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SciLake at the EOSC-CoARA workshop for Advancing Research Assessment


Workshop

SciLake participates in EOSC-CoARA workshop for Advancing Research Assessment

By Stefania Amodeo, Zenia Xenou, Angeliki Tzouganatou, Giulia Malaguarnera

On April 10th, 2024, Thanasis Vergoulis from Athena RC, project coordinator of SciLake, represented our project at the EOSC-CoARA workshop for advancing research assessment, presenting how SciLake is contributing to  open infrastructures for research assessment. This blog post summarizes the key takeaways from the event.

CoARA and EOSC Commitments

The workshop hosted discussions on advancing the European Research Area's Policy Agenda for 2022-2024 focusing on promoting open sharing and reuse of research outputs and improving research assessment systems (i.e., Actions 1 and 2). To this end, the workshop aimed at collaboration and strategic alignment between the Coalition for Advancing Research Assessment (CoARA) and the European Open Science Cloud (EOSC), two relevant, pivotal initiatives:  CoARA aims to reform research assessment practices and policies to recognize a broader range of scientific contributions while promoting transparency and inclusivity. EOSC, on the other hand, provides the necessary infrastructure for easy access to research data across Europe. Together, they ensure that the new assessment criteria encouraged by CoARA align with the open and interoperable data environment EOSC provides. This collaboration fosters a research landscape that is more collaborative, transparent, inclusive, and effective in advancing open science principles across Europe.

In this context, SciLake, PathOS, OPUS, and GraspOS have been invited to inform stakeholders about their project goals and status. Their mission is to align with the overarching vision of the European Commission, EOSC, and CoARA in reforming research assessment. The discussion contributed to the publication of the European Commission's Action Plan To Implement The Ten Commitments On The Agreement on Reforming the Research Assessment.

SciLake's Mission

As an INFRAEOSC project, SciLake is expected to have substantial and long-term impact in the EOSC ecosystem. During the workshop, Thanasis Vergoulis presented the main objectives of our project highlighting its three key contributions in the  research assessment field:

  1. Enhancing the interoperability and accessibility of Scientific Knowledge Graphs (SKGs)

Scientific Knowledge Graphs (SKGs) form the fundamental input for research assessment practices. Enhancing the interoperability and accessibility of SKGs is a key focus of SciLake, and thus SciLake is expected to significantly facilitate research assessment practices. SciLake researchers collaborate closely with the members of the Research Data Alliance's (RDA) SKG-Interoperability Framework group to refine a common data exchange model for domain-agnostic SKGs. At the same time, SciLake extends this work by leading the effort to design extensions to the basic SKG-IF model, supporting domain-specific entities and relationship types in the fields of the project pilots. Regarding accessibility, SciLake’s APIs offer advanced graph querying capabilities through the AvantGraph analytics engine. This enhances the simplicity and efficiency of SKG querying, aiding in the revelation of research insights and further supporting effective research assessment.

  1. Developing modules that provide enrichments for research data that can be valuable for research assessment use cases.

Among the various modules SciLake is developing, some are specifically designed to add value to research data, making them highly beneficial for implementing research assessment practices. Indicative examples include the module that produces classifications of research works based on relevant Fields of Science and the modules that calculate a range of indicators that can offer valuable insights into various aspects of citation-based scientific impact or the reproducibility of research works.

  1. Recognising and incorporating discipline-specific contributions.

SciLake is closely collaborating with domain experts conducting four pilots focused on analyzing research in distinct scientific fields: Neuroscience, Cancer research, Transportation research, and Energy research. This work is invaluable for identifying domain-specific research activities and contributions, enabling them to be effectively tracked and recognized within research assessment practices.

Conclusions

In conclusion, SciLake is contributing to research assessment through its innovations in the field of Scientific Knowledge Graphs enhancing their interoperability, generating deeper research insights, and incorporating discipline-specific contributions. Through these efforts, SciLake is laying the groundwork for a more cohesive and responsible approach to research assessment.

The slides of the presentation can be found on Zenodo: https://zenodo.org/records/10959719

Read more …SciLake at the EOSC-CoARA workshop for Advancing Research Assessment

Discover SciLake Maritime Transport Pilot


Scilake Pilots

Pioneering Knowledge Graph in Maritime Transport Research

SciLake is in full swing with its pilot programs in the fields of neuroscience, cancer research, transportation, and energy. These initiatives aim to create or enrich domain-specific Scientific Knowledge Graphs that capture valuable knowledge from each scientific field.

The SciLake Maritime Transport Pilot aims to develop innovative knowledge management and discovery solutions for the transport research community, serving several categories of stakeholders, including technology providers, research bodies and funding agencies.

Leading the pilot are researchers of the Hellenic Institute of Transport (HIT) at the Centre for Research and Technology Hellas (CERTH), Greece.

Read the press release


transportation

Read more …Discover SciLake Maritime Transport Pilot

Discover SciLake CCAM Transport Pilot


Scilake Pilots

Guiding CCAM Research through Scientific Knowledge Graphs

SciLake is in full swing with its pilot programs in the fields of neuroscience, cancer research, transportation, and energy. These initiatives aim to create or enrich domain-specific Scientific Knowledge Graphs that capture valuable knowledge from each scientific field.

The SciLake CCAM Transport Pilot aims to consolidate the existing knowledge around Cooperative Connected Automated Mobility (CCAM) to enrich the Transportation Scientific Knowledge Graph (SKG) of the OpenAIRE Community.

