Results for “Data Curation” — Page 22

NASA NTRS2018

Air Quality Satellite Monitoring by TROPOMI on Sentinel-5P

The recently launched Sentinel satellite mission, the Sentinel-5 Precursor (Sentinel-5P), is one of the European Space Agency's (ESA) new mission family – Sentinels. The sole payload on Sentinel-5P is the TROPOspheric Monitoring Instrument (TROPOMI), a nadir-viewing 108⁰ field-of-view push-broom grating hyperspectral spectrometer, covering the wavelengths of ultraviolet-visible (270 nm - 495 nm), near infrared (675 nm - 775 nm), and shortwave infrared (2305 nm - 2385 nm). Sentinel-5P is the first of the Atmospheric Composition Sentinels, and is providing measurements of atmospheric chemistry, aerosols, and clouds at high spatial, temporal, and spectral resolution. The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) supports over a thousand data collections in the focus areas of Atmospheric Composition, Water & Energy Cycles, and Climate Variability. Sentinel-5P TROPOMI Level-1B (L1B) and Level-2 (L2) products are curated at the GES DISC. Sentinel-5P data are provided by the European Union and the European Space Agency (ESA) through an agreement between ESA and NASA. Through its convenient and enhanced tools/services, such as OPeNDAP and L2 Subsetting, GES DISC offers the air quality remote sensing user community facile solutions for using complex Earth science data and applications. This presentation will demonstrate up-to-date TROPOMI products including EarthView (EV) radiance, solar irradiance, Aerosol Index, Carbon Monoxide, Total column Ozone, Nitrogen Dioxide, and cloud, as well as easy ways to access, visualize and subset TROPOMI data.

TROPOMI↗

NASA NTRSDate not supplied

Senteniel-6 Radio Occultation Product Released by NASA GES DISC to Supplement Satellite Remote Sensing Datasets for PBL Study

The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) curates hyperspectral atmospheric sounder remote sensing and numerical model reanalysis datasets which have been utilized in the Planetary Boundary Layer (PBL) research and applications. The hyperspectral sounder remote-sensing datasets include the Atmospheric Infrared Sounder (AIRS) on the Aqua satellite to the Cross-track Infrared Sounder (CrIS) on Suomi--National Polar- orbiting Partnership (NPP) and National Oceanic and Atmospheric Administration -20 (N NOAA-20)/ Joint Polar-orbiting Satellite System -1 (JPSS-1). The Modern-Era Retrospective analysis for Research and Applications Version 2 (MERRA-2) global reanalysis product provides a data record commencing in 1980. The sounder remote sensing and reanalysis datasets include temperature, water vapor, and trace gas profile down to the PBL, and also have a derived PBL height as well. A nearly 10-year (June 2006 to December 2015) seasonal and annual PBL height climatology dataset from COSMIC Global Navigation Satellite System (GNSS) radio occultation (RO) measurement is also available from the GES DISC. In collaboration with Sentinel-6 Project, the GES DISC is implementing curation activities for GNSS RO products from the Sentinel-6A/Sentinel-6 Michael Freilich satellite launched on November 21, 2020. Sentinel-6A RO products provide refractivity, temperature, and humidity profile with finer vertical resolution, leveraging PBL research and application as a supplement to the hyperspectral sounder remote sensing and reanalysis products. The public release of Sentinel- 6A RO products is scheduled for mid-October of 2021. In this presentation, we will introduce all Senitnel-6A products and services, and demonstrate use cases studying the PBL by combining these products with other GES DISC archived data products.

Feng Ding↗

NASA NTRSDate not supplied

Scientific Content Curation in an Open Science Era

Today’s open science environment, in combination with the Big Data era, means more scientific data, software, tools, documentation, publications and other resources are available than ever. The promise of the open science era is that scientists will spend less time reinventing the wheel and more time doing actionable research. Yet navigating this vast and complex information landscape can feel overwhelming to scientists trying to get their bearings. In this presentation, we define and discuss the importance of scientific content curation for enhancing discovery and use of scientific data and information. We also share two examples of scientific content curation in action: the Catalog of Archived Suborbital Earth Science Investigations (CASEI) and the Science Discovery Engine (SDE).

