Dataset Open Access

ProGene - A Large-scale, High-Quality Protein-Gene Annotated Benchmark Corpus

Faessler, Erik; Modersohn, Luise; Lohr, Christina; Hahn, Udo

The Pro(tein)/Gene corpus was developed at the JULIE Lab Jena under supervision of Prof. Udo Hahn.

The goals of the annotation project were

  • to construct a consistent and (as far as possible) subdomain-independent/-comprehensive protein-annotated corpus
  • to differentiate between protein families and groups, protein complexes, protein molecules, protein variants (e.g. alleles) and elliptic enumerations of proteins.

The corpus has the following annotation levels / entity types:

  • protein
  • protein_familiy_or_group
  • protein_complex
  • protein_variant
  • protein_enum

For definitions of the annotation levels, please refer to the Proteins-guidelines-final.doc file that is found in the download package.

To achieve a large coverage of biological subdomains, document from multiple other protein / gene corpora were reannotated. For further coverage, new document sets were created. All documents are abstracts from PubMed/MEDLINE. The corpus is made up of the union of all the documents in the different subcorpora.
All document are delivered as MMAX2 (http://mmax2.net/) annotation projects.

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progene.zip
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  • Faessler et al. (2020). PROGENE—A Large-scale, High-Quality Protein-Gene Annotated Benchmark Corpus, LREC 2020

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