Title: Mastering Literature Review Data Extraction Forms Made Easy

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Those who conduct systematic reviews know well the degree of missing information sought to
summarize a group of studies. You are a close professional associate of any of the authors (e.g.
scientific mentor, recent student). Not applicable Are the conclusions drawn adequately supported by
the results presented in the review. Reviewer Expertise: Evidence-based medicine, systematic
reviews, automation techniques. Continue reading READ ALL Data extraction in a systematic
review is a hard and time-consuming task. Romi Satria Wahono. SD Sompok Semarang (1987)
SMPN 8 Semarang (1990) SMA Taruna Nusantara Magelang (1993). We listed many ongoing
challenges in the field of data extraction for systematic review (semi) automation, including
ambiguity in clinical trial texts, incomplete data, and previously unseen data. It was selected by
Cochrane to become the standard production platform for Cochrane Reviews. Although the specifics
will be different, each review will likely extract data on the following aspects of the studies:
Participants Interventions Outcomes Results These bullets represent data from the study only.
MEDLINE was the most popular source of data, with abstracts usually described as being retrieved
via searches on PubMed, or full texts from PubMed Central. Competing Interests Policy Provide
sufficient details of any financial or non-financial competing interests to enable users to assess
whether your comments might lead a reasonable person to question your impartiality. Olorisade
3,5,6, James Thomas 4, Julian P. T. Higgins 3 Lena Schmidt 1-3, Ailbhe N. References 56 and 76
showed how the decision of extracting the top two or N predictions impacts the evaluation scores,
for example precision or recall. In the base-review we assessed the included publications based on a
list of 17 items in the domains of reproducibility (3.4.1), transparency (3.4.2), description of testing
(3.4.3), data availability (3.4.4), and internal and external validity (3.4.5). The list of items was
reduced to six items for the update, more information about the removed items can be found in the
methods section of this LSR. Develop the Review’sProtocol 5.1 PLANNING 1. Identify the
RelevantLiterature 2. We thank Sarah Dawson for developing and evaluating the search strategy, and
for providing advice on databases to search for this review. Cochrane Handbook for Systematic
Reviews of Interventions version 6.1 (updated September 2020). The (semi) automation of data
extraction in systematic reviews is an advantage for researchers and ultimately for evidence-based
clinical practice. Commonly, randomized controlled trials (RCT) text was at least one of the target
text types used in the included publications. 3.2.3.2 Data extraction targets Mining P, IC, and O
elements is the most common task performed in the literature of systematic review (semi-)
automation (see Table A1 in Underlying data, 127 and Figure 6 ). Resources for students and
trainees some key resources are highlighted in the next few pages researchers around the world have
found these useful its worth a look and it might save you a lot of time. The funders had no role in
study design, data collection and analysis, decision to publish, or preparation of the manuscript. Key
to Reviewer Statuses VIEW HIDE Approved The paper is scientifically sound in its current form
and only minor, if any, improvements are suggested Approved with reservations A number of small
changes, sometimes more significant revisions are required to address specific details and improve
the papers academic merit. For the LSR update, the strongest trend was the increasing application of
BERT (Bidirectional Encoder Representations from Transformers). Embedding and neural
architectures are increasingly being used in literature over the past seven years. Raja K, et al.:
Towards Evidence-based Precision Medicine: Extracting Population Information from Biomedical
Text using Binary Classifiers and Syntactic Patterns. Of the included publications in the base-review,
47 out of 53 (88%) described using at least one third-party framework for their data extraction
systems. The following list is likely to be incomplete, due to non-available code and incomplete
reporting in the included publications. It’s easy to collaborate across the whole team and to keep the
project running smoothly. This creates opportunities for support through intelligent software, which
identify and extract information automatically. Nine publications (12%) use rule-bases alone, while
the rest of the publications use them in combination with other classifiers (data shown in Underlying
data: Appendix A and D 127 ). For named-entity recognition, EBM-NLP 55 is the most popular
dataset, used by at least 10 other publications and adapted and used by another four.
The field of systematic review (semi) automation is evolving rapidly along with advances in
language processing, machine learning, and deep learning. Between review updates, trends for
sharing data and code increased strongly: in the base-review, data and code were available for 13 and
19% respectively, these numbers increased to 78 and 87% within the 23 new publications. In
between updates, the screening process and current state of the data extraction is visible via the
living review website. At the time of publication of these documents, methods such as topic
modelling (Latent Dirichlet Allocation) and support vector machines (SVM) were considered state-
of-the art for language models. Yes Competing Interests No competing interests were disclosed.
