ernestojimenezruiz / logmap-matcher

LogMap: An Ontology Alignment and Alignment Repair System

LogMap: An Ontology Alignment and Alignment Repair System

News (July 2022):

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 >500 citations according to Google Scholar!
2. Check out...
   • A proof-of-concept interface to offer LogMap as a service: KGAS documentation and codes, Web app, REST API
   • The new interface with the MELT platform here.
   • 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.

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) (OWL2Vec* work)

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.

logmap-matcher's Issues

Error processing labels: trying to cast IRI to OWLLiteral

What steps will reproduce the problem?
Error when matching
1. http://sensormeasurement.appspot.com/naturopathy# 
2. http://kmi.open.ac.uk/projects/smartproducts/ontologies/food_taxonomy.owl 

Error:

java.lang.ClassCastException: org.semanticweb.owlapi.model.IRI$IRIImpl cannot 
be cast to org.semanticweb.owlapi.model.OWLLiteral
        at uk.ac.ox.krr.logmap2.overlapping.OntologyProcessing4Overlapping.extractLabels4OWLCls(OntologyProcessing4Overlapping.java:256)
        at uk.ac.ox.krr.logmap2.overlapping.OntologyProcessing4Overlapping.processOntologyClassLabels(OntologyProcessing4Overlapping.java:134)
        at uk.ac.ox.krr.logmap2.overlapping.LexicalOverlappingExtractor.createOverlapping(LexicalOverlappingExtractor.java:222)
        at uk.ac.ox.krr.logmap2.overlapping.LexicalOverlappingExtractor.createOverlapping(LexicalOverlappingExtractor.java:147)
        at uk.ac.ox.krr.logmap2.web_service.LogMap_WebService.OverlappingEstimation(LogMap_WebService.java:301)
        at uk.ac.ox.krr.logmap2.web_service.LogMap_WebService.<init>(LogMap_WebService.java:137)
        at uk.ac.ox.krr.logmap2.web_service.LogMapRequest$LogMapThread.run(LogMapRequest.java:652)
        at java.lang.Thread.run(Thread.java:722)

Original issue reported on code.google.com by [email protected] on 5 Sep 2013 at 4:43

Can't send the matching request via web interface

I try to run LogMap via the web interface: http://krrwebtools.cs.ox.ac.uk/logmap/. I successfully upload 2 ontologies in the form of head entity, relation and tail entity seperated by "\t" in every line. But I can't send the matching request and the button is still greyed out.

question regarding matching CoNLL output with NER tags containing B-ORG GPE

Hi,

I have been successfully able to extract entities into CoNLL-RDF into a NER annotation for a Word class.

See below for the source CoNLL-RDF:
acoli-repo/conll-rdf#84 (comment)

And created resulting ttl:
Source:
https://www.richmondfed.org/publications/research/coronavirus/economic_impact_covid-19_11-10-21
How Charlotte’s Banks Responded to COVID-19
By Elizabeth Medlin - The Federal Reserve Bank of Richmond (
Views expressed in this article are those of the authors and not necessarily those of their respective Reserve Banks or the Federal Reserve System.)

economic_impact_covid_ner.ttl.zip

But would like to match this output to an ontology - in particular the NER annotations , I'm not having a lot of luck doing so. I thinks some of it has to do with my source ttl and I'm missing some necessary steps?

Any suggestions in what I could try with LogMap? I would be glad to try to clarify if I'm not asking the right question.

Hits@K and MRR for OAEI 2022 data

Hi, I am trying to generate the results for LogMap (Table 4 in https://arxiv.org/pdf/2205.03447.pdf) using the standalone release.

I am using the mappings file generated by LOGMAP ( as stated in https://code.google.com/archive/p/logmap-matcher/wikis/LogMapCommandLine.wiki) for computing all the metrics. Though I am getting precision, recall and f1 score the same as reported in Table 4 in https://arxiv.org/pdf/2205.03447.pdf, I get different values for Hits@K and MRR.

Am I looking at the correct mapping file for generating Hits@K and MRR or do we need to generate the score for the negative candidates separately and then compute these metrics?

For calculating Hits@K and MRR, I follow the same logic as in https://github.com/KRR-Oxford/DeepOnto. Is this correct?

Add SSSOM or alignment-xml output

I would like to analyze results using sssom tools; see:

• mapping-commons/sssom-py#377

sssom-py has an adapter for the OAEI alignment-xml but this doesn't seem to be one of the formats produced?

