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http://dx.doi.org/10.5808/GI.2019.17.2.e14

Biotea-2-Bioschemas, facilitating structured markup for semantically annotated scholarly publications  

Garcia, Leyla (EMBL-EBI, Wellcome Genome Campus)
Giraldo, Olga (Ontology Engineering Group, Campus de Montegancedo, Boadilla del Monte, Universidad Politecnica de Madrid)
Garcia, Alexander (BASF SE)
Rebholz-Schuhmann, Dietrich (ZB MED-Information Centre for Life Sciences)
Publication Information
Genomics & Informatics / v.17, no.2, 2019 , pp. 14.1-14.6 More about this Journal
Abstract
The total number of scholarly publications grows day by day, making it necessary to explore and use simple yet effective ways to expose their metadata. Schema.org supports adding structured metadata to web pages via markup, making it easier for data providers but also for search engines to provide the right search results. Bioschemas is based on the standards of schema.org, providing new types, properties and guidelines for metadata, i.e., providing metadata profiles tailored to the Life Sciences domain. Here we present our proposed contribution to Bioschemas (from the project "Biotea"), which supports metadata contributions for scholarly publications via profiles and web components. Biotea comprises a semantic model to represent publications together with annotated elements recognized from the scientific text; our Biotea model has been mapped to schema.org following Bioschemas standards.
Keywords
biomedical text mining; literature metadata; semantic annotations; structured data; web page markup;
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  • Reference
1 Lapeyre D. Introduction to JATS (Journal Article Tag Suite). Rockville: Mulberry Technologies, Inc., 2018. Accessed 2019 Mar 11. Available from: https://www.xml.com/articles/2018/10/12/introduction-jats/.
2 Gray AJ, Goble C, Jimenez RC; The Bioschemas Community. Bioschemas: from potato salad to protein annotation. In: International Semantic Web Conference. Berlin: Springer-Verlag, 2017. Accessed 2019 Mar 11. Available from: https://pdfs.semanticscholar.org/74ec/a9c89622bff731b21b03acb4f2400a0f00fa.pdf.
3 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 2013;4 Suppl 1:S5.   DOI
4 Garcia A, Lopez F, Garcia L, Giraldo O, Bucheli V, Dumontier M. Biotea: semantics for Pubmed Central. PeerJ 2018;6:e4201.   DOI
5 Jonquet C, Shah NH, Youn CH, Musen MA, Callendar C, Storey MA. NCBO Annotator: semantic annotation of biomedical data. In: International Semantic Web Conference. Berlin: Springer-Verlag, 2009. Accessed 2019 Mar 11. Available from: http://www.lirmm.fr/-jonquet/publications/documents/Demo-ISWC09-Jonquet.pdf.
6 Ciccarese P, Ocana M, Garcia Castro LJ, Das S, Clark T. An open annotation ontology for science on web 3.0. J Biomed Semantics 2011;2 Suppl 2:S4.
7 Sanderson R, Ciccarese P, Van de Sompel H. Open Annotation Data Model. Open Annotation Community Group, 2013. Accessed 2019 Mar 14. Available from: http://www.openannotation.org/spec/core/.
8 Kim JD, Wang Y. PubAnnotation: a persistent and shareable corpus and annotation repository. In: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing, 2012 Jun 8, Montreal, Canada. Stroudsburg: Association for Computational Linguistics, 2012. pp. 202-205.
9 Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 2016;3:160018.   DOI