Effectiveness of tagging laboratory data using Dublin Core in an electronic scientific notebook

Laura M. Bartolo1, Cathy S. Lowe2, Austin C. Melton3,4, Monica Strah5, Louis Feng3, Christopher J. Woolverton5

1College of Arts & Sciences, 2 School of Library and Information Sciences, 3Department of Computer Science, 4Department of Mathematics,

5Department of Biological Sciences

Kent State University

Thursday, August 29, 2002

Scientific Notebooks record and document daily in-house activities manage research results

Objectives of scientific electronic notebook project provide high quality resource discovery and retrieval for primary

data objects adapt for a multidisciplinary, biotechnology research laboratory

Current Work: one stage of a multi-stage project record, store, and manipulate multidisciplinary, multi-institutional scientific information raw data to finished research papers

Today’s presentation laboratory data early in the scientific process prototype modified relational database Dublin Core metadata

Long-term Project Goals

1. Organize biotechnology information to encourage multidisciplinary use of information;

2. Apply knowledge gained and tools developed to the organization of other scientific information; and

3. Make scientific information from different disciplines more accessible

Biotechnology Research Team

Interdisciplinary, multi-institutional research team: Department of Biological Sciences Liquid Crystal Institute at Kent State University, Northeastern Ohio Universities College of Medicine Summa City Hospital

Workplace and research needs collectively conceive new ideas prevent redundancy exchange results, write papers perform daily activities in different physical locations

Tagging Data with Dublin Core Metadata

Link data across users and institutions – individual data, – analogous data types– non-chronological data entries

Enable the retrieval of laboratory data– facilitate data acquisition and analysis – share data more readily

Ensure reliable quality control– enhanced data integrity – better data analysis

Immediate Research Questions:

1. Is it feasibly to use DC to describe laboratory data (i.e., does it adequately capture necessary information)?

2. Does DC adequately support functions required in a laboratory environment?

Advantages of Dublin Core:

1. Concise, simple, and easy to learn Scientists & staff: little time to create metadata

records 2. Supports multiple formats

Scientific laboratory:text, still images, video, audio, and datasets

3. Facilitates Internet resource discovery Scientific data: rapidly and widely available

4. Approved ANSI/NISO standard Seeking approval as international standard: resource

discovery and information exchange

Scientific Notebook Database Design

Main Notebook is organized hierarchically and includes:

Topic: descriptions of past, present and planned projects;

Experiment Goals: experiment design concepts for a given project

Materials & Methods: procedures and materials used in experiments

Experiment Results/ Materials & Methods Results: data tables, graphs, images and datasets

Topic Results: Results would include drafts and finished papers

Main Notebook

Experiment Goals (6)

Materials & Methods Results (119)

T/N&As

EG/N&As (1)

Topic

MM/N&As (42)

Mat’ls & Methods (32)

Topic Results

Experiment Results (2)

Supplementary Tables

Materials: detailed information such as MSDS (material safety data sheets), specification sheets, and Materials Lot Analyses about organisms and liquid crystal substances involved with experiments.

User: basic contact information about individual researchers involved with the scientific investigation specifing authentication and access rights.

 

Memos: entities such as correspondence, equipment issues, and notes for future experiments.

Dublin Core Records

Materials Memos

Users

MainNotebook

Supplementary Tables Design

Image DC record

Title = "Bacterial Toxicity Assay of CPCl treated Klebsiella pneumoniae"Creator = "Woolverton, Christopher J."Subject= “Cetylpyridinium” (MeSH)Subject= “Klebsiella pneumoniae” (MeSH)Subject= “Toxicity Tests” (MeSH)Subject= “Biological Assay” (MeSH)Subject= “Bacterial Toxins” (MeSH)Description = "Graph of Bacterial Toxicity Assay of CPCl treated Klebsiella pneumoniae. % live standard curve used to evaluate CPCl effects."Date = " Created 2000-09-06"Type = "image"Format = "image/jpg 183 KB"Identifier = "CJW2_043001.JPG"Identifier = "Materials and Methods Result #39"Language = "en-US" (rfc1766)Relation = "IsPartOf Materials and Methods #18"Source = "topic #4"

LC Image DC record

Title = " Slide 'B' of strepavidin-bead: anti-strepavidin AB Dose Response Assay"Creator = "Woolverton, Christopher J."Subject= “Streptavidin” (MeSH)Subject= “Polymers” (MeSH)Subject= “Microspheres” (MeSH)Subject= “LC-5” (uncontrolled)Description = " % BEADS= 1.25; AB Concentration 100. Big aggregates, occasional isotropic regions, phase shift around larger eggs. Birefringence 5."Date = " Created 2000-10-17"Type = "image"Format = "image/jpg 67 KB"Identifier = " 101700\B 10x.jpg"Identifier = "Materials and Methods Result #100"Language = "en-US" (rfc1766)Relation = "IsPartOf Materials and Methods #35"Source = "topic #4"

