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
Bibliographic record
Abstract
BACKGROUND: The 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. OBJECTIVE: The 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. METHODS: To 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. RESULTS: REDASA (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. CONCLUSIONS: This 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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.075 | 0.124 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.007 | 0.005 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.005 | 0.007 |
| Open science | 0.003 | 0.010 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.005 | 0.006 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".