Crossover 2 (CR2) contributes to the work of collecting and structuring existing knowledge of gene regulation. The work is part of a comprehensive international effort to construct open digital research infrastructures for the future life sciences. The assumption is that a) an ecosystems of knowledge databases - a "Knowledge Commons" (KC) - can release a research and innovation potential if the life sciences and b) if successful these KC structures will be transformative not only for the life sciences as structures of innovation simultaneously need to be rebuilt calling for c) interdisciplinary scrutiny of what responsibility issues these changes pose. CR2 is also part of an ongoing international effort to experiment on ways to increase the humanities? and social sciences? ability to critically support research and technology-driven societal development, since such collaborations are not adequately supported within existing research structures and cultures. CR2 focuses on two related questions: how can this potential be released, and how can it be done in a responsible manner?
The two Co-PI?s, Kuiper and Lægreid, initiated an international consortium to coordinate knowledge retrieval in the domain of gene regulation (GRECO, www.theGRECO.org). During the first project year of CR2 (https://www.ntnu.edu/crossover-research) GRECO received support as an EU COST action (GREEKC http://greekc.org/) led by Kuiper. CR2 was further complemented by two research projects utilizing knowledge infrastructures: DrugLogics led by Lægreid and funded by NTNU and the ERACoSysMed project COLOSYS, led by Kuiper. The three research projects are organized under the heading DrugLogics (http://www.druglogics-ntnu.org/), that has hired 11 PhD and postdoctoral fellows at three Faculties.
These activities positioned us well to pursue the plans of the CR2: to investigate what conditions the KC by studying our own work of constructing and using knowledge databases in an innovation context that aim to enable better predictive modeling for drug development. This study, along with stakeholder engagement should help identify key obstacles and bottlenecks, articulate conditions for feasible solutions along with the responsibility challenge they pose. CR2's four work packages consist of seminars and workshops (wp1), building knowledge databases (wp2), utilizing knowledge databases in building computer models (wp3) and studies that capitalize from and feed into WP1-3 (wp4).
The first year of the project focused on recruitment, frequent internal seminars, 5 workshops with project partners and user groups to discuss project design, methodology, technical and conceptual issues.
Key activities second year were a) the GRECO startup meeting in Malta, April -17, gathering stakeholders from Europe and the US with interest in the subfield of gene regulation, b) completion of biocuration from scientific literature of more than 500 transcription factors and c) development of the biocuration tool SciCura (http://scicura.org/info.html) that assists professional and volunteer curators in knowledge curation, d) literature studies of sustainability challenges to digital resource commons with a focus on bio curators and e) interviews of bio curators at EBI.
Key outcomes third and fourth year. A) Consolidating the GRECO initiative with workshop in Lisbon, Ljubljana, Hinxton, Malaga, Lausanne and Marseille, targeting identified action points in Malta. B) Writing papers on i) the development of curation tools, ii) curation strategies including sustainable structures for community governance, iii) key role of curators as care takers and iv) threats to the knowledge commons in the domain of gene regulation focusing on issues of trust and v) the projects RRI strategy C) This work was discussed at interdisciplinary workshops with partners and invited researchers at a) Arizona State University, Oct. -17 and b) at NTNU Trondheim (https://druglogics.eu/activity/trondheim-workshop/) May -18. The final workshop was prepared in a seminar in May -19 and held June -19 inviting scientists and humanists to jointly formulate ten simple rules for how to construct a knowledge commons resource (https://www.druglogics.eu/events/).
The project was extended seven months allowing for A) the postdocs and two Ph.D candidates affiliated to CR to finalize papers and B) research visits to Berkley lab (Vercruysse) and Arizona State University (Lægreid and Nydal).
CR2 has contributed to the KC at many levels working under the assumption that different tasks of the work need to be mutually informed and adjusted by each other. Contextualizing the CR2 in the GRECO and DrugLogics initiatives have enabled such mechanisms. In addition to such stakeholder engagements, the RRI work have included the identification analysis of responsibility issues that arise in the context where KC is build. CR2 have focused on issues of trust, sustainability and the key role of curators.
The Crossover project (CR) has helped build national capacities and international collaboration structures enabling the construction of open digital infrastructures for the future life sciences. CR has illustrated ways in which local research groups can contribute, emphasizing the need for a digital infrastructure ability to mobilize and support local research groups. Digital infrastructures call for stakeholder engagements at all levels for this to happen as well as scrutiny of possible social and ethical aspects. The crossover model for building and appropriating digital infrastructures will continue after the project period.
The GRECO consortium will join the Disease Maps consortium to apply for a follow-up COST Action. The CR work further continues into a the RCN-funded innovation project PRESORT and we will submit a stage-2 ERAPerMed-proposal June 2020. These efforts cover all disciplines (humanities/ethics; medicine, biology, computing).
A Life Sciences Knowledge Commons calls for the innovation of comprehensive knowledge management systems implying novel forms of organization and collaboration, both materially and socially. The nature of such an effort has to be demonstrated in terms of the answerability of pertinent research questions. The project is founded on collaborative work of Nydal, Lægreid and Kuiper in the area of Knowledge Management (KM), and will address challenges faced when designing and using KM for the engineering of a Knowledge Commons (KC) for enabling precise and individuated diagnosis, prevention and treatment of diseases. A sandbox KC development and application project will itself be further articulated in the process, as research questions, technological apparatus, theoretical frameworks and interpreted empirical data will be reciprocally adjusted. The KC project provides the experimental model for joint ethical-political and epistemic quality measures, ensuring symmetrical integration of humanities in an interdisciplinary research project needed to demonstrate viable Knowledge Commons building approaches.
The project is organised in four Work Packages. WP1: Identification of a stakeholder group, and planning of workshops and communication structures, as mutual engagement is key for developing responsible and viable ICT solutions; WP2: Constructing a Gene Regulation Consortium KC (www.theGRECO.org). WP3: Using the GRECO KC in the computational modelling of biological networks for rational drug design.WP4: Capitalise and feed into WP1-3 researching the ethos of KC. The experimental system of Lægreid's and Kuiper's research groups contextualises KC in the research context it is to enable and provides an experimental model for improvements of the quality of the infrastructures of KC both in terms of epistemic and ethical-political measures, identified, discussed and refined in workshops and seminars.