OpenScientist verdicts vs current prediction reviews
OpenScientist adjudication report · ProtNLM2 Evaluation · Generator · Transcribed verdicts · Reconciliation TSV
Generated by reconcile_openscientist.py; do not edit by hand. The OpenScientist column is transcribed from the adjudication report. The current column is read from each gene's *-protnlm-predictions-review.yaml. The current YAML assessment is the project's call of record.
31 GO terms across 21 genes: 12 agree, 5 differ within the same polarity group, 13 are overridden by the current YAML, and 1 had no OpenScientist verdict. Reviews citing the OpenScientist investigation: A0A061AL94, A0A2G9RZF1, A0A2U1PS28, A0A3B6RKV1, A0A4W3GVU1, A0A6I8W8A2, A0A8B6GS20, A0A8C5FPT8, A0A8J0SCI2, A0A8M9QG43, B4MAQ2, B7FXQ8, B8BAB0, C6T1A2, D3VIU4, F4JLB7, F6LAX4, Q2U1U6, Q6YYC5, Q9L243.
Polarity groups: supported = COR/CNN/LSP; uncertain = UNC; incorrect = NPI/PLI/REP. The rationale column quotes the current review summary verbatim (checked by the generator). Where it is blank, no reason for the difference is recorded.
| Round | Gene | GO term | OpenScientist | Current YAML | Status | Cites OpenScientist | Current review's stated rationale |
|---|---|---|---|---|---|---|---|
| 1 | ARTAN/A0A2U1PS28 | GO:0009507 chloroplast | Supported: COR | COR | AGREE | true | |
| 1 | DROVI/B4MAQ2 | GO:0005737 cytoplasm | Supported (incomplete): COR | CNN | SAME_DIRECTION | true | "Cytoplasm is already present in cached GOA and UniProt." |
| 1 | CALMI/A0A4W3GVU1 | GO:0005634 nucleus | Supported: COR | CNN | SAME_DIRECTION | true | "The gene already carries nucleus in GOA (accepted in the gene review), so the prediction is correct but not novel." |
| 1 | STRCO/Q9L243 | GO:0009264 deoxyribonucleotide catabolic process | Over-annotated: NPI | UNC | OVERRIDE | true | override not documented |
| 1 | AQUCT/A0A2G9RZF1 | GO:0007338 single fertilization | Refuted: NPI | UNC | OVERRIDE | true | override not documented |
| 1 | ORYSI/B8BAB0 | GO:0010152 pollen maturation | Refuted: NPI | PLI | SAME_DIRECTION | true | |
| 1 | WHEAT/A0A3B6RKV1 | GO:0010099 regulation of photomorphogenesis | Split: NPI | UNC | OVERRIDE | true | "Orthology supports a conserved nuclear JmjC oxygenase but does not establish that the wheat protein sits in an equivalent light-signalling circuit, so the term can be neither confirmed nor refuted." |
| 1 | WHEAT/A0A3B6RKV1 | GO:0010476 gibberellin mediated signaling pathway | Split: NPI | NPI | AGREE | true | "That is regulation of hormone synthesis, not participation in gibberellin perception or signal transduction, and the reviewed JMJ22 record describes the role as triggering GA biosynthesis." |
| 1 | WHEAT/A0A3B6RKV1 | GO:0010114 response to red light | Split: NPI | UNC | OVERRIDE | true | "conservation of the catalytic domain does not establish conservation of its transcriptional control, and no wheat expression or genetic study was found by PubMed search." |
| 1 | WHEAT/A0A3B6RKV1 | GO:0010030 positive regulation of seed germination | Split: NPI | UNC | OVERRIDE | true | "A related germination role is plausible but not established, and the term is absent from the target's GOA annotations." |
| 1 | PHATC/B7FXQ8 | GO:0009651 response to salt stress | Over-annotated: NPI | UNC | OVERRIDE | true | "Characterised sHSP client binding (PMID:29983375) does not establish a salt-triggered response." |
| 1 | PHATC/B7FXQ8 | GO:0042542 response to hydrogen peroxide | Over-annotated: NPI | UNC | OVERRIDE | true | "No peroxide induction, protection or perturbation data exist for B7FXQ8 or a characterised protein in its diatom lineage, and the OpenScientist analysis flags the peroxide prediction as an outlier." |
| 1 | ORYSJ/Q6YYC5 | GO:0070534 protein K63-linked ubiquitination | Undecidable: UNC | UNC | AGREE | true | |
| 1 | SOYBN/C6T1A2 | GO:0009788 negative regulation of abscisic acid-activated signaling pathway | Undecidable: UNC | UNC | AGREE | true | |
| 1 | ABRPR/A0A8B8L1Z3 | GO:0005783 endoplasmic reticulum | Run failed: no verdict | NPI | NO_VERDICT | false | |
| 2 | ARATH/F4JLB7 | GO:0016301 kinase activity | confirmed: PLI | NPI | SAME_DIRECTION | true | |
| 2 | ARATH/F4JLB7 | GO:0016310 phosphorylation | confirmed: PLI | UNC | OVERRIDE | true | "Nothing on the target establishes or excludes a role in phosphorylation, so the prediction remains uncertain." |
| 2 | MYTGA/A0A8B6GS20 | GO:0004438 phosphatidylinositol-3-phosphate phosphatase activity | confirmed: NPI | NPI | AGREE | true | |
| 2 | ASPOR/Q2U1U6 | GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds | confirmed: NPI | NPI | AGREE | true | |
| 2 | WHEAT/F6LAX4 | GO:0046982 protein heterodimerization activity | confirmed: NPI | COR | OVERRIDE | true | override not documented |
| 2 | WHEAT/F6LAX4 | GO:0043025 neuronal cell body | confirmed: NPI | NPI | AGREE | true | |
| 2 | WHEAT/F6LAX4 | GO:0007059 chromosome segregation | confirmed: NPI | UNC | OVERRIDE | true | "Support for the exact segregation term is therefore insufficient." |
| 2 | WHEAT/F6LAX4 | GO:0043005 neuron projection | confirmed: NPI | NPI | AGREE | true | |
| 2 | WHEAT/F6LAX4 | GO:0000775 chromosome, centromeric region | confirmed: NPI | COR | OVERRIDE | true | "Centromere targeting depends on the regulatory subunit rather than on the scaffold itself, but the A subunit is a member of the holoenzyme residing there, which suffices for a cellular component annotation." |
| 2 | WHEAT/F6LAX4 | GO:1990405 protein antigen binding | confirmed: NPI | NPI | AGREE | true | |
| 2 | CAEEL/A0A061AL94 | GO:0006367 transcription initiation at RNA polymerase II promoter | confirmed: NPI | UNC | OVERRIDE | true | override not documented |
| 2 | XENTR/A0A8J0SCI2 | GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | confirmed: NPI | UNC | OVERRIDE | true | "Absence of a recognizable activation domain is not decisive because activation can depend on partners or short interaction regions." |
| 2 | DANRE/A0A8M9QG43 | GO:0016311 dephosphorylation | confirmed: NPI | NPI | AGREE | true | |
| 2 | DROPS/A0A6I8W8A2 | GO:0016874 ligase activity | confirmed: NPI | NPI | AGREE | true | |
| 2 | XENNA/D3VIU4 | GO:0015276 ligand-gated monoatomic ion channel activity | confirmed: NPI | NPI | AGREE | true | |
| 2 | GADMO/A0A8C5FPT8 | GO:0005776 autophagosome | overturned: CNN | COR | SAME_DIRECTION | true | "This is a justified orthology transfer of experimentally grounded evidence." |