Kaylin Bugbee↗

DOE OSTI2022

Reviews and syntheses: The promise of big diverse soil data, moving current practices towards future potential

Abstract. In the age of big data, soil data are more available and richer than ever, but – outside of a few large soil survey resources – they remain largely unusable for informing soil management and understanding Earth system processes beyond the original study. Data science has promised a fully reusable research pipeline where data from past studies are used to contextualize new findings and reanalyzed for new insight. Yet synthesis projects encounter challenges at all steps of the data reuse pipeline, including unavailable data, labor-intensive transcription of datasets, incomplete metadata, and a lack of communication between collaborators. Here, using insights from a diversity of soil, data, and climate scientists, we summarize current practices in soil data synthesis across all stages of database creation: availability, input, harmonization, curation, and publication. We then suggest new soil-focused semantic tools to improve existing data pipelines, such as ontologies, vocabulary lists, and community practices. Our goal is to provide the soil data community with an overview of current practices in soil data and where we need to go to fully leverage big data to solve soil problems in the next century.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRSDate not supplied

Multi-Decadal Nitrogen Dioxide and Derived Products from Satellites (MINDS) Datasets Released by NASA GES DISC and Their Applications for Air Quality

Nitrogen dioxide (NO2), a pervasive air pollutant, comes from vehicles, power plants, industrial emissions, and off-road sources such as construction or lawn and gardening equipment. The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) curates many remote sensing datasets with NO2 retrievals, which have been utilized for air quality research and applications. The remotely-sensed datasets include those generated by the Ozone Monitoring Instrument (OMI) on the Aura satellite, the TROPOspheric Monitoring Instrument (TROPOMI) onboard the Copernicus Sentinel-5 Precursor (S5P), and the Ozone Mapping and Profiling Suite (OMPS) Nadir-Mapper (NM) instrument on the Suomi National Polar-orbiting Partnership (S- NPP). In collaboration with the NASA Making Earth System Data Records for Use in Research Environments (MEaSUREs) Multi-Decadal Nitrogen Dioxide and Derived Products from Satellites (MINDS) project, the GES DISC recently released MINDS datasets. The NASA MEaSUREs MINDS project aims to develop long-term NO2 global data records by adapting a consistent retrieval algorithm to multiple instrument measurements. Long-term data records will be achieved by applying consistent retrieval approaches to multiple satellite instruments, including OMI (2004 - ); the Global Ozone Monitoring Experiment (GOME, 1995-2011) onboard the second European Remote Sensing satellite (ERS-2); the Scanning Imaging Spectrometer for Atmospheric Cartography (SCIAMACHY, 2002-2012) onboard the ENVIronmental SATellite (ENVISAT); GOME-2 on the Meteorological Operational satellites (MetOp-A and MetOp-B, 2006 - ); and TROPOMI onboard the Copernicus S5P (2017 - ). The long-term record (1995 to present) of MINDS datasets makes them very useful for air quality trend studies. Some MINDS datasets with high spatial resolution of only a few kilometers can be used for air quality research and applications at regional scales. In this presentation, we will introduce all of the MINDS products and services, and demonstrate use cases of MINDS data for studying air quality. We will also present a few other NO2 datasets acquired from NASA’s Health and Air Quality Applied Sciences Team (HAQAST), to be archived and distributed by the GES DISC, and highlight some of their applications for air quality and health.

