Papers by Elizabeth Record
The procedures outlined in this document describe how Anatomical Structures, Cell Types and Bioma... more The procedures outlined in this document describe how Anatomical Structures, Cell Types and Biomarkers (ASCT+B) tables are authored. The tables are a critical part of the evolving Human Reference Atlas. See Börner et al. 2021 for background information.<strong> </strong>
Bookmarks Related papers MentionsView impact
Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) Master tables aim to capture the nest... more Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) Master tables aim to capture the nested part_of structure of anatomical human body organ systems from gross anatomical structure scale to subcellular biomarker scale. Functional tissue units (FTUs) for an organ system should be identified as well as the typology of cells and biomarkers used to uniquely identify cell types within that organ system and FTUs (e.g., gene, protein, proteoforms, lipid or metabolic markers). Ontology terms and unique identifiers are matched to AS, CT, and B wherever possible for semantic search capability within MC-IU products: Registration User Interface (RUI), Exploration User Interface (EUI), ASCT+B Reporter. The tables are authored and reviewed by an international team of anatomists, pathologists, physicians, and other experts. This document is intended for subject matter experts (pathologists, surgeons, dissectionists, molecular biologists, bioinformaticians, human organ or cell atlas consort...
Bookmarks Related papers MentionsView impact
This SOP describes procedures for communicating with those involved in the effort to develop tabl... more This SOP describes procedures for communicating with those involved in the effort to develop tables that document agreed-upon naming conventions for Anatomical Structures (AS), Cell Types (CT), and Biomarkers (B) tables and associated 3D reference organs authored by multiple consortia to support a Common Coordinate Framework (CCF) and Human Reference Atlas (HRA). The effort is led by a cross-consortium open working group (WG), organized under the auspices of the HuBMAP consortium. This SOP documents the timing, tools, and processes used to communicate with members of this working group and is designed for administrative staff from the Indiana University Mapping Component (MC-IU) of the HuBMAP HIVE who support this working group.
Bookmarks Related papers MentionsView impact
The procedures outlined in this document describe how 3D reference objects are reviewed,<br>... more The procedures outlined in this document describe how 3D reference objects are reviewed,<br> refined, and approved by subject matter experts (SMEs). Models appear in the CCF Portal 3D<br> Reference Object Library on the CCF Portal and are used in the Registration User Interface (RUI)<br> and Exploration User Interface (EUI). This document is intended for subject matter experts (SMEs), many of whom are organ experts<br> from funded components of HuBMAP or other projects.
Bookmarks Related papers MentionsView impact
Several international consortia are collaborating to construct a human reference atlas, which is ... more Several international consortia are collaborating to construct a human reference atlas, which is a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Laboratories around the world are collecting tissue specimens from donors varying in sex, age, ethnicity, and body mass index. However, integrating and harmonizing tissue data across 20+ organs and more than 15 bulk and spatial single-cell assay types poses diverse challenges. Here we present the software tools and user interfaces developed to annotate (“register”) and explore the collected tissue data. A key part of these tools is a common coordinate framework, which provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions linked to existing ontologies. As of December 2021, the “registration” user interface has been used to harmonize and make publicly available data on 6,178 tissue sections from 2,698 tissue blocks collec...
Bookmarks Related papers MentionsView impact
ArXiv, 2020
The National Institutes of Health's (NIH) Human Biomolecular Atlas Program (HuBMAP) aims to c... more The National Institutes of Health's (NIH) Human Biomolecular Atlas Program (HuBMAP) aims to create a comprehensive high-resolution atlas of all the cells in the healthy human body. Multiple laboratories across the United States are collecting tissue specimens from different organs of donors who vary in sex, age, and body size. Integrating and harmonizing the data derived from these samples and 'mapping' them into a common three-dimensional (3D) space is a major challenge. The key to making this possible is a 'Common Coordinate Framework' (CCF), which provides a semantically annotated, 3D reference system for the entire body. The CCF enables contributors to HuBMAP to 'register' specimens and datasets within a common spatial reference system, and it supports a standardized way to query and 'explore' data in a spatially and semantically explicit manner. [...] This paper describes the construction and usage of a CCF for the human body and its referenc...
Bookmarks Related papers MentionsView impact
Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact, 2017
Interactive data visualizations known as macroscopes have great potential as tools for exploring,... more Interactive data visualizations known as macroscopes have great potential as tools for exploring, understanding, and communicating science [1]. Macroscopes empower individuals to interact with data in order to better understand it from multiple perspectives. Joël de Rosnay [2] first introduced the concept of the macroscope in his 1979 book, The Macroscope: A New World Scientific System, where he describes macroscopes as tools "not used to make things larger or smaller, but to observe what is at once too great, too slow, and too complex for our eyes." The Cyberinfrastructure for Network Science Center, in partnership with Indiana University's Advanced Visualization Laboratory, developed a touchscreen kiosk to showcase the macroscopes in the international science mapping exhibit, Places & Spaces: Mapping Science [2]. The exhibit showcases best examples of visualization techniques from a range of disciplines in order to stimulate the development of new algorithms, workflows, and techniques for visualizing the fields of science, technology, and innovation. New exhibit pieces are selected with the input of an advisory board of prominent data visualization experts from both academia and industry. The 2016 collection of interactive data visualizations showcases innovative examples of how to visualize large scientific data sets with user-friendly interfaces for interacting with data, developing new questions, and discovering new insights. It includes a diverse collection of interactive visualizations that draw on multiple types of data, ranging from geo-tagged social media posts to metadata from a digital library to citation counts and ship transponder data. The first macroscope uses social media posts to map smells across 12 cities. Humans can differentiate thousands of different odors, yet city officials and urban planners deal only with the management of a few bad odors. In creating Smelly Maps [3, 4, 5, 6, 7, 8], University of Turin computer science professor Rossano1 Schifanella and Bell Labs researchers Luca Maria Aiello and Daniele Quercia teamed up to introduce a new stream of research that celebrates the complex aromas of our cities and makes it possible to use this information in urban design. To map urban smellscapes, the project team first created a lexicon of smell-related words. Then, they gathered geotagged social media posts from Flickr, Instagram, and Twitter that included smell-related words. Finally, smell information was mapped by street segment. The second macroscope provides a visual approach to the vast digital collections of the HathiTrust Digital Library, a collective "elephant's memory" or storehouse of knowledge. Run by a consortium of international research libraries, HathiTrust serves as a shared and growing repository for digital copies of more than 14 million publications that span 2000 years. Visualization software developer David Reagan, curator Lisel Record, and information scientist Katy Börner developed this visualization to provide access to the geographic and temporal diversity of the collection using freely available metadata. Yellow circles show publication locations, with the size of the circle showing how many publications were printed in that location. Lines connect publication locations to places where that language is spoken, illustrating the connection between publication location and potential readers. The third macroscope concerns itself with collaborative scientific research activity at the world's top institutions. While it may be simple to estimate which research institutions are at the top of their game, it is hard to create a statistical model to measure and map this. Lutz Bornmann, a sociologist of science at the Max Planck Society; Rüdiger Mutz, a Swiss researcher in social psychology and higher education; Moritz Stefaner, an independent data visualization expert; and Félix de Moya Anegón, senior researcher at SCImago, took up the challenge and created Excellence Networks [9, 10, 11]. This interactive web application shows how universities and other research institutions collaborate. Institutions in the SCImago Institutions Rankings were categorized by subject area. Each institution was then mapped in relation to its collaborators. The resulting networks show how successfully---in terms of citations---an institution has collaborated with others working in the same field. Created by FleetMon, a company that provides live vessel tracking, the last macroscope animates a week of ship traffic on the seven seas as seen from space [12]. The movements of hundreds of thousands of vessels were captured using shore and satellite-based tracking data from FleetMon and its partner, Luxspace. Many cargo ships, tankers, ferries, cruise ships, yachts, and tugs carry transponders that transmit their locations. That data is then made available to amateur ship spotters and maritime businesses alike through the interactive FleetMon Explorer tool. Using the tool, one can follow the…
Bookmarks Related papers MentionsView impact
Bookmarks Related papers MentionsView impact
PLoS ONE, 2020
Understanding the emergence, co-evolution, and convergence of science and technology (S&T) areas ... more Understanding the emergence, co-evolution, and convergence of science and technology (S&T) areas offers competitive intelligence for researchers, managers, policy makers, and others. This paper presents new funding, publication, and scholarly network metrics and visualizations that were validated via expert surveys. The metrics and visualizations exemplify the emergence and convergence of three areas of strategic interest: artificial intelligence (AI), robotics, and internet of things (IoT) over the last 20 years (1998-2017). For 32,716 publications and 4,497 NSF awards, we identify their topical coverage (using the UCSD map of science), evolving co-author networks, and increasing convergence. The results support data-driven decision making when setting proper research and development (R&D) priorities; developing future S&T investment strategies; or performing effective research program assessment.
Bookmarks Related papers MentionsView impact
Uploads
Papers by Elizabeth Record