How to extract data from your paper for systemic review - Pubrica

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How to Extract Data from your Paper for
Systemic Review
Dr. Nancy Agnes, Head, Technical Operations, Pubrica, sales@pubrica.com
In-brief
Data should be extracted based on previously
identified interventions and outcomes developed
during the formulation of the study topic,
inclusion/exclusion requirements, and search
procedure. It should not be challenging to classify
the data elements that need to be retrieved from
each included sample if those phases have been
completed properly. To analyze and assess findings,
extract data from related studies. It is important to
use sound data collection techniques when the data
is being collected (1)
. Data processing can begin as
soon as you begin collecting data, and it can even
determine which data types you retain.
I. INTRODUCTION
Researchers in evidence-based medicine are
overwhelmed by the volume of primary research
papers, both old and modern. Since it is currently
impractical to scan for appropriate data with
accuracy, support for the early stages of the
systematic review phase – searching and screening
studies for eligibility – is needed. Not only could
better automatic data extraction help with the stage of
analysis known as "data extraction," but it could also
help with other aspects of the review process.
Systematic review (semi)automation research lies at
the intersection between evidence-based medicine
and computer science. Besides the advancement in
computing power and storage space, computers'
capacity to serve humans grows. Data extraction for
systematic analysis is a time-consuming process (2)
. It
opens up possibilities for sophisticated machines to
assist. In this domain, tools and methods are often
based on automating data processing relevant to the
PICO framework (Population, Intervention,
Comparator, and Outcome).
Table 1 A summary of included extraction methods and their evaluation

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II. WORK FLOW AND STUDY DESIGN
Two critics will separately screen both titles and
abstracts. Any discrepancies in judgement would be
addressed and, if possible, overcome with the
assistance of a third reviewer. The evaluation process
for complete texts would be the same, a single
reviewer will extract data, and a random 10%
selection from each reviewer will be reviewed
separately. We plan to contact the writers of reports
for confirmation or additional material if necessary.
We will provide a cross-sectional overview of the
data from our searches in the case study and any
published update. The analysis will include the
features of each reviewed method or tool, as well as a
summary of our outcomes. In addition, we will
evaluate the quality of reporting at the publication
level (3)
.
III. ELIGIBILITY CRITERIA
1. Eligible papers
 Full-text articles describing an initial natural
language processing method to extract data for
structured reviewing activities will be included.
The Extended data contains data areas of concern
adapted from the Cochrane Handbook for
Systematic Reviews of Interventions. The whole
spectrum of natural language processing (NLP)
techniques includes regular expressions, rule-
based structures, machine learning, and deep
artificialnetworks.
 Papers must detail the whole process of
implementing and evaluating a system.
 The data used for mining in the included articles
must be abstracts, conference proceedings, full
texts, or portions of full texts from randomized
clinical experiments, comparative cohort studies,

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or case management articles in the form of
abstracts, conference proceedings, full texts, or
parts of full texts.
2. Ineligible papers
We will exclude papers reporting:
 image editing and downloading biomedical data
from PDF files without the use of natural
language processing (NLP), including data
retrieval from graphs;
 any study that focuses merely on protocol
planning, synthesis of previously extracted data,
write-up, text pre-processing, and dissemination
will be disqualified;
 Methods or tools that do not use natural language
processing and instead focus on administrative
interfaces, document storage, databases, or
version control; or
• All articles relating to electronic health records
or genomic data mining may be disqualified.
IV. KEY ITEMS FOR DATA EXTRACTION
Primary
Machine learning approaches used
Reported performance metrics used for evaluation
Type of data
 Scope: full text, abstract, or conference
proceedings
 Study type: randomized clinical experiment,
cohort, and case-control
 Input data format: For example, data imported as
standardized results of literature searches (e.g.
RIS), APIs, or data imported from PDF or text
files.
 Output format: The format in which the data is
exported after extraction is a text file.
Secondary:
 Data mining granularity: Does the machine
retrieve individual entities, words, or whole
sections of text?
 Other indicators that have been published,
such as the effect on systemic review
processes (e.g. time saved during data
extraction)(4)
.
V. LIMITATIONS
First, there's a chance that data extraction algorithms
haven't been published in journals or that our search
has missed them. We searched several bibliographic
databases, including PubMed, IEEExplore, and the
ACM Digital Library, to overcome this limit. Second,
we did not publish a protocol ahead of time, and our
preliminary results may have affected our procedures.
To eliminate potential bias in our systematic analysis,
we duplicated main steps such as sampling, full-text
review, and data extraction.
VI. FUTURE WORK
According to a systematic analysis, information
retrieval technology positively affects physicians in
decision-making—the need for new methods to report
on and searching for organized data in written
literature. The use of an automated knowledge
extraction process to retrieve data elements can aid
comprehensive reviewers and, in the long run,
simplify the searching and data extraction steps (5)
.
VII. CONCLUSIONS
The studies have described methods to extract these
data elements, so data extraction for systematic
reviews outlines previously reported methods to
categorize sentences containing some of the data
extraction elements. Data extraction approaches may
serve as checks for currently conducted manual data
extraction, then serve to verify manual data extraction
achieved by a single reviewer, then become the
primary source for data element extraction that a
person will check, and finally full data extraction to
allow live systematic reviews(6)
.
REFERENCES
1. Splieth, Christian H., et al. "How to intervene in
the caries process: proximal caries in adolescents
and adults—a systematic review and meta-
analysis." Clinical oral investigations 24.5
(2020): 1623-1636.
2. Van Rensburg, Dina C. Christa Janse, et al.
"How to manage travel fatigue and jet lag in
athletes? A systematic review of
interventions." British journal of sports
medicine 54.16 (2020): 960-968.
3. Miake-Lye, Isomi M., et al. "Unpacking
organizational readiness for change: an updated
systematic review and content analysis of
assessments." BMC health services research 20.1
(2020): 106.
4. Karunananthan, Sathya, et al. "PROTOCOL:
When and how to replicate systematic
reviews." Campbell Systematic Reviews 16.2
(2020): e1087.
5. Muka, Taulant, et al. "A 24-step guide on how to
design, conduct, and successfully publish a
systematic review and meta-analysis in medical
research." European journal of
epidemiology 35.1 (2020): 49-60.
6. Haddaway, N. R., Bethel, A., Dicks, L. V.,
Koricheva, J., Macura, B., Petrokofsky, G., ... &

4
Stewart, G. B. (2020). Eight problems with
literature reviews and how to fix them. Nature
Ecology & Evolution, 1-8.

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