Chemistry Central Blog
NIGMS funds new structure-activity database
The National Institute of General Medical Sciences (NIGMS), which is one of the National Institutes of Health, has announced funding of a project to enhance computer-aided drug design.
The University of Michigan will lead the project to expand and enhance the molecular data needed to develop computer programs that more accurately predict potential drug candidates. The data will be presented in a free access online database. The project is estimated to receive up to US$5 million over 5 years from the NIGMS.
Chemist Heather Carlson of the University of Michigan will oversee the creation and operation of the new Community Structure-Activity Resource.
To build it, Carlson and her co-investigators at the University of Michigan will gather molecular data from existing resources as well as generating new data. A major activity will be the collection of unpublished data from pharmaceutical company scientists, who emphasized both the need for this information and a willingness to share it.
The team also will draw from published literature as well as from Carlson’s Binding MOAD (“Mother of All Databases”), which contains more than 11,000 protein-ligand complexes, and the PDBbind database, which was developed by co-investigator Shaomeng Wang, and provides experimentally measured binding data. The team will conduct experiments to address any gaps in the data and sponsor community-wide events to facilitate collaboration among scientists.
Posted by Jan Kuras at 12:54 Comments (0)
Chemistry Central host OA session at EuCheMS Congress
Chemistry Central hosted an engaging open session - An Introduction to Open Access Publishing in Chemistry - at the recent EuCheMS Chemistry Congress in Torino, Italy.
Jan Kuras, Associate Publisher at Chemistry Central, provided an overview of the strategy and business model of OA publishing and positioned it within the publishing landscape, highlighting the beneficiaries throughout the research community.
Dr Livia Simon Sarkadi, from the Budapest University of Technology and Economics, then examined the benefits (as well as some disadvantages) of OA publishing to the chemistry community and shared some initiatives that could be implemented to progress OA in chemistry. These included: soliciting articles from leading chemists in areas of high topicality to raise the profile of an OA journal; engaging with young chemists for whom OA publications will be part of their careers; and seeking support for OA publishing from national societies and divisions.
Please contact us if you would like to find out more about the session. Also, if you are organising a chemistry conference in the future and would like to include a session on open access publishing please contact us.
Posted by Jan Kuras at 15:25 Comments (0)
Open Access session at EuCheMS Congress in Torino
Chemistry Central will be hosting An Introduction to Open Access Publishing in Chemistry on Thursday 18th September from 12-12.30 pm during the 2nd EuCheMS Chemistry Congress in the Madrid Room of the Lingotto Conference Centre, Torino, Italy.
This is a great opportunity to find out more about open access publishing and Chemistry Central, and will include an open floor debate for your questions to be answered.
We are pleased to announce that we will be joined by guest speaker Dr. Livia Simon Sarkadi, Associate Professor from the Budapest University of Technology and Economics in Hungary, who will discuss the benefits of open access publishing from the academic perspective.
The session is free to attend, so we look forward to seeing you there.
Posted by Jan Kuras at 15:07 Comments (0)
Meet us at the EuCheMS Congress in Torino
The 2nd EuCheMS Chemistry Congress takes place in Torino, Italy, 16-20 September at the Lingotto Convention Centre.
Chemistry Central will be attending the congress, and you can visit the Chemistry Central stand (#31) any time from Tuesday 16th to Saturday 20th September, where we will be promoting open access publishing and our journal portfolio. Leave your details at the stand to enter our prize draw to win a fantastic 8GB MP4 Watch Player with 1.5 inch LCD screen.
The congress is co-organised by the European Association for Chemical and Molecular Sciences (EuCheMS) and the Società Chimica Italiana (SCI). The 4-day programme includes plenary, keynote, and invited lectures as well as contributed oral communications and poster sessions. The scope of the congress will cover the 6 following themes: Advances in Synthesis; Advances in Understanding; Chemistry and Life Sciences; Energy and Industry; Environment; Materials and Devices. Participants include Nobel Laureates in Chemistry Peter Agre, Robert H. Grubbs, Hartmut Michel and K. Barry Sharpless.
We look forward to seeing you in Torino!
Posted by Jan Kuras at 11:10 Comments (0)
Chemistry Central Journal indexed by ISI
We are delighted to announce that Thomson Reuters has just accepted Chemistry Central Journal for indexing - beginning with Vol. 1 (1) 2007. The journal will be included in the Science Citation Index Expanded available through the Web of Science, and in the Chemistry Citation Index. Chemistry Central Journal will receive an Impact Factor in 2009.