Feng Ding↗

NASA NTRS2020

Accelerating Space Life Sciences: Successes and Challenges of Biospecimen and Data Sharing

NASA's current human space flight research is directed towards enabling human space exploration beyond Low Earth Orbit (LEO). To that end, NASA Space Flight Payload Projects; Rodent Research, Cell Science, and Microbial Labs, flown on the International Space Station (ISS), benefit the global life sciences and commercial space communities. Verified data sets, science results, peer-reviewed publications, and returned biospecimens, collected and analyzed for flight and ground investigations, are all part of the knowledge base collected by NASA's Human Exploration and Operations Mission Directorate's Space Life and Physical Sciences Research and Applications (SLPSRA) Division, specifically the Human Research and Space Biology Programs. These data and biospecimens are made available through the public Life Sciences Data Archive (LSDA) website to promote basic discovery, pre-clinical and clinical science.The NASA Institutional Scientific Collection (ISC), stores flight and ground biospecimens from Space Shuttle and ISS programs. These specimens are curated and managed by the Ames Life Sciences Data Archive (ALSDA), an internal node of NASA's LSDA. The ISC stores over 30,000 specimens from experiments dating from 1984 to present. Currently available specimens include tissues from the circulatory, digestive, endocrine, excretory, integumentary, muscular, neurosensory, reproductive, respiratory and skeletal systems.NASA's biospecimen collection represents a unique and limited resource of unique spaceflight payload and ground control research subjects. These specimens are harvested according to well established SOPs that maintain their quality and integrity. Once the primary scientific objectives have been met, the remaining specimens are made available to provide secondary opportunities for complementary studies or new investigations to broaden research without large expenditures of time or resources. Website: https://lsda.jsc.nasa.gov/

Scott, Ryan T.↗

NASA NTRS2017

NASA Ames Institutional Scientific Collection (ISC)

NASA's current human space flight research is directed towards enabling human space exploration beyond Low Earth Orbit (LEO). The Space Flight Payload Projects; Rodent Research, Cell Science, and Microbial Labs, flown on the International Space Station (ISS), benefit both the global life sciences and commercial space communities. Verified data sets, science results, peer-reviewed publications, and returned biospecimens, collected and analyzed for flight and ground investigations, are all part of the knowledge base within NASA’s Human Exploration and Operations Mission Directorate’s Space Life and Physical Sciences Research and Applications (SLPSRA) Division, specifically the Human Research and Space Biology Programs. These data and biospecimens are made available through the public LSDA website. The Ames Institutional Scientific Collection (ISC), or ARC Biobank, stores flight and ground biospecimens from Space Shuttle and ISS programs. These specimens are curated and managed by the Ames Life Sciences Data Archive (ALSDA), an internal node of NASA's Life Sciences Data Archive (LSDA). The ARC Biolbank stores over 15,000 specimens from experiments dating from 1984 to present. Currently available specimens include tissues from the circulatory, digestive, endocrine, excretory, integumentary, muscular, neurosensory, reproductive, respiratory and skeletal systems. The most recent contributions include RNA, DNA and protein extracts from Rodent Research 1 and tissues from Rodent Research 4. NASA's biospecimen collection represents a unique and limited resource. The use of these biospecimens maximizes utilization and scientific return from these unique spaceflight payload and ground control research subjects. These biospecimens are harvested following complex, costly NASA research activities to meet primary scientific objectives. Once the primary scientific objectives have been met, the remaining specimens are made available to provide secondary opportunities for complementary studies or new investigations to broaden research without large expenditures of time or resources. Innovative ways of sharing this information ultimately advances the frontiers of human space exploration as well as scientific understanding of the effects of gravity on life on earth.

