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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
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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
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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
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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
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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
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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?
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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
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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
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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)
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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.
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Dublin Core Records
Materials Memos
Users
MainNotebook
Supplementary Tables Design
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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"
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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"
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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).
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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
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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
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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
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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
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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
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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
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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
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"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:
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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
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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
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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: