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NIOSH Industry Day

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Centralized Database for Diverse Biological Research and ... Engineering and Control Technology Branch (ECTB) Health Communication Research Branch (HCRB) ... – PowerPoint PPT presentation

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Title: NIOSH Industry Day


1
NIOSH Industry Day May 31, 2000
WELCOME
2
Administrative
3
Request for Information
Centralized Database for Diverse Biological
Research and Development Laboratory Data
4
Agenda
  • Introduction
  • Information from selected laboratories
  • Definition of the system needs
  • Solution to the system needs
  • Questions and answers

5
NIOSH Vision Statement
  • Delivering on the Nations Promise Safety and
    Health at Work for All PeopleThrough Research
    and Prevention

6
NIOSH Mission
  • To provide national and world leadership in the
    prevention of work-related illness, injury and
    death. We accomplish this by a scientific
    approach to gathering information, assembling and
    creating knowledge, translating it into products
    and services, and delivering it to all who can
    effect prevention.

7
Divisions in NIOSH
  • Division of Applied Research and Technology
    (Cincinnati, OH)
  • Division of Respiratory Disease Studies
    (Morgantown, WV)
  • Division of Safety Research (Morgantown)
  • Division of Surveillance, Hazard Evaluations, and
    Field Studies (Cincinnati)
  • Education and Information Division (Cincinnati)
  • Pittsburgh Research Laboratory (Pittsburgh, PA)
  • Spokane Research Laboratory (Spokane, WA)
  • Health Effects Laboratory Division (Morgantown)

8
Health Effects Laboratory Division (HELD)
  • HELD is a basic and applied research
  • laboratory with a testing component.

9
Research Areas in HELD
  • Agricultural Immunotoxicology Group (AIG)
  • Analytical Services Branch (ASB)
  • Biostatistics Branch (BB)
  • Exposure Assessment Branch (EAB)
  • Engineering and Control Technology Branch
    (ECTB)
  • Health Communication Research Branch (HCRB)
  • Pathology and Physiology Research Branch (PPRB)
  • Toxicology and Molecular Biology Branch
    (TMBB)

10
Market Research
  • It is our initial assessment that off-the-shelf
    laboratory information management systems
    (LIMS) designed for testing laboratories do not
    adequately fulfill the requirements... as we
    know them.

11
Purpose of Industry Day
  • Enhance information given in the CBD
  • Define the characteristics of an electronic
    database system for HELD
  • Questions and answers

12
Current Environment
  • Diverse research environment many techniques and
    technologies
  • No centralized data collection facility
  • No standard backup/archival solution
  • Not all laboratory systems/instruments are
    accessible from the Local Area Network
  • Proprietary file formats output by software and
    instruments

13
Database Project Concept
  • Main products of HELD are reports and
    publications in the scientific literature
  • Goal Storage and retrieval of all processes and
    information that are relevant to the final
    reports and publications

14
Scope of the Problem
  • There are currently 95 research projects being
    conducted in HELD.

15
Examples of Laboratory Data
  • Vera Kommineni Lung pathology
  • Travis Goldsmith Developmental bioengineering
  • Ainsley Weston DNA sequencing/oligonucleotide
    arrays
  • Ren Dong/Paul Smutz Hand/arm vibration
    mechanical engineering
  • Jennifer Hornsby-Myers Surface spectroscopy
    analysis/particle physics
  • Steve Reynolds Genetic susceptibility

16
Examples of Laboratory Data
  • Vera Kommineni
  • Lung pathology

17
Pathology
  • Animal protocols
  • Animal in life observations
  • Animal weight data
  • Animal organ weight data
  • Animal necropsy observations
  • Gross photographs
  • Tissue trimming observations
  • Accession records
  • Tissue processing records

18
Histopathology
  • Diagnosis on each of maximum 60 organs for each
    animal
  • Tabulation of diagnoses (Group)
  • By cause of death
  • By gender
  • By nature of lesion
  • By neoplasm
  • By organ
  • By sacrifice interval
  • Free text diagnoses (when not using available
    nomenclature)
  • Gross and microscopic correlation of lesions
  • Immunohistochemistry
  • Re-cuts
  • Special stains
  • Statistical analysis

19
Examples of Laboratory Data
  • Travis Goldsmith
  • Developmental bioengineering

20
Developmental Engineering Research Team
  • Data Storage Issues

21
Example Signals
Air Flow
Air Flow During A Cough
Expire
Time
Inspire
Sound Pressure During A Cough
Sound Pressure
Time
Recorded at 65536 Hz with 16 bits
resolution. File size 257 KB.
1 SECOND
22
File Formats
  • ASCII
  • Used for smaller data files.
  • Ease of viewing with text editors.
  • Binary
  • Used for large data files to save drive space
  • Mixtures
  • Header Data
  • Custom written files are used to extract data
  • Matlab, Labview, C, etc.

23
(No Transcript)
24
Considerations
  • Large range of file sizes (up to 80 MB).
  • Extraction files must also be archived in order
    to make sense of data file and to calculate
    indexes derived from data.

