Article
Biochemistry & Molecular Biology
Shuai Jiang, Qiheng Qian, Tongtong Zhu, Wenting Zong, Yunfei Shang, Tong Jin, Yuansheng Zhang, Ming Chen, Zishan Wu, Yuan Chu, Rongqin Zhang, Sicheng Luo, Wei Jing, Dong Zou, Yiming Bao, Jingfa Xiao, Zhang Zhang
Summary: Single-cell studies have uncovered a growing number of previously uncharacterized cell types in complex tissues. To understand cellular heterogeneity and tumorigenesis at single-cell resolution, a comprehensive and curated repository of cell types and associated cell markers, called Cell Taxonomy, has been established. This database provides well-structured taxonomy for 3,143 cell types and collects a comprehensive collection of 26,613 associated cell markers across various species, tissues, and conditions. With the integration of literature curation and data, Cell Taxonomy offers multifaceted characterization for cell types and cell markers, enabling better understanding of cellular biology across species.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Chen Cao, Mengting Shao, Chunman Zuo, Devin Kwok, Lin Liu, Yuli Ge, Zilong Zhang, Feifei Cui, Mingshuai Chen, Rui Fan, Yijie Ding, Hangjin Jiang, Guishen Wang, Quan Zou
Summary: Rare variants are important for genetic causes of complex traits, but there is currently no systematic collection of these associations. This study presents the Rare Variant Association Repository (RAVAR), which collects a large number of rare variant associations and provides an interactive interface with search functionality.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Pharmacology & Pharmacy
Sadhana Tripathi, Neelam Sharma, Leimarembi Devi Naorem, Gajendra P. S. Raghava
Summary: Over the years, numerous vaccines have been developed against viral infections, but a comprehensive database providing detailed information on viral vaccines has been lacking. In this review, we introduce our freely accessible database ViralVacDB, which includes details of viral vaccines, their types, routes of administration, and approving agencies. This repository systematically covers additional information on 422 viral vaccines, including 145 approved vaccines and 277 in clinical trials. We believe that this database will greatly benefit researchers and professionals in pharmaceuticals and immuno-informatics.
DRUG DISCOVERY TODAY
(2023)
Article
Biochemistry & Molecular Biology
Jonas Coelho Kasmanas, Alexander Bartholomaeus, Felipe Borim Correa, Tamara Tal, Nico Jehmlich, Gunda Herberth, Martin von Bergen, Peter F. Stadler, Andre Carlos Ponce de Leon Ferreira de Carvalho, Ulisses Nunes da Rocha
Summary: Metagenomics has become a standard strategy for understanding the functional potential of microbial communities, with an increasing number of metagenomes in public repositories. However, challenges arise from misannotated metadata in these repositories. HumanMetagenomeDB aims to simplify the identification and utilization of public human metagenomes, containing metadata from nearly 70,000 metagenomes across multiple countries, diagnoses, and age ranges.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Soeren Doose
Summary: Single-molecule localization microscopy has become an important tool in biomedical research. The LOCAN Python library provides well-defined data structures and analysis methods for analyzing localization data in a script or computable notebook.
Article
Mathematical & Computational Biology
Stano Pekar, Jonas O. Wolff, Ludmila Cernecka, Klaus Birkhofer, Stefano Mammola, Elizabeth C. Lowe, Caroline S. Fukushima, Marie E. Herberstein, Adam Kucera, Bruno A. Buzatto, El Aziz Djoudi, Marc Domenech, Alison Vanesa Enciso, Yolanda M. G. Pinanez Espejo, Sara Febles, Luis F. Garcia, Thiago Goncalves-Souza, Marco Isaia, Denis Lafage, Eva Liznarova, Nuria Macias-Hernandez, Ivan Magalhaes, Jagoba Malumbres-Olarte, Ondrej Michalek, Peter Michalik, Radek Michalko, Filippo Milano, Ana Munevar, Wolfgang Nentwig, Giuseppe Nicolosi, Christina J. Painting, Julien Petillon, Elena Piano, Kaina Privet, Martin J. Ramirez, Candida Ramos, Milan Rezac, Aurelien Ridel, Vlastimil Ruzicka, Irene Santos, Lenka Sentenska, Leilani Walker, Kaja Wierucka, Gustavo Andres Zurita, Pedro Cardoso
Summary: Spiders, as ubiquitous predators in terrestrial ecosystems, play an important role and are suitable for testing eco-evolutionary hypotheses. An online database has been developed to archive and access diverse spider traits data globally, curated by an expert team and aimed at facilitating cross-taxon assays in functional ecology and comparative biology.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Chemistry, Multidisciplinary
Tran B. Nguyen, Kelvin H. Bates, Reina S. Buenconsejo, Sophia M. Charan, Eric E. Cavanna, David R. Cocker III, Douglas A. Day, Marla P. DeVault, Neil M. Donahue, Zachary Finewax, Luke F. Habib, Anne V. Handschy, Lea Hildebrandt Ruiz, Chung-Yi S. Hou, Jose L. Jimenez, Taekyu Joo, Alexandra L. Klodt, Weimeng Kong, Chen Le, Catherine G. Masoud, Matthew S. Mayernik, Nga L. Ng, Eric J. Nienhouse, Sergey A. Nizkorodov, John J. Orlando, Jeroen J. Post, Patrick O. Sturm, Bridget L. Thrasher, Geoffrey S. Tyndall, John H. Seinfeld, Steven J. Worley, Xuan Zhang, Paul J. Ziemann
Summary: ICARUS is an open access infrastructure for storing, sharing, discovering, and utilizing atmospheric chamber data. It supports the evaluation and revision of atmospheric model mechanisms, intercomparison of data and models, and the development of new model frameworks.
