Biology subjects

Bandrowski, A.

Publications and source records attributed to Bandrowski, A..

5 recordsLinked to original sources

bioRxiv2024

Automatic Detection and Extraction of Key Resources from Tables in Biomedical Papers

Tables are useful information artifacts that allow easy detection of data "missingness" by humans and have been deployed by several publishers to improve the amount of information present for key resources and reagents such as antibodies, cell lines, and other tools that constitute the inputs to a study. The STAR*Methods tables, specifically, have increased the "findability" of these key resources, but they have not been commonly available outside of the Cell Press journal family. To improve the availability of these tables in the broader biomedical literature, we have attempted to automatically process BioRxiv preprints to create tables from text or to recognize tables already created by authors and structure them for later use by publishers and search systems, to improve "findability" of resources in a larger amount of the scientific literature. The extraction of key resource tables in PDF files by the best in class tools resulted in Grid Table Similarity (GriTS) score of 0.12, so we have created several multimodal pipelines employing machine learning approaches for key resource table page identification, Table Transformer models for table detection and table structure recognition and a new table-specific language model for row over-segmentation to improve the extraction of text in tables created by biomedical authors and published on BioRxiv to around GriTS score of 0.90 enabling the deployment of automated research resource extraction tools onto BioRxiv. Author summaryTables are useful information artifacts that allow for easy detection of data "missingness" by humans and have been implemented by several publishers to improve the amount of information present for key resources and reagents such as antibodies, cell lines, and other tools that constitute the inputs to a study. To improve the availability of these tables in the broader biomedical literature, we introduced four pipelines for key resource table extraction from biomedical documents in PDF format. Our approach reconstructs key resource tables using image level table detection and structure detection generated table boundary, column (and row) bounding box information together with PDF text alignment. To remedy row over-segmentation resulting from overflowing table cell contents, we introduced a language modeling (LM) based row merging solution where a character-level generative pre-trained transformer (GPT) model was pre-trained on more than 11 million scientific table contents from PubMed Central Open Access Subset (PMC OAS). All introduced pipelines significantly outperformed GROBID baseline while our Table LM based row merging based pipeline, significantly outperformed all other pipelines including our OCR based pipeline.

bioinformatics↗

bioRxiv2022

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

Characterizing cellular diversity at different levels of biological organization across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also required to manipulate cell types in controlled ways, and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data generating centers, data archives and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain and demonstration of prototypes for human and non-human primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed, and to accessing and using the BICCN data and its extensive resources, including the BRAIN Cell Data Center (BCDC) which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted by the BICCN toward FAIR (Wilkinson et al. 2016a) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.

bioinformatics↗

bioRxiv2021

The SPARC DRC: Building a resource for the autonomic nervous system community

The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. A data portal has been developed that allows discovery of data and models both via semantic search and via an interface that includes Google Map-like 2D flatmaps for displaying connectivity, and 3D anatomical organ scaffolds that provide a common coordinate framework for cross-species comparisons. We discuss examples that illustrate the data pipeline, which includes data upload, curation, segmentation (for image data), registration against the flatmaps and scaffolds, and finally display via the web portal, including the link to freely available online computational facilities that will enable neuromodulation hypotheses to be investigated by the autonomic neuroscience community and device manufacturers.

neuroscience↗

bioRxiv2021

SPARC Data Structure: Rationale and Design of a FAIR Standard for Biomedical Research Data

The NIH Common Funds Stimulating Peripheral Activity to Relieve Conditions (SPARC) initiative is a large-scale program that seeks to accelerate the development of therapeutic devices that modulate electrical activity in nerves to improve organ function. Integral to the SPARC program are the rich anatomical and functional datasets produced by investigators across the SPARC consortium that provide key details about organ-specific circuitry, including structural and functional connectivity, mapping of cell types and molecular profiling. These datasets are provided to the research community through an open data platform, the SPARC Portal. To ensure SPARC datasets are Findable, Accessible, Interoperable and Reusable (FAIR), they are all submitted to the SPARC portal following a standard scheme established by the SPARC Curation Team, called the SPARC Data Structure (SDS). Inspired by the Brain Imaging Data Structure (BIDS), the SDS has been designed to capture the large variety of data generated by SPARC investigators who are coming from all fields of biomedical research. Here we present the rationale and design of the SDS, including a description of the SPARC curation process and the automated tools for complying with the SDS, including the SDS validator and Software to Organize Data Automatically (SODA) for SPARC. The objective is to provide detailed guidelines for anyone desiring to comply with the SDS. Since the SDS are suitable for any type of biomedical research data, it can be adopted by any group desiring to follow the FAIR data principles for managing their data, even outside of the SPARC consortium. Finally, this manuscript provides a foundational framework that can be used by any organization desiring to either adapt the SDS to suit the specific needs of their data or simply desiring to design their own FAIR data sharing scheme from scratch.

bioinformatics↗

bioRxiv2020

A multimodal cell census and atlas of the mammalian primary motor cortex

We report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, our results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

neuroscience↗