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

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.