chem-bla-ics: January 2016

Adding chemical compounds to Wikidata

Adding chemical compounds to Wikidata is not difficult. You can store the chemical formula (P274), (canonical) SMILES (P233), InChIKey (P235) (and InChI (P234), of course), as well various database identifiers (see what I wrote about that here). It also allows storing of the provenance, and has predicates for that too.

So, to enter a new structure for a compound, you should enter the compound information to Wikidata. Of course, make sure to create the needed accounts, particularly one for Wikidata (create account) (not sure if the next steps needs a more general Wikimedia account too).

Entering the research paper

Magnus Manske pointed me to this helper tool. If you have the DOI of the paper, it is easy to add a new paper.

Jan

Publishing H2020 Proposals

Over a year ago Daniel Mietchen invited me to join writing a H2020 proposal around Open Science. Well, that combines two of my current worlds, so interesting indeed. But there was more: Daniel wanted to do the writing openly, and that was certainly new to me. But since I see piles of benefits in open science, this is sort of the next step. Not obvious, perhaps, but certainly a step I wanted to try.

Jan

ELIXIR is setting up a Tools and Data Services Registry

ELIXIR is setting up a Tools and Data Services Registry. Recently, they organized a workshop in Amsterdam that I attended and where I learned how to add tools and services to their database. I played with the entry for WikiPathways, and one of the nice things is that it inherits from past European registry projects and allows the encoding if the input and output format, for tools and services alike.

Jan

Open Spectral Database

Stuart Chalk wrote on the CHMINF-L mailing list about Open Spectral Database (OSDB). This new database is more of an idea than something with critical mass yet. But the idea seems right: it has a CCZero waiver for the data, is Open Source (see github.com/stuchalk/OSDB), and API. The webinterface looks good too:

It supports various spectral types and maybe it can be seeded with data from one of the Massbank instances.

Jan

Project "Chemical Safety Library", aka redistributable MSDS data

The Pistoia Alliance has an interesting project proposal:

This project consists of two distinct phases:

development of a collaborative system for sharing information about known laboratory hazard based on an existing system developed and implemented by a member of the Pistoia Alliance working with chemical suppliers and publishers to define and adopt standards for hazard information making MSDS and handbooks more accessible and more easily used One reason this has never happened is that in ce