Semi-Automated Identification of Ontological Labels in the Biomedical Literature with goldi
Bibliographic record
Abstract
Abstract Recent growth in both the scale and the scope of large publicly available ontologies has spurred the development of computational methodologies which can leverage structured information to answer important questions. However, ontological labels, or “terms” have thus far proved difficult to use in practice; text mining, one crucial aspect of electronically understanding and parsing the biomedical literature, has historically had difficulty identifying “terms” in literature. In this article, we present goldi, an open source R package whose goal it is to identify terms of variable length in free form text. It is available at https://github.com/Chris1221/goldi or through CRAN. The algorithm works through identifying words or synonyms of words present in individual terms and comparing the number of present words to an acceptance function for decision making. In this article we present the theoretical rationale behind the algorithm, as well as practical advice for its usage applied to Gene Ontology term identification and quantification. We additionally detail the options available and describe their respective computational efficiencies.
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 | 0.008 | 0.033 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.020 | 0.009 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.005 | 0.003 |
| Open science | 0.002 | 0.006 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.005 | 0.005 |
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".