It would be great if this tool could produce either format

Running logmap's docker image over local track and getting 0 correspondences

Hi,

I was running logmap's docker image over local dataset, though there are no errors, getting 0 correspondences.

Please take a look at the below log and if you find something that maybe the issue please let me know.

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
2022-09-28 16:55:16,871 INFO  MeltUtil                  - Welcome to
 __  __ ______ _   _______
|  \/  |  ____| | |__   __|
| \  / | |__  | |    | |
| |\/| |  __| | |    | |
| |  | | |____| |____| |
|_|  |_|______|______|_|    3.4-SNAPSHOT (git commit f281487)
2022-09-28 16:55:16,877 INFO  Track                     - Track cache folder is: C:\Users\user\oaei_track_cache
Recognized MELT WEB DOCKER package:
.\logmap-melt-oaei-2021-web-latest.tar.gz
2022-09-28 16:55:16,881 INFO  Main                      - Please make sure that docker is running on your system.
2022-09-28 16:55:17,785 INFO  MatcherDockerFile         - Connected to docker machine: docker-desktop
2022-09-28 16:55:17,785 INFO  MatcherDockerFile         - Load docker image from file .\logmap-melt-oaei-2021-web-latest.tar.gz to docker local registry. If image is already there, use constructor MatcherDockerFile(String imageName).
2022-09-28 16:55:21,952 INFO  MatcherDockerFile         - Starting container from image logmap-melt-oaei-2021-web (port 8080 from container is mapped to port 64007 in host)
2022-09-28 16:55:22,729 INFO  MatcherDockerFile         - Container started with id cff3121683ac3f1a0e2826cda9a293aaf3221ad31042ea52bb5ba2f0d47a154c
2022-09-28 16:55:22,731 INFO  Main                      - Running matching systems...
2022-09-28 16:55:22,752 INFO  ExecutionRunner           - Running matcher .\logmap-melt-oaei-2021-web-latest.tar.gz on testcase Local TC (track LocalTrack).
2022-09-28 16:55:23,103 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 170  in log                  - Logging initialized @381ms to org.eclipse.jetty.util.log.Slf4jLog
2022-09-28 16:55:23,208 INFO  MatcherHTTPCall           - Execute now the following HTTP request: POST http://localhost:64007/match HTTP/1.1
2022-09-28 16:55:23,226 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 68   in Main                 - Matching service runs at: http://localhost:8080/match
2022-09-28 16:55:23,229 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 375  in Server               - jetty-9.4.41.v20210516; built: 2021-05-16T23:56:28.993Z; git: 98607f93c7833e7dc59489b13f3cb0a114fb9f4c; jvm 1.8.0_212-b04
2022-09-28 16:55:23,240 INFO  RetryExec                 - I/O exception (java.net.SocketException) caught when processing request to {}->http://localhost:64007: Software caused connection abort: socket write error
2022-09-28 16:55:23,240 INFO  MatcherHTTPCall           - Endpoint is not ready / an exception occurred. Waiting 10 seconds. Trial 1/5
2022-09-28 16:55:23,277 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 916  in ContextHandler       - Started o.e.j.s.ServletContextHandler@5ae63ade{/,null,AVAILABLE}
2022-09-28 16:55:23,308 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 331  in AbstractConnector    - Started ServerConnector@5a61f5df{HTTP/1.1, (http/1.1)}{0.0.0.0:8080}
2022-09-28 16:55:23,308 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 415  in Server               - Started @586ms
2022-09-28 16:55:33,246 INFO  MatcherHTTPCall           - Execute now the following HTTP request: POST http://localhost:64007/match HTTP/1.1
2022-09-28 16:55:33,317 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:33 INFO  [qtp1748225580-19              ] 90   in Main                 - Got multipart request - start matching
2022-09-28 16:55:33,361 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:33 INFO  [qtp1748225580-19              ] 206  in Main                 - Server starts matcher class uk.ac.city.logmap.melt.LogMap_MELT for task:
Source:file:/tmp/MELT-fileupload8654086080574412052/source-8453155817845026653.rdf
Target:file:/tmp/MELT-fileupload8654086080574412052/target-1887410882821678633.rdf
InputAlignment:null
Parameter:null
2022-09-28 16:55:33,387 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:33 INFO  [qtp1748225580-19              ] 486  in Parameters           - Reading LogMap parameters from file.
2022-09-28 16:55:33,964 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:33 INFO  [qtp1748225580-19              ] 395  in LogMap2Core          - LogMap: ontology loading and overlapping extraction
2022-09-28 16:55:34,420 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:34 INFO  [qtp1748225580-19              ] 1307 in OWLRDFConsumer       - dumping remaining triples
2022-09-28 16:55:34,421 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:34 INFO  [qtp1748225580-19              ] 1341 in OWLRDFConsumer       - done dumping remaining triples
2022-09-28 16:55:35,061 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 1307 in OWLRDFConsumer       - dumping remaining triples
2022-09-28 16:55:35,065 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 1341 in OWLRDFConsumer       - done dumping remaining triples
2022-09-28 16:55:35,087 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 404  in LogMap2Core          - LogMap indexation
2022-09-28 16:55:35,208 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 423  in LogMap2Core          - LogMap anchor extraction
2022-09-28 16:55:35,219 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 428  in LogMap2Core          - LogMap class mapping extraction
2022-09-28 16:55:35,226 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 471  in LogMap2Core          - LogMap property mapping extraction
2022-09-28 16:55:35,324 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 479  in LogMap2Core          - LogMap instance mapping extraction
2022-09-28 16:55:35,325 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 39   in LogMap_MELT          - Matching with LogMap completed
2022-09-28 16:55:35,333 INFO  DockerLogCallback         - STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 158  in Main                 - Finished matching
2022-09-28 16:55:35,345 INFO  ExecutionRunner           - Running matcher .\logmap-melt-oaei-2021-web-latest.tar.gz on testcase Local TC (track LocalTrack) completed in 12 seconds.
2022-09-28 16:55:35,369 INFO  Main                      - Evaluating matching system results...
2022-09-28 16:55:35,587 INFO  EvaluatorCSV              - Evaluate matcher .\logmap-melt-oaei-2021-web-latest.tar.gz
2022-09-28 16:55:35,635 INFO  OntologyCacheJena         - Reading model into cache (file:/C:/Users/user/OneDrive/conference-conference-de-hi/source.rdf)
2022-09-28 16:55:35,745 INFO  OntologyCacheJena         - Reading model into cache (file:/C:/Users/user/OneDrive/conference-conference-de-hi/target.rdf)
2022-09-28 16:55:35,807 INFO  ExecutionRunner           - Running matcher baseLineMatcher on testcase Local TC (track LocalTrack).
2022-09-28 16:55:35,854 INFO  ExecutionRunner           - Running matcher baseLineMatcher on testcase Local TC (track LocalTrack) completed in 0 seconds.
2022-09-28 16:55:35,886 INFO  EvaluatorCSV              - Writing alignment cube
2022-09-28 16:55:35,886 INFO  AlignmentsCube            - Writing LocalTrack | Local TC | .\logmap-melt-oaei-2021-web-latest.tar.gz [to file: C:\Users\user\AppData\Local\Temp\melt-client-results-2315723151985622977\alignmentCube.csv]
Results written to: C:\Users\user\AppData\Local\Temp\melt-client-results-2315723151985622977
2022-09-28 16:55:35,933 INFO  Main                      -

Matcher: .\logmap-melt-oaei-2021-web-latest.tar.gz
Macro Precision: 0.0
Macro Recall: 0.0
Macro F1: 0.0
Micro Precision: 0.0
Micro Recall: 0.0
Micro F1: 0.0
Total Runtime (HH:MM:SS): 00:00:12
Since F1 is 0, you can find the full log of .\logmap-melt-oaei-2021-web-latest.tar.gz below:
2022-09-28 16:55:35,955 INFO  Main                      - STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 170  in log                  - Logging initialized @381ms to org.eclipse.jetty.util.log.Slf4jLog
STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 68   in Main                 - Matching service runs at: http://localhost:8080/match
STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 375  in Server               - jetty-9.4.41.v20210516; built: 2021-05-16T23:56:28.993Z; git: 98607f93c7833e7dc59489b13f3cb0a114fb9f4c; jvm 1.8.0_212-b04
STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 916  in ContextHandler       - Started o.e.j.s.ServletContextHandler@5ae63ade{/,null,AVAILABLE}
STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 331  in AbstractConnector    - Started ServerConnector@5a61f5df{HTTP/1.1, (http/1.1)}{0.0.0.0:8080}
STDOUT: 2022-09-28 11:25:23 INFO  [main                          ] 415  in Server               - Started @586ms
STDOUT: 2022-09-28 11:25:33 INFO  [qtp1748225580-19              ] 90   in Main                 - Got multipart request - start matching
STDOUT: 2022-09-28 11:25:33 INFO  [qtp1748225580-19              ] 206  in Main                 - Server starts matcher class uk.ac.city.logmap.melt.LogMap_MELT for task:
STDOUT: Source:file:/tmp/MELT-fileupload8654086080574412052/source-8453155817845026653.rdf
STDOUT: Target:file:/tmp/MELT-fileupload8654086080574412052/target-1887410882821678633.rdf
STDOUT: InputAlignment:null
STDOUT: Parameter:null
STDOUT: 2022-09-28 11:25:33 INFO  [qtp1748225580-19              ] 486  in Parameters           - Reading LogMap parameters from file.
STDOUT: 2022-09-28 11:25:33 INFO  [qtp1748225580-19              ] 395  in LogMap2Core          - LogMap: ontology loading and overlapping extraction
STDOUT: 2022-09-28 11:25:34 INFO  [qtp1748225580-19              ] 1307 in OWLRDFConsumer       - dumping remaining triples
STDOUT: 2022-09-28 11:25:34 INFO  [qtp1748225580-19              ] 1341 in OWLRDFConsumer       - done dumping remaining triples
STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 1307 in OWLRDFConsumer       - dumping remaining triples
STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 1341 in OWLRDFConsumer       - done dumping remaining triples
STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 404  in LogMap2Core          - LogMap indexation
STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 423  in LogMap2Core          - LogMap anchor extraction
STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 428  in LogMap2Core          - LogMap class mapping extraction
STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 471  in LogMap2Core          - LogMap property mapping extraction
STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 479  in LogMap2Core          - LogMap instance mapping extraction
STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 39   in LogMap_MELT          - Matching with LogMap completed
STDOUT: 2022-09-28 11:25:35 INFO  [qtp1748225580-19              ] 158  in Main                 - Finished matching