Leading the pilot are researchers from I-SENSE, a Research Group of the Institute of Communication and Computer Systems (ICCS) of the National Technical University of Athens.

Read the press release


transportation

Read more …Discover SciLake CCAM Transport Pilot

SciLake’s “Energy pilot” launches “Regional Energy Planning Pilot”

Discover SciLake Energy Pilot


Scilake Pilots

SciLake Regional Energy Planning Pilot for Sustainable Regions

SciLake is in full swing with its pilot programs in the fields of neuroscience, cancer research, transportation, and energy. These initiatives aim to create or enrich domain-specific Scientific Knowledge Graphs that capture valuable knowledge from each scientific field.

The SciLake Regional Energy Planning (REP) pilot focuses on sustainable energy solutions tailored to regional contexts.

The pilot's goal is to improve the accessibility and interoperability of scientific knowledge in order to facilitate the Regional Energy Transition.

Leading the pilot are researchers from HES-SO School of Engineering in Switzerland.

Read the press release


energy

Read more …Discover SciLake Energy Pilot

Unlocking insights in Cancer Research through Knowledge Graphs


Case Study

Unlocking insights in Cancer Research through Knowledge Graphs

By Stefania Amodeo

In a recent meeting with the EOSC4Cancer Cancer Landscape Partnering (CLP), SciLake took center stage as it introduced its vision and roadmap for unlocking insights in cancer research. Project coordinator, Thanasis Vergoulis (Athena RC), and Leily Rabbani, bioinformatician at the Department of Molecular Medicine and Surgery in Karolinska Institute, discussed the ongoing work towards creating a Cancer Research Knowledge Graph. This innovative tool will provide context and connections for what is known about specific research questions, helping researchers as they design new experiments.

The SciLake Cancer Research pilot involves the Institute of Applied Bioscience (INAB-CERTH) in Greece and Karolinska Institutet in Sweden. Focused on meeting the needs of researchers and clinicians, the project aims to harness the wealth of information available in public resources to address ongoing research questions. 

The ultimate goal? To deepen our understanding of the molecular biology and immunopathology of Chronic Lymphocytic Leukemia (CLL) and study the potential effects of different mutations.

With the assistance of SciLake technical partners, members of the pilot project are utilising advanced algorithms to discover new insights from the knowledge graph. For example, one interesting question they are exploring is, "how might a specific genetic mutation forecast a patient's overall health status and what insights might related literature offer in this regard?"


Chronic Lymphocytic Leukemia (CLL)

  • Characterized by the accumulation of neoplastic B cells in the bone marrow, blood cells, and secondary lymph nodes.

  • Patients can have a very diverse genetic landscape leading to heterogeneous clinical outcomes. This means progression rates and responses to drugs can vary greatly among patients.

  • The most common type of leukemia in adults.

  • Currently incurable.

Knowledge Graph: Benefits

The use of a scientific knowledge graph offers several benefits. It empowers research in precision medicine and diagnostics by facilitating the discovery of potential associations between identified biomarkers and other elements, such as genes, biological or functional pathways, and drugs. Furthermore, it is easily deployable and flexible, capable of integrating data from various sources, thereby offering a comprehensive view of the research landscape.

Challenges

Developing a knowledge graph comes with its own set of challenges. The objective is to provide tools for creating and enriching the graph, and the primary concern is extracting latent knowledge to create the graph. Another significant challenge is establishing a common language among people of different expertise, such as clinicians and technical developers. This is crucial to facilitate effective communication and collaboration in the development and application of the knowledge graph. Finally, an important step to validate the graph involves manual curation to assess hidden associations and existing connections and ensure they are relevant to the specific biology experiment.

Where are we

The development of the knowledge graph is progressing by leveraging several pre-existing state-of-the-art knowledge graphs. One is PrimeKG, which is used to query networks of genes or proteins connected to a specific disease. For example, the graph shows connections between CLL and TP53, a gene known for its potential to increase the risk of various forms of cancer significantly when altered. Other larger state-of-the-art knowledge graphs, based on various biomedical databases, are also being integrated along with Prime KG. This strategy aims to capitalise on a broader set of databases and underlying connections, potentially uncovering new missing links. An example of this is the revealed relation between CLL and the gene SOD1, known for being overexpressed in many human cancers.

A variety of knowledge graphs exist, each drawing from a different biomedical source, and we can collect more information through their combination. In fact, many details are unique to a particular graph and there is minimal overlap between them.

Our data flow involves using a variety of knowledge graphs, including those previously mentioned, along with different ontologies and other data sources. We utilize tools provided by SciLake to establish connections among them and generate a comprehensive cancer knowledge graph.

Dataflow towards a CLL KG

Goals

The ultimate vision is to create a comprehensive network of interconnected nodes and relationships. These nodes can represent various entities such as institutions, grants, patents, publications, software, anatomical structures, diseases, drugs, compounds, gene targets, and many more. These relationships can take on different forms and can signify different types of connections such as mentions, associations, or other types of relationships. By creating this extensive web of connections, the network can be navigated and queried in a semi-automated manner to answer specific research questions. Moreover, the impact and reproducibility analysis services offered by SciLake can be utilized to prioritize findings.

This approach will enhance the understanding of the molecular biology and immunopathology of Chronic Lymphocytic Leukemia. It will also assist in studying the potential effects of different mutations. The advantage of this method lies in its ability to incorporate information from multiple sources simultaneously, offering a comprehensive and insightful analysis.

Cancer

Read more …Unlocking insights in Cancer Research through Knowledge Graphs