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3. Pathways to Data: From Plans to Datasets

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4. From data to information: automating data science to explore the U.S. court system

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   null (Ed.)

   The U.S. court system is the nation's arbiter of justice, tasked with the responsibility of ensuring equal protection under the law. But hurdles to information access obscure the inner workings of the system, preventing stakeholders - from legal scholars to journalists and members of the public - from understanding the state of justice in America at scale. There is an ongoing data access argument here: U.S. court records are public data and should be freely available. But open data arguments represent a half-measure; what we really need is open information. This distinction marks the difference between downloading a zip file containing a quarter-million case dockets and getting the real-time answer to a question like "Are pro se parties more or less likely to receive fee waivers?" To help bridge that gap, we introduce a novel platform and user experience that provides users with the tools necessary to explore data and drive analysis via natural language statements. Our approach leverages an ontology configuration that adds domain-relevant data semantics to database schemas to provide support for user guidance and for search and analysis without user-entered code or SQL. The system is embodied in a "natural-language notebook" user experience, and we apply this approach to the space of case docket data from the U.S. federal court system. Additionally, we provide detail on the collection, ingestion and processing of the dockets themselves, including early experiments in the use of language modeling for docket entry classification with an initial focus on motions. 

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5. TIMSCONVERT: a workflow to convert trapped ion mobility data to open data formats

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   Abstract MotivationAdvances in mass spectrometry have led to the development of mass spectrometers with ion mobility spectrometry capabilities and dual-source instrumentation; however, the current software ecosystem lacks interoperability with downstream data analysis using open-source software and pipelines. ResultsHere, we present TIMSCONVERT, a data conversion high-throughput workflow from timsTOF Pro/fleX mass spectrometer raw data files to mzML and imzML formats that incorporates ion mobility data while maintaining compatibility with data analysis tools. We showcase several examples using data acquired across different experiments and acquisition modalities on the timsTOF fleX MS. Availability and implementationTIMSCONVERT and its documentation can be found at https://github.com/gtluu/timsconvert and is available as a standalone command-line interface tool for Windows and Linux, NextFlow workflow and online in the Global Natural Products Social (GNPS) platform. Supplementary informationSupplementary data are available at Bioinformatics online. 

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