Systematic curation of protein and genetic interaction data for computable biology
Bibliographic record
Abstract
Research over the past three decades has revealed that cellular behavior is governed by dynamic, complex networks of interactions among proteins, RNA, DNA, lipids and metabolites [1]. As such, each discrete interaction represents the minimal input unit for computational models of biological system responses. This principle in turn requires that biological interactions be rigorously documented in a readily computable format to enable mathematical models of network function that are able to predict nonobvious behavior. Despite the foundational shifts in our conception of biology, however, we still use the same primary method to disseminate scientific information that was used by Darwin over 150 years ago, namely the freetext, descriptive narrative style of conventional publications. The vast and everincreasing biomedical literature thus poses a formidable challenge for the annotation of biological data and computational analysis [2].Our 2006 publication describing the comprehensive curation of protein and genetic interactions for the budding yeast
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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 | 0.008 | 0.020 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.003 | 0.002 |
| Bibliometrics | 0.017 | 0.013 |
| Science and technology studies | 0.001 | 0.003 |
| Scholarly communication | 0.003 | 0.005 |
| Open science | 0.006 | 0.005 |
| Research integrity | 0.002 | 0.003 |
| Insufficient payload (model declined to judge) | 0.005 | 0.007 |
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".