AnnoTree: Functionally Annotated Tree of Life
Bibliographic record
Abstract
<strong>Current version:</strong><br> 2019-02-01: This file is a MySQL (v5.7) dump for AnnoTree, a functionally annotated tree of life. It includes the databases 'gtdb_bacteria_RS86' and 'gtdb_archaea_RS86'. Both databases include Pfam (v27), KEGG Ontology (from the UniRef100 database downloaded March 6, 2018), and TIGRFAM (v15) annotations for the representative genomes in GTDB release 03-RS86. Please refer to http://annotree.uwaterloo.ca for the full site. <strong>Older versions:</strong><br> 2018-10-22: MySQL dump file (v5.7) containing the 'gtdb_bacteria' database for GTDB release 02-RS83 for use with AnnoTree. Functional annotations include Pfam (v27) and KEGG Ontology (from the UniRef100 database downloaded March 6, 2018). Corresponds to AnnoTree version 1.0.0 before the integration of Archaea.
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 distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.034 | 0.004 |
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; both teacher heads 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".