Rathbone et al., 28 for example, used hand-crafted Boolean searches specific to a systematic
review’s PICO criteria to support the screening process of a review within Endnote. Comparability
between models might be further decreased by comparing results between publications that use
relaxed vs. It also ensures neither the research was done before nor it is a replication study. In section
2.4 about searching Pubmed, can the authors clarify that the Pubmed 2.0 API or GUI will be used to
access candidate literature. MEDLINE was the most popular source of data, with abstracts usually
described as being retrieved via searches on PubMed, or full texts from PubMed Central. The arrival
of transformer-based methods in 2018 marked the last big change in the field, as documented by this
LSR. Additionally, the authors may want to consider commenting on the topic areas covered by the
included studies and whether that has an impact on any of the metrics measured. Examples of
'Financial Competing Interests' You expect to receive, or in the past 4 years have received, any of the
following from any commercial organisation that may gain financially from your submission: a
salary, fees, funding, reimbursements. Data are available from 25 (33%), and code from 30 (39%)
publications. Conflicting judgements were resolved by the authors who made the initial screening
decisions. We found a variety of topics discussed in these publications and summarised them under
seven different domains. In the base-review we assessed the included publications based on a list of
17 items in the domains of reproducibility (3.4.1), transparency (3.4.2), description of testing (3.4.3),
data availability (3.4.4), and internal and external validity (3.4.5). The list of items was reduced to six
items for the update, more information about the removed items can be found in the methods section
of this LSR. When criticisms of the article are based on unpublished data, the data should be made
available. The authors included more than 50 publications in this version of their review that
addressed extraction of data from abstracts, while less (26%) used full texts. Here are the steps to
follow when creating a literary review. In short, for the base-review we screened all retrieved
publications using the Abstrackr tool. Yes Are the conclusions drawn adequately supported by the
results presented in the review. The views expressed in this article are those of the authors and do
not necessarily represent those of the NHS, the NIHR, MRC, or the Department of Health and
Social Care. They conclude that tools facilitating screening are widely accessible and usable, while
data extraction tools are still at piloting stages or require a higher amount of human input. After
extraction we structured them into six different domains: 1. Due to the increased number of available
corpora we stopped downloading the data and provide links instead. We listed many ongoing
challenges in the field of data extraction for systematic review (semi) automation, including
ambiguity in clinical trial texts, incomplete data, and previously unseen data. Yes Are sufficient
details of the methods and analysis provided to allow replication by others. Both micro and macro
scores were reported by Singh et al. (2021), 45 Kilicoglu et al. (2021), 38 Kiritchenko et al. (2010),
46 Fiszman et al. (2007) 47 whereas Karystianis et al. (2014, 2017) 48, 49 reported micro across
documents, and macro across the classes.
Estimate an effect size for each individual study 3. Any deviations from the protocol have been
described below. Around three in ten publications made their datasets available to the public, and
more than half of all included publications reported training or evaluating on these datasets. If you
do not have access to your original account, please contact us. Publications that did provide the
source code were exclusively published or last updated in the last seven years. Examples of 'Financial
Competing Interests' You expect to receive, or in the past 4 years have received, any of the
following from any commercial organisation that may gain financially from your submission: a
salary, fees, funding, reimbursements. Norman C, Leeflang M, Neveol A: Data Extraction and
Synthesis in Systematic Reviews of Diagnostic Test Accuracy: A Corpus for Automating and
Evaluating the Process. Publications in the neural and deep-learning domain described approaches
such as early stopping, dropout, L2-regularisation, or weight decay. 59, 96, 106 Some publications
did not specifically discuss overfitting in the text, but their open-source code indicated that the latter
techniques were used. 55, 75 3.4.5.4 Is the process of splitting training from validation data
described. Reference 72 shows four cut-offs, whereas Ref. 95 shows different probability thresholds
for their classifier, and describe the impacts of this on precision, recall, and F1 curves. We searched
only for pre-print or published literature and therefore did not search sources such as GITHUB or
other source code repositories. However, the re-use of benchmark corpora increased with the
publications in the LSR update, where we found 40 publications that report results on one of the
previously published benchmark datasets (see Table 4 ). Conclusions are drawn adequately supported
by the results presented in the review. Within-Company Cost Estimation Studies, IEEE Transactions
on Software Engineering, 33 (5), 2007 Example of PICOC (Wahono, 2015) Romi Satria Wahono, A
Systematic Literature Review of Software Defect Prediction: Research Trends, Datasets, Methods
and Frameworks, Journal of Software Engineering, Vol. 1, No. 1, pp. 1-16, April 2015 Example of
RQs (Kitchenham, 2007) Kitchenham et al., A Systematic Review of Cross- vs. While the aim is laid
out well in section 1.2, the large amount of missing performance data (reported to be 87%) is unable
to address the “Is it reliable?” question. Of these, 23 corpora were available online and a total of 40
publication mentioned using one of these public benchmarking sets. We automated the export of
PDF reports for each included publication. Some of the less-frequent data extraction targets in the
literature can be categorised as sub-classes of a PICO, 55 for example, by annotating hierarchically
multiple entity types such as health condition, age, and gender under the P class. We found a variety
of topics discussed in these publications and summarised them under seven different domains. Yes
Have the search and update schedule been clearly defined and justified. Discrepancies must be
resolved here and a consensus reached. Nine publications (12%) use rule-bases alone, while the rest
of the publications use them in combination with other classifiers (data shown in Underlying data:
Appendix A and D 127 ). Methods: We systematically and continually search PubMed, ACL
Anthology, arXiv, OpenAlex via EPPI-Reviewer, and the dblp computer science bibliography. There
were several approaches and justifications of using macro- or micro-averaged precision, recall, or F1
scores in the included publications. This living systematic review examines published approaches for
data extraction from reports of clinical studies. Could the authors comment on the implications of
this in terms of using tools in a live review as it's not common to manually only extract data from an
abstract. Review teams can assess the suitability of each tool and switch between them at any time
during this step. This image is reproduced under the terms of a Creative Commons Attribution 4.0
International license (CC-BY 4.0) from Schmidt et al. 15 The decision for full review updates is
made every six months based on the number of new publications added to the review. DeYoung J,
Beltagy I, van Zuylen M, et al.: Ms2: Multi-document summarization of medical studies. Six (8%)
implemented publicly available tools Conclusions: This living systematic review presents an
overview of (semi)automated data-extraction literature of interest to different types of literature
review. On Page 5, the exclusions listed have the use of pre-processing of text, yet the results discuss
the many papers that appear to have used that in their methods.