ESciDoc Services Annotator

IN PROGRESS

Introduction

The motivation for defining an Annotator service comes from MPI MB Demonstrator proposal. Main aim is to be able to enrich publications with references or short descriptions/comments on resources about which a publication (or another form of work) is about. There is an assumption that most of these are external resources and are not managed by MPDL services. However, this does not have to be the case.

Some premisses:

• The solution shall not be heavy for PubMan and shall be applicable to other applications as well
• The solution shall be flexible enough and allow for extensions of various types of resources
• The solution shall be scalable
• ...

Related concepts/implementations

• see RDF Metadata store
• see Open Annotation Collaboration (OAC)

Data Model

• For basic data model and definitions please check OAC
• The ontology developed for the Annotator service at MPDl is shown below

• A Resource is a class of all individuals representing content which is managed in the system. In the depicted ontology, Annotation(SylvaAnnotation) and Body are considered as a Resource.
• An Annotation is a subclass of managed Resource class. It is class of individuals that relate the Body and the Target individuals, and may have some additional metadata.
• A Body is the class of individuals which holds any kind of information about the Target individual associated through the Annotation individual.
• A Target is the class of individuals about which the Body in general is.
• A SylvaAnnotation is a subclass of an Annotation referencing Sylva database resources (see MPDL Demonstrator Marine Microbiology for more details)
• A Service is a class of individual services that may be associated with particular types of annotations, e.g. Sylva browser

In particular cases Target individual is not related with the Annotation to a Body individual. In this case for the Annotation individual it is assumed that it is an e.g. "textual" annotation (e.g. it is described via a "datatype" property as a content of the annotation rather than an "object" property).

Example

• pubman:P-1 is a publication about a "Marine metagenome 1096626369196, whole genome shotgun sequence".

    Environmental Genome Shotgun Sequencing of the Sargasso Sea, 
    J. Craig Venter,Karin Remington,John F. Heidelberg,Aaron L. Halpern,Doug Rusch,Jonathan A. Eisen,Dongying Wu,Ian Paulsen,Karen E. Nelson,William Nelson,
    Derrick E. Fouts,Samuel Levy,Anthony H. Knap,Michael W. Lomas, Ken Nealson, Owen White,Jeremy Peterson,Jeff Hoffman,Rachel Parsons,Holly Baden-Tillson,
    Cynthia Pfannkoch, Yu-Hui Rogers, and Hamilton O. Smith
    Science 2 April 2004: 66-74.Published online 4 March 2004, http://www.sciencemag.org/content/304/5667/66
     

• sylva:AACY020292957 is the resource in the Sylva database, providing some more details on the sequence (see http://www.arb-silva.de/browser//AACY020292957 )

Max Planck Digital Library

Publication Management

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