2022-09-28 16:55:35,957 INFO  MatcherDockerFile         - JVM shutdown detected and container cff3121683ac3f1a0e2826cda9a293aaf3221ad31042ea52bb5ba2f0d47a154c is shut down now. Please call close method of MatcherDockerFile to remove this message.

Thanks
Abhisek

OAEI format contains measures > 1.0

What steps will reproduce the problem?
1. Perform matching between two ontologies where Logmap is highly certain about 
some correspondences
2. Example: 
http://csu6325.cs.ox.ac.uk/output/matching_14_07_2015__10_00_20_963/index.html

What is the expected output? What do you see instead?
Measure should be 1.0 if Logmap is entirely sure, instead some values are 1.0x
This, in turn, crashes the Alignment API command line interface for determining 
F-measures w.r.t. reference alignments

What version of the product are you using? On what operating system?
Happens with the online version and the standalone tool v.2.4

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 14 Jul 2015 at 9:37

Want to use in python project

Dears,
I want to integrate LogMap in my python project, could you give me some suggestions:

How can I integrate it conveniently, or I can only rewrite LogMap in python by myself ? I would be grateful if there is a logmap-python available.

Thanks a lot & Best Regards,
KilinChange

Error saving mapping

Dears,

kindly I need your help in the following issue

I have faced some (attached) errors in the console for some of the alignments found by the tool. However the output files were generated. Can you please guide me why these errors were generated and how to solve them.

Another question is, there are two output files generated with two different directories, the first is in the assigned directory in the written command, and the second is in the same directory where the ontologies are found. Can you also please explain to me why this happens, am I doing the matching process wrong ?

Thanks a lot & Best Regards,
Engy Nasr

Update instructions for running the CLI

It would be great if there were more instructions on how to run the CLI, and if these could be updated

In order to run on java 17, I had to add --add-opens java.base/java.lang=ALL-UNNAMED

e.g.

java --add-opens java.base/java.lang=ALL-UNNAMED -jar tools/logmap-matcher-standalone-july-2021/logmap-matcher-4.0.jar

See https://stackoverflow.com/questions/41265266/how-to-solve-inaccessibleobjectexception-unable-to-make-member-accessible-m

Could not find an appropriate factory to load ontology from ontology document

org.semanticweb.owlapi.model.OWLOntologyFactoryNotFoundException: Could not find an appropriate factory to load ontology from ontology document: <E://logmap//a//data//OAEI2018//LargeBioMed_dataset_oaei2012//oaei2012_FMA_small_overlapping_nci.owl>
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1072)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:947)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:903)
at UsingLogMapMatcher.(UsingLogMapMatcher.java:41)
at UsingLogMapMatcher.main(UsingLogMapMatcher.java:87)

what is the situation with https IRIs?

the web interface didn't handle an ontology with https IRIs - is this the same situation for the standalone version?

