GeneLab is currently being developed by NASA to accelerate 'open science' biomedical research in support of the human exploration of space and the improvement of life on earth. Phase I of the four-phase GeneLab Data Systems (GLDS) project emphasized capabilities for submission, curation, search, and retrieval of genomics, transcriptomics and proteomics ('omics') data from biomedical research of space environments. The focus of development of the GLDS for Phase II has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics

Berrios, Daniel C.

Costes, Sylvain V.

Tran, Peter B.

GeneLab is currently being developed by NASA to accelerate open science biomedical research in support of the human exploration of space and the improvement of life on earth. Phase I of the four-phase GeneLab Data Systems (GLDS) project emphasized capabilities for submission, curation, search, and retrieval of genomics, transcriptomics and proteomics (omics) data from biomedical research of space environments. The focus of development of the GLDS for Phase II has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics

Tran, Peter

Costes, Sylvain

NASA Technical Reports Server

National Aeronautics and Space AdministrationNational Aeronautics and Sp ce Administration
NASA’s GeneLab Phase II: 
Federated Search and Data Discovery
Daniel C. Berrios MD PhD MPH
Sylvain Costes PhD
Peter Tran MS
NASA Ames Research Center
https://ntrs.nasa.gov/search.jsp?R=20180000803 2019-08-30T13:43:29+00:00Z
• GeneLab
• Federated Search
– Common Metadata Model
– Metadata Export
• Next Steps
Agenda
October 2017 2ASGSR 2017
• Goals 
– An integrated repository and bioinformatics data system for analysis and 
modeling
– Enable the discovery and validation of molecular networks that are 
influenced by space conditions through ground-based and flight research 
using next-generation omics technologies
– Engage the broadest possible community of researchers, industry, and the 
general public to foster innovation
– Strengthen international partnerships by leveraging existing capabilities and 
data sharing
Strategic Plan
3October 2017 ASGSR 2017
Phased Implementation
4
Phase 1
Searchable Data
FY2014 –2015
Phase 2
Data Exchange
FY2016-2017
Phase 3
System Integration
FY2018– 2019
Data System
 Public Website
 Searchable Data Repository
 Top Level Requirements
 New Data and Legacy Data
Data System
• Link to Public Databases via Metadata 
Federation
• Integrated Search
Data System
• Provide collaboration framework and tools 
• Build Community via collaborative science analysis 
& modeling
• Provide access to biocomputational tools for omics 
analysis
Cytoscape
October 2017 ASGSR 2017
• What?
– Search using 1 system over multiple data sources
– For example, Google web search
• Why?
– Facilitates discovery of data similar to known data
– Improves search efficiency: no need to switch and search multiple source 
systems
• How?
– Metadata Mapping of Data Sources
– If systems have search interfaces:
• Dynamic query translation
– If systems do not have search interfaces, or for greater reliability:
• Metadata warehousing
Federated Search
October 2017 5ASGSR 2017
Metadata Source Mappings
October 2017 6
Investigation
Study
Assay
Accession No GSE60473
Title Gravitational signature of synchronized cell cultures in particular cell 
cycle stages
Summary Cell cycle and cell proliferation are decoupled under altered gravity 
conditions…
Organism Arabidopsis thaliana
Experiment Type Expression profiling by array
Status Public on Aug 23, 2014
Accession No PXD005035
Title Mouse muscle LC-MSMS upon weightlessness
Description Upon weightlessness and microgravity, deleterious effects on the 
neurosensory and neurovestibular systems, haematological
changes…
Species Mus musculus (Mouse)
Tissue muscle
Experiment Type Shotgun proteomics
Accession No mgp4026
principle 
investigator
Peter Girguis, Harvard University
Description -
funding source NASA
Visibility Public
Accession No
Study Title Gravitational signature of synchronized cell cultures in particular cell 
cycle stages
Study Description Cell cycle and cell proliferation are decoupled under altered gravity 
conditions…
Organism Arabidopsis thaliana
Assay Type Transcription Profiling by Array
Release Date 23-Aug-2014
Accession No GSE60473
Study Title Gravitational signature of synchronized cell cultures in particular cell 
cycle stages
Study Description Cell cycle and cell proliferation are decoupled under altered gravity 
conditions…
Organism Arabidopsis thaliana
Assay Type Transcription Profiling by Array
Release Date 23-Aug-2014
ASGSR 2017
Common Metadata Model
October 2017 7
Accession GSE466
Title mRNA expression in regenerated mdx mouse skeletal muscle
Summary … A fourfold decrease in myostatin mRNA in the mdx muscle was 
noted. Differential upregulation of actin-related protein 2/3 (subunit 
4), beta-thymosin, calponin, mast cell chymase, and 
guanidinoacetate methyltransferase mRNA in the more benign mdx 
was also observed. …
Accession GLDS-131
Study Title Rodent Research-3-CASIS: Mouse liver transcriptomic proteomic 
and epigenomic data
Study Description The Rodent Research-3 (RR-3) mission was designed to study the 
effectiveness of a potential countermeasure for the loss of muscle 
and bone mass that occurs during spaceflight. Myostatin is a 
protein secreted by myoblasts that inhibits muscle cell growth and 
differentiation. Mutations in myostatin or drugs that block myostatin
cause increases in muscle mass. The RR-3 experiment was 
sponsored by pharmaceutical company Eli Lilly and Co. and the 
Center for the Advancement of Science in Space and assessed the 
efficacy of myostatin inhibition to prevent skeletal muscle atrophy 
and weakness….
ASGSR 2017
Federated Search Example 1
October 2017 8
“mouse”
“myostatin”
ASGSR 2017
Federated Search Example 2
October 2017 9
“mouse”
“liver”
ASGSR 2017
• Support development of federated searches initiated using extramural 
systems
– Export metadata (and data, if necessary) from GeneLab to these systems
– Provide link to “authoritative” source data (GeneLab)
• Semi-automated (scripted) process
– GeneLab metadata used as input
– Data products for submission to extramural data system are the output 
Extramural Federated Search 
October 2017 10
Accession No GSE60473
Title Gravitational signature of synchronized cell cultures in particular cell 
cycle stages
Summary Cell cycle and cell proliferation are decoupled under altered gravity 
conditions…
Organism Arabidopsis thaliana
Experiment Type Expression profiling by array
Status Public on Aug 23, 2014
ASGSR 2017
Extramural Federated Search 
October 2017 11ASGSR 2017
• Support federated queries initiated using PRIDE, MG-RAST
– Export metadata to these data systems
• Implement federated searches to other sources
– MODs
– NGOs, OGOs
• Expand search capabilities using ontologies (beyond UMLS 
translations) to increase discovery further
Next Steps/Directions
October 2017 12ASGSR 2017
Acknowledgements
October 2017 13
Chris Barreras
Afshin Beheshti
Valery Boyko
Sonja Caldwell
Jairon Camarillo
Kaushik Chakravarty
Egle Cekanaviciute
John Costa
Sylvain Costes
Marie Dinh
Sandy Dueck
Homer Fogel
Jon Galazaka
Samrawit Gebre
Dennis Heher
Lynn Hutchison
Yared Kidane
San-Huei Lai Polo
Tristan Le
Qiang Li
Shu-Chun Lin
Debora Pletcher
Sneha Raghunandan
Shayoni Ray
Sigrid Reinsch
Mike Skidmore
David Smith
Marla Smithwick
Olga Stotzky
Hao Thai
Serena Trieu
Andrew Williamson
ASGSR 2017