This is great news, and demonstrates the growing importance and acceptance of open access journals. Chemistry Central Journal is already indexed by PubMed Scopus, CAS, DOAJ and Google Scholar, and is archived in PubMed Central and LOCKSS.
If you have not visited the Chemistry Central Journal website recently, please do take a look at the latest articles published. You can also register to receive regular Chemistry Central updates about our journals, development plans and events.
So I do encourage you and your colleagues to submit your research to Chemistry Central, and experience the benefits of open access publishing!
Posted by Jan Kuras at 14:33 Comments (0)
Chemistry Central will once again be exhibiting at the American Chemical Society National Meeting, to be held in Philadelphia 17-21 August. Come and see Jan Kuras, Lisa Prickett or me at booth 305 and enter our draw to win a pretty cool MP4 watch!
Once again energy is high on the agenda with a Presidential session on Global Energy Challenges in the 21st Century, Monday, August 18 (cosponsored by Committee on International Activities and Committee on Science) 1:30 to 5 p.m. Philadelphia Marriott, Grand Ballroom Salon F.
Several excellent sessions combine to form Chemistry for Health: Catalyzing Translational Research.
Advice is on hand from the Younger Chemists programming in the form of 3 sessions:
- Getting Your First Industrial Job
- From Test-Tube to Start-Up Companies
- Opportunities and Challenges for Non-Tenure Track Faculty
For more of a publishing bias turn to the Division of Chemical Information (CINF). Rob McFarland and Andrea Twiss-Brooks have pulled together an interesting session Preservation Issues for the Digital Library where I'm particularly looking forward to Leah Solla's presentation to find out what role a university library can play in riding the rising tide of research data.
In the Datamining and Textmining Approaches to Drug Discovery session Matthew Stahl (OpenEye Scientific Software) will present on medium throughput methods for extracting chemical information out of a number of document sources.
In the same session Igor V. Filippov (National Cancer Institute, National Institutes of Health) will present the latest developments of Optical Structure Recognition Application (OSRA), an open source project which has been designed to extract chemical structure images from documents such as patents and scientific publications and convert the extracted images into the computer-readable SMILES format.
Peter Johnson (University of Leeds) will cover the main problems involved with Chemical OCR
i) identification of chemical images within a document
ii) compilation of chemical graphs of individual molecules from chemical images, and
iii) interpretation of complex objects such as generic molecules and reaction schemes using the retrieved chemical graphs
while highlighting CLiDE Pro, the latest incarnation of software to emerge from the long-term CLiDE (Chemical Literature Data Extraction) project.
It should be an interesting few days.
Again, do stop by our booth (#305) to discuss open access to the chemical literature. We look forward to seeing you in Philadelphia!
Posted by Bryan Vickery at 13:00 Comments (0)
It's certainly informative and engaging, and shows some real chemistry in action.
Posted by Jan Kuras at 11:14 Comments (0)
Jan Kuras joins Chemistry Central
Greetings! I join Chemistry Central as the new Associate Publisher.
After a brief sojourn away from science publishing - and a couple of exciting vacations - I am back on familiar territory.
I garnered an interest in how chemists can efficiently communicate their research findings when I was studying chemistry, and then specializing in analytical chemistry. My first meaningful employment was at Thomson Scientific (in what was then Derwent). I worked on pharmaceutical information products, and was involved in the development of the company’s first structure searchable and web-based databases.
This stimulated an interest in the application of Web technologies to search and display scientific data. I joined BioMedNet and then ChemWeb at Elsevier. My roles encompassed product development, publisher relations and community site development, and I was fortunate to collaborate with some prestigious publishers and database vendors. We were motivated by producing intuitive website functionality and easily accessible information. Our highest usage was always for free access, high quality journals and databases.
I am now pleased to be joining Chemistry Central, where we are striving to accelerate the growth in open access publishing of chemistry research, and I look forward to keeping you informed through the Chemistry Central blog.
Posted by Jan Kuras at 14:07 Comments (1)
Chemistry Central Journal author joins the editorial board
We are delighted to announce the appointment of Dr Sébastien Sauvé, associate professor in the department of chemistry at the university of Montreal, Canada, to the editorial board. He will act as an editorial adviser on analytical, aquatic and environmental chemistry, in addition to geochemistry and mass spectrometry.
