Abstract
BackgroundThere is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges.MethodsInitial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work.ResultsThis paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables “stand-off” or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO’s Google Code page: http://code.google.com/p/annotation-ontology/ .ConclusionsThe Annotation Ontology meets critical requirements for an open, freely shareable model in OWL, of annotation metadata created against scientific documents on the Web. We believe AO can become a very useful common model for annotation metadata on Web documents, and will enable biomedical domain ontologies to be used quite widely to annotate the scientific literature. Potential collaborators and those with new relevant use cases are invited to contact the authors.
Highlights
There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers
The framework we have developed need not be the sole way of annotating web documents using the annotation ontology, and we hope additional such tools are built wherever needed
The annotation ontology: core features The core of Annotation Ontology (AO) is inspired by the Annotea model with a few important differences:
Summary
There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. Bridging the gap between ontologies and documents Much current work in biomedical ontologies focuses on detailed formal classification of objects, functions and processes, using description logics [1,2,3,4,5,6,7,8,9,10,11,12,13,14] This approach creates a set of fixed categories for searching, navigating and integrating ontology-annotated content on the web, whether in the standard journal publications or in web “collaboratories” [15] or other web publication vehicles. The purpose of this paper is to provide an open, shareable representational structure for dynamic integration of biomedical domain ontologies with the scientific document
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