Dataset Open Access

Biotea-2-Bioschemas test data

Garcia, Leyla; Giraldo, Olga; Garcia, Alexander; Rebholz-Schuhmann, Dietrich

Biotea-2-Bioschemas mapps Biotea model to schema.org following the approach proposed by Bioschemas. Here we present the test data used in Biotea GitHub pages, corresponding to 2596 PubMed Open Access (PMC-OA) subset publications together with the software used to render schema.org markup.

Date deposited includes (i) publications retrieved from PMC-OA API, i.e., full text in JATS/XML, (ii) ontology terms recognized in the abstracts and obtained from the NCBO Annotator, i.e., semantic annotations, and (iii) the same annotations following the PubAnnotation format.

Software deposited includes (i) biotea-bioschemas-metadata which parses JATS/XML files and creates Bioschemas markup including metadata, abstract and references, (ii) biotea-bioschemas-annotations which parses PubAnnotation annotations and creates Bioschemas markup, and (iii) biotea-bioschemas-showcase which uses the other two in order to display markup in a graphical basic way and render it as a script element in the HTML following the JSON-LD format. The corresonding GitHub repositories are: (i) https://github.com/biotea/biotea-bioschemas-metadata, (ii) https://github.com/biotea/biotea-bioschemas-annotations, and (iii) https://github.com/biotea/biotea-bioschemas-showcase.

Biotea-2-bioschemas can be seen in action at http://biotea.github.io/bioschemas/

Files (114.9 MB)
Name Size
biotea-bioschemas-annotations.zip
md5:c34f1f84a88028552e7c3e97e73ba2d7
302.9 kB Download
biotea-bioschemas-metadata.zip
md5:26b922758381dd1ddfa721573d56c26b
374.3 kB Download
biotea-bioschemas-showcase.zip
md5:6ac6e567eafc4d49c7ef273b04fb8adf
779.7 kB Download
NCBO.zip
md5:73d13456195ba596a7a764432c23a30d
41.1 MB Download
PMC.zip
md5:6c21ac3b985c4164085e99725517d0f9
62.8 MB Download
PubAnnotation.zip
md5:567cf1ac315e9be5c34e718fa79d1938
9.5 MB Download
  • Garcia A, Lopez F, Garcia L, Giraldo O, Bucheli V, Dumontier M. Biotea: semantics for Pubmed Central. PeerJ. PeerJ Inc.; 2018;6: e4201.

  • Garcia Castro LJ, McLaughlin C, Garcia A. Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data. J Biomed Semantics. BioMed Central; 2013;4: S5.

  • Gray AJG, Goble CA, Jiménez R. Bioschemas: From Potato Salad to Protein Annotation. International Semantic Web Conference. 2017; Available: https://pdfs.semanticscholar.org/74ec/a9c89622bff731b21b03acb4f2400a0f00fa.pdf

  • Jonquet C, Shah NH, Youn CH, Musen MA, Storey M-A. NCBO Annotator: Semantic Annotation of Biomedical Data. Proceedings of the 2009 International Semantic Web Conference. 2009. Available:

  • Kim J-D, Wang Y. PubAnnotation: a persistent and shareable corpus and annotation repository. Proceedings of the 2012 Workshop on Biomedical Natural Language Processing. Association for Computational Linguistics; 2012. pp. 202–205.

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