French, Alison J.↗

NASA NTRSDate not supplied

Maximizing Spaceflight Biological Data with Omics Analytics: The NASA GeneLab Database

NASA’s GeneLab includes an open-access repository of some 250+ omics datasets generated by biological experiments relevant to spaceflight including simulated cosmic radiation and microgravity. In order to maximize the intelligibility of these data, particularly for users with limited bioinformatics background, GeneLab has become a knowledgebase platform converting raw genetic and proteomic signatures found in flight samples into biological and physiological meanings. A large community of more than 100 scientists has rallied behind GeneLab and organized into four Analysis Working Groups (AWGs: Animal, Plant, Microbe, and Multi-Omics). Together, the AWGs have gained scientific recognition worldwide by establishing a consortium in charge of adopting new complex standards for data analysis workflows and omics sample processing in a rapidly evolving field. We will demonstrate the usage of the repository with smart search capability, an online controlled-access toolshed "Galaxy" to process user data with vetted standard workflows, a workspace for data sharing and a data submission portal with ontology control for better metadata curation. The GeneLab visualization portal will also be demonstrated, showing how anyone without formal training in bioinformatics can now browse the space biology omics data to discover new biology and potential solutions to improve life in space.

Sylvain Vincent Costes↗

NASA NTRSDate not supplied

GeneLab: The NASA System Biology Platform for Space Omics Repository, Analysis and Visualization

NASA’s GeneLab includes an open-access repository of some 250+ omics datasets generated by biological experiments relevant to spaceflight including simulated cosmic radiation and microgravity. In order to maximize the intelligibility of these data, particularly for users with limited bioinformatics background, GeneLab has become a knowledgebase platform converting raw genetic and proteomic signatures found in flight samples into biological and physiological meanings. A large community of more than 100 scientists has rallied behind GeneLab and organized into four Analysis Working Groups (AWGs: Animal, Plant, Microbe, and Multi-Omics). Together, the AWGs have gained scientific recognition worldwide by establishing a consortium in charge of adopting new complex standards for data analysis workflows and omics sample processing in a rapidly evolving field. We will demonstrate the usage of the repository with smart search capability, an online controlled-access toolshed "Galaxy" to process user data with vetted standard workflows, a workspace for data sharing and a data submission portal with ontology control for better metadata curation. The GeneLab visualization portal will also be demonstrated, showing how anyone without formal training in bioinformatics can now browse the space biology omics data to discover new biology and potential solutions to improve life in space.

GeneLab↗

NASA NTRSDate not supplied

Exploring Innovative Methods for Earth Science Communication Through NASA’s Earth Information Center

Environmental challenges stemming from unprecedented changes in our planet have increased the need to communicate our understanding of Earth as a connected system. In June 2023, NASA unveiled the Earth Information Center (EIC), part of NASA’s Earth Action Strategy aimed at amplifying NASA’s Earth science impact by engaging decision-makers beyond the scientific community. Existing in both physical and virtual space, the EIC provides critical information on how the planet is changing and affecting livelihoods across the globe. For over fifty years, NASA has utilized the unique vantage point space offers to monitor Earth in collaboration with Federal partners. Through an expanding fleet of Earth observing satellites and sensors, NASA informs local to global decision making within nine thematic areas: agriculture, biodiversity, disasters, greenhouse gases, health and air quality, sea level rise and coastal impacts, sustainable energy, water resources, and wildfires. Visitors to the inaugural location of the EIC at NASA Headquarters in Washington D.C., can interact with Earth observation data and models through innovative exhibits and storytelling. Designed by an interdisciplinary team, the EIC is designed for multiple modality learning to reach a wide base of end-users. Data driven visualizations, near real-time information, and curated stories highlight the applications of Earth observations to address environmental challenges. Complementary exhibits and immersive storytelling allow visitors to physically step inside environmental data and connect with information on an emotional level. Taken together, the collective EIC provides scientists and non-scientists alike with the ability to see our home planet as NASA sees it, as a system of systems, while delivering easily accessible information to those who need it most.

