Table 2.
Groups contributing literature-based annotations. Includes all annotations traceable to the literature (EXP, including HTP, TAS, NAS, and IC; see http://geneontology.org/docs/guide-go-evidence-codes; see below for information). Direct annotations to the term “protein binding” are listed separately, since without information about interacting partner(s), protein binding represents an activity that most proteins possess, and therefore the GO class itself provides little information (see text for further description). The statistics for groups that have contributed more than 700 manual annotations. Other contributing groups include the following: HGNC, JaponicusDB, PHI-base, PAMGO, JCVI, MENGO, and GDB. Current GO Consortium members are labeled with an asterisk. See http://geneontology.org/docs/annotation-contributors/ for more details.
| Group | Organism or area of focus | Number of literature-based annotations, excluding direct protein binding | Number of literature-based annotations directly to protein binding |
|---|---|---|---|
| UniProt* (UniProt: the universal protein knowledgebase 2017) | Human and also a wide variety of organisms not covered by other GOC members | 185,121 | 30,927 |
| MGI* (Bult et al. 2019) | Mouse | 106,435 | 8,051 |
| Reactome* (Fabregat et al. 2018) | Human pathways | 92,178 | 6 |
| TAIR* (Lamesch et al. 2012) | A. thaliana (model plant) | 64,633 | 4,695 |
| FlyBase* (Sian et al. 2022) | D. melanogaster (fruit fly) | 55,203 | 892 |
| UCL* | Human | 54,595 | 2,935 |
| RGD* (Smith et al. 2020) | Rat | 47,694 | 1,894 |
| SGD* (Lang et al. 2018) | Saccharomyces cerevisiae (Baker's yeast) | 48,811 | 165 |
| ZFIN* (Howe et al. 2021) | Zebrafish | 28,261 | 488 |
| PomBase* (Harris et al. 2022) | Schizosaccharomyces pombe (fission yeast) | 26,128 | 2,201 |
| GeneDB | Microbial pathogens | 23,884 | 756 |
| ComplexPortal* (Meldal et al. 2019) | Protein complexes | 18,343 | 0 |
| WormBase* (Davis et al. 2022) | C. elegans (nematode) | 17,171 | 560 |
| CGD* (Skrzypek et al. 2017) | Candida albicans (yeast pathogen) | 17,113 | 0 |
| EcoCyc* (Keseler et al. 2017) | E. coli (bacterium) | 13,372 | 829 |
| AgBase | Agricultural animals, primarily chicken | 11,198 | 1,110 |
| dictyBase* (Basu et al. 2015) | Dictyostelium discoideum (slime mold) | 9,615 | 844 |
| HPA | Human protein subcellular localization | 9,963 | 0 |
| SynGO (Koopmans et al. 2019) | Neuron–neuron synapses | 9,552 | 0 |
| PINC | Human and mouse | 6,746 | 0 |
| MTBBASE | Mycobacterium tuberculosis (bacterial pathogen) | 6,160 | 463 |
| IntAct* (Del Toro et al. 2022) | Protein–protein interactions | 4,849 | 216,488 |
| CAFA (Radivojac et al. 2013) | Various | 4,818 | 371 |
| CACAO* (Ramsey et al. 2021) | Various | 4,382 | 0 |
| AspGD (Cerqueira et al. 2014) | Aspergillus niger (fungal pathogen) | 4,099 | 0 |
| PseudoCAP (Winsor et al. 2005) | Pseudomonas aeruginosa (bacterium) | 2,323 | 0 |
| EcoliWiki* (McIntosh et al. 2012) | E. coli (bacterium) | 2,123 | 55 |
| TIGR | Bacteria | 2,150 | 0 |
| GO_Central* | Various | 3,643 | 160 |
| CollecTF | Bacterial transcription factors | 1,850 | 0 |
| NTNU_SB | Human, mouse, and rat transcription factors | 1,733 | 0 |
| GR | Rice | 1,260 | 0 |
| SGN | Tomato | 1,255 | 0 |
| DisProt | Disordered proteins | 933 | 156 |
| Xenbase* (Fortriede et al. 2020) | Xenopus (frog) | 731 | 0 |