I am interested in the exploitation of Semantic Web technology (RDF, OWL, etc.) to improve knowledge management in several domains, most importantly Life Sciences and Open Data. The realisation of this interest involves the creation of semantic resources (Ontologies, Knowledge Bases, Linked Data datasets, Semantic Web Services, etc.), and the development of tools for creating and using such resources.
I have been involved in the following funded projects:
- 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: 24M EUR; Eurohelp: 300.000 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). (40.000 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)
I have done 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).
- Intellimedis (Ontology Engineering).
I am or have been involved in the following technical developments:
- Linked Open Data Euskadi: migration of current Open Data Euskadi to Linked Open Data. [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]
- Linked Data Server: a different version of Life Sciences Linked Data, using Stardog as a triple store and a custom NodeJS script instead of Pubby. The script is technically worse than Pubby, obviously, but the overall configuration is way easier. [https://github.com/mikel-egana-aranguren/LinkedDataServerNodeJSStardog]
- 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]