Web version different than the standalone ?

Both the below scenarios work perfect with the web version. Finds the match for Dim_patient
http://krrwebtools.cs.ox.ac.uk/logmap/output/matching_07_04_2020__20_47_14_29/mappings.txt

http://hl7.org/fhir/integer|http://watsonhealth.ibm.com/cro/integer|=|0.7|CLS
http://hl7.org/fhir/string|http://watsonhealth.ibm.com/cro/string|=|0.7|CLS
http://hl7.org/fhir/boolean|http://watsonhealth.ibm.com/cro/boolean|=|0.7|CLS
http://hl7.org/fhir/Patient|http://watsonhealth.ibm.com/cro/Dim_Patient|=|0.52|CLS
http://hl7.org/fhir/value|http://watsonhealth.ibm.com/cro/value|=|1.0|DPROP

Standalone (build from Github)

1. with ELK reasoner turned on in parameters.txt I get
   Running LogMap Matcher ....
   SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
   SLF4J: Defaulting to no-operation (NOP) logger implementation
   SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
   org.semanticweb.owlapi.model.OWLRuntimeException: No current axiom; is the walker being used outside of an ontology visit?
   at org.semanticweb.owlapi.util.OWLOntologyWalkerVisitor.getCurrentAxiom(OWLOntologyWalkerVisitor.java:48)
   at org.semanticweb.owlapi.profiles.OWL2DLProfile$OWL2DLProfileObjectVisitor.visit(OWL2DLProfile.java:477)
   at uk.ac.manchester.cs.owl.owlapi.OWLAnnotationPropertyImpl.accept(OWLAnnotationPropertyImpl.java:83)
   at org.semanticweb.owlapi.util.OWLObjectWalker.passToVisitor(OWLObjectWalker.java:137)
   at org.semanticweb.owlapi.util.StructureWalker.process(StructureWalker.java:87)
   at org.semanticweb.owlapi.util.StructureWalker.visit(StructureWalker.java:687)
   at uk.ac.manchester.cs.owl.owlapi.OWLAnnotationPropertyImpl.accept(OWLAnnotationPropertyImpl.java:83)
   at org.semanticweb.owlapi.profiles.OWLOntologyProfileWalker$1.visit(OWLOntologyProfileWalker.java:56)
   at uk.ac.manchester.cs.owl.owlapi.OWLAnnotationImpl.accept(OWLAnnotationImpl.java:141)
   at org.semanticweb.owlapi.util.StructureWalker.process(StructureWalker.java:101)
   at org.semanticweb.owlapi.util.StructureWalker.visit(StructureWalker.java:116)
   at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.accept(OWLImmutableOntologyImpl.java:852)
   at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyImpl.accept(ConcurrentOWLOntologyImpl.java:396)
   at org.semanticweb.owlapi.util.OWLObjectWalker.walkStructure(OWLObjectWalker.java:181)
   at org.semanticweb.owlapi.profiles.OWL2DLProfile.checkOntology(OWL2DLProfile.java:146)
   at org.semanticweb.owlapi.profiles.OWL2ELProfile.checkOntology(OWL2ELProfile.java:106)
   at uk.ac.ox.krr.logmap2.reasoning.profiles.CheckOWL2Profile.isInOWL2ELProfile(CheckOWL2Profile.java:59)
   at uk.ac.ox.krr.logmap2.indexing.OntologyProcessing.setUpReasoner_ELK(OntologyProcessing.java:2809)
   at uk.ac.ox.krr.logmap2.indexing.OntologyProcessing.setTaxonomicData(OntologyProcessing.java:2625)
   at uk.ac.ox.krr.logmap2.LogMap2Core.IndexLexiconAndStructure(LogMap2Core.java:942)
   at uk.ac.ox.krr.logmap2.LogMap2Core.IndexLexiconAndStructure(LogMap2Core.java:886)
   at uk.ac.ox.krr.logmap2.LogMap2Core.(LogMap2Core.java:421)
   at uk.ac.ox.krr.logmap2.LogMap2Core.(LogMap2Core.java:214)
   at uk.ac.ox.krr.logmap2.LogMap2_Matcher.(LogMap2_Matcher.java:63)
   at uk.ac.ox.krr.logmap2.LogMap2_CommandLine.main(LogMap2_CommandLine.java:106)