Earth Information Center↗

DOE OSTI2021

ClimateNet: an expert-labeled open dataset and deep learning architecture for enabling high-precision analyses of extreme weather

Abstract. Identifying, detecting, and localizing extreme weather events is a crucial first step in understanding how they may vary under different climate change scenarios. Pattern recognition tasks such as classification, object detection, and segmentation (i.e., pixel-level classification) have remained challenging problems in the weather and climate sciences. While there exist many empirical heuristics for detecting extreme events, the disparities between the output of these different methods even for a single event are large and often difficult to reconcile. Given the success of deep learning (DL) in tackling similar problems in computer vision, we advocate a DL-based approach. DL, however, works best in the context of supervised learning – when labeled datasets are readily available. Reliable labeled training data for extreme weather and climate events is scarce. We create “ClimateNet” – an open, community-sourced human-expert-labeled curated dataset that captures tropical cyclones (TCs) and atmospheric rivers (ARs) in high-resolution climate model output from a simulation of a recent historical period. We use the curated ClimateNet dataset to train a state-of-the-art DL model for pixel-level identification – i.e., segmentation – of TCs and ARs. We then apply the trained DL model to historical and climate change scenarios simulated by the Community Atmospheric Model (CAM5.1) and show that the DL model accurately segments the data into TCs, ARs, or “the background” at a pixel level. Further, we show how the segmentation results can be used to conduct spatially and temporally precise analytics by quantifying distributions of extreme precipitation conditioned on event types (TC or AR) at regional scales. The key contribution of this work is that it paves the way for DL-based automated, high-fidelity, and highly precise analytics of climate data using a curated expert-labeled dataset – ClimateNet. ClimateNet and the DL-based segmentation method provide several unique capabilities: (i) they can be used to calculate a variety of TC and AR statistics at a fine-grained level; (ii) they can be applied to different climate scenarios and different datasets without tuning as they do not rely on threshold conditions; and (iii) the proposed DL method is suitable for rapidly analyzing large amounts of climate model output. While our study has been conducted for two important extreme weather patterns (TCs and ARs) in simulation datasets, we believe that this methodology can be applied to a much broader class of patterns and applied to observational and reanalysis data products via transfer learning.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

An Open Combinatorial Diffraction Dataset Including Consensus Human and Machine Learning Labels with Quantified Uncertainty for Training New Machine Learning Models

Modern machine learning and autonomous experimentation schemes in materials science rely on accurate analysis of the data ingested by these models. Unfortunately, accurate analysis of the underlying data can be difficult, even for domain experts, complicating the training of the models intended to drive experiments. This is especially true when the goal is to identify the presence of weak signatures in diffraction or spectroscopic datasets. In this work, we examine a set of as-obtained diffraction data that track the phase transition from monoclinic to tetragonal in a Nb-doped VO2 film as a function of temperature and dopant concentration. We then task a set of domain experts and a set of machine learning experts with identifying which phase is present in each diffraction pattern manually and algorithmically, respectively; in both cases, the labels can vary dramatically, especially at the phase boundaries. We use the mode of the labels and the Shannon entropy as a method to capture, preserve and propagate consensus labels and their variance. Further we use the expert labels as a benchmark and demonstrate the use of Shannon entropy weighted scoring to test the performance of machine learning generated labels. Finally, we propose a material data challenge centered around generating improved labeling algorithms. This real-world dataset curated with expert labels can act as test bed for new algorithms. The raw data, annotations and code used in this study are all available online at data.gov and the interested reader is encouraged to replicate and improve the existing models

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2011

Nuts and Bolts - Techniques for Genesis Sample Curation

The Genesis curation staff at NASA Johnson Space Center provides samples and data for analysis to the scientific community, following allocation approval by the Genesis Oversight Committee, a sub-committee of CAPTEM (Curation Analysis Planning Team for Extraterrestrial Materials). We are often asked by investigators within the scientific community how we choose samples to best fit the requirements of the request. Here we will demonstrate our techniques for characterizing samples and satisfying allocation requests. Even with a systematic approach, every allocation is unique. We are also providing updated status of the cataloging and characterization of solar wind collectors as of January 2011. The collection consists of 3721 inventoried samples consisting of a single fragment, or multiple fragments containerized or pressed between post-it notes, jars or vials of various sizes.

