Review Comment:
The paper Publishing DisGeNET as Nanopublications, presents the release of a very valuable source, gene disease associations, using the nanopublication model and trusty URIs. This paper is also indicative of the natural evolution in publishing information in science. Adopting semantic web standards for publishing information together with provenance metadata and cryptographic hash values in the URIs. The paper is well written and structured and well motivated. The potential of such an effort is apparent and I find it an excellent effort towards knowledge discovery. I definitely accept this paper, but I do have some minor comments that need to be addressed by the authors.
Minor revision comments
1. Virtuoso can be configured differently, more properly in order to provide a message for the errors that result from the sparql query.
2. It is not very clear to me what exactly is already in nanopublication format and what is not. For example substituting the disease id of the 4.1 section with the huntington's disease id, C0020179, does not give any hits back. Like what percentage of the RDF data source has been already transformed into nanopublications?
3. I would personally find it very helpful to include a picture of the nanopublication schema. This can help a lot the reader to understand the model and it also saves a lot of time and effort when you want to perform sparql queries over this dataset.
4. It is not very clear to me (and maybe this also relates to the previous comment about the figure), how to retrieve with the current model, assertions that are talking about the same GDA (e.g. geneX is associated with diseaseY) but have different types of evidence e.g. literature and predicted.
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Comments
Link to access the nanopub query examples
Apologizes,
The link to see the nanopub queries in the paper is DisGeNET nanopub queries.
Best,
Núria
Hyperlink to the paper query
Dear all,
Apologizes, in the submitted manuscript the hyperlink to the full nanopublication query example is missed. Please, follow this following link in order to access it:
http://www.disgenet.org/web/DisGeNET/v2.1/rdf#nanoQueries
Kind regards,
Núria