Dataset Open Access

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

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


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    <subfield code="a">&lt;p&gt;The Pro(tein)/Gene corpus was developed at the JULIE Lab Jena under supervision of Prof. Udo Hahn.&lt;/p&gt;

&lt;p&gt;The goals of the annotation project were&lt;/p&gt;

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

&lt;p&gt;The corpus has the following annotation levels / entity types:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;protein&lt;/li&gt;
	&lt;li&gt;protein_familiy_or_group&lt;/li&gt;
	&lt;li&gt;protein_complex&lt;/li&gt;
	&lt;li&gt;protein_variant&lt;/li&gt;
	&lt;li&gt;protein_enum&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;For definitions of the annotation levels, please refer to the Proteins-guidelines-final.doc file that is found in the download package.&lt;/p&gt;

&lt;p&gt;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.&lt;br&gt;
All document are delivered as MMAX2 (http://mmax2.net/) annotation projects.&lt;/p&gt;</subfield>
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