# Presentation: 487684

## WELCOME

- NIOSH Industry Day
- May 31, 2000

**WELCOME**

## Administrative

## Request for Information 

- Request for Information** **

## Agenda

- Introduction
- Information from selected laboratories
- Definition of the system needs
- Solution to the system needs
- Questions and answers

## NIOSH Vision Statement

- Delivering on the Nation’s Promise: Safety and Health at Work for All People...Through Research and Prevention

## 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.

## 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)

## Health Effects Laboratory Division (HELD)

- HELD is a basic and applied research
- laboratory with a testing component.

## 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)

## 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.

## Purpose of Industry Day

- Enhance information given in the CBD
- Define the characteristics of an electronic database system for HELD
- Questions and answers

## 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

## 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

## Scope of the Problem

- There are currently 95 research projects being conducted in HELD.

## 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

## Examples of Laboratory Data

- Vera Kommineni
- Lung pathology

## 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

## 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

## Examples of Laboratory Data

- Travis Goldsmith
- Developmental bioengineering

## Developmental Engineering Research Team

- Data Storage Issues

## Example Signals

**During A Cough**

- Sound
- Pressure

- Time

**Air Flow During **
**A Cough**

- Air Flow

- Time

- Expire

- Inspire

- 1 SECOND

- Recorded at 65536 Hz
- with 16 bits resolution.
- File size : 257 KB.

## 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.

## Slide 23

## 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.

## Examples of Laboratory Data

- Ainsley Weston
- DNA sequencing/oligonucleotide arrays

## Molecular Carcinogenesis Team

- PHS/DHHS/CDC
- NIOSH/HELD/TMBB

***Ainsley Weston, Ph.D.,***
***May 31, 2000***

## Ambiguous Haplotypes

**I/L65**

**K/E69**

**A-T-C-----------------------------------A-A-G****	****01011**
**A-T-C-----------------------------------G-A-G****	****0201**
**C-T-C-----------------------------------A-A-G****	****0301**
**C-T-C-----------------------------------G-A-G****	****2901**

## 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

## High Density Oligonucleotide Arrays (gene-chip)

- 7000 – 200,000 pieces of data per scan
- Numerical
- Zip/Jazz – drive/disc

## Photomicrographs

***Photomicrographs***

**A**

**B**

**D**

**C**

## Examples of Laboratory Data

- Ren Dong & Paul Smutz
- Hand-arm vibration; mechanical engineering

## Types of Raw Data

- <date/time>

- General test information manually recorded
- Data recorded on a tape
- Digitized data saved in a file
- Questionnaire
- Diagnostic Tests
- Photographs and video recordings

## General Test Information

-  Test date, time, location
-  Environmental conditions
-  Tool types, test devices and setup
-  Test staff
-  Technical notes and comments
-   Etc.

- <date/time>

## Data Recorded on a Tape

- <date/time>

- 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.

## 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.

## Questionnaire

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

## 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

## Photographs and video recordings

- Workers in Field Studies
- 	Posture
- 	Task analysis
- Infrared Camera

## Examples of Laboratory Data

- Jennifer Hornsby-Myers for Joel Harrison
- Surface spectroscopyanalysis/particle physics

## 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

## Focusing in on just the SEM/EDS method.

- We perform automated analysis of dust samples using commercial and custom software.
- Browsers
- Spreadsheets
- 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.

## 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.

## Examples of Laboratory Data

- Steve Reynolds
- Genetic susceptibility

## Definition of the Problem

- Project
- Protocols

- Chemical
- records

- Animals

- Equipment

- Facility
- Management

- Testing

- Data

- Prep. Report  &
- Manuscript

- Test Article

- Original Idea
- or Project

- SOPs

- Security

- Procurement

- Personnel

- Training

- Safety

- Reports &
- Manuscript

- Isotope
- Records

## Archive

- Project
- Protocols

- Chemical
- records

- Animals

- Equipment

- Facility
- Management

- Testing

- Data

- Prep. Report  &
- Manuscript

- Test Article

- Original Idea
- or Project

- SOPs

- Security

- Procurement

- Personnel

- Training

- Safety

- Reports &
- Manuscript

- Isotope
- Records

## “Data”

- Acquired data
- Transformed data
- Statistically-analyzed data

## Equipment Records

- Acquisition of equipment
- Calibration
- Maintenance and repair
- Authorization
- User training
- Log of usage

## Good Laboratory Practices (GLP)

- Leon Pringle, QA Officer

## 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

## HELD Laboratory Experiences

- Basic applied research
- Testing component

## Archive

- Project
- Protocols

- Chemical
- records

- Animals

- Equipment

- Facility
- Management

- Testing

- Data

- Prep. Report  &
- Manuscript

- Test Article

- Original Idea
- or Project

- SOPs

- Security

- Procurement

- Personnel

- Training

- Safety

- Reports &
- Manuscript

- Isotope
- Records

## GLP Concerns

- Test Article
- Animals
- Security
- SOPs
- Equipment
- Testing
- Chemicals records
- Chemicals
- Isotopes
- Safety
- Procurement
- Personnel/training
- Archive

## Archive

- Facilitator:
- Physical entity:

- Track
- Locate
- Retrieve
- Recreate
- Data

## 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

## Closing Date

- Friday, June 30, 2000

## Questions & Answers

- Please use the microphone