Adding bibliographic data to Open Annotation

One of the challenges for achieving interoperability between annotation clients that deal with different formats (for example PDF and HTML, see previous post Domeo and Utopia integration through Annotopia) is to be able to identify the annotated content.

For example, let's consider the paper about Annotation Ontology: Ciccarese P, Ocana M, Castro LJG, Das S, Clark, T. An open annotation ontology for science on web 3.0. J Biomed Semantics 2011, 2(Suppl 2):S4 (17 May 2011) [doi:10.1186/2041-1480-2-S2-S4]

Besides this PDF version (there might be others) of the article:
* PDF at Journal of Biomedical Semantics

The manuscript can be found in HTML format at least in these two locations (which exhibits different layouts):
* PubMed Central
* Journal of Biomedical Semantics

We know that the same content can be identified through identifiers:
* DOI (Digital Object Identifier) 10.1186/2041-1480-2-S2-S4
* PMID (PubMed ID) 21624159
* PMCID (PubMed Central ID) PMC3102893
* PII (Publisher Item Identifier) 2041-1480-2-S2-S4

In order to take into account all the available identifiers, it is possible to include in the annotation target the additional information. So if the client is annotating the PubMed Central version of the document (identified by the URL http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102893/), the source of the target will be identified by:

 ...
    "hasSource": {
        "@id": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102893/",
        "@type": "dctypes:Text",
        "frbr:embodimentOf" : 
        { 
            "prism:doi": "10.1186/2041-1480-2-S2-S4",
            "fabio:hasPII":"2041-1480-2-S2-S4",
            "fabio:hasPubMedCentralId":"PMC3102893",
            "fabio:hasPubMedId":"21624159"
        }
        
    }

Where I made use of the FaBiO (FRBR aligned bibliographic Ontology) ontology which, in turns, reuse term from the FRBR ontology and the PRISM vocabulary. Kudos to Silvio Peroni for pointing out that the relationship between the Manifestation (HTML page) and the Expression should be frbr:embodimentOf and not fabio:manifestationOf. The latter would assume the identifiers are identifying the Work.

Domeo and Utopia integration through Annotopia

Here is a very recent demo of annotation created on a HTML document through Domeo and then seen on the correspondent PDF with the Utopia PDF viewer. All through Open Annotation and Annotopia.

Thanks to Steve Pettifer and Dave Thorne (for the Utopia plugin development); Thomas Wilkins for OAuth implementation in Annotopia. Annotopia is currently architected and developed by me.