ACS EARTH AND SPACE CHEMISTRY
(2023)
Article
Genetics & Heredity
Muhammad Kabiru Nata'ala, Anderson P. Avila Santos, Jonas Coelho Kasmanas, Alexander Bartholomaeus, Joao Pedro Saraiva, Sandra Godinho Silva, Tina Keller-Costa, Rodrigo Costa, Newton C. M. Gomes, Andre Carlos Ponce de Leon Ferreira de Carvalho, Peter F. Stadler, Danilo Sipoli Sanches, Ulisses Nunes da Rocha
Summary: The MarineMetagenomeDB is a valuable resource for researchers to find marine metagenome samples with curated metadata and facilitate meta-studies involving marine microbiomes. The database contains over 11,000 marine metagenomes from all oceans and provides user-friendly search and download tools.
ENVIRONMENTAL MICROBIOME
(2022)
Article
Multidisciplinary Sciences
Ryley McConkey, Eugene Yee, Fue-Sang Lien
Summary: The surge in machine learning augmented turbulence modelling offers a promising approach to address RANS models' limitations. This work introduces the development of an open-source dataset curated for immediate use in machine learning augmented corrective turbulence closure modelling, reducing effort required for training and testing new RANS models.
Article
Biochemistry & Molecular Biology
Guobang Shi, Xinyue Kang, Fanyi Dong, Yanchao Liu, Ning Zhu, Yuxuan Hu, Hanmei Xu, Xingzhen Lao, Heng Zheng
Summary: The new version of the antimicrobial peptide database (DRAMP) focuses on the development of stapled antimicrobial peptides and includes a subclass for storing information on these special chemically modified AMPs. It also adds cytotoxicity property of AMPs and expands newly discovered AMP data, with a total of 22259 entries and links to experimentally determined structures in the Protein Data Bank.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Nayang Shan, Yao Lu, Hao Guo, Dongyu Li, Jitong Jiang, Linlin Yan, Jiudong Gao, Yong Ren, Xingming Zhao, Lin Hou
Summary: This study develops a publicly accessible database, CITEdb, which facilitates interactive exploration of cell-cell interactions in specific physiological contexts and provides a benchmark dataset to interpret and evaluate computationally derived cell-cell interactions from different tools.
Review
Imaging Science & Photographic Technology
Sofia Amaru, Davide Marelli, Gianluigi Ciocca, Raimondo Schettini
Summary: Data augmentation is a crucial technique in machine learning that enhances the generalization and robustness of models by applying various transformations or modifications to existing data. This paper focuses on the most widely adopted data augmentation libraries in computer vision tasks, providing a comprehensive survey and organized classification of their approaches along with application examples. A dedicated public website named DALib has been created to ensure accessibility to this valuable information.
JOURNAL OF IMAGING
(2023)
Article
Biochemical Research Methods
Ruohua Shi, Keyan Bi, Kai Du, Lei Ma, Fang Fang, Lingyu Duan, Tingting Jiang, Tiejun Huang
Summary: Cell membrane segmentation in electron microscopy (EM) images is an important task. Current approaches perform well on low-resolution datasets but struggle with high-resolution datasets. Through eye movement and perceptual consistency experiments, we found that humans are more sensitive to membrane structure and can tolerate misalignment. Based on these findings, we propose a computational framework that incorporates human perception characteristics, including the perceptual Hausdorff distance (PHD) evaluation metric and a PHD-guided segmentation network (PS-Net).
