MolBank: First Fully Web-Based Publication of Chemical Reaction Data of Individual Molecules with Structure Search and Submission
Shu-Kun Lin1* and Luc Patiny2
1Molecular Diversity Preservation International (MDPI),
Saengergasse 25, CH-4054 Basel, Switzerland;
2Institute of Organic Chemistry, University Lausanne, ICO-BCH, 1015 Lausanne, Switzerland.
Keywords: Chemical information, chemical journal, MolBank, online journal, electronic publication, structure search, substructure search, online submission
Publication date: Jan 11 2000 14:19:00 GMT
Since August 1999, we initiated the MolBank section of Molecules (http://www.mdpi.org/molecules/, ISSN 1420-3049) at the http://www.molbank.org server as a substructure searchable electronic journal in chemistry. All the published compounds can be readily searched on the website www.molbank.org by 2D substructure search.
At the very beginning in 1997, we launched the MolBank section of Molecules
where small pieces of experimental work of individual compound preparation
and structural characterization can be rapidly and easily published in
the MolBank column of the monthly chemistry journal
Many small pieces of very useful experimental findings cannot find a
way to be formally recorded in the literature. This is a tremendous loss
of useful chemical information. We believe the way to publish the MolBank
column in Molecules is a very significant step towards the preservation
of the information aspect of molecular diversity of precious experimental
findings and an interesting experiment in electronic publishing. We would
like to discuu it and hope more journals can join us to publish electronically
the experimental findings.
Many chemists working in industry research and development have accumulated a large amount of synthetic and structural characterization results. However, many of them have never been published. It is understandable that if the chemists have done a good job and are well-paid, both sides, the chemists themselves and the companies are satisfied. They do not need to publish anything.
Their interests in publishing their works are further discouraged by
the conventional standard of chemical paper publications: they do not want
to spend a lot of time painstakingly preparing the "introduction" and the
"discussion" sections required by conventional chemistry journals. The
preparation of these two sections are tricky. Many very good experimental
works have been rejected because the authors failed to prepare good paragraphs
for these sections. Even published "experimental work" can be published
virtually without any experimental data presented if you are a good writer:
It is not rare in some prestigious journals of chemistry to find papers
without any experimental data except a statement such as "all the compounds
give satisfactory elemental analysis (C,N,H), IR and NMR". Examples are
not rare in Chemical Communication and Tetrahedron Letters
For similar reasons, chemists in universities also have this problem and feel reluctant to publish fully their experimental findings, particularly if they are scattered unassembled experimental data of individual compounds.
Therefore, most (we estimate at least 2/3) of the experimental data for organic molecules was previously never published.
On the other hand, we know that chemistry is a typical experimental
science. Chemical knowledge as written in the text books is based on experimental
findings. The recording as fully as possible of all these experimental
findings would on any account be very useful
Can we do something better to change the situation of chemical information
Authors are not required to prepare "introduction" and "discussion" parts - it is not necessary to be asked to tell why you want to prepare these compounds.
MolBank papers are short notes of synthetic works and the data of the structural characterization which can be one molecule (one structure) per paper and can be as short as one page only. Such publications in Molecules will serve as the experimental data deposit.
|Figure 1||A MolBank short note in html format.|
This project might be interesting because a large volume of very precious chemical information, particularly the very diverse works of synthesis and structural characterization have either never been published -- the submitted papers were rejected by editors because they were too trivial (normally because it belonged to the classical scope of chemistry, i.e., pure synthetic or pure spectroscopic measurements), or the chemists themselves never planned to publish such works for individual compounds and isolated data because they thought them not publishable in a traditional journal. We believe that synthesis and structural elucidation of individual compounds are still the essence of chemistry and the material foundation of other research.
The ready publication of all scattered unassembled data for individual
compounds in Molecules as short posters will provide a bank for
chemists to deposit all of their information of synthesis and structural
characterization, together with the sample availability information. Those
works that have no compound samples available will also be published. When
a large volume of (say 1 million) structures is published in this way and
also constructed as a retrievable databank, it will be a very useful treasure
to all chemists and other related scientists. If every synthetic chemist
contributes 100 such posters, this number will be easily reached within
|Figure 2||Online submission of paper for consideration and publication in MolBank section.|
A chemist started to serve as the MolBank section Editor of Molecules
(http://www.mdpi.org/molecules/editors.htm#molbank) in August 1999.
Thus, Molecules publishes in the section of MolBank (http://www.mdpi.org/molbank) very short notes of experimental data records for individual molecules. Any scattered, unassembled experimental data for individual compounds which is conventionally not publishable is particularly welcomed, to be published as one-paper one-page for one structure and given special page numbers (M1, M2, etc.). They have been published in HTML format, with at least a formula of the target molecule. MDL MOL file is also included for every MolBank short notes. All papers submitted for consideration and publication in this column of "MolBank" have been refereed and the accepted papers edited (English corrected and format unified). The related chemical samples are in most cases available and the availability information is also published.
So far all papers published in the MolBank section have been indexed and abstracted by several leading indexing and abstracting services, including Chemical Abstracts; CAPLUS; Science Citation Index Expanded; SciSearch, Research Alert; Chemistry Citation Index; Current Contents/Physical, Chemical & Earth Sciences.
We would say that this is only an interesting experiment.
This awork was originally presented at the Third
International Electronic Conference on Synthetic Organic Chemistry (ECSOC-3),
www.mdpi.org/ecsoc-3.htm, September 1-30, 1999, and the 218th ACS
National Meeting August 22-26, 1999.
|1||Online-only journals monitored by CAS are available at http://info.cas.org/EO/ejourn2.html.|
|2||Examples are Rzepa, H. R. (Organizer); ECTOC-1, June 12-July 7, 1995 (http://www.ch.ic.ac.uk/ectoc/ectoc-1.html) and the other three ECTOC meetings in the series at the website. Substructure searching, similar in style to what is described here, was utilized in ECTOC-2.|
|3||The MolBank website is http://www.mdpi.org/molbank/.|
|4||The MolBank server http://www.molbank.org/ has the MolBank section papers in searchable database form. The web-based submission and reviewing systems are also installed there.|
|5||S.-K. Lin and L. Patiny
MolBank: Preservation and Publication of Chemical Reaction Data, presented at the 218th ACS National Meeting August 22-26, 1999.
MolBank: Rapid and Easy Publication of Short Notes of Individual Molecules, presented at the First International Electronic Conference on Synthetic Organic Chemistry (ECSOC-1), www.mdpi.org/ecsoc/, September 1-30, 1997
"A Good Yield and a High Standard"
Molecules 1996, 1, 1-2
"Preserving and Exploiting Molecular Diversity: Deposit and Exchange of Chemical Information and Chemical Samples"
Molecules 1997, 2, 1-2
Chemical and Engineering News May 26 1997, 4
|10||The "high yield" standard is another questionable standard for many publishable synthetic works [see Reference 7]. As reasonably skillful synthetic organic experimentalists, we found quite a number of papers that claimed (higher) yields which can never be reproduced. Normally 20% higher than what we find if we repeat a synthesis. Therefore, the chemistry journal Molecules does not set the "high yield" as a high standard of organic synthesis [see Reference 7] and authors can be encouraged to be honest and to report reproducible yields.|
|11||As synthetic organic chemists, we may read carefully only the experimental section, sometimes making a Xerox copy of only the specific experimental paragraphs of a paper or a patent.|