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WikiGOA: Gene set enrichment analysis based on Wikipedia and the Gene Ontology

Lubiana, T.; Dias, T. L.; Peixe, D. G.; Nakaya, H. T. I.

2022-09-17 bioinformatics
10.1101/2022.09.15.508149 bioRxiv
Show abstract

O_LIGene sets curated to Gene Ontology terms are widely used by the transcriptomics community C_LIO_LIPresence in Wikipedia is a common proxy for the relevance of a concept. C_LIO_LIIn this work, we describe the use of Wikidata to generate a dataset comprising only gene sets with a corresponding Wikipedia page. C_LIO_LIWe refer to the dataset as "WikiGOA", standing for "Wikipedia Gene Ontology Annotations" C_LIO_LIWe use the dataset to analyze gene expression data and show that it provides readily understandable results. C_LIO_LIWe envision WikiGOA to be useful for exploring complex biological datasets both in academic research and educational contexts. C_LI NoteThis report was written in a non-standard, experimental format, where assertions are expressed in bullet points. This was done to clarify statements and assumptions, simplify reading and pave the way for conversion to structured formats (e.g., nanopublications). [1]

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.