GExplore 1.5: a comprehensive <i>Caenorhabditis elegans</i> database for the analysis of gene function with a new user-friendly web interface
Bibliographic record
Abstract
GExplore is an online tool to assist with large-scale data mining of selected datasets related to gene and protein function in Caenorhabditis elegans. Here, we describe the current version GExplore 1.5, which contains new datasets and display options as well as a completely redesigned web interface. GExplore now consists of six databases. The gene database contains protein domain information, general expression, and phenotype data as well as interacting genes, gene ontology annotations, and disease associations. The mutation database contains a curated list of more than 200 000 mutations affecting the protein sequences of all protein-coding genes. The protein database contains proteome data from 19 different nematode species, four genetic model organisms and the human proteome for comparison. Three genome-scale RNAseq expression databases contain expression profiles of different developmental stages from embryo to adult, tissues-specific expression profiles at the L2 stage, and expression profiles of the major tissues in the developing embryo at five different time points from gastrulation to the beginning of terminal differentiation. The web-based user interface has been completely redeveloped for the current version. The search interfaces allow users to explore content of the individual databases in detail. The interactive display pages enable the user to fine-tune the results, display additional data, and download the results. GExplore is a tool to quickly obtain an overview of biological and biochemical functions of large groups of genes or identify genes with a certain combination of features for further experimental analysis. Database URL: https://genome.science.sfu.ca/gexplore.
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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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.004 | 0.002 |
| Meta-epidemiology (broad) | 0.003 | 0.002 |
| Bibliometrics | 0.004 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.005 | 0.003 |
| Research integrity | 0.002 | 0.003 |
| Insufficient payload (model declined to judge) | 0.073 | 0.066 |
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".