______________________________________________________________ / \ | AML (AgreementMakerLight) | | Demo GUI / CLI version | | Copyright 2013-2016 LASIGE | | | | This product includes software developed at LASIGE by the | | SOMER team (http://somer.fc.ul.pt) in collaboration with | | the ADVIS Lab (http://www.cs.uic.edu/Advis) and the UBI | | (http://bioinformatics.igc.gulbenkian.pt/ubi/). | | | | 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 | | | | This software is provided on an "AS IS" BASIS, WITHOUT | | WARRANTIES OR CONDITIONS OF ANY KIND, either express or | | implied, including, without limitation, any warranties or | | conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, | | or FITNESS FOR A PARTICULAR PURPOSE. | \______________________________________________________________/ / \ | ABOUT AML: | | | | AML is a lightweight ontology matching system specialized | | on the biomedical domain but applicable to any ontologies. | | It can be used to generate alignments automatically, as a | | platform for reviewing alignments, or as an alignment | | repair system (both automatically and interactively). | | AML has achieved top resuls in the last two editions of the | | Ontology Alignment Evaluation Initiative: | | - D. Faria, C. Martins, A. Nanavaty, et al. "AML Results | | for OAEI 2015", ISWC Workshop on Ontology Matching, 2015. | | - D. Faria, C. Martins, A. Nanavaty, et al. | | "AgreementMakerLight Results for OAEI 2014", ISWC Workshop | | on Ontology Matching, 2014. | | | | If you use AML, please cite the following publication: | | - D. Faria, C. Pesquita, E. Santos, M. Palmonari, I. Cruz, | | and F. Couto, The AgreementMakerLight ontology matching | | system, ODBASE 2013. | | | | The AML GUI uses Gephi, an open source graph visualization | | and manipulation software. Like AML, Gephi is lightweight | | and efficient. | \______________________________________________________________/ / \ | SYSTEM REQUIREMENTS: | | | | AML requires Java SE Runtime Environment 7+. Its GUI may | | not function properly on older Java versions. | | | | Memory usage depends on the size of the ontologies you are | | working with. We recommend a minimum of 2 GB RAM for small | | ontologies (<1,000 classes), 4 GB RAM for medium-sized | | ontologies (<10,000 classes), 8 GB RAM for large ontologies | | (<100,000 classes), and 16 GB RAM for larger ontologies. | | | | Please keep in mind that opening large ontologies may take | | several minutes. Likewise, matching large ontologies may | | also take several minutes, particularly when WordNet or | | large ontologies are used as background knowledge sources | | and/or the repair option is selected. | | | | Please do not move the AgreementMakerLight.jar file from | | the AML folder, as it will not work without this folder | | structure. | \______________________________________________________________/ / \ | AML GUI USAGE: | | | | You can run the AML GUI by simply double-clicking the file | | AgreementMakerLight.jar or through the command line, by | | typing 'java -jar AgreementMakerLight.jar' without any | | arguments. | | | | If you want to use external ontologies as background | | knowledge sources, just place them in 'store/knowledge/' | | and they will be automatically listed by AML. | \______________________________________________________________/ / \ | AML CLI USAGE: | | | | For running AML through the command line (without calling | | the GUI, type: | | | | java -jar AgreementMakerLight.jar OPTIONS | | | | The options are: | | | | -h (--help) -> print the help menu | | -s (--source) 'path_to_source_ontology' | | -t (--target) 'path_to_target_ontology' | | -i (--input) 'path_to_input_alignment' | | (mandatory in repair mode, where it will be | | the alignment to repair; optional in match | | mode, where it will be used as the reference | | alignment, to evaluate the match result) | | -o (--output) 'path_to_ouput_alignment' | | (if you want to save the resulting alignment) | | -a (--auto) -> automatic match mode | | OR | | -m (--manual) -> manual match mode (you can configure the | | matcher in the store/config.ini file) | | OR | | -r (--repair) -> repair alignment mode | | | | Examples: | | | | 1) Use AML to automatically match two ontologies and save | | output alignment: 'java -jar AgreementMakerLight.jar | | -s store/anatomy/mouse.owl -t store/anatomy/human.owl | | -o store/anatomy/alignment.rdf -a' | | | | 2) Use AML to manually match two ontologies and evaluate | | the output alignment: 'java -jar AgreementMakerLight.jar | | -s store/anatomy/mouse.owl -t store/anatomy/human.owl | | -i store/anatomy/reference.rdf -m' | | Note that you can configure the options manually in the | | store/config.ini file. | | | | 3) Use AML to repair the input alignment between two | | ontologies: 'java -jar AgreementMakerLight.jar | | -s store/anatomy/mouse.owl -t store/anatomy/human.owl | | -i store/anatomy/alignment.rdf -r | | -o store/anatomy/repaired_alignment.rdf' | \______________________________________________________________/ / \ | AML TRANSLATION MODULE: | | | | AML's translation module is based on the Microsoft (Bing) | | translator. To use it, you MUST get your own access token | | from microsoft as detailed here: | | https://msdn.microsoft.com/en-us/library/hh454950.aspx | | | | Once you have an access token, create a file called | | exactly 'microsoft-translator-id' and place it in the | | store/ folder. This file should contain your client_id in | | the first line and your access_token in the second line. It | | should contain no other information. | | | | Finally, you should create a 'dictionary/' folder within | | AML's 'store/' folder and ensure that java has write | | permission in this folder. This folder will be used by AML | | to store computed translations, so as to avoid overloading | | Microsoft translator with redundant queries. | | | \______________________________________________________________/