chem-bla-ics: March 2014

Linked Open Drug Data: three years on

Almost three years ago I collaborated with others in the W3C Health Care and Life Sciences interest group. One of the results of that was a paper in the special issue around the semantic web conference at one of the bianual, national ACS meeting (look at this nice RDFa-rich meeting page!). My contribution was around the ChEMBL-RDF, which I recently finally published, though it was already described earlier in an HCLS note.

Anyway, when this paper reached the most viewed paper position in the JChemInf journal, and I tweeted that event, I was asked for an update of the linked data graph (the darker nodes are the twelve the LODD task force worked on).

Mar

"Bridging WikiPathways and metabolomics data using the ChEBI ontology"

This week the ChEBI 3rd User Workshop took place, and I presented how WikiPathways is using ChEBI, and how I have been using it in the BridgeDb identifier mapping database for metabolites, and in mapping metabolites to WikiPathways using the ChEBI ontology.

Mar

Breaking News: CC-NC only for personal use!

What some of us already interpreted is that the Non-Commercial (NC) clause of the Creative Commons (CC) is a killer. German court has ruled that the NC clause means that the material is only for personal use. And that is literally breaking news! It means that such material is not Open Access in the context of (European) universities. I learned from Lessig's Free Culture (a must read) that academic use falls under fair use under USA law. but as far as I know this is not the case in Europe.

Mar

Publishers #fail to innovate knowledge dissemination

I have ranted often enough about publishing. I have also often enough indicated how publishers (or journals) could improve their act. Enough to find in the archives of this blog. Even the more innovative publishers have a long way to go. The reason why I blog about this, is why I can be happy with something like a rrdf package (doi:10.7287/peerj.preprints.185v3). Seriously, it is far away from where my heart is: understanding the underlying chemistry of biology.

Mar

CiteULike to Twitter? IFTTT!

Twitter is great! Minutes after I asked this online:

can I have @citeulike automatically tweet new papers I bookmark?

— Egon Willighagen (@egonwillighagen) March 15, 2014 Sarah Pohl replied:

@egonwillighagen I would have suggested @IFTTT for that, but they don't support @citeulike, it seems.

— Sarah Pohl (@LilithElina) March 15, 2014 Alex Henderson complemented the answer informing me RSS is supported:

@egonwillighagen @citeulike Library RSS to @IFTTT then twitter should work fine.

Mar

Reviewing CDK patches in the Maven era

Three weeks ago the CDK project migrated from Ant to Maven as the primary build tool. That means that my workflow for making and, importantly, reviewing patches is completely turned upside down. Well, that happens.