Henning Hermjakob - Community SARS-CoV-2 Curation Driven Emergent Experiences скачать в хорошем качестве

Henning Hermjakob - Community SARS-CoV-2 Curation Driven Emergent Experiences

Title: Community SARS-CoV-2 Curation Driven Emergent Experiences - Increased Curation Efficiency and Learned Lessons for the Future Session: April 26 - Community 2 Abstract: In April 2019, Reactome began a COVID-19 curation project. This project differed in multiple ways from Reactome's standard curation practices, but ultimately provided critical procedural insights. Reactome is an open-source, open access, manually curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic and clinical research, genome analysis, modeling, systems biology and education. At the beginning of the COVID-19 pandemic the Reactome group joined the COVID-19 Disease Map community, a broad community-driven effort developing a COVID-19 Disease Map. This group combined the biocuration practices and philosophies of Reactome, Cell Designer, and WikiPathways communities. The parallell curation of of the the viral lifecycle and host cell interactions provided each curation community with a unique opportunity to learn, compare, and adopt best curation practices. Shared data repositories, weekly meetings, chat and knowledge exchange software was present from the very beginning of this communal effort, and the software and mechanisms to compare each communities work only grew as the effort proceeded. Curation of a molecular pathway often starts with a set of expert assertions found in literature reviews covering a wide range of experiments and knowledge. For SARS-CoV-2 no such literature existed. Reactome used an orthoprojection approach, first curating the well supported SARS-CoV-1 viral lifecycle, and then using Reactomes orthologous projection tools to create the associated pathways for SARS-CoV-2. This approach produced a logical scaffolding for SARS-CoV-2 curation, rapidly accelerating the curation of an emerging pathogen. The process of adding SARS-CoV-2 experimental support was accelerated, allowing curators and other researchers with a global view of each new facts impact on the model. Assessing the literature support for those curatorial assertions posed another challenge. The experimental work around SARS-CoV-2 was growing far quicker than any one curator or community could manage. Pre-prints, which were never part of Reactome or most other molecular pathway curation efforts, were critical to this endeavor. What emerged was a pipeline that combined human expertise with automated computational paper identification. A literature triage system grew that connected curators and editors across the community all building a central repository of papers tagged to specific molecular entities and steps in the pathway. As annotated modeles emerged the communities provided rapid review and revision. Groups of curators provided an additional layer of review. These review groups were precisely positioned, building similar networks, using similar sets of literature support, and could understand the nuances of the different data models that each each community worked with. This process identified four areas: Use of orthoprojection, literature triage, alignment of curatorial communities working in the same area but using different tools, and a new layer of curatorial community review. All of these steps would be enhanced using current computational approaches. Rather than look to replace manual curation, we should focus on using the best aspects of curation across communties and approaches.