Dr Sauvé's numerous areas of research interest include: soil and environmental chemical and ecotoxicological evaluations, such as the environmental fate of contaminants and pharmaceuticals; quantification of the occurrence and transformation of nanoparticles and nanotechnology in the environment; and chemical speciation, including the kinetics of complication and dissociation, as well as adsorption and desorption rates at the solid-liquid interface. His research also focuses on creating conceptual and computational models that integrate environmental fate, chemical speciation and bioavailability.
Dr Sauvé recently published a preliminary communication in Chemistry Central Journal reporting the use of graphite
furnace atomic absorption spectrometry in studying the effects of two complexing agents on the fractionation
of beryllium in human serum.
Preliminary communication
Study
on the effects of nitrilotriproprionic acid and
4,5-dihydroxy-1,3-benzene disulphonate on the fractionation of
beryllium in human serum using graphite furnace atomic absorption
spectrometry
Chadi H Stephan, Michel Fournier, Pauline Brousseau, Sebastien Sauve
Chemistry Central Journal 2008, 2:10 (14 May 2008)
[Abstract] [Provisional PDF]
Posted by Gino D'Oca at 10:15 Comments (0)
Chempedia: "a free and continuously-updated" chemical compound encyclopaedia
Each compound monograph outlines information about the "structure, uses, history, and significance of a chemical compound". Users can search for compounds through the 'ChemWriter Structure Editor' or by text using a title, CAS Number, or PubChem CID. There is also the option to search the compound listings alphabetically or by most recent items.
The compound entries can be updated as soon as possible to reflect newly available information. Here users are well placed to know when an existing Wikipedia compound monograph ought to appear in Chempedia yet does not, when an existing monograph needs to be updated, or when a new monograph has been written and needs to be linked. All users need to do in order to create a new or updated link from Chempedia to Wikipedia, is to provide the Wikipedia link via the 'create' tab found on the site's main menu.
Posted by Gino D'Oca at 16:18 Comments (0)
New, free-to-access life sciences search engine
A new, free-to-access life sciences search engine has been recently made available to the general public. NextBio allows users to search over 10,000 public experimental results, 1.2 billion data points, and 16 million PubMed literature abstracts, making "massive amounts of disparate biological, clinical and chemical data from public and proprietary sources searchable, regardless of data type and origin....".
The search engine's framework, which connects heterogeneous data and textual information, was previously only provided in an "enterprise version" for life science R&D and drug development, with notable users including Johnson & Johnson Pharmaceutical Research & Development. The "enterprise accounts" differ from the free version in that they include "added data integration services, security and support".
The research areas covered by NextBio's publicly searchable data range from pharmacogenomics to oncology. Functionality exists to allow users to import their own analysed experimental results, where they can choose to share their data with the network or restrict access to a limited audience. Users can also create their own profiles to more easily develop collaborations with other scientists.
NextBio's founders state that it
"...provides a unique opportunity for the research
community to collaborate through information sharing and to perform an important
part of their biological work in silico... [allowing users]... to glean new
insights into gene function, disease progression and compound effects, as well
as into their own studies using the world's quality public experiments..."
There
are plans to incorporate further content into the platform in due course, such as
sequence-centric and phenotypic data types. Helpful and informative video demonstrations can be found on the site, offering an overview of the initiative's "open biology" ethos, as well as a tutorial on how to use the search engine.
Posted by Gino D'Oca at 16:19 Comments (0)
Open database for insect semiochemicals
To continue our theme of providing overviews of free-to-access chemical databases, I feel Pherobase, a interesting database of insect behaviour modifying chemicals, to be well worth a mention.
The database, hosted by the chemical ecology group, HortResearch, New Zealand, is aimed at "convert[ing] scientific data and knowledge from the literature and publish[ing] peer-reviewed information about behavioural modifying chemicals in insects into electronically searchable database entries." Chemical signals are the main channel of communication in arthropods, especially insects, finding uses in, amongst other things, sexual attraction and defence. The project's author believes the database will "...definitely aid and [accelerate] the process of semiochemicals' (Ed: chemical substance that carries a message) identification and... will provide an overview of the hetero-specific overlap in the chemical signals between different animal groups."
