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go-bp

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license: cc-by-4.0
tags:
  - biology
  - rna
  - genomics

Overview

Gene Ontology (GO) is a database of gene-level functional annotations. This specific dataset collects the biological process and activities of specific genes. The GO exists as a heirarchy, and we subset to GO terms at most 3 levels away from the biological process root.

This dataset is redistributed as part of mRNABench: https://github.com/morrislab/mRNABench

Data Format

Description of data columns:

  • target: Multihot label indicating GO terms applicable to transcript.
    The label positions correspond to: ["GO:0007267": 0, "GO:0009410": 1, "GO:0001666": 2, "GO:0007186": 3, "GO:0016477": 4, "GO:0035556": 5, "GO:0007204": 6, "GO:0001525": 7, "GO:0098609": 8, "GO:0000226": 9, "GO:0007166": 10, "GO:0006897": 11, "GO:0030154": 12, "GO:0007283": 13, "GO:0045087": 14, "GO:0030036": 15, "GO:0006914": 16, "GO:0008360": 17, "GO:0000278": 18, "GO:0002250": 19]
  • cds: Binary track which reports position of first nucleotide in each codon in CDS.
  • splice: Binary track which reports position of the 3' end of each exon, indicating splice sites.

Data Source

This dataset is processed using data collected in the Gene Ontology Resource, which is licensed under the Creative Commons Attribution 4.0 Unported License.

Original papers:

Original dataset source: https://geneontology.org/docs/download-go-annotations/
Citations:

  • Ashburner et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000 May;25(1):25-9. DOI: 10.1038/75556
  • The Gene Ontology Consortium. The Gene Ontology knowledgebase in 2023. Genetics. 2023 May 4;224(1):iyad031. DOI: 10.1093/genetics/iyad031