Challenges and Opportunities in Data Management for Biomedical Research
Evolution of the Traditional Repositories
Eric Brunskill, Ph.D.
A HUMAN KIDNEY DISEASE ATLAS AND
DATA REPOSITORY:
KIDNEY PRECISION MEDICINE PROJECT
atlas.kpmp.org
The GenitoUrinary Development Molecular
Anatomy Project (GUDMAP) provides data
and tools that facilitate research on the
GenitoUrinary (GU) tract for the scientific and
medical community.
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https://www.gudmap.org/
https://www.rebuildingakidney.org/
NIH/NIDDK: DATA STEWARDS
NIH/NIDDK Data Challenges:
1.
Heterogeneity of Data
: NIH repositories often house data
from diverse sources and studies, including genomic, clinical,
imaging, and behavioral data. Integrating these disparate
datasets can be challenging due to differences in data
formats, standards, and data collection methods.
2.
Data Quality and Consistency
: Ensuring the quality and
consistency of data across different collections is crucial
for meaningful secondary research. Variations in data quality,
missing data (Data sparsity
)
, and inconsistencies in data
coding can hinder integration efforts.
3.
Data Privacy and Security
: NIH repositories typically
contain sensitive and personally identifiable information.
Balancing the need for data sharing with strict data privacy
and security requirements can be complex. Ensuring
compliance with regulations like HIPAA (Health Insurance
Portability and Accountability Act) is a significant challenge.
4.
Data Standardization
: NIH repositories may contain data in
different formats and standards. Harmonizing data to a
common standard can be time-consuming and resource-
intensive.
6.
Metadata Standardization
: Metadata is critical for
understanding and using the data effectively. Standardizing
metadata across different collections is essential for
discoverability and interoperability.
7.
Technical Infrastructure
: Integrating and managing large and
diverse datasets requires robust technical infrastructure and
data management systems. Ensuring compatibility and
scalability of these systems can be challenging.
8.
Data Access and Permissions
: Establishing access policies
and procedures that balance the need for open access with
the protection of sensitive information can be a complex task.
9.
Ethical Considerations
: Ensuring that data integration
respects ethical principles, such as informed consent and data
sharing agreements, is crucial in biomedical research.
Ensuring that machine learning does not incorporate bias.
10.
Funding and Resources
: Developing and maintaining the
infrastructure required for integrating and managing diverse
collections can be costly. As datasets become larger and more
complex, so do associated storage costs.
11.
User Training and Support
: Researchers may need to be
educated on how to access, use, and analyze integrated
datasets effectively. Providing training and support services
can be resource-intensive.
Democratization of data and
analysis!
1.
Data Integration Platforms
: Advanced data integration
platforms, including data lakes and data warehouses, can help
consolidate diverse datasets into a unified repository.
2.
Machine Learning and AI
: Machine learning algorithms and
artificial intelligence can assist in data mapping,
transformation, and harmonization. Natural language
processing (NLP) techniques can be employed to standardize
metadata and extract valuable information from unstructured
data sources.
3.
Cloud Computing
: Cloud computing services provide scalable
and cost-effective infrastructure for data storage,
processing, and analysis. Cloud-based platforms like AWS,
Azure, and Google Cloud offer tools and services for data
storage, integration and analytics.
4.
Blockchain and Data Provenance
: Blockchain technology can
enhance data security and traceability, ensuring that data is
tamper-proof and that its origins and modifications are
transparent. This is particularly important for maintaining
data integrity in multi-institutional collaborations.
5.
Data Standards and Ontologies
: The adoption of
standardized data formats, metadata schemas, and
biomedical ontologies helps ensure data consistency and
interoperability.
6.
APIs and Web Services
: Application Programming Interfaces
(APIs) and web services provide a standardized way for different
systems to interact and exchange data. They can facilitate the
integration of data from multiple sources into a unified platform.
7.
Data Visualization and Exploration Tools
: Interactive data
visualization tools can help researchers explore and analyze
integrated datasets effectively. HuBMAP Vitesse/KPMP
Explorer.
8.
Open Science Platforms
: Open science platforms and research
data repositories promote data sharing and collaboration. They
often come equipped with tools for data integration, metadata
management, and version control.
9.
Collaborative Research Ecosystems
: Building collaborative
research ecosystems that involve data scientists,
bioinformaticians, and domain experts can help address both
technical and governance challenges. Cross-disciplinary teams can
work together to integrate and analyze data effectively.
10.
Data Linkage and Federated Databases
: Federated databases
and distributed data linkage techniques allow data to remain in its
original location while enabling seamless querying and analysis
across different datasets.
NIH/NIDDK:
OPPORTUNITIES TO ADDRESS DATA
CHALLENGES THROUGH TECHNOLOGY
Managing data in biomedical research repositories poses challenges such as data heterogeneity, quality issues, privacy concerns, standardization, and technical infrastructure requirements. Addressing these challenges through technology like data integration platforms, machine learning, cloud computing, and blockchain can enhance data management efficiency and effectiveness for researchers.
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Presentation Transcript
Evolution of the Traditional Repositories Eric Brunskill, Ph.D.
NIH/NIDDK: DATA STEWARDS A HUMAN KIDNEY DISEASE ATLAS AND DATA REPOSITORY: KIDNEY PRECISION MEDICINE PROJECT The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) provides data and tools that facilitate research on the GenitoUrinary (GU) tract for the scientific and medical community. https://www.gudmap.org/ (Re)Building a Kidney consortium coordinating research to generate or repair nephrons that can function within the kidney. is an NIDDK-funded https://www.rebuildingakidney.org/ atlas.kpmp.org
NIH/NIDDK Data Challenges: 1. Heterogeneity of Data: NIH repositories often house data from diverse sources and studies, including genomic, clinical, imaging, and behavioral data. Integrating these disparate datasets can be challenging due to differences in data formats, standards, and data collection methods. 2. Data Quality and Consistency: Ensuring the quality and consistency of data across different collections is crucial for meaningful secondary research. Variations in data quality, missing data (Data sparsity), and inconsistencies in data coding can hinder integration efforts. 3. Data Privacy and Security: NIH repositories typically contain sensitive and personally identifiable information. Balancing the need for data sharing with strict data privacy and security requirements can be complex. Ensuring compliance with regulations like HIPAA (Health Insurance Portability and Accountability Act) is a significant challenge. 4. Data Standardization: NIH repositories may contain data in different formats and standards. Harmonizing data to a common standard can be time-consuming and resource- intensive. 6. Metadata Standardization: understanding and using the data effectively. Standardizing metadata across different collections is essential for discoverability and interoperability. 7. Technical Infrastructure: Integrating and managing large and diverse datasets requires robust technical infrastructure and data management systems. Ensuring compatibility and scalability of these systems can be challenging. 8. Data Access and Permissions: Establishing access policies and procedures that balance the need for open access with the protection of sensitive information can be a complex task. 9. Ethical Considerations: Ensuring that data integration respects ethical principles, such as informed consent and data sharing agreements, is crucial in biomedical research. Ensuring that machine learning does not incorporate bias. 10. Funding and Resources: Developing and maintaining the infrastructure required for integrating and managing diverse collections can be costly. As datasets become larger and more complex, so do associated storage costs. 11. User Training and Support: Researchers may need to be educated on how to access, use, and analyze integrated datasets effectively. Providing training and support services can be resource-intensive. Democratization of data and analysis! Metadata is critical for
NIH/NIDDK: OPPORTUNITIES TO ADDRESS DATA CHALLENGES THROUGH TECHNOLOGY 1. Data Integration Platforms: Advanced data integration platforms, including data lakes and data warehouses, can help consolidate diverse datasets into a unified repository. 2. Machine Learning and AI: Machine learning algorithms and artificial intelligence can transformation, and harmonization. processing (NLP) techniques can be employed to standardize metadata and extract valuable information from unstructured data sources. 3. Cloud Computing: Cloud computing services provide scalable and cost-effective infrastructure processing, and analysis. Cloud-based platforms like AWS, Azure, and Google Cloud offer tools and services for data storage, integration and analytics. 4. Blockchain and Data Provenance: Blockchain technology can enhance data security and traceability, ensuring that data is tamper-proof and that its origins and modifications are transparent. This is particularly important for maintaining data integrity in multi-institutional collaborations. 5. Data Standards and Ontologies: standardized data formats, biomedical ontologies helps ensure data consistency and interoperability. 6. APIs and Web Services: Application Programming Interfaces (APIs) and web services provide a standardized way for different systems to interact and exchange data. They can facilitate the integration of data from multiple sources into a unified platform. 7. Data Visualization and Exploration Tools: Interactive data visualization tools can help researchers explore and analyze integrated datasets effectively. HuBMAP Vitesse/KPMP Explorer. 8. Open Science Platforms: Open science platforms and research data repositories promote data sharing and collaboration. They often come equipped with tools for data integration, metadata management, and version control. 9. Collaborative Research Ecosystems: research ecosystems that bioinformaticians, and domain experts can help address both technical and governance challenges. Cross-disciplinary teams can work together to integrate and analyze data effectively. 10. Data Linkage and Federated Databases: Federated databases and distributed data linkage techniques allow data to remain in its original location while enabling seamless querying and analysis across different datasets. assist in data mapping, language Natural for data storage, Building collaborative scientists, involve data The adoption schemas, of and metadata