The database, which has now grown to over 50,000 entries - of which 3,000 contain details on molecules -, also contains mass spectral data on over 1,500 of the compounds. Users can search by text, or browse a large number of categories, including genus, species, and functional group, but also application, such as 'lure and kill' and 'mating disruption'. In addition to having an interactive Jmol molecular model, each compound page contains links to spectra, as well as references regarding synthesis and behavioural function.
Pherobase is yet another
example of a free-to-access database, which benefits from being enriched and augmented by contributions from
interested specialists, and that in spite of attracting a somewhat
niche audience, nonetheless has high practical utility.
***
On a related note, it is
worth highlighting Anthony Williams' (ChemSpider) review of the
status of public chemical databases that was recently published in BioMed
Central's Current Opinion in Drug Discovery and
Development. The following is an excerpt from the abstract:
“...The increasing array of chemistry-related resources that are now available provides chemists with a direct path to the information that was previously accessed via library services and was limited by commercial and costly resources. The diversity of the information that can be accessed online is expanding at a dramatic rate, and the support for publicly available resources offers significant opportunities in terms of the benefits to science and society. While the data online do not generally meet the quality standards of manually curated sources, there are efforts underway to gather scientists together and 'crowdsource' an improvement in the quality of the available data...” Public chemical compound databases: Current Opinion in Drug Discovery and Development 2008, 11:393-404 (18 April 2008).
Posted by Gino D'Oca at 16:14 Comments (0)
Chemistry Central appoints new Section Editor
We are delighted to announce the appointment of Professor Yang Gan (Harbin Institute of
Technology, China) as Section Editor for geochemistry, nuclear and radiochemistry and
surface/interfacial chemistry.
Prof Gan, who also serves as an editorial adviser for physical chemistry, joined the board in October 2007. His research interests lie in the use of Atomic Force Microscopy (AFM) in various areas, such as in the study of the interaction of oxide particles in high salt concentrations, the relationship between atomic scale structure and surface charge behaviour of hydroxylated alpha alumina, and crack extension behaviour in brittle solids.
Posted by Gino D'Oca at 12:02 Comments (0)
Chemistry Central to attend the 235th ACS national meeting in New Orleans
Chemistry Central will be exhibiting and speaking at The 235th American Chemical Society National Meeting, in New Orleans from 6-10th of April.
Do visit us at booth 1305 in the Morial Convention Center and hear us speak on 'Open access: Toward the mainstream?' at 11.35 a.m. on Monday the 7th of April (Division: Division of Chemical Education; Session: Using Social Networking Tools to Teach Chemistry).
Posted by Gino D'Oca at 16:08 Comments (0)
CAS agrees to cooperate with Wikipedia
In a positive turnaround Chemical Abstracts Service (CAS) has announced that it will support the 'CAS Number Validation project' started at Wikipedia Chemistry to assist in producing a curated dataset.
"CAS, a division of the American Chemical Society... will contribute to the Wikipedia project... to help provide accurate CAS Registry Numbers for current substances listed in Wikiprojects-Chemicals... that are of widespread general public interest...". The statement goes on to say that "CAS views Wikipedia as an important societal tool for the general public, and this collaboration with Wikipedia is in line with CAS' mission as a Division of the American Chemical Society."
The declaration comes after CAS had earlier made clear its objection "to anyone encouraging the use of SciFinder and STN to curate third-party databases or chemical substance collections, including the one found in Wikipedia. SciFinder and STN are provided to researchers under formal license agreements, under which the researchers agree to refrain from using these tools to build databases. We urge and expect those researchers to respect the explicit terms of the agreements they have entered into..."
CAS's agreement to
cooperate comes on the back of discussions with Martin Walker of WP:Chem and the ChemSpider
Advisory Group, in addition to much debate that ensued elsewhere.
The aim of the validation project is to address various concerns, which
include CAS numbers not matching the structure drawn in the Wikipedia's 'Chemical
Box' or 'Drug Box'. The import of CAS's cooperation was reiterated on the ChemSpider blog: "...there is general agreement by all participants at WP:Chem
that CAS Numbers have value... so the presence of a CAS number in the
[Wikipedia] boxes makes absolute sense and, of course, the correct CAS number
for the structure makes sense in an encyclopedia."
Posted by Gino D'Oca at 11:18 Comments (0)