2. With HemiT

It just simply ignores the custom datatypes

http://hl7.org/fhir/string|http://watsonhealth.ibm.com/cro/string|=|0.7|CLS
http://hl7.org/fhir/boolean|http://watsonhealth.ibm.com/cro/boolean|=|0.7|CLS
http://hl7.org/fhir/integer|http://watsonhealth.ibm.com/cro/integer|=|0.7|CLS
http://hl7.org/fhir/value|http://watsonhealth.ibm.com/cro/value|=|1.0|DPROP

Web Interface Bug

The submit button on the web interface seems to be broken.

Mvn package failure

I downloaded logmap-matcher from sourceforge and since the readme file said:
"Development requires a clone of this git repository. You can use the pre-configured Eclipse (Maven) project (dependencies are automatically downloaded). To generate a JAR file for LogMap from the command line using Maven, run: mvn package". I ran mvn package but it gives the error:

[MVNVM] Using maven: 3.2.5
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for logmap-matcher:logmap-matcher:jar:3.0.0-SNAPSHOT
[WARNING] 'dependencies.dependency.systemPath' for com.googlecode:google-api-translate-java:jar should not point at files within the project directory, ${basedir}/lib/google-api-translate-java-0.97.jar will be unresolvable by dependent projects @ line 102, column 17
[WARNING] 'dependencies.dependency.systemPath' for eu.sealsproject.omt:omt-client:jar should not point at files within the project directory, ${basedir}/lib/seals-omt-client.jar will be unresolvable by dependent projects @ line 109, column 17
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building LogMap 3.0.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ logmap-matcher ---
[WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent!
[INFO] skip non existing resourceDirectory /Amrapali/AAStanford/Projects/SIO-Bio2RDF/logmap-matcher/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ logmap-matcher ---
[INFO] Changes detected - recompiling the module!
[WARNING] File encoding has not been set, using platform encoding UTF-8, i.e. build is platform dependent!
[INFO] Compiling 156 source files to /Amrapali/AAStanford/Projects/SIO-Bio2RDF/logmap-matcher/target/classes
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] /Amrapali/AAStanford/Projects/SIO-Bio2RDF/logmap-matcher/src/main/java/uk/ac/ox/krr/logmap2/indexing/LightTarjan.java:[17,58] diamond operator is not supported in -source 1.5
(use -source 7 or higher to enable diamond operator)
[ERROR] /Amrapali/AAStanford/Projects/SIO-Bio2RDF/logmap-matcher/src/main/java/uk/ac/ox/krr/logmap2/indexing/JointIndexManager.java:[403,64] diamond operator is not supported in -source 1.5
(use -source 7 or higher to enable diamond operator)
[INFO] 2 errors
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 4.978 s
[INFO] Finished at: 2016-06-28T21:29:29-07:00
[INFO] Final Memory: 9M/245M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project logmap-matcher: Compilation failure: Compilation failure:
[ERROR] /Amrapali/AAStanford/Projects/SIO-Bio2RDF/logmap-matcher/src/main/java/uk/ac/ox/krr/logmap2/indexing/LightTarjan.java:[17,58] diamond operator is not supported in -source 1.5
[ERROR](use -source 7 or higher to enable diamond operator)
[ERROR] /Amrapali/AAStanford/Projects/SIO-Bio2RDF/logmap-matcher/src/main/java/uk/ac/ox/krr/logmap2/indexing/JointIndexManager.java:[403,64] diamond operator is not supported in -source 1.5
[ERROR](use -source 7 or higher to enable diamond operator)
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

StackOverflow Error in Structural reasoner

What steps will reproduce the problem?
1. Matching ontologies 
http://csu6325.cs.ox.ac.uk/ontologies/matching_29_11_2012/dbpedia_3.8.owl and 
http://csu6325.cs.ox.ac.uk/ontologies/matching_29_11_2012/Wikipedia.zip

The error has been detected and it will be fixed in next LogMap's release.