NASAs GeneLab Phase II: Federated Search and Data Discovery

NASA’s GeneLab Phase II: Federated Search and Data Discovery 
Daniel C. Berrios, MD MPH PhD1,2, Sylvain V. Costes, PhD2, Peter B. Tran, PhD2 
1Universities Space Research Association; 2NASA Ames Res. Ctr., Moffett Field, CA 
Purpose 
GeneLab is currently being developed by NASA to accelerate “open science” biomedical research in support of the 
human exploration of space and the improvement of life on earth.1,2 Phase I of the four-phase GeneLab Data Systems 
(GLDS) project emphasized capabilities for submission, curation, search, and retrieval of genomics, transcriptomics 
and proteomics (“omics”) data from biomedical research of space environments. The focus of development of the 
GLDS for Phase II has been federated data search for and retrieval of these kinds of data across other open-access 
systems, so that users are able to conduct biological meta-investigations using data from a variety of sources.  Such 
meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems 
biology knowledge and, eventually, therapeutics.   
System Design 
The GLDS currently serves over 100 omics investigations 
to the biomedical community via open access.  In order to 
expand the scope of metadata record searches via the 
GLDS, we designed a metadata warehouse that collects and 
updates metadata records from external systems housing 
similar data.  To demonstrate the capabilities of federated 
search and retrieval of these data, we imported metadata 
records from three open-access data systems into the GLDS 
metadata warehouse: NCBI’s Gene Expression Omnibus 
(GEO), EBI’s PRoteomics IDEntifications (PRIDE) 
repository, and the Metagenomics Analysis server (MG-
RAST).  Each of these systems defines metadata for omics 
data sets differently.  One solution to bridge such 
differences is to employ a common object model (COM) to 
which each systems’ representation of metadata can be 
mapped.  Warehoused metadata records are then 
transformed at ETL to this single, common representation. 
Queries generated via the GLDS are then executed against 
the warehouse, and matching records are shown in the 
COM representation (Fig. 1).  While this approach is 
relatively straightforward to implement, the volume of the 
data in the omics domain presents challenges in dealing 
with latency and currency of records.  Furthermore, the lack 
of a coordinated, universal registry of these kinds of data creates the issue of data duplication in federated search 
systems.       
Results 
Prototype federated data search capabilities are currently accessible to internal (NASA) users, with open access to 
these capabilities anticipated in the GLDS no later than Sep. 2017.  We will demonstrate the flexibility, performance, 
and power of our metadata representation mapping approach.  The execution of these kinds of studies will be furthered 
in Phases III and IV through the development of collaborative omics meta-analysis workspaces.   
References 
1. Berrios DC, Thompson TG, Fogle HW, Rask JC, Coughlan JC. GeneLab: NASA's Open Access, Collaborative
Platform for Systems Biology and Space Medicine. AMIA Annual Symposium Proceedings 2015.
2. Berrios DC, Welch, JD, Fogle HW, Skidmore, M, Marcu O. GeneLab: NASA’s GeneLab: Phase I Results and
Plans. AMIA Annual Symposium Proceedings 2016.
Figure 1. Federated Search of Omics Data 
https://ntrs.nasa.gov/search.jsp?R=20170010665 2019-08-31T01:38:20+00:00Z


NASA's GeneLab Phase II: Federated Search and Data Discovery

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