Browsing NTNU Open by Author "Vercruysse, Steven"

Now showing items 1-9 of 9

    • CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator 

      Touré, Vasundra; Zobolas, John; Kuiper, Martin; Vercruysse, Steven (Journal article; Peer reviewed, 2021)
      Molecular causal interactions are defined as regulatory connections between biological components. They are commonly retrieved from biological experiments and can be used for connecting biological molecules together to ...

    • Gene regulation knowledge commons: community action takes care of DNA binding transcription factors 

      Tripathi, Sushil; Vercruysse, Steven; Chawla, Konika; Christie, Karen R.; Blake, Judith A; Huntley, Rachael P.; Orchard, Sandra; Hermjakob, Henning; Thommesen, Liv; Lægreid, Astrid; Kuiper, Martin (Journal article; Peer reviewed, 2016)
      A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge ...

    • Gene regulation knowledge commons: community action takes care of DNA binding transcription factors 

      Tripathi, Sushil; Vercruysse, Steven; Chawla, Konika; Christie, Karen R.; Blake, Judith A; Huntley, Rachael P.; Orchard, Sandra; Hermjakob, Henning; Thommesen, Liv; Lægreid, Astrid; Kuiper, Martin (Journal article; Peer reviewed, 2016)
      A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge ...

    • The gene regulation knowledge commons: the action area of GREEKC 

      Kuiper, Martin; Bonello, Joseph; Fernández-Breis, Jesualdo Tomás; Bucher, Philipp; Futschik, Matthias E; Gaudet, Pascale; Kulakovskiy, Ivan V.; Licata, Luana; Logie, Colin; Lovering, Ruth C.; Makeev, Vsevolod J; Orchard, Sandra; Panni, Simona; Perfetto, Livia; Sant, David; Schulz, Stefan M.; Vercruysse, Steven; Zerbino, Daniel; Lægreid, Astrid (Peer reviewed; Journal article, 2022)
      As computational modeling becomes more essential to analyze and understand biological regulatory mechanisms, governance of the many databases and knowledge bases that support this domain is crucial to guarantee reliability ...

    • Improving the FAIRness of causal interactions in systems biology 

      Touré, Vasundra (Doctoral theses at NTNU;2020:293, Doctoral thesis, 2020)
      In molecular systems biology, regulatory process models are built and computationally simulated to represent and analyse the behaviour of cellular systems and how they respond to perturbations. A considerable amount of ...

    • Jointly creating digital abstracts: dealing with synonymy and polysemy 

      Vercruysse, Steven; Kuiper, Martin (Journal article; Peer reviewed, 2012)
      Background Ideally each Life Science article should get a ‘structured digital abstract’. This is a structured summary of the paper’s findings that is both human-verified and machine-readable. But articles can contain a ...

    • The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST) 

      Touré, Vasundra; Vercruysse, Steven; Acencio, Marcio Luis; Lovering, Ruth C.; Orchard, Sandra; Bradley, Glyn; Casals-Casas, Cristina; Chaouiya, Claudine; del-Toro, Noemi; Flobak, Åsmund; Gaudet, Pascale; Hermjakob, Henning; Hoyt, Charles Tapley; Licata, Luana; Lægreid, Astrid; Mungall, Christopher; Niknejad, Anne; Panni, Simona; Perfetto, Livia; Porras, Pablo; Pratt, Dexter; Saez-Rodriguez, Julio; Thieffry, Denis; Thomas, Paul; Türei, Dénes; Kuiper, Martin (Peer reviewed; Journal article, 2020)
      Motivation A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a ...

    • OLSVis: an animated, interactive visual browser for bio-ontologies 

      Vercruysse, Steven; Venkatesan, Aravind; Kuiper, Martin (Journal article; Peer reviewed, 2012)
      Background: More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS). Although OLS provides ample possibility for querying and browsing terms, ...

    • UniBioDicts: Unified access to biological dictionaries 

      Zobolas, John; Touré, Vasundra; Kuiper, Martin; Vercruysse, Steven (Peer reviewed; Journal article, 2020)
      We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts ...