Research

Currently ongoing projects:

• 2024. Knowledge Graphs. Universidad de Murcia (UM), SIEMENS (Through Euskoiker foundation).
• 2023 - 2024. Methods for automatic generation of Knowledge Graph. Universidad de Murcia (UM), BASF (Through Euskoiker foundation).
• 2021 - 2024. SUPPORT4LS (Process Mining and Knowledge Representation technologies to Support the Learning Health System). PID2020-113723RB-C22. Agencia Estatal de Investigación, “Proyectos I+D+i 2020” - Modalidades “Retos Investigación” y “Generación de Conocimiento” (Plan Estatal de Investigación Cientı́fica y Técnica y de Innovación 2017-2020). 136.972,00 EUR. 01/09/2021 - 31/08/2024
• 2024. EHUkhi: una plataforma para el desarrollo del potencial fotovoltaico de la UPV/EHU (Campus Bizia Lab).

Finished projects:

• 2020 - 2021. Linked Open Data Fase 2 (Through Euskoiker foundation). Basque Government, Spain.
• 2018. Servicios Directorio Linked Open Data. Basque Government, Spain. (70.000 EUR)
• 2016 - 2018. REPLICATE: Renaissance of Places with Innovative Citizenship And TEchnology (Project 691735).  EU. (Consortium:  24.965.263,09; Eurohelp:  328.580,00 EUR)
• 2016 - 2018. Servicios OpenLinkedData (Linked Data implementation of Open Data Euskadi). Basque Government, Spain. (90.000 EUR)
• 2015 - 2016. Linking Open Domains, Plataforma para la generación de datos enlazados (LODGen). Ministerio de Industria, Energia y Turismo, Acción Estratégica Economía y Sociedad Digital (AEESD) 1/2015, Spain (TSI-100105-2015-0012).  (40.182,54 EUR)
• 2017 - 2018. SOLDAGE (Semantic Open Linked DAta GEnerator), a FAIR data generator. Hazitek, Basque Government. (150.000 EUR)
• 2015. Enlazando Gipuzkoa con el Mundo (ENGIMU). Gipuzkoako Foru Aldundia, Gipuzkoa IKT: Innovación digital Empresas, Spain. (40.000 EUR)
• 2012 - 2014. Genes And Proteins for AutoImmunity Diagnostics (GAPAID).FP7-SME - Specific Programme "Capacities": Research for the benefit of SMEs (7PM-CAPACITIES-SMEs12/01)
• 2010 - 2015 Grupo de Investigación del Sistema Universitario Vasco. "Análisis genómicos de la variación del ADN" (GIC10/58-IT558-10)
• 2007 - 2010. Plataforma web para gestión de conocimientos guiada por ontologı́as en genómica funcional. Proyecto Industrial-Regional Murcia (BIO-TEC 06/01-0005)

Past freelance work:

• I wrote the Public tender for two projects under the Hércules initiative, a federation of University research data through Linked Open Data (5 million EUR).
• Cognizone (Ontology Engineering).

Current technical developments:

• Transparent Relations Ontology (TRO): TRO offers a vocabulary to publish information about relations that should be more transparent, usually between powerful parties. [https://github.com/mikel-egana-aranguren/Transparent-Relations-Ontology]
• Basque Country Institutions Transparent Relations Graph: RDF Knowledge Graph for Transparent relations involving Basque Country institutions. The aim of this project is to build a graph to integrate information about entities and individuals that might have a conflict of interest, in order to analyse such information. [https://github.com/mikel-egana-aranguren/BasqueCountryInstitutionsTransparentRelationsGraph]
• OntoGenix: The project utilizes the OpenAI GPT-4 model to develop a semi-automatic system that generates OWL ontologies and RML mappings from CSV datasets using LLMs. [https://github.com/tecnomod-um/OntoGenix]

Past technical developments:

• Semantic Manfred Awesomic CV: a prototype for a semantic version of the MAC, based on JSON-LD. [https://github.com/mikel-egana-aranguren/mac/tree/semantic_mac]
• Linked Open Data Euskadi: migration of current Open Data Euskadi to Linked Open Data (Phases I and II). [https://github.com/opendata-euskadi]
• Guerra Civil en Euskadi: this resource integrates data about the spanish civil war in Euskadi, through RDF graphs, and it offers nice visualisations. [http://guerracivileuskadi.eurohelp.es/]
• Linked Data Test Suite: Tests and reporting for Linked Data systems. [https://github.com/mikel-egana-aranguren/LinkedDataTestSuite]
• ALDAPA: Assistant for Linked DAta Production Automation. [https://github.com/mikel-egana-aranguren/ALDAPA]
• SADI-Galaxy is a wrapper of SADI services for Galaxy. [http://github.com/mikel-egana-aranguren/SADI-Galaxy]. There are also two Docker versions for easy deployment, each of them with a different approach: SADI-Docker-Galaxy provides the SADI tools as a Docker image and how to configure Galaxy to run Docker images; SADI-Galaxy-Docker provides the whole Galaxy server, preconfigured with SADI tools, as a Docker image.
• OpenLifeData2SADI is a set of SADI services that wraps the Linked Data resources from Open Life Data (formerly known as Bio2RDF). I wrote the Galaxy pipelines to demonstrate how to use the SADI services. [http://github.com/wilkinsonlab/OpenLifeData2SADI]
• BIOM-LD is a mapping of the BIOM format to a Linked Open Data setting, including an ontology defining the mapping (BIOMO). This is a very preliminary development. [http://github.com/mikel-egana-aranguren/biom-ld]
• Life Sciences Linked Data: This is a standalone, light-weight, configuration-free bundle to publish Linked Data. It is meant as an educational tool that students can use to become familiar with Linked Data, by publishing their own dataset at localhost with only the necessary hassle, but still being aware of the overal technical setting. It can also be used for rapid prototyping and deployment of a Linked Data system. [http://github.com/mikel-egana-aranguren/LSLD]. A different version, using Blazegraph as triple store and Trifid as web frontend: [https://github.com/mikel-egana-aranguren/MSc-UM-2020-FAIR/tree/main/LinkedDataServer]
• DDx2NP: This programme can be used to add Nanopublications to a given medical Knowledge Base. [http://github.com/wilkinsonlab/DDx2NP]
• PPIO: The Plant-Pathogen Interactions Ontology (http://purl.oclc.org/PPIO) offers an axiomisation of plant-pathogen interactions in order to annotate, query and reason over such domain of knowledge. [https://github.com/wilkinsonlab/PPIO]
• NCBO-Galaxy: NCBO-Galaxy provides graphical interfaces for the NCBO web services available at BioPortal, to access and exploit biomedical ontologies as part of Galaxy workflows. It can be found in Ontology Manipulation in the Galaxy Toolshed. [http://toolshed.g2.bx.psu.edu/]
• OGO: OGO integrates orthology information with diseases from OMIM, exploiting OWL, SPARQL and OBO ontologies. [http://miuras.inf.um.es:9080/OGO-1.0/]
• OGOLOD is a Linked Data version of OGO. [http://miuras.inf.um.es/~ogo/ogolod.html]
• ODPs catalogue: A repository of ontology engineering best practices, focused on biological knowledge. [http://odps.sf.net]
• BioGateway: An RDF store holding information integrated from different bioinformatics resources, like the OBO ontologies, GOA files and SwissProt. [http://www.semantic-systems-biology.org/biogateway]
• CCO: The Cell Cycle Ontology is an application ontology that describes different aspects of the cell cycle, integrating information from  UniProt, IntAct, GOA, NCBI taxonomy and GO. [http://cellcycleontology.org]
• OPPL: The Ontology Pre-Processor Language is a scripting language for defining and performing axiomatic changes in OWL ontologies, thus offering an abstraction of the OWL API that works directly with axioms instead of programmatic procedures. [http://oppl.sourceforge.net/]
• OPPL-Galaxy: this tool can be used to execute OPPL scripts as part of Galaxy. It can be found in Ontology Manipulation in the Galaxy Toolshed. [http://toolshed.g2.bx.psu.edu/]
• ONTO-PERL: An API for manipulating OBO ontologies, written in Perl. [http://search.cpan.org/~easr/]
• GONG: Gene Ontology Next Generation is a methodology for enriching OBO ontologies by adding OWL axioms based on dissecting the structure of the term names with regular expressions. [http://www.gong.manchester.ac.uk]
• Linked Data Open Data Euskadi: pack para publicar Linked Data con un dataset de Open Data Euskadi, como demostración de como implementar Linked Data apropiadamente, desarrollado en el Open Data Day Deusto 2014. [http://github.com/OpenDataDayBilbao/Linked-Data-Open-Data-Euskadi]