NIOSH Industry DayMay 31, 2000

WELCOME

Administrative

Centralized Database for Diverse Biological Research and

Development Laboratory Data

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 researchlaboratory 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

PathologyAnimal 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 GoldsmithDevelopmental bioengineering

Developmental Engineering Research Team

Data Storage Issues

Sound Pressure During A Cough

Sou

ndP

ress

ure

Time

Air Flow During A Cough

Air Flow

Time

Expire

Inspire

1 SECOND

Recorded at 65536 Hzwith 16 bits resolution.File size : 257 KB.

Example Signals

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.

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/L65K/E69

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

A B

DC

Examples of Laboratory Data

Ren Dong & Paul Smutz

Hand-arm vibration; mechanical engineering

Types of Raw Data

1. General test information manually recorded

2. Data recorded on a tape

3. Digitized data saved in a file

4. Questionnaire

5. Diagnostic Tests

6. 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.

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.

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 TestsBlood flow

Skin temperature

Nerve conduction velocity

Data will be different for each testSingle number

Large ACSII file

Chart or graph

Photographs and video recordings

Workers in Field StudiesPosture

Task analysis

Infrared Camera

Examples of Laboratory Data

Jennifer Hornsby-Myers for Joel HarrisonSurface 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:

NMRFTIRRamanAuger/XPSSEM/EDS/WDSHPLC

Focusing in on just the SEM/EDS method.

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

BrowsersSpreadsheetsWord processorJava, 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 ReynoldsGenetic susceptibility

Definition of the Problem

ProjectProtocols

Chemicalrecords

Animals

Equipment

FacilityManagement

Testing

DataPrep. Report &

Manuscript

Test Article

Original Ideaor Project

SOPs

Security

Procurement

Personnel Training

Safety

Reports &Manuscript

IsotopeRecords

Archive

ProjectProtocols

Chemicalrecords

Animals

Equipment

FacilityManagement

Testing

DataPrep. Report &

Manuscript

Test Article

Original Ideaor Project

SOPs

Security

Procurement

Personnel Training

Safety

Reports &Manuscript

IsotopeRecords

“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

ProjectProtocols

Chemicalrecords

Animals

Equipment

FacilityManagement

Testing

DataPrep. Report &

Manuscript

Test Article

Original Ideaor Project

SOPs

Security

Procurement

Personnel Training

Safety

Reports &Manuscript

IsotopeRecords

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