Text DC record

Title = "Culture purity confirmed via streak plate."Creator = "Woolverton, Christopher J."Subject= "Escherichia coli" (MeSH)Subject= "Klebsiella pneumoniae" (MeSH)Subject= "Pseudomonas aeruginosa" (MeSH)Subject= "Biological Assay" (MeSH)Subject= "Bacterial Toxins" (MeSH)Subject= "Toxicity Tests" (MeSH)Description = "All three organisms grew well on nutrient agar, 37, overnight. E. coli and Klebsiella grew single colonial morphologies, Pseudomonas grew as two colonial types; a small + larger colony type as expected. Prep to repeat BacLight Assay - E. coli + K. P"Date = " Created 2000-08-24"Type = "text"Format = "ascii"Identifier = "Materials and Methods Attachments #38"Language = "en-US" (rfc1766)Relation = "IsPartOf Materials and Methods #17"Source = "topic #4"

Written notebook entry

240800Culture purity confirmed via streak plate.All three organisms grew well on nutrient agar, 37, overnight. E. coli and Klebsiella grew single colonial morphologies, Pseudomonas grew as two colonial types; a small + larger colony type as expected.Prep to repeat BacLight Assay - E. coli + K. Pneumo sub'ed to NB (30 ml).

Distribution of DC descriptions:202 (88.5%) of the 228 records

Type of database record # of records in database

# of DC records

% of DC records

Topic 1 0 0

notes/attachments 0 0 0

results 0 0 0

Experimental Goals 6 6 100.0

notes/attachments 6 1 16.6

results 6 2 33.3

Materials and Methods 32 32 100.0

notes/attachments 52 42 80.7

results 125 119 95.2

Totals 228 202 88.5

Problems Encountered:

Involved descriptions of higher-level records.

type designation for records: "text" or "collection"

"text" was used.

subject element: extent and level of detail that should be provided

relation element:provide a link between Material and Methods notes and results

not used

DC Records: Computerized Content Analysis

Use frequency of elements for different types of information objectsTotal and unique instances of elements included in frequency counts DC records visually analyzed to identify any nonstandard DC usages Good fit between the metadata schema and the data exists if DC elements follow with established standards Indicate ability of DC element set to be applied to laboratory data as information objects

DC Element Use Frequencies:

Element n Freq Ave Min Max Unique instances

Title 202 202 1 1 1 184

Creator 202 202 1 1 1 1

Subject 202 843 4.173 1 9 35

Description 202 202 1 1 1 196

Contributor 5 9 1.8 0 3 5

Date 202 202 1 1 1 39

Type 202 202 1 1 1 2

Format 202 202 1 1 1 92

Identifier 202 341 1.69 1 2 341

Source 202 202 1 1 1 1

Language 202 202 1 1 1 1

Relation 202 441 2.183 1 17 270

DC Element Qualifier Use Frequencies

Element Q Avail Q Used Instances n frequency Average

Title Yes No 0 202 0 0

Creator No ----- ----- 202 ----- -----

Subject Yes Yes 1 202 677 3.351

Description Yes No 0 202 0 0

Contributor No ----- ----- 5 ----- -----

Date Yes Yes 1 202 202 1

Type Yes Yes 1 202 202 1

Format Yes No 0 202 0 0

Identifier Yes No 0 202 0 0

Source Yes No 0 202 0 0

Language Yes Yes 1 202 202 1

Relation Yes Yes 4 202 441 2.183

Observations:

11 of the 15 DC elements may be qualified: title, subject, description, date, type, format, identifier, source, language, relation, and coverage.

at least one qualifier was used for those five elements: subject, date, type, language, relation

Qualified vs. Unqualified Subject Element Frequencies

Qualifer n frequencyAv

FreqMin Freq

Max Freq

# of Unique Instances

MeSH 202 677 3.351 1 7 26

Unqualified 202 166 0.822 0 4 9

Totals ----- 843 4.173 ----- ----- 35

"MeSH" Medical Subject Headings (NLM 2002) qualifier was used with the subject element in the 677 occurrences an average frequency of occurrence of 3.351 Twenty-six unique instances

MeSH" very useful in describing the organisms and microbiological techniques used in the laboratory 166 occurrences (average frequency 0.822)

Unqualified subjects contained keywords generated by the persons entering the metadata 154 occurrences describe different types of liquid crystals

MeSH general descriptor "Polymer" applied to liquid crystals

Observations:

Examine four specific types of metadata classes:

discovery, use, authentication and administration (Greenberg 2001)

aggregate content analysis element frequencies for each class

identify DC’s effectiveness regarding specific functions among data types

Functionality of the DC elements

DC Schema’s Ability to Sustain Required Information Functions

Discovery(14)

Use(5)

Authentication(8)

Administration(4)

Title 202 ------- ------- -------

Creator 202 ------- 202 -------

Subject 844 ------- ------- -------

Description 202 ------- ------- -------

Contributor 9 ------- 9 -------

Date 202 202 202 202

Type 202 202 202 -------

Format 202 202 ------- -------

Identifier 341 341 ------- 341

Source 202 ------- 202 202

Relation 441 ------- 441 -------

freq totals 3251 947 1258 745

# DC 202 202 202 202

freq/class 1.14 0.94 0.78 0.92

Further database development needed XML database

Small amount of data in the database Enlarge lab participation

It is feasible to use DC to describe lab data. many elements used once in each DC record

DC supports functions required in a lab setting. each function represented reasonably well

Preliminary Conclusions: