| « Back Open research project manager position (24 month) for OntoPortal in Montpellier, France
TitleOntoPortal project manager (Montpellier, France) Information
KeywordsScientific project management, Web development, ontologies & semantic web, ontology repository, knowledge engineering, semantic interoperability. ContextTerminologies, vocabularies and ontologies are key elements to achieve data interoperability. LIRMM (U. Montpellier/CNRS) and MISTEA (SupAgro/INRAE) design, develop and maintain two vocabulary and ontology repositories: (i) SIFR BioPortal (http://bioportal.lirmm.fr) which targets the French biomedical community and offers an ontology-based annotation workflow to semantically index text biomedical and clinical data; (ii) AgroPortal (http://agroportal.lirmm.fr) a reference repository for semantic artefacts in agri-food. These platforms allow us to tackle scientific problems in data integration and interoperability, ontology engineering, semantic annotation, ontology alignment, FAIRness assessment, while being driven by concrete use cases with impacts in biomedicine and agronomy. These two ontology repositories are based on the OntoPortal technology originally developed by BMIR at Stanford University for the NCBO BioPortal (https://bioportal.bioontology.org), the reference and most comprehensive repository of biomedical ontologies and terminologies. In 2020, several research organizations, led by Stanford BMIR, have joined into the OntoPortal Alliance (https://ontoportal.org) to co-develop, maintain and disseminate a shared, generic technology to develop ontology repositories. The current research project manager position is to manage and coordinate the collaboration within the Alliance, especially the French actors (INRAE, CNRS, U. Montpellier). Extended descriptionThe semantic Web offers the methods and technologies to transform big data into actionable knowledge. It relies on standard vocabularies and ontologies to formally capture the knowledge of a domain into semantic resources computers use to index, search or reason on the data. Ontologies formalize the knowledge of a domain by means of concepts, relations and rules that apply to that domain. The FAIR principles have established the importance of using standard vocabularies to describe FAIR data and to facilitate interoperability and reuse. However, in recent years, we have seen an explosion in the number of semantic resources or artefacts being developed in various domains so it becomes mandatory to offer open repositories to host and serve them to relevant scientific communities. With such a number of ontologies, new problems have raised such as describing, selecting, evaluating, trusting and interconnecting ontologies. Plus, ontologies are spread out, in different formats, of different sizes, with different structures and from overlapping domains. Therefore, there is a need for platforms to receive and host them, align them, and enable their use in multiple data integration, mining and annotation. Different scientific communities have already developed ontology Web portals to assist researchers and scientists in the use of ontologies. The Stanford Center for Biomedical Informatics Research (BMIR) group at Stanford University (http://bmir.stanford.edu), develops and maintains the NCBO BioPortal an open repository of ontologies and terminologies in biology and medicine originally spread out over the Web and in different formats. There are +800 ontologies in this collection, mostly related to biomedicine, but also going beyond these domains. Using the portal, health professionals and biologists can browse, search, visualize and comment on ontologies both interactively, through a Web interface, and programmatically, via Web services. Within BioPortal, ontologies are used to develop an annotation workflow that can be used to index text biomedical data resources (in English). BioPortal’s web pages are accessed over 10,000 times daily, and its API server handles over one million requests daily. The NCBO technology is domain-independent and open source and has already been adopted for different use cases or communities. For instance, in the context of the Semantic Indexing of French Biomedical Data Resources (SIFR) ANR project (www.lirmm.fr/sifr), LIRMM have developed the SIFR BioPortal, an open platform to host French biomedical ontologies and terminologies. As of today, the portal contains 30 public ontologies and terminologies with French content. One of the main motivation to build the SIFR BioPortal was to design the SIFR Annotator, a publicly accessible and easily usable ontology-based annotation web service to annotate with ontology concepts French biomedical text and clinical notes. Since 2015, LIRMM has also developed AgroPortal, an ontology repository for agri-food. The platform currently hosts 130+ semantic artefacts, has more than 250 registered users and some semantic artefacts are visited more than 100 times a month over some 10,000 annual sessions. However, the current AgroPortal platform only partially addresses the needs of the community: it is not multilingual, it is limited in terms of ontology alignment capabilities and does not provide semantic-search and retrieval of agronomy or agri-food data. Some of these challenges are at the core of the Data to Knowledge in Agronomy and Biodiversity (D2KAB) ANR project (www.d2kab.org). More recently, LIRMM and BMIR have started to collaborate with LifeWatch ERIC, which is committed to build EcoPortal, a similar platform with a dedicated focus on ecology/biodiversity and environment. In the context of the FAIR-IMPACT Horizon Europe project (2022-2025) other adopters are expected. Building atop of a strong long-standing collaboration between LIRMM and BMIR (explicitly supported by both an International Research Project from the CNRS and International Research Team from the NUMEV Labex), we are establishing since 2020 a collaborative alliance representing OntoPortal adopters and end users. The OntoPortal Alliance objectives are: (i) to maximize OntoPortal value (state-of-the-art service portfolio); (ii) to improve OntoPortal software while managing several parallel and different installations; (iii) to increase semantic uptake in science communities and facilitate adoption of the FAIR principles; (iv) to increase the ecosystem’s long term operational and financial health. Adoption of the OntoPortal virtual appliance has increased to the point that we have a significant community of developers, operators, and end users adopting and improving the OntoPortal code as well as using this environment for experimental computer science research. There are three main major motivations for ontology repositories to rely on a shared product: (i) to avoid re-developing tools that have already been designed and extensively used; (ii) to contribute to long term support of the commonly used technology; and (ii) to offer the same tools, services and formats to different communities, to facilitate the interface and interaction between their domains. Please refer to our GitHub repository for more detail:
Related Technologies: Ruby/Rails, Java/JEE, RESTful web services, XML/JSON, Web technologies (HTML5, Bootstrap, JavaScript, etc.), Collaboration/versioning (Git), Semantic web technologies (OWL, RDF, SPARQL, triplestore, Linked data), OntoPortal ontology repository, DevOps( Linux, Server administration, etc.). Missions and profileWe are seeking a motivated, curious and interested-by-research-application project manager with experience in developing web applications possibly with semantics technologies. The candidate will hold an engineer (in France CTI-accredited) or doctorate degree in computer science, informatics or information technologies. Master degree in the same area can only be accepted with significant experience (>4 years). The scientific project manager (hired as a research engineer or researcher) will have:
You will work with a group (3-4 persons) at LIRMM & MISTEA in both a national and international context. The candidate will demonstrate aptitudes or matches with most of the following aspects:
ApplicationApplication for this position must be done solely via this form: https://bit.ly/3QzkKMz
Remote and face to face interviews will be organized.
Documents (PDF) required are:
For more information about this position, please contact Clement Jonquet (jonquet@lirmm.fr). | |