Burkett, Patti J.↗

NASA NTRS2017

GES DISC Datalist Improves Earth Science Data Discoverability

At American Geophysical Union(AGU) 2016 Fall Meeting, Goddard Earth Sciences Data Information Services Center (GES DISC) unveiled a novel way to access data: Datalist. Currently, datalist is a collection of predefined data variables from one or more archived datasets, curated by our subject matter expert (SME). Our science support team has curated a predefined Hurricane Datalist and received very positive feedback from the user community. Datalist uses the same architecture our new website uses and have the same look and feel as other datasets on our web site. and also provides a one-stop shopping for data, metadata, citation, documentation, visualization and other available services. Since the last AGU Meeting, we have further developed a few new datalists corresponding to the Big Earth Data Initiative (BEDI) Societal Benefit Areas and A-Train data. We now have four datalists: Hurricane, Wind Energy, Greenhouse Gas and A-Train. We have also started working with our User Working Group members to create their favorite datalists and working with other DAAC to explore the possibility to include their products in our datalists that may also lead to a future of potential federated (cross-DAAC) datalists. Since our datalist prototype effort was a success, we are planning to make datalist operational. It's extremely important to have a common metadata model to support datalist, this will also be the foundation of federated datalist. We mapped our datalist metadata model to the unpublished UMM(Universal Metadata Model)-Var (Variable) (June version) and found that the UMM-var together with UMM-C (Collection) and possible UMM-S (Service) will meet our basic requirements. For example: Dataset shortname, and version are already specified in UMM-C, variable name, long name, units, dimensions are all specified in UMM-Var. UMM-Var also facilitates Science Keywords to allow tagging at variable level and Characteristics for optional variable characteristics. Measurements is useful for grouping of the variables and Set is promising to define datalist. And finally, the UMM-Service model to specify the available services for the variable will be very beneficial. In summary, UMM-Var, UMM-C and UMM-S are the basis of federated datalist and the development and deployment of datalist will contribute to the evolution of the UMM.

datalist↗

DOE OSTI2023

Ontologizing health systems data at scale: making translational discovery a reality

Common data models solve many challenges of standardizing electronic health record (EHR) data but are unable to semantically integrate all of the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68–99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

NASA NTRSDate not supplied

Metadata Entry Optimization for NASA's Biological Institutional Scientific Collection (NBISC)

The NASA Biological Institutional Sample Collection (NBISC) at NASA’s Ames Research Center is a critical resource housing non-human samples collected from spaceflight missions and ground analog studies, primarily consisting of specimens from rats, mice, and select microbes. The primary objective of NBISC is to systematically receive, document, preserve, and facilitate access to these samples for the global scientific community. NBISC promotes international collaboration and maximizes the return on investment for precious tissues from spaceflight and analog experiments. Researchers can request physical samples through an online request form and subsequent written proposal review process. This study addresses two core research objectives: streamlining the NBISC sample lifecycle processes and strategizing for managing an influx of 50,000 tissue samples from a series of cosmic radiation analog experiments carried out at the NASA Space Radiation Laboratory (NSRL) by Drs. Eleanor Chang (Lawrence Berkeley Laboratory) and Polly Blakely (SRI). The Chang/Blakely studies investigated Harderian gland (HG) tumorigenesis in mice exposed to low dose and LET radiation comprising 8 different exposure protocols in over 4000 mice. NBISC sample metadata is stored in a Laboratory Information Management System (SLIMS). To streamline sample data entry, we customize python scripts using information extracted from the individual experimental protocols. The scripts automate entry into multiple SLIMS data fields including protocol name, unique sample barcode, tissue and sub-tissue information, freezer location, sample preservation method, etc. The semi-automated procedure significantly decreases the time spent on data entry by several orders of magnitude. Automation and data organization are essential, as they free up time for curation and promotion of the collection which, in turn, increase the accessibility of samples to the broader research community. NBISC benefits from streamlined data ingestion, and the methodologies developed here are applicable to other projects which use SLIMS including the NASA Biospecimen Sharing Program and GeneLab. As of Fall 2023, plans include transferring sample data from SLIMS to public facing repositories (OSDR and NLSP), expanding the reach of the Chang/Blakely sample collection. The Human Research Program Space Radiation Element plans to transfer non-human tissues from many more investigations to NBISC in the coming year.