Original issue reported on code.google.com by [email protected] on 29 Nov 2012 at 6:55

No result from LogMap web service

Dear Ernesto,
since Saturday I could not get back any results from http://krrwebtools.cs.ox.ac.uk/logmap/. While the website says very quickly that a message has been sent to my email address, I never get that progress or results email. I would be very glad if this could be repaired because I would like to show LogMap to my students tomorrow.
Best regards,
Monika

Num unsat classes after integration: 0

Getting Num unsat classes after integration: 0 while running logmap using jar file.

Could you suggest what should I do? I might be missing something.

Thanks & Regards
Abhisek

g

Error processing URIs without local names

URIs without a local name associated to an entity causes an error: e.g. 
"http://www.opengis.net/citygml/appearance/2.0/"

This error will be solved in LogMap version 2.4.

Original issue reported on code.google.com by [email protected] on 5 Nov 2012 at 9:28

Problems with the owl api 3 version

Hii,

when i try to use the branch with the owl api 3 it gives me the following result:
'Number of mappings computed by LogMap: 0'.
it works fine with the master branch but this branch is not giving any result for any pairs of ontologies

Thank you

Update to improved locality module extractor method

A slightly faster version of the locality module extractor is available.

Original issue reported on code.google.com by [email protected] on 9 Jan 2013 at 5:06

Adding google translate

On windows when adding google translate with Maven, you need quotes around "com.googlecode" and "0.97".

So you have:
mvn install:install-file -Dfile=/home/ernesto/git/logmap3-matcher/lib/google-api-translate-java-0.97.jar -DgroupId="com.googlecode" -DartifactId=google-api-translate-java -Dversion="0.97" -Dpackaging=jar

PreIntervalLabelledHierarchy StackOverflowError

This error has been detected in a few cases:

Exception in thread "main" java.lang.StackOverflowError
at 
uk.ac.ox.krr.logmap2.indexing.labelling_schema.PreIntervalLabelledHierarchy.walk
AscNode(PreIntervalLabelledHierarchy.java:76)

Original issue reported on code.google.com by [email protected] on 23 Mar 2013 at 5:09

No result and error on standalone version

Hi,
I also did not receive the mail with the results.
Additionally, attempting to run the standalone version gives me the following error:

C:\Users\utente\Downloads\logmap-matcher-standalone-july-2021>java -jar logmap-matcher-4.0.jar LITE file:rswo-1.3.0.ttl file:rswo-1.3.0.ttl C://Users/utente/Downloads/logmap-matcher-standalone-july-2021

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$2 (file:/C:/Users/utente/Downloads/logmap-matcher-standalone-july-2021/java-dependencies/guice-4.0.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$2
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Size LogMap Lite mappings: 111
Time loading ontos (s): 1.895
LogMap Lite Matching Time (s): 0.09200000000000008
java.lang.IllegalArgumentException: URI is not hierarchical
        at java.base/java.io.File.<init>(File.java:420)
        at org.semanticweb.owlapi.util.AbstractOWLStorer.prepareActualOutput(AbstractOWLStorer.java:80)
        at org.semanticweb.owlapi.util.AbstractOWLStorer.storeOntology(AbstractOWLStorer.java:63)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1217)
        at uk.ac.ox.krr.logmap2.io.OWLAlignmentFormat.saveOutputFile(OWLAlignmentFormat.java:329)
        at uk.ac.ox.krr.logmap2.io.OutPutFilesManager.closeAndSaveFiles(OutPutFilesManager.java:143)
        at uk.ac.ox.krr.logmap_lite.LogMap_Lite.saveMapping(LogMap_Lite.java:447)
        at uk.ac.ox.krr.logmap_lite.LogMap_Lite.<init>(LogMap_Lite.java:246)
        at uk.ac.ox.krr.logmap2.LogMap2_CommandLine.main(LogMap2_CommandLine.java:124)

Any idea about these?
Many thanks

Missing Artifact "com.googlecode:google-api-translate-java"

When I clone the project I get a "missing artifact" error.
Missing artifact com.googlecode:google-api-translate-java:jar:0.97
The other dependencies seem to be fine. I also deleted the dependency from the .m2 directory and redownloaded it but it is still not working.

"the results will be sent to you by e-mail." No email received.

"the results will be sent to you by e-mail."
No email received.
Tested with various email addresses and spam checked

Error with mailing exceptions

See https://groups.google.com/forum/#!topic/play-framework/vRDjO5bJTc8

Original issue reported on code.google.com by [email protected] on 24 Jun 2013 at 3:26