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This enables a relatively quick search for literature evidence supporting (or not) annotations in the iVS941 Model.
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Most of these genes code for known proteins and have been annotated with start and stop codons suggesting that these genes are not annotation artifacts, although a few genes were annotated as hypothetical proteins.
These cases are however not annotation errors according to the class definition of the FAMILY class in Kolarik et al. [16], where "Substances used as bases for building various derivatives and analogs were tagged as IUPAC, not as FAMILY (e.g. 1,4-dihydronaphthoquinones)", but they are not expected to be found in ChemSpider since ChemSpider focuses on single compounds.
Overall, all three analyses demonstrate that orphans are not annotation artifacts, but evolutionary conserved genes.
This result suggests that most of the hypothetical proteins are real genes and not annotation artifacts.
Changes to the relationships do not affect annotations, because annotations always refer to specific terms, not their location within the GO.
Uncharacterized proteins where that annotation matches the protein ID are not considered annotations.
During the calculation of gene product weight, we do not propagate annotations to ancestor terms, and thus, only explicit annotations are considered.
The updated PFPDB database did not include annotations from Swiss-Prot keywords and added two new annotation resources to the previous ones (PIRSF [ 48] and Reactome [ 49]).
This work does not present annotations but a KDM extension.
The environment did not support annotations in the visual representation thereby avoiding problems with visual clutter.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com