Cloud‐based archived metabolomics data: A resource for in‐source fragmentation/annotation, meta‐analysis and systems biology
Bibliographic record
Abstract
Abstract Archived metabolomics data represent a broad resource for the scientific community. However, the absence of tools for the meta‐analysis of heterogeneous data types makes it challenging to perform direct comparisons in a single and cohesive workflow. Here, we present a framework for the meta‐analysis of metabolic pathways and interpretation with proteomic and transcriptomic data. This framework facilitates the comparison of heterogeneous types of metabolomics data from online repositories (eg, XCMS Online, Metabolomics Workbench, GNPS, and MetaboLights) representing tens of thousands of studies, as well as locally acquired data. As a proof of concept, we apply the workflow for the meta‐analysis of (a) independent colon cancer studies, further interpreted with proteomics and transcriptomics data, (b) multimodal data from Alzheimer's disease and mild cognitive impairment studies, demonstrating its high‐throughput capability for the systems level interpretation of metabolic pathways. Moreover, the platform has been modified for improved knowledge dissemination through a collaboration with Metabolomics Workbench and LIPID MAPS. We envision that this meta‐analysis tool combined with our in‐source fragmentation/annotation (ISA) technology will help overcome the primary bottleneck in analyzing diverse datasets and facilitate the full exploitation of archival metabolomics data for addressing a broad array of questions in metabolism research and systems biology.
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 | 0.014 | 0.015 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.003 |
| Bibliometrics | 0.009 | 0.009 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.007 | 0.004 |
| Open science | 0.004 | 0.007 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.005 | 0.004 |
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".