Rebecca Sutton Koeser bio photo

Rebecca Sutton Koeser

Lead Developer, The Center for Digital Humanities at Princeton University

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I realize it’s been a while since the Open Repositories conference; I thought that those of us who attended were going to have a debrief and share some of the interesting things we learned about, but that hasn’t happened yet, so I decided I would try to blog about some of the interesting things from my notes.

Introduction to the Topaz Framework and the Ambra Publishing Platform

Richard Cave from the Public Library of Science (PLos)

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PLoS has been using Ambra/Topaz since December 2006, and all of their journals are now on that platform. The original intent was for an end-to-end peer review system with opportunities for post publication, annotations, semantic relationships, etc. The core of it is built on Fedora, used as a blob store; metadata, annotations, etc. are stored as triples in Mulgara.

Topaz is an object triples mapping (like Hibernate ORM) with an objects based query language; this allows for storage & retrieval of files and triples in a single transaction.

Ambra is a web 2.0 frontend for Topaz with the goal of turning readers into knowledge contributors. Right now, it can only handle NLM xml; it has no workflow engine or peer review - it is not an out-of-the-box solution. However, features in development are article metrics (impact factor), usage data (views, downloads), semantic enhancement - e.g., highlighting specific terms (proteins, genes, locations, etc).

Potential relevance/applicability for us? The only project that these technologies might fit right now is Molecular Vision, which uses NLM xml. Hopefully, this will also be a good project to keep an eye on as they develop more features and add support for other kinds of content types.