{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2011/02/21/ckan-and-rdf-nice-example-on-why.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/qgd1w-x2514", "url": "https://chem-bla-ics.linkedchemistry.info/2011/02/21/ckan-and-rdf-nice-example-on-why.html", "title": "CKAN and RDF: a nice example of why ontologies matter", "content_html": "

\nFor a while now I have been a so-called invited expert\nto the Linking Open Drug Data (LODD) task\nforce of the W3C’s Health Care and Life Sciences Interest Group\n(HCLSIG). I also participate in the open-science\ngroup of the Open Knowledge Foundation (OKF). This is not\nreally worth blogging about if the two are not being mashed up. Members from\nboth sides are interested in learning how Open (think Is It Open Data?)\nthe open data from the LODD network really is.

\n\n

In fact, the Open Data definition as outlined in the Panton Principles \ndoes not allow for a non-commercial clause, which several LODD data sets are\nlabeled with. Clear copyright and license statements are really important. This\napplies to source code ,\nbut most certainly to data too.

\n\n

So, early March there will be a virtual, online hack session on making a start\nclarifying the licensing and copyrights of the various LODD data sets. CKAN,\nthe OKF’s registry of data sets sounds like a suitable place to organize things.\nAnd, they support RDF making it even a nicer match. Or…

\n\n

Records, data sets, packages, lists, …
\nWell, I am running into a number of problems that need to be solved. The first\none is, in fact, rather fundamental. A record in the CKAN catalog is typed as\na CatalogRecord. Nothing more, nothing\nless. However, looking at the database content each record is like a data set.\nThe GUI confirms that with links like ‘Add a dataset’. Then again, following\nthe link, it is described as a ‘data package’\nas well as a ‘dataset’. This is confusing.

\n\n

Yes, it is! Really! Just look at how people are using it.

\n\n

Take for example the record for LODD\n(well, there is a second LODD record and\nI haven’t found a way to delete records). But, the LODD data is not a single\ndata set, but a aggregation (package?) of data sets. This is basically one of\nthe standing issues with Linked Open Data: license incompatibilities, just like\nwith mixing GPL v2 and v3 in source code. As such, these records which are basically\nlists of datasets typically not have a license listed, as multiple license apply.

\n\n

There seem two solutions: the use of groups and of\ntags. I opted for a new W3C’s HCLSIG LODD task force\ngroup.

\n\n

Small issues
\nAs said, I could not find a way yet to remove datasets, so cleaning up the catalog\nis a bit difficult. You can add comments, but I am not sure if these get read.\nEarlier, I noted that the GNU FDL license was missing, but that is available\nfrom the list now, so I have updated the NMRShiftDB record.\nThe combination of Attribution and Share-Alike for the Creative Commons license\nis missing from the list though, affecting the ChEMBL record.

\n\n

Redistribution?
\nAnother issue that must be addressed in CKAN is how to deal with redistributions.\nFor example, the above cited ChEMBL data is also available as SPARQL end \npoint by me, and this end point currently has a different record.\nShould those records be merged? I guess not, because there is only place for\none maintainer. So, perhaps a CKAN catalog record is not even a dataset, but\na data set provider?

\n\n

Well, this does make a really nice example of what can go wrong if terms are\nnot well-defined, e.g. using an ontology. People do not know how to fill the\ndatabase, leading to noisy content, limiting the usefulness of the data. I do\nhope we get to see definitions for what groups and datasets are in the catalog\nbefore our hack session in March.

", "summary": "For a while now I have been a so-called invited expert to the Linking Open Drug Data (LODD) task force of the W3C’s Health Care and Life Sciences Interest Group (HCLSIG). I also participate in the open-science group of the Open Knowledge Foundation (OKF). This is not really worth blogging about if the two are not being mashed up. Members from both sides are interested in learning how Open (think Is It Open Data?) the open data from the LODD network really is.", "date_published": "2011-02-21T00:00:00+00:00", "date_modified": "2026-11-01T00:00:00+00:00", "tags": ["chembl","nmrshiftdb","rdf"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }