Standardizing gene product nomenclature—a call to action
Bibliographic record
Abstract
The current lack of a standardized nomenclature system for gene products (e.g., proteins) has resulted in a haphazard counterproductive system of labeling. Different names are often used for the same gene product; the same name is sometimes used for unrelated gene products. Such ambiguity causes not only potential harm to patients, whose treatments increasingly rely on laboratory tests for multiple gene products, but also miscommunication and inefficiency, both of which hinder progress of broad scientific fields. To mitigate this confusion, we recommend standardizing human protein nomenclature through the use of a Human Genome Organisation (HUGO) Gene Nomenclature Committee (HGNC) gene symbol accompanied by its unique HGNC ID. We call for action across all biomedical communities and scientific and medical journals to standardize nomenclature of gene products using HGNC gene symbols to enhance accuracy in scientific and public communication. We call on all biomedical communities and scientific and medical journals to standardize nomenclature of gene products to enhance accuracy in scientific and public communication. Image credit: Shutterstock/greenbutterfly. Use of gene symbols designated by the HGNC [www.genenames.org (1)] is nearly universal. DNA- and RNA-level sequence variation nomenclature has been standardized to use HGNC gene symbols, the Single Nucleotide Polymorphism database (dbSNP) IDs, and genetic variant nomenclature designated by the Human Genome Variation Society (HGVS) to unambiguously designate variants. In striking contrast to the use of universal identifiers for genes and gene variants, there are no universal identifiers for the peptides and proteins that these genes encode. Many gene products have multiple nomenclatures in widespread use, and many common nomenclatures are used for multiple gene products. For example, the symbol “PD-1” is shared by multiple unrelated gene products and is used to describe PDCD1 , SNCA , and SPATA2 gene products. The PDCD1 (PD-1) protein is a well-known target for cancer immunotherapy. … [↵][1]1To whom correspondence may be addressed. Email: elspeth@ebi.ac.uk, timothy.oleary@va.gov, or sogino{at}bwh.harvard.edu. [1]: #xref-corresp-1-1
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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 | 0.250 | 0.286 |
| Meta-epidemiology (narrow) | 0.003 | 0.002 |
| Meta-epidemiology (broad) | 0.005 | 0.004 |
| Bibliometrics | 0.007 | 0.006 |
| Science and technology studies | 0.007 | 0.036 |
| Scholarly communication | 0.023 | 0.042 |
| Open science | 0.017 | 0.017 |
| Research integrity | 0.041 | 0.072 |
| Insufficient payload (model declined to judge) | 0.014 | 0.023 |
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; the direct Gemma label and the distilled Codex classifier agree on what is shown here.
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".