Article
Biochemistry & Molecular Biology
Ben Te Aika, Libby Liggins, Claire Rye, E. Owen Perkins, Jun Huh, Rudiger Brauning, Tracey Godfery, Michael A. Black
Summary: The Aotearoa Genomic Data Repository (AGDR) is an initiative that aims to securely store and share non-human genomic data from Aotearoa New Zealand, following the principles of Maori Data Sovereignty. The repository allows access to data only to those who hold guardianship rights and have been approved to access the data. This article describes the development of AGDR from both cultural and technical perspectives and outlines its operational processes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Geosciences, Multidisciplinary
Irene DeFelipe, Juan Alcalde, Monika Ivandic, David Marti, Mario Ruiz, Ignacio Marzan, Jordi Diaz, Puy Ayarza, Imma Palomeras, Jose-Luis Fernandez-Turiel, Cecilia Molina, Isabel Bernal, Larry Brown, Roland Roberts, Ramon Carbonell
Summary: Seismic reflection data are valuable assets for solid Earth sciences, providing critical information about lithosphere properties and shallow subsurface geology. SeisDARE is a comprehensive open-access online database storing seismic data with a permanent identifier (DOI), promoting easy access and utilization of both old and newly acquired seismic data.
EARTH SYSTEM SCIENCE DATA
(2021)
Article
Neurosciences
Adam R. Ferguson, Jessica L. Nielson, Melissa H. Cragin, Anita E. Bandrowski, Maryann E. Martone
NATURE NEUROSCIENCE
(2014)
Editorial Material
Behavioral Sciences
Maryann E. Martone
BRAIN AND BEHAVIOR
(2014)
Article
Mathematical & Computational Biology
Janna Hastings, Gwen A. Frishkoff, Barry Smith, Mark Jensen, Russell A. Poldrack, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica A. Turner, Maryann E. Martone
FRONTIERS IN NEUROINFORMATICS
(2014)
Article
Mathematical & Computational Biology
Vinay K. Chaudhri, Daniel Elenius, Andrew Goldenkranz, Allison Gong, Maryann E. Martone, William Webb, Neil Yorke-Smith
JOURNAL OF BIOMEDICAL SEMANTICS
(2014)
Article
Mathematical & Computational Biology
B. Nolan Nichols, Jose L. V. Mejino, Landon T. Detwiler, Trond T. Nilsen, Maryann E. Martone, Jessica A. Turner, Daniel L. Rubin, James F. Brinkley
JOURNAL OF BIOMEDICAL SEMANTICS
(2014)
Editorial Material
Neurosciences
Eric M. Prager, Karen E. Chambers, Joshua L. Plotkin, David L. McArthur, Anita E. Bandrowski, Nidhi Bansal, Maryann E. Martone, Hadley C. Bergstrom, Anton Bespalov, Chris Graf
JOURNAL OF NEUROSCIENCE RESEARCH
(2019)
Editorial Material
Behavioral Sciences
Eric M. Prager, Karen E. Chambers, Joshua L. Plotkin, David L. McArthur, Anita E. Bandrowski, Nidhi Bansal, Maryann E. Martone, Hadley C. Bergstrom, Anton Bespalov, Chris Graf
BRAIN AND BEHAVIOR
(2019)
Article
Multidisciplinary Sciences
Joe Menke, Martijn Roelandse, Burak Ozyurt, Maryann Martone, Anita Bandrowski
Article
Multidisciplinary Sciences
Fiona Murphy, Michael Bar-Sinai, Maryann E. Martone
Summary: The increasing focus on biomedical data repositories aims to improve long-term availability of scientific data. Various principles like open science, data citation, and trustworthiness, along with FAIR data principles, guide the functions of these repositories. The framework OFCT, consisting of Open, FAIR, Citable, and Trustworthy principles, provides a comprehensive approach to enhance the design of biomedical data repositories.
