Internship opportunity for the EarthPortal service at CNRS Data Terra

Opportunity

CNRS Data Terra Portal

Internship topic: Improvement and optimisation of the O'FAIRe tool

The volume of data in science is growing rapidly. Data integration and semantic interoperability are essential for new scientific discoveries, as is the adoption of FAIR principles.

The Semantic Web helps transform big data into actionable knowledge through standard vocabularies and ontologies, enabling computers to index, search and reason about the data. Semantic artefacts (ontologies, vocabularies, terminologies, thesauri, etc.) are key elements in ensuring data interoperability. There are several Semantic Web languages for encoding semantic artefacts: RDFS, SKOS, OWL, OBO, etc. 

The explosion in the number of semantic artefacts has led to the need to build open portals to host them and serve the scientific communities. OntoPortal is a technology for setting up catalogues of semantic artefacts, enabling its users to deposit, share and utilise the vocabularies and ontologies they produce as part of their activities. EarthPortal is the catalogue for semantic artefacts relating to the Earth System. 

EarthPortal is part of the OntoPortal Alliance (https://ontoportal.org), whose aim is to coordinate efforts and mutualise technological developments within an open-source project. Each member of this alliance contributes to the development of new features. Among the services shared within the OntoPortal Federation, EarthPortal hosts and provides access to O’FAIRe, a tool for assessing the FAIRness of ontologies.

Internship topic: Improvement and optimisation of the O'FAIRe tool

O’FAIRe is a tool for assessing the FAIRness of ontologies developed by LIRMM/INRAE and used by EarthPortal. The methodology associated with the tool is described in the following scientific article: https://www.inderscience.com/storage/f141268935112710.pdf  

A technical review of the O’FAIRe code (https://github.com/earthportal/fairness), cross-referenced with open issue tickets, has highlighted several limitations in terms of reliability, performance and generality:

  • Storage in a single file. All scores for a portal are stored in a single JSON file (save.json), which is completely rewritten with every refresh 
  • No incremental recalculation. Updating an ontology does not trigger any targeted recalculation 
  • Lack of automated testing; incomplete generality across portals. 

Objectives

This intern aims to contribute to making O’FAIRe more reliable, more generalisable and improved, building on what already exists.

  • To analyse the existing system and contribute to the consolidation of the caching mechanism, taking into account community work already underway.
  • Develop the data storage method towards a more persistent and granular solution, in order to facilitate targeted reads and writes.
  • Implement a more incremental approach to score recalculations during ontology updates.
  • Enhance the isolation of processing tasks and the robustness of network calls to limit the impact of a local incident on the entire portal.
  • Investigate the generalisation of scoring rules to make them applicable to several portals within the federation.
  • Design and deploy a suite of automated tests to ensure the security of changes and verify non-regression cases.
  • Propose a feature to assist with the interpretation of scores, based on an explanation in natural language and exportable as a report.

This internship is being carried out in coordination with the AgroPortal development team to ensure that the improvements benefit the entire OntoPortal Federation.

Keywords & technologies

Java, Maven, Ruby, Servlet/Tomcat; Semantic Web (RDF, OWL, SPARQL); Databases (SQL, schema design); REST APIs; LLMs (application-level use, no fine-tuning); Development tools: Docker, GitHub, CI/CD, JUnit.

Profile

Master’s students in computer science or engineering, with a preference for working on existing production code (refactoring, improving reliability, testing) rather than developing from scratch. A keen interest in learning about Semantic Web concepts and the FAIR principles is essential. A good command of English is useful for communicating with the OntoPortal Alliance community.

 

References

Source code

Documentation

Key scientific articles

Application and information

For further information on this internship opportunity, please contact:
Christelle Pierkot (christelle.pierkot@cnrs.fr ) and Hakim Allem (hakim.allem@cnrs.fr ) 

To apply, please send an email with links (DO NOT INCLUDE ANY ATTACHED DOCUMENTS) to:

  • a cover letter explaining YOUR interest in the placement;
  • a brief CV outlining your experience and how it matches the required profile;
  • your most recent academic transcripts;
  • names and contact details of referees.

We are looking for students with a master’s degree in computer science (or, in some cases, information science) who have studied data and knowledge sciences and web technologies. Ideally, you will have taken a course on the Semantic Web as part of your degree. Expertise in earth sciences is not strictly necessary, but an interest in and understanding of this discipline would, of course, be appreciated.

We will contact suitable students by email to arrange an interview if their profile matches our requirements and we consider their application to be motivated and relevant.

Internships are remunerated at the current rate (approximately €650 per month). You will work with a team (4–5 people) at Data Terra in a national and international context. Some placements may lead to a fixed-term contract, even if this is not explicitly mentioned in the vacancy. On-site attendance is compulsory. The statutes and regulations of our respective organisations apply to all interns, including in terms of ethics and professional conduct.

 

Location : 
CNRS Data Terra, Agropolis, Montpellier

Duration : 
Academic year 2026–2027 (5–6-month placement, postgraduate level)