Model overview
PhenDB uses Support Vector Machine (SVM) models for the prediction of traits. Below is a list of all models (click model name for further information). For each model, the maximal mean balanced accuracy (given a 100% complete, 0% contaminated metagenomic bin) is given.
Legend: T = from text mining E = from expert opinion M = inferred from marker gene presence C = from Feldbauer et al 2015
| Model name | Description | Training date | Maximal accuracy |
|---|---|---|---|
| ARCHAEA | Organism is an archaeon (C) | 2018-06-19 08:50:24 | |
| PEN_180 | Organism is resistant to penicillin (trained on S. aureus) (E) | 2018-06-19 08:55:24 | |
| THERM | Organism has a thermophilic lifestyle (C) | 2018-06-19 08:58:05 | |
| THERM_OR_TOLERANT | Organism has a thermophilic lifestyle or is thermotolerant (C) | 2018-06-19 08:58:27 | |
| Aerobe | Organism is capable of aerobic respiration (T) | 2018-06-19 08:59:19 | |
| Anaerobe | Organism is capable of anaerobic respiration (T) | 2018-06-19 08:59:52 | |
| gram_stain | Cells of organism stain Gram-positive (+) or Gram-negative (-) (T) | 2018-06-19 09:00:19 | |
| motility | Organism is capable of self-propelled motion (T) | 2018-06-19 09:00:54 | |
| sporulation | Organism is capable of producing endospores for persistence (T) | 2018-06-19 09:01:24 | |
| Sulfate_reducer | Organism is capable of using sulfate as terminal electron acceptor (T) | 2018-06-19 09:01:56 | |
| amikacin_resistant | Organism is resistant to amikacin. (Trained on Acinetobacter baumannii.) (E) | 2018-09-11 09:32:47 | |
| ciprofloxacin_resistant | Organism is resistant to ciprofloxacin. (Trained on Acinetobacter baumannii.) (E) | 2018-09-11 09:32:49 | |
| alkb | Organism is capable of degrading alkanes (M) | 2019-02-01 14:12:13 | |
| AOB | Organism is part of the clade of ammonia-oxidizing bacteria (E) | 2019-02-01 14:12:28 | |
| ars | Organism is capable of arsenic detoxification (M) | 2019-02-01 14:12:36 | |
| avre | Organism is a plant pathogen (based on AvrE virulence factor) (M) | 2019-02-01 14:12:49 | |
| baicd | Organism is capable of producing secondary bile acids (M) | 2019-02-01 14:12:54 | |
| bena | Organism is capable of degrading benzoate via hydroxylation (M) | 2019-02-01 14:13:02 | |
| bpp | Organism is capable of hydrolyzing phytate (M) | 2019-02-01 14:13:21 | |
| bsh | Organism is capable of deconjugating glycine and taurine from bile salts (M) | 2019-02-01 14:13:29 | |
| buk2 | Organism is capable of producing butyrate (M) | 2019-02-01 14:13:37 | |
| chb | Organism is capable of degrading chitine (M) | 2019-02-01 14:13:59 | |
| cnta | Organism is capable of aromatic ring hydroxylation (M) | 2019-02-01 14:14:07 | |
| coos | Organism is capable of assimilating CO (M) | 2019-02-01 14:14:12 | |
| cutc | Organism is capable of producing trimethylamine via choline (M) | 2019-02-01 14:14:28 | |
| dbfa4 | Organism is capable of performing dibenzofuran degradation (M) | 2019-02-01 14:14:38 | |
| FACULTATIVE | Organism is a facultative anaerobe (C) | 2019-02-01 14:14:59 | |
| HALO | Organism has a halophilic lifestyle (C) | 2019-02-01 14:15:25 | |
| hsdh | Organism is capable of degrading bile acids (M) | 2019-02-01 14:15:40 | |
| hyda | Organism is capable of producing H2 gas (M) | 2019-02-01 14:15:49 | |
| METHANOTROPH | Organism is capable of growth with methane as the sole carbon source (C) | 2019-02-01 14:16:08 | |
| naph2 | Organism is capable of degrading naphtalene (M) | 2019-02-01 14:16:25 | |
| nif | Organism is capable of fixing N2 (E) | 2019-02-01 14:16:31 | |
| NOB | Organism is part of the clade of nitrite-oxidizing bacteria (E) | 2019-02-01 14:16:53 | |
| p450 | Organism is capable of degrading fatty acids (M) | 2019-02-01 14:16:59 | |
| phnx | Organism is capable of hydrolyzing phosphonate (M) | 2019-02-01 14:17:19 | |
| phod | Organism is capable of recycling organic phosphorus (M) | 2019-02-01 14:17:45 | |
| PHOTO | Organism is capable of photon capture for energy acquisition (C) | 2019-02-01 14:18:05 | |
| psa | Organism is capable of synthesizing capsular polysaccharide (M) | 2019-02-01 14:18:23 | |
| PSYCHRO | Organism has a psychrophilic lifestyle (C) | 2019-02-01 14:18:28 | |
| soxb | Organism is capable of oxidizing thiosulfate (M) | 2019-02-01 14:18:55 | |
| SYMBIONT | Organism has an obligate intracellular lifestyle (C) | 2019-02-01 14:19:08 | |
| T3SS | Organism expresses a Type III secretion system (C) | 2019-02-01 14:19:22 | |
| T4SS | Organism expresses a Type IV secretion system (C) | 2019-02-01 14:19:48 | |
| T6SS | Organism expresses a Type VI secretion system (C) | 2019-02-01 14:20:09 | |
| txta | Organism is a plant pathogen (based on thaxtomin synthesis capability) (M) | 2019-02-01 14:20:35 | |
| urea | Organism is capable of degrading urea (M) | 2019-02-01 14:20:49 | |
| xen | Organism is capable of reducing various alpha-beta-unsaturated and nitro compounds (M) | 2019-02-01 14:21:02 | |
| AUTO | Organism is capable of growth with CO2 as sole carbon source (C) | 2019-02-01 14:21:46 |
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