Big Data to Knowledge (BD2K) is a project of the National Institutes of Health for knowledge extraction from big data.
BD2K was founded in 2013 in response to a report from the Working Group on Data and Informatics for the Advisory Committee to the Director of the National Institutes of Health. [1]
A significant part of BD2K's plans is to have organizations make plans to share their research data when they make a proposal in response to a funding opportunity announcement. [2]
Philip Bourne was the lead in managing the project until early 2017. [3]
Health informatics is the study and implementation of computer structures and algorithms to improve communication, understanding, and management of medical information. It can be viewed as branch of engineering and applied science.
The Biomedical Informatics Research Network, commonly referred among analysts as “BIRN” is a national proposed project to assist biomedical researchers in their bioscience investigations through data sharing and online collaborations. BIRN provides data-sharing infrastructure, advisory services from a single source and software tools and techniques. This national initiative is funded by NIH Grants, the National Center for Research Resources and the National Institute of General Medical Sciences (NIGMS), a component of the United States National Institutes of Health (NIH).
Biomedical text mining refers to the methods and study of how text mining may be applied to texts and literature of the biomedical domain. As a field of research, biomedical text mining incorporates ideas from natural language processing, bioinformatics, medical informatics and computational linguistics. The strategies in this field have been applied to the biomedical literature available through services such as PubMed.
The ICMJE recommendations are a set of guidelines produced by the International Committee of Medical Journal Editors for standardising the ethics, preparation and formatting of manuscripts submitted to biomedical journals for publication. Compliance with the ICMJE recommendations is required by most leading biomedical journals. Levels of real compliance are subject to debate. As of 9 January 2020, 5570 journals worldwide claim to follow the ICMJE recommendations.
Philip Eric Bourne is an Australian bioinformatician, non-fiction writer, and businessman. He is currently Stephenson Chair of Data Science and Director of the School of Data Science and Professor of Biomedical Engineering and was the first associate director for Data Science at the National Institutes of Health, where his projects include managing the Big Data to Knowledge initiative, and formerly Associate Vice Chancellor at UCSD. He has contributed to textbooks and is a strong supporter of open-access literature and software. His diverse interests have spanned structural biology, medical informatics, information technology, structural bioinformatics, scholarly communication and pharmaceutical sciences. His papers are highly cited, and he has an h-index above 50.
Apache cTAKES: clinical Text Analysis and Knowledge Extraction System is an open-source Natural Language Processing (NLP) system that extracts clinical information from electronic health record unstructured text. It processes clinical notes, identifying types of clinical named entities — drugs, diseases/disorders, signs/symptoms, anatomical sites and procedures. Each named entity has attributes for the text span, the ontology mapping code, context, and negated/not negated.
Translational bioinformatics (TBI) is a field that emerged in the 2010s to study health informatics, focused on the convergence of molecular bioinformatics, biostatistics, statistical genetics and clinical informatics. Its focus is on applying informatics methodology to the increasing amount of biomedical and genomic data to formulate knowledge and medical tools, which can be utilized by scientists, clinicians, and patients. Furthermore, it involves applying biomedical research to improve human health through the use of computer-based information system. TBI employs data mining and analyzing biomedical informatics in order to generate clinical knowledge for application. Clinical knowledge includes finding similarities in patient populations, interpreting biological information to suggest therapy treatments and predict health outcomes.
The field of population informatics is the systematic study of populations via secondary analysis of massive data collections about people. Scientists in the field refer to this massive data collection as the social genome, denoting the collective digital footprint of our society. Population informatics applies data science to social genome data to answer fundamental questions about human society and population health much like bioinformatics applies data science to human genome data to answer questions about individual health. It is an emerging research area at the intersection of SBEH sciences, computer science, and statistics in which quantitative methods and computational tools are used to answer fundamental questions about our society. [[File:Data science.png|alt=Data Science|thumb|Data Science]
Robert Lee Grossman is an American computer scientist and bioinformatician at the University of Chicago. His primary research interests are data science and data-intensive computing.
Ron Kikinis is an American physician and scientist best known for his research in the fields of imaging informatics, image guided surgery, and medical image computing. He is a professor of radiology at Harvard Medical School. Kikinis is the founding director of the Surgical Planning Laboratory in the Department of Radiology at Brigham and Women's Hospital, in Boston, Massachusetts. He is the vice-chair for Biomedical Informatics Research in the Department of Radiology.
Daniela M. Witten is an American biostatistician. She is a professor and the Dorothy Gilford Endowed Chair of Mathematical Statistics at the University of Washington. Her research investigates the use of machine learning to understand high-dimensional data.
Betsy L. Humphreys is an American medical librarian and health informatician known for leading the cross-institutional efforts to establish biomedical terminology standards such as SNOMED CT and the Unified Medical Language System. She was the deputy director of the National Library of Medicine from 2005 until her retirement in 2017, serving as acting director from 2015 to 2016.
Dean Forrest Sittig is an American biomedical informatician specializing in clinical informatics. He is a professor in Biomedical Informatics at the University of Texas Health Science Center at Houston and Executive Director of the Clinical Informatics Research Collaborative (CIRCLE). Sittig was elected as a fellow of the American College of Medical Informatics in 1992, the Healthcare Information and Management Systems Society in 2011, and was a founding member of the International Academy of Health Sciences Informatics in 2017. Since 2004, he has worked with Joan S. Ash, a professor at Oregon Health & Science University to interview several Pioneers in Medical Informatics, including G. Octo Barnett, MD, Morris F. Collen, MD, Donald E. Detmer, MD, Donald A. B. Lindberg, MD, Nina W. Matheson, ML, DSc, Clement J. McDonald, MD, and Homer R. Warner, MD, PhD.
Hixny is a not-for-profit, health information exchange (HIE) serving the Hudson Valley, Capital, Southern Tier, and North Country regions of New York State. A health information exchange connects fragmented personal health information between different organizations for improved overall healthcare.
Biological data refers to a compound or information derived from living organisms and their products. A medicinal compound made from living organisms, such as a serum or a vaccine, could be characterized as biological data. Biological data is highly complex when compared with other forms of data. There are many forms of biological data, including text, sequence data, protein structure, genomic data and amino acids, and links among others.
Kathy Lynn Hudson is an American microbiologist specializing in science policy. She was the deputy director for science, outreach, and policy at the National Institutes of Health from October 2010 to January 2017. Hudson assisted in the creation and launch of All of Us, the BRAIN initiative, and the National Center for Advancing Translational Sciences. She founded the Genetics and Public Policy Center at Johns Hopkins University in 2002. Hudson is an advocate for women in science.
Noémie Elhadad is an American data scientist who is an associate professor of Biomedical Informatics at the Columbia University Vagelos College of Physicians and Surgeons. As of 2022, she serves as the Chair of the Department of Biomedical Informatics. Her research considers machine learning in bioinformatics, natural language processing and medicine.
Peipei Ping is an academic specializing in cardiac physiology, system biology and data science.
Daniel Richard Masys is an American biotechnologist and academic. He is an Affiliate Professor of Biomedical and Health Informatics at the University of Washington.
The Observational Health Data Sciences and Informatics, or OHDSI is an international collaborative effort aimed at improving health outcomes through large-scale analytics of health data. The OHDSI effort includes diverse researchers and health databases worldwide, with its central coordinating center located at Columbia University.