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

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


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  <identifier identifierType="DOI">10.5281/zenodo.3698568</identifier>
  <creators>
    <creator>
      <creatorName>Faessler, Erik</creatorName>
      <givenName>Erik</givenName>
      <familyName>Faessler</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1193-5103</nameIdentifier>
      <affiliation>Jena University Language &amp; Information Engineering (JULIE) Lab,Friedrich-Schiller-Universität Jena, Jena, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Modersohn, Luise</creatorName>
      <givenName>Luise</givenName>
      <familyName>Modersohn</familyName>
      <affiliation>Jena University Language &amp; Information Engineering (JULIE) Lab,Friedrich-Schiller-Universität Jena, Jena, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Lohr, Christina</creatorName>
      <givenName>Christina</givenName>
      <familyName>Lohr</familyName>
      <affiliation>Jena University Language &amp; Information Engineering (JULIE) Lab,Friedrich-Schiller-Universität Jena, Jena, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Hahn, Udo</creatorName>
      <givenName>Udo</givenName>
      <familyName>Hahn</familyName>
      <affiliation>Jena University Language &amp; Information Engineering (JULIE) Lab,Friedrich-Schiller-Universität Jena, Jena, Germany</affiliation>
    </creator>
  </creators>
  <titles>
    <title>ProGene - A Large-scale, High-Quality Protein-Gene Annotated Benchmark Corpus</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>Genes and proteins</subject>
    <subject>text corpus</subject>
    <subject>annotation</subject>
    <subject>biomedical corpus</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-03-12</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3698568</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3698567</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/julie-lab</relatedIdentifier>
  </relatedIdentifiers>
  <version>1.1</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&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;</description>
    <description descriptionType="Other">{"references": ["Faessler et al. (2020). PROGENE\u2014A Large-scale, High-Quality Protein-Gene Annotated Benchmark Corpus, LREC 2020"]}</description>
  </descriptions>
</resource>
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