The IntAct database:Efficient access to fine-grained molecular interaction data

The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way

Overview of the interactive task in BioCreative V

Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration and the TM communities. In BioCreative V, the IAT track followed a format similar to previous interactive tracks, where the utility and usability of TM tools, as well as the generation of use cases, have been the focal points. The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated. Two levels of user participation were offered to broaden curator involvement and obtain more feedback on usability aspects. The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey. The partial level participation was designed to focus on usability aspects of the interface and not the performance per se. In this case, biocurators navigated the system by performing pre-designed tasks and then were asked whether they were able to achieve the task and the level of difficulty in completing the task. In this manuscript, we describe the development of the interactive task, from planning to execution and discuss major findings for the systems tested

Example of a visual agenda.

<p>This was created for an internal workshop held to gather ideas for a website redesign process. Visual agendas are useful for setting the creative tone needed for successful interactive workshops.</p

Example room layout for an interactive workshop.

<p>This bird's-eye view shows the setup for supporting group-based, facilitated activities around a specific topic, problem, or project. The moderator oversees the workshop with the help of facilitators, who are briefed in the aims and methods of the activities. Alternatives include “circuit training” layout, where each table is an activity station and the participants move around the room.</p

Example of a workshop artefact: The output of the “Speed Boat” activity.

<p>The aim of this activity is to identify improvements that need to be made, for instance, to a product or service. The boat and anchors are drawn on paper as a template before the workshop. During the activity, the groups add their ideas in pen: they write the goal of the workshop on the boat and the challenges to achieving this goal by the anchors. We also include “positive forces for change”—things that are moving the project towards the goal—as “wind arrows” flanking the boat. The sticky notes have been added after the activity by the facilitator during the presenting-back stage and group discussion. The sticky notes have been labelled with the letters A to E for reference; note that a labelling scheme may be helpful for the analysis and report. This activity was adapted from p. 206 in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003485#pcbi.1003485-Gray1" target="_blank">[5]</a>; also watch this video for more hints: <a href="http://www.youtube.com/watch?v=xwVbcioYvdM" target="_blank">http://www.youtube.com/watch?v=xwVbcioYvdM</a>.</p

Overview of the interactive task in BioCreative V

Publisher's PDFFully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting Developmentelopment of useful TM tools, and providing a communication channel between the biocuration and the TM communities. In BioCreative V, the IAT track followed a format similar to previous interactive tracks, where the utility and usability of TM tools, as well as the generation of use cases, have been the focal points. The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated. Two levels of user participation were offered to broaden curator involvement and obtain more feedback on usability aspects. The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey. The partial level participation was designed to focus on usability aspects of the interface and not the performance per se. In this case, biocurators navigated the system by performing pre-designed tasks and then were asked whether they were able to achieve the task and the level of difficulty in completing the task. In this manuscript, we describe the Developmentelopment of the interactive task, from planning to execution and discuss major findings for the systems tested.University of Delaware, Center for Bioinformatics and Computational Biology University of Delaware, Department of Computer and Information Sciences University of Delaware, College of Agriculture & Natural Resource