WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content.

Data sharing and reuse are crucial to enhance scientific progress and maximize return of investments in science. Although attitudes are increasingly favorable, data reuse remains difficult due to lack of infrastructures, standards, and policies. The FAIR (findable, accessible, interoperable, reusable) principles aim to provide recommendations to increase data reuse. Because of the broad interpretation of the FAIR principles, maturity indicators are necessary to determine the FAIRness of a dataset. In this work, we propose a reproducible computational workflow to assess data FAIRness in the life sciences. Our implementation follows principles and guidelines recommended by the maturity indicator authoring group and integrates concepts from the literature. In addition, we propose a FAIR balloon plot to summarize and compare dataset FAIRness. We evaluated the feasibility of our method on three real use cases where researchers looked for six datasets to answer their scientific questions. We retrieved information from repositories (ArrayExpress, Gene Expression Omnibus, eNanoMapper, caNanoLab, NanoCommons and ChEMBL), a registry of repositories, and a searchable resource (Google Dataset Search) via application program interfaces (API) wherever possible. With our analysis, we found that the six datasets met the majority of the criteria defined by the maturity indicators, and we showed areas where improvements can easily be reached. We suggest that use of standard schema for metadata and the presence of specific attributes in registries of repositories could increase FAIRness of datasets.

The need to rank items based on user input arises in many practical applications such as elections, group-decision making and recommendation systems. The primary challenge in such scenarios is to decide a global ranking based on partial preferences provides by users. The standard approach to address this challenge is to ask users to provide explicit numerical ratings (cardinal information) of a subset of items. The main appeal of such an approach is the ease of aggregation. However, the rating scale as well as the individual ratings are often arbitrary and may not be consistent from one user to another. A more natural alternative to numerical ratings requires users to compare pairs of items (ordinal information). In contrast to cardinal information, such comparisons provide an "absolute" indicator of the user's preference. However, it is often hard to combine or aggregate comparisons to obtain a consistent global ranking.In this work, we provide a tractable framework for utilizing comparison data as well as first-order marginal information for the purpose of ranking. We treat the available information as partial samples from an unknown distribution over permutations. Using the Principle of Maximum Entropy, we devise a concise parameterization of distribution consistent with observations using only O(n 2 ) parameters, where n is the number of items in question. We propose a distributed, iterative algorithm for estimating the parameters of the distribution. We establish the correctness of the algorithm as well as identify the rate of convergence explicitly. Using the learnt distribution, we provide efficient approach to (a) learn the mode of the distribution using 'maximum weight matching', (b) identification of top k items, and (c) an aggregate ranking of all n items. Through evaluation of our approach on real-data, we verify effectiveness of our solutions as well as the scalability of the algorithm.

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