📓 content/R- Genuine semantic publishing.md by @scalingsynthesis ☆

Core Questions

#references
- Title: Genuine semantic publishing
  - Tags:: #references#ref/Paper #[[Semantic Web]] #[[semantic publishing]]
- Authored by:: [[Tobias Kuhn]] , Michel Dumontier
- Year: 2017
- Publication: Data Science
- URL: https://content.iospress.com/articles/data-science/ds010
- PDF
  - Placeholder
- #lit-context
  - Lead author is originator and proponent of [[std/Nanopublications]]
- #[[📝 lit-notes]]
  - Argues that we don’t yet have genuine semantic publishing. Most approaches so far "tack on" semantics (broadly construed) to existing papers, without changing what is published in the first place.
  - Includes history of attempts, ranging from [[std/Research Objects]] to [[Structured Digital Abstracts]] to [[std/Micropublication]] and [[std/Nanopublications]], and [[Scholarly HTML]] (p. 142-145)
    - ⥅ [[https://firebasestorage.googleapis.com/v0/b/firescript-577a2.appspot.com/o/imgs%2Fapp%2Fmegacoglab%2FCp2k6dGc07.png?alt=media&token=b7794f73-426b-48a3-b424-7d7f080cf052]]
  - Claims that we have all the tech we need already; problem remaining is an [[Authoring Bottleneck]] one (p. 148)
    - Also talks about better ontologies, but I think that is related to the [[Authoring Bottleneck]]; seems to me that the ontology needs authors to grow (can’t predefine everything!)
    - ⥅ [[https://firebasestorage.googleapis.com/v0/b/firescript-577a2.appspot.com/o/imgs%2Fapp%2Fmegacoglab%2FBtCE-k-dxP.png?alt=media&token=c0103e5c-c9b6-4e41-b7be-e86785c63d0e]]
    - "It turns out that all the technologies needed for applying genuine semantic publishing are already available and most of them are very mature and reliable. There are no technical obstacles preventing us from releasing our results from today on as genuine semantic publications, even though more work is needed on ontologies that cover all relevant aspects and areas and on nice and intuitive end-user interfaces to make this process as easy as possible." (p. 148)
      - #from p. 148
  - Past efforts on technical infrastructure
    - ⥅ [[https://firebasestorage.googleapis.com/v0/b/firescript-577a2.appspot.com/o/imgs%2Fapp%2Fmegacoglab%2FMqFIhHPg-8.png?alt=media&token=db6c3b90-6401-4583-a850-2ce62e686fba]]
    - ⥅ [[https://firebasestorage.googleapis.com/v0/b/firescript-577a2.appspot.com/o/imgs%2Fapp%2Fmegacoglab%2FKO6kU5N29G.png?alt=media&token=baa411eb-864c-4157-bb87-1bb5db69735a]]
    - [[std/Semantic Publishing and Reference Ontologies (SPAR)]]
      - [37] S. Peroni and D. Shotton, FaBiO and CiTO: Ontologies for describing bibliographic resources and citations, Web Semantics: Science, Services and Agents on the World Wide Web 17 (2012), 33–43. doi:10.1016/j.websem.2012.08.001.
      - [38] S. Peroni, D. Shotton and F. Vitali, Scholarly publishing and Linked Data: Describing roles, statuses, temporal and contextual extents, in: Proceedings ofthe 8th International Conference on Semantic Systems, ACM, 2012, pp. 9–16.
    - [[std/Annotation Ontology]]
      - P. Ciccarese, M. Ocana, L.J.G. Castro, S. Das and T. Clark, An open annotation ontology for science on web 3.0, Journal ofbiomedical semantics 2(2) (2011), 1. doi:10.1186/2041-1480-2-S2-S4. [[@ciccareseOpenAnnotationOntology2011]]
    - [[std/W3C Web Annotation recommendations]]
    - [[std/PROV Ontology]] for [[provenance]]
      - T. Lebo, S. Sahoo, D. McGuinness, K. Belhajjame, J. Cheney, D. Corsar, D. Garijo, S. Soiland-Reyes, S. Zednik and J. Zhao, PROV-O: The PROV ontology, W3C Recommendation, 2013, [Online]. Available at https://www.w3.org/TR/prov-o/.
    - [[std/Semanticscience Integrated Ontology (SIO)]]
      - M. Dumontier, C.J. Baker, J. Baran, A. Callahan, L. Chepelev, J. Cruz-Toledo, N.R. Del Rio, G. Duck, L.I. Furlong, N. Keath et al., The semanticscience integrated ontology (SIO) for biomedical research and knowledge discovery, Journal ofbiomedical semantics 5(1) (2014), 14. doi:10.1186/2041-1480-5-14.
    - [[std/Linked Science Core Vocabulary]]
    - Argumentation / [[discourse]] [[@schneiderReviewArgumentationSocial2013]]
    - MOdels of evidence
      - B.M.H. Brush, K. Shefchek and M. Haendel, SEPIO: A semantic model for the integration and analysis of scientific evidence, in: ICBO/BioCreative, CEUR-WS, 2016, [Online]. Available at http://ceur-ws.org/Vol-1747/IT605_ICBO2016.pdf. [[@brushSEPIOSemanticModel2016]]
    - formalizing [[uncertainty]]
      - A. De Waard and J. Schneider, Formalising uncertainty: An ontology of reasoning, certainty and attribution (ORCA), in: Semantic Technologies Applied to Biomedical Informatics and Individualized Medicine, 2012, [Online]. Available at http://dl.acm.org/citation.cfm?id=2887634. [[@dewaardFormalisingUncertaintyOntology2012]]