Article
Biochemical Research Methods
Chun-Nan Hsu, Chia-Hui Chang, Thamolwan Poopradubsil, Amanda Lo, Karen A. William, Ko-Wei Lin, Anita Bandrowski, Ibrahim Burak Ozyurt, Jeffrey S. Grethe, Maryann E. Martone
Summary: This study investigates the feasibility of automatically generating alerts for users of problematic antibodies by extracting statements about antibody specificity reported in the literature. A deep neural network system was developed and tested with a corpus of over two thousand articles. The system accurately performed the task of identifying and classifying snippets about antibody specificity, as well as linking these snippets to specific antibodies mentioned. Leveraging Research Resource Identifiers (RRIDs), the study demonstrates the feasibility of constructing a reliable knowledge base about problematic antibodies through text mining.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Computer Science, Interdisciplinary Applications
Thomas H. Gillespie, Shreejoy J. Tripathy, Mohameth Francois Sy, Maryann E. Martone, Sean L. Hill
Summary: Defining and organizing knowledge about the building blocks of the brain is a challenge that requires a standardized approach. This article proposes the Neuron Phenotype Ontology (NPO) as a standardized and automatable method for naming cell types and normalizing their properties. The NPO allows for interoperability between different neuron naming schemes and provides a framework for organizing knowledge about cellular properties.
Article
Biochemistry & Molecular Biology
Michael Hawrylycz, Maryann E. Martone, Giorgio A. Ascoli, Jan G. Bjaalie, Hong-Wei Dong, Satrajit S. Ghosh, Jesse Gillis, Ronna Hertzano, David R. Haynor, Patrick R. Hof, Yongsoo Kim, Ed Lein, Yufeng Liu, Jeremy A. Miller, Partha P. Mitra, Eran Mukamel, Lydia Ng, David Osumi-Sutherland, Hanchuan Peng, Patrick L. Ray, Raymond Sanchez, Aviv Regev, Alex Ropelewski, Richard H. Scheuermann, Shawn Zheng Kai Tan, Carol L. Thompson, Timothy Tickle, Hagen Tilgner, Merina Varghese, Brock Wester, Owen White, Hongkui Zeng, Brian Aevermann, David Allemang, Seth Ament, Thomas L. Athey, Cody Baker, Katherine S. Baker, Pamela M. Baker, Anita Bandrowski, Samik Banerjee, Prajal Bishwakarma, Ambrose Carr, Min Chen, Roni Choudhury, Jonah Cool, Heathe Creasy, Florence D'Orazi, Kylee Degatano, Benjamin Dichter, Song-Lin Ding, Tim Dolbeare, Joseph R. Ecker, Rongxin Fang, Jean-Christophe Fillion-Robin, Timothy P. Fliss, James Gee, Tom Gillespie, Nathan Gouwens, Guo-Qiang Zhang, Yaroslav O. Halchenko, Nomi L. Harris, Brian R. Herb, Houri Hintiryan, Gregory Hood, Sam Horvath, Bingxing Huo, Dorota Jarecka, Shengdian Jiang, Farzaneh Khajouei, Elizabeth A. Kiernan, Huseyin Kir, Lauren Kruse, Changkyu Lee, Boudewijn Lelieveldt, Yang Li, Hanqing Liu, Lijuan Liu, Anup Markuhar, James Mathews, Kaylee L. Mathews, Chris Mezias, Michael I. Miller, Tyler Mollenkopf, Shoaib Mufti, Christopher J. Mungall, Joshua Orvis, Maja A. Puchades, Lei Qu, Joseph P. Receveur, Bing Ren, Nathan Sjoquist, Brian Staats, Daniel Tward, Cindy T. J. van Velthoven, Quanxin Wang, Fangming Xie, Hua Xu, Zizhe Yao, Zhixi Yun, Yun Renee Zhang, W. Jim Zheng, Brian Zingg
Summary: The BICCN is a comprehensive network aiming to systematically profile and characterize cell types in the brain using multimodal approaches. It provides a guide to cellular and spatial methods employed by the network and highlights analysis and visualization tools. The emerging standards of the BICCN ecosystem align with the principles of FAIR neuroscience.
Article
Multidisciplinary Sciences
Heidi Kleven, Thomas H. Gillespie, Lyuba Zehl, Timo Dickscheid, Jan G. Bjaalie, Maryann E. Martone, Trygve B. Leergaard
Summary: Brain atlases are crucial for accurate anatomical description of neuroscience data, but the lack of standardized description hinders their use in analytic tools and data registration. To address this issue, we developed an Atlas Ontology Model (AtOM) that provides a standardized framework for communication and use of brain atlases. By applying AtOM to different species' brain atlases, we demonstrate its potential in facilitating data integration and complying with FAIR guiding principles.
Article
Information Science & Library Science
Heather Staines, Maryann E. Martone
INSIGHTS-THE UKSG JOURNAL
(2018)
Article
Psychology, Multidisciplinary
Maryann E. Martone, Alexander Garcia-Castro, Gary R. VandenBos
AMERICAN PSYCHOLOGIST
(2018)
