Chemistry society goes head to head with NIH in fight over public database

Call for a Public Open Database of All Chemical Reactions

Today there exists no public, freely downloadable, comprehensive database of all known chemical reactions and associated information. Such a database not only would serve chemical sciences and technologies around the world but also would enable the power of modern AI and machine learning methods to be unleashed on a host of fundamental problems. In time, this could lead to important scientific discoveries and economic developments for the benefit of humanity. While ideally such a repository ought to be created and maintained by an international consortium, in the near future, it may be easier to begin the process through governmental agencies such as the National Science Foundation or the National Institutes of Health. Working together, we could use a multipronged approach that could combine negotiations with commercial stakeholders, crowd-sourcing efforts, automated extraction methods, and legislative actions.

A Provisional System to Evaluate Journal Publishers Based on Partnership Practices and Values Shared with Academic Institutions and Libraries

Background: Journals with high impact factors (IFs) are the “coin of the realm” in many review, tenure, and promotion decisions, ipso facto, IFs influence academic authors’ views of journals and publishers. However, IFs do not evaluate how publishers interact with libraries or academic institutions. Goal: This provisional system introduces an evaluation of publishers exclusive of IF, measuring how well a publisher’s practices align with the values of libraries and public institutions of higher education (HE). Identifying publishers with similar values may help libraries and institutions make strategic decisions about resource allocation. Methods: Democratization of knowledge, information exchange, and the sustainability of scholarship were values identified to define partnership practices and develop a scoring system evaluating publishers. Then, four publishers were evaluated. A high score indicates alignment with the values of libraries and academic institutions and a strong partnership with HE. Results: Highest scores were earned by a learned society publishing two journals and a library publisher supporting over 80 open-access journals. Conclusions: Publishers, especially nonprofit publishers, could use the criteria to guide practices that align with mission-driven institutions. Institutions and libraries could use the system to identify publishers acting in good faith towards public institutions of HE.

ChemDB: a public database of small molecules and related chemoinformatics resources

MOTIVATION

The development of chemoinformatics has been hampered by the lack of large, publicly available, comprehensive repositories of molecules, in particular of small molecules. Small molecules play a fundamental role in organic chemistry and biology. They can be used as combinatorial building blocks for chemical synthesis, as molecular probes in chemical genomics and systems biology, and for the screening and discovery of new drugs and other useful compounds.

RESULTS

We describe ChemDB, a public database of small molecules available on the Web. ChemDB is built using the digital catalogs of over a hundred vendors and other public sources and is annotated with information derived from these sources as well as from computational methods, such as predicted solubility and three-dimensional structure. It supports multiple molecular formats and is periodically updated, automatically whenever possible. The current version of the database contains approximately 4.1 million commercially available compounds and 8.2 million counting isomers. The database includes a user-friendly graphical interface, chemical reactions capabilities, as well as unique search capabilities.

AVAILABILITY

Database and datasets are available on http://cdb.ics.uci.edu.