Sample Repository↗

NASA NTRSDate not supplied

Metadata Entry Optimization For NASA's Biological Institutional Scientific Collection (NBISC)

The NASA Biological Institutional Sample Collection (NBISC) at NASA’s Ames Research Center is a critical resource housing non-human samples collected from spaceflight missions and ground analog studies, primarily consisting of specimens from rats, mice, and select microbes. The primary objective of NBISC is to systematically receive, document, preserve, and facilitate access to these samples for the global scientific community. NBISC promotes international collaboration and maximizes the return on investment for precious tissues from spaceflight and analog experiments. Researchers can request physical samples through an online request form and subsequent written proposal review process. This study addresses two core research objectives: streamlining the NBISC sample lifecycle processes and strategizing for managing an influx of 50,000 tissue samples from a series of cosmic radiation analog experiments carried out at the NASA Space Radiation Laboratory (NSRL) by Drs. Eleanor Chang (Lawrence Berkeley Laboratory) and Polly Blakely (SRI). The Chang/Blakely studies investigated Harderian gland (HG) tumorigenesis in mice exposed to low dose and LET radiation comprising 8 different exposure protocols in over 4000 mice. NBISC sample metadata is stored in a Laboratory Information Management System (SLIMS). To streamline sample data entry, we customize python scripts using information extracted from the individual experimental protocols. The scripts automate entry into multiple SLIMS data fields including protocol name, unique sample barcode, tissue and sub-tissue information, freezer location, sample preservation method, etc. The semi-automated procedure significantly decreases the time spent on data entry by several orders of magnitude. Automation and data organization are essential, as they free up time for curation and promotion of the collection which, in turn, increase the accessibility of samples to the broader research community. NBISC benefits from streamlined data ingestion, and the methodologies developed here are applicable to other projects which use SLIMS including the NASA Biospecimen Sharing Program and GeneLab. As of Fall 2023, plans include transferring sample data from SLIMS to public facing repositories (OSDR and NLSP), expanding the reach of the Chang/Blakely sample collection. The Human Research Program Space Radiation Element plans to transfer non-human tissues from many more investigations to NBISC in the coming year.

Biospecimen↗

DOE OSTI2021

Identifying Genomic Islands with Deep Neural Networks

Background Horizontal gene transfer is the main source of adaptability for bacteria, through which genes are obtained from different sources including bacteria, archaea, viruses, and eukaryotes. This process promotes the rapid spread of genetic information across lineages, typically in the form of clusters of genes referred to as genomic islands (GIs). Different types of GIs exist, and are often classified by the content of their cargo genes or their means of integration and mobility. While various computational methods have been devised to detect different types of GIs, no single method is capable of detecting all types. Results We propose a method, which we call Shutter Island, that uses a deep learning model (Inception V3, widely used in computer vision) to detect genomic islands. The intrinsic value of deep learning methods lies in their ability to generalize. Via a technique called transfer learning, the model is pre-trained on a large generic dataset and then re-trained on images that we generate to represent genomic fragments. We demonstrate that this image-based approach generalizes better than the existing tools. Conclusions We used a deep neural network and an image-based approach to detect the most out of the correct GI predictions made by other tools, in addition to making novel GI predictions. The fact that the deep neural network was re-trained on only a limited number of GI datasets and then successfully generalized indicates that this approach could be applied to other problems in the field where data is still lacking or hard to curate.

Computer Vision↗