chem 2.0

Chem 2.0: ChemRank – You decide the quality of the literature

Dissociating the good literature from the bad literature is an endeavor we all do individually(but not for long: ChemRank). If only there was some website where we could tell whether that syn. prep. is accurate or that physical model is valid. The current methods to determine the validity of the literature are: to perform the same experiment, try to determine this from how many people cite that article, go ask around the department for someone who did something similar, try to relate the quality of the paper from the h-index of the author.

But, what if you still want more? What if you want something more than a numerical qualifier of a paper’s worthiness, or of an author’s scientific quality? What if you want to have a discussion beyond the scope of your labmates? What if you want to have an intellectual discussion about the current chemical literature with every other chemist on the planet? How do you do this and where do you begin?

The chemical blogosphere has done a rather good job in keeