Additional file 2 of Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem
Bibliographic record
Abstract
Additional file 2: Supplementary Table S1 Metagenomics sample information and environmental factors. Metagenomics sequencing data were obtained from the European Nucleotide Archive (ENA) database: accession numbers PRJEB41834 (Broman et al., 2022; Rodríguez-Gijón et al., 2023), PRJEB22997 (Alneberg et al., 2018), and PRJEB34883 (Alneberg et al., 2020). The environmental parameters, i.e., depth (m), salinity (PSU), and temperature (°C), compiled by Rodríguez-Gijón et al. (2023) were used in this study. Table S2 Metagenomics data processing information: Sequence codes, read processing counts (from quality-filtering to contig assembly), prodigal annotations and binning stat values. The Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD; Khot et al., 2022) counts highlighted in blue. Table S3 Metagenome-assembled genome (MAG) stats and taxonomic classification based on using GTDB-Tk v2.4.0 with R220 (Chaumeil et al., 2022). Table S4 The Calgary approach to ANnoTating HYDrocarbon degrading enzymes database (CANT-HYD) annotations (Khot et al. 2022). Table S5 Count and annotation table of the annotated hydrocarbon degradation genes (HDGs). Reads per kilobase million (RPKM) absolute counts. Table S6. The annual average of total oil spills during the assessment period 2016-2021 (m³) values (Supplementary Table S6) from HELCOM (2023b). Table S7 Average metagenome-assembled genome (MAG) quality stats per environment. Table S8 Total metagenome-assembled genome (MAG) counts per environment and relative abundance based on species-level classification.Table S9 Statistical results of the permutation test for homogeneity of multivariate dispersions and permutation test for adonis under a reduced model of the hydrocarbon degradation genes (HDG) dataset. Table S10 Differential abundance test by Random Forests for the HDGs per environment and per subbasin. Table S11 Statistical results of the permutation test for distance-based redundancy analysis (dbRDA) analyses in R of the ARG composition and environmental factors. Table S12 Spearman rank correlations between environmental variables and the RPKM abundance of the hydrocarbon degradation genes (HDG)
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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 | 0.009 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.005 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.795 | 0.127 |
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".