, Patrick Lambrix and Catia Pesquita. User validation in ontology alignment: functional assessment and impact. Knowledge Engineering Review journal, Volume 34 , 2019. (PDF) (HTML)

• Ian Harrow, Ernesto Jiménez-Ruiz, Andrea Splendiani, Martin Romacker, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, James Malone, and Arild Waaler. Matching Disease and Phenotype Ontologies in the Ontology Alignment Evaluation Initiative. Journal of Biomedical Semantics 8, 55, 2017. (PDF) (HTML)

Applications

• Ian Harrow, Rama Balakrishnan, Ernesto Jimenez-Ruiz, Simon Jupp, Jane Lomax, Jane Reed, Martin Romacker, Christian Senger, Andrea Splendiani, Jabe Wilson, Peter Woollard. Ontology mapping for semantically enabled applications. Drug Discovery Today, Volume 24, 2019 (HTML)

• Erik B. Myklebust, Ernesto Jimenez Ruiz, Jiaoyan Chen, Raoul Wolf, Knut Erik Tollefsen. Prediction of Adverse Biological Effects of Chemicals Using Knowledge Graph Embeddings. Semantic Web Journal. (arXiv) (HTML) (GitHub)

Additional list of LogMap-related publications.

Acknowledgements

LogMap was originally designed and developed in the Knowledge Representation and Reasoning group at the Department of Computer Science of the University of Oxford by Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau and Ian Horrocks. LogMap is currently maintained by Ernesto Jiménez-Ruiz at the Department of Computer Science (City, University of London]).

Development has been supported by The Royal Society, the EPSRC project LogMap, the EU FP7 projects SEALS and Optique, the AIDA project, and the SIRIUS Centre for Scalable Data Access.

We would like to thank Jiaoyan Chen, Alessandro Solimando, Valerie Cross, Anton Morant, Yujiao Zhou, Weiguo Xia, Xi Chen, Yuan Gong, Shuo Zhang and Rob Upson, who have also contributed to the LogMap project.

We also thank the organisers of the OAEI evaluation campaigns for providing test data and infrastructure.

License

Copyright 2022 Department of Computer Science (University of Oxford) and Department of Computer Science (City, University of London)

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.