25
Examples of Laboratory Data
  • Ainsley Weston
  • DNA sequencing/oligonucleotide arrays

26
Molecular Carcinogenesis Team
  • PHS/DHHS/CDC
  • NIOSH/HELD/TMBB

Ainsley Weston, Ph.D., May 31, 2000
27
Ambiguous Haplotypes
I/L65
K/E69
A-T-C-----------------------------------A-A-G 0101
1 A-T-C-----------------------------------G-A-G 02
01 C-T-C-----------------------------------A-A-G 0
301 C-T-C-----------------------------------G-A-G
2901
28
Case Control Study
  • 1000 Participants
  • 8 amplicons (300 base pairs)
  • 2 complete sequences
  • 2 alleles, 1000 samples, 300 bases
  • 600,000 pieces of information to link

29
High Density Oligonucleotide Arrays (gene-chip)
  • 7000 200,000 pieces of data per scan
  • Numerical
  • Zip/Jazz drive/disc

30
Photomicrographs
A
B
D
C
31
Examples of Laboratory Data
  • Ren Dong Paul Smutz
  • Hand-arm vibration mechanical engineering

32
Types of Raw Data
  • General test information manually recorded
  • Data recorded on a tape
  • Digitized data saved in a file
  • Questionnaire
  • Diagnostic Tests
  • Photographs and video recordings

33
General Test Information
  • Test date, time, location
  • Environmental conditions
  • Tool types, test devices and setup
  • Test staff
  • Technical notes and comments
  • Etc.

34
(No Transcript)
35
Data Recorded on a Tape
  • A tape recorder is portable and convenient for a
    field test.
  • It can be analog and digital signals
  • The tape can only be replayed with the tape
    recorder.
  • Analog signal will be digitized and processed
    using a software.

36
Digitized Data Saved in a File
  • Many measurement devices come with their own
    software and data are save in a file with a
    special format.
  • In many cases, the file can only be read by a
    specific software.
  • The data may also be saved in a ASCII format so
    that many other software can read it. However, An
    ASCII takes several times more memory and it is
    not desired.
  • In most cases, we will keep the file in their
    original formats.

37
Questionnaire
  • Medical History
  • Hand Written Data
  • Filled out by the test subjects
  • 20-50 Questions
  • 400 to 500 Test Subjects

38
Diagnostic Tests
  • 5 to 6 Diagnostic Tests
  • Blood flow
  • Skin temperature
  • Nerve conduction velocity
  • Data will be different for each test
  • Single number
  • Large ACSII file
  • Chart or graph

39
Photographs and video recordings
  • Workers in Field Studies
  • Posture
  • Task analysis
  • Infrared Camera

40
Examples of Laboratory Data
  • Jennifer Hornsby-Myers for Joel Harrison
  • Surface spectroscopyanalysis/particle physics

41
Exposure Assessment Branch in HELD Are there
physical and chemical surface properties that
make certain particles more toxic than
others? We investigate this question by using
various spectroscopy methods and HPLC
NMR FTIR Raman Auger/XPS SEM/EDS/WDS HPLC
42
Focusing in on just the SEM/EDS method. We
perform automated analysis of dust samples using
commercial and custom software. Browsers Spreadsh
eets Word processor Java, Perl and C-shell
scripts Data is generated and analyzed on UNIX
systems and can be transferred via ftp to Windows
systems for further analysis. We use both Sun
and SGI UNIX computers to perform the data
analysis.
43
We use Exceed as the interface between the UNIX
and Windows operating systems. A typical
automated dust analysis experiment generates text
and SunOS RAS digital image files. The amount
of data generated is about 20 megabytes. Data is
currently being stored and archived on 1 gigabyte
Jaz discs. Most of our computer systems are
connected to the Loca Area Network.
44
Examples of Laboratory Data
  • Steve Reynolds
  • Genetic susceptibility

45
Definition of the Problem
Equipment
SOPs
Animals
Testing
Test Article
Safety
Prep. Report Manuscript
Reports Manuscript
Project Protocols
Data
Original Idea or Project
Facility Management
Security
Procurement
Chemical records
Personnel
Training
Isotope Records
46
Archive
Equipment
SOPs
Animals
Testing
Test Article
Safety
Prep. Report Manuscript
Reports Manuscript
Project Protocols
Data
Original Idea or Project
Facility Management
Security
Procurement
Chemical records
Personnel
Training
Isotope Records
47
Data
  • Acquired data
  • Transformed data
  • Statistically-analyzed data

48
Equipment Records
  • Acquisition of equipment
  • Calibration
  • Maintenance and repair
  • Authorization
  • User training
  • Log of usage

49
Good Laboratory Practices (GLP)
  • Leon Pringle, QA Officer

50
Regulatory Compliance
  • GLP Regulations
  • 21 CFR 58 FDA
  • 40 CFR160 FIFRA
  • Federal Insecticide, Fungicide, and Rodenticide
    Act
  • 40 CFR 792 TSCA
  • Toxic Substances Control Act

51
HELD Laboratory Experiences
  • Basic applied research
  • Testing component

52
Archive
Equipment
SOPs
Animals
Testing
Test Article
Safety
Prep. Report Manuscript
Reports Manuscript
Project Protocols
Data
Original Idea or Project
Facility Management
Security
Procurement
Chemical records
Personnel
Training
Isotope Records
53
GLP Concerns
  • Test Article
  • Animals
  • Security
  • SOPs
  • Equipment
  • Testing
  • Chemicals records
  • Chemicals
  • Isotopes
  • Safety
  • Procurement
  • Personnel/training
  • Archive

54
Archive
  • Facilitator
  • Physical entity
  • Track
  • Locate
  • Retrieve
  • Recreate
  • Data

55
Solutions
  • Will include all the processes in the diagrams
  • Will be user-friendly
  • Will involve an integrated electronic laboratory
    notebook
  • Will be scalable and able to accommodate a large
    amount of expandable, diverse data
  • Will involve a partnership that facilitates a
    reliable system from design through implementation

56
Closing Date
  • Friday, June 30, 2000

57
Questions Answers Please use the microphone
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