Evidence map›Paper›PMID 33835932›Full record

ArticleJournal of medical Internet research2021

Using a Secure, Continually Updating, Web Source Processing Pipeline to Support the Real-Time Data Synthesis and Analysis of Scientific Literature: Development and Validation Study.

Uddhav Vaghela, Simon Rabinowicz, Paris Bratsos, Guy Martin, Epameinondas Fritzilas, Sheraz Markar, Sanjay Purkayastha, Karl Stringer, Harshdeep Singh, Charlie Llewellyn and 6 more

Abstract readValidation Study
In one paragraph

Article in Journal of medical Internet research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Observational
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Uddhav Vaghela *PanSurg Collaborative, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.ORCID 0000-0003-3525-4388
Simon Rabinowicz *PanSurg Collaborative, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.ORCID 0000-0002-3593-3770
Paris BratsosPanSurg Collaborative, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.ORCID 0000-0002-2281-2726
Guy MartinPanSurg Collaborative, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.ORCID 0000-0002-5759-962X
Epameinondas FritzilasAmazon Web Services UK Limited, London, United Kingdom.ORCID 0000-0002-8621-2690
Sheraz MarkarPanSurg Collaborative, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.ORCID 0000-0001-8650-2017
Sanjay PurkayasthaPanSurg Collaborative, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.ORCID 0000-0003-0187-8328
Karl StringerMirrorWeb Limited, Manchester, United Kingdom.ORCID 0000-0001-5944-2100
Harshdeep SinghCloudwick Technologies, Newark, CA, United States.ORCID 0000-0002-0466-378X
Charlie LlewellynAmazon Web Services UK Limited, London, United Kingdom.ORCID 0000-0001-7539-7469
Debabrata DuttaCloudwick Technologies, Newark, CA, United States.ORCID 0000-0002-6912-1439
Jonathan M ClarkePanSurg Collaborative, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.ORCID 0000-0003-1495-7746
Matthew HowardAmazon Web Services UK Limited, London, United Kingdom.ORCID 0000-0002-6515-4751
PanSurg REDASA Curators *PanSurg Collaborative, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
Ovidiu SerbanData Science Institute, Imperial College London, London, United Kingdom.ORCID 0000-0001-5359-3661
James KinrossPanSurg Collaborative, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.ORCID 0000-0002-0427-7643

Funding

Randomized Controlled Trial of Resistant Starch to Reduce Colon Cancer Risk in Alaska Native PeopleR01CA204403 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI O'KEEFE, STEPHEN J.D., THOMAS, TIMOTHY K · 2017 to 2021
$2.8M
NCI NIH HHS R01 CA204403
6 · The paper itself

Abstract

backgroundThe scale and quality of the global scientific response to the COVID-19 pandemic have unquestionably saved lives. However, the COVID-19 pandemic has also triggered an unprecedented "infodemic"; the velocity and volume of data production have overwhelmed many key stakeholders such as clinicians and policy makers, as they have been unable to process structured and unstructured data for evidence-based decision making. Solutions that aim to alleviate this data synthesis-related challenge are unable to capture heterogeneous web data in real time for the production of concomitant answers and are not based on the high-quality information in responses to a free-text query.

objectiveThe main objective of this project is to build a generic, real-time, continuously updating curation platform that can support the data synthesis and analysis of a scientific literature framework. Our secondary objective is to validate this platform and the curation methodology for COVID-19-related medical literature by expanding the COVID-19 Open Research Dataset via the addition of new, unstructured data.

methodsTo create an infrastructure that addresses our objectives, the PanSurg Collaborative at Imperial College London has developed a unique data pipeline based on a web crawler extraction methodology. This data pipeline uses a novel curation methodology that adopts a human-in-the-loop approach for the characterization of quality, relevance, and key evidence across a range of scientific literature sources.

resultsREDASA (Realtime Data Synthesis and Analysis) is now one of the world's largest and most up-to-date sources of COVID-19-related evidence; it consists of 104,000 documents. By capturing curators' critical appraisal methodologies through the discrete labeling and rating of information, REDASA rapidly developed a foundational, pooled, data science data set of over 1400 articles in under 2 weeks. These articles provide COVID-19-related information and represent around 10% of all papers about COVID-19.

conclusionsThis data set can act as ground truth for the future implementation of a live, automated systematic review. The three benefits of REDASA's design are as follows: (1) it adopts a user-friendly, human-in-the-loop methodology by embedding an efficient, user-friendly curation platform into a natural language processing search engine; (2) it provides a curated data set in the JavaScript Object Notation format for experienced academic reviewers' critical appraisal choices and decision-making methodologies; and (3) due to the wide scope and depth of its web crawling method, REDASA has already captured one of the world's largest COVID-19-related data corpora for searches and curation.

Indexed as

Natural Language ProcessingCOVID-19Data Interpretation, StatisticalDatasets as TopicHumansInternetLongitudinal StudiesSARS-CoV-2Search EngineCOVID-19critical analysisdatadatabasedata sciencedata synthesisdecision makinginfodemicinfrastructureliteraturemethodologymisinformationpipelineresearchstructured data synthesisweb crawl data

Identifiers

PMID33835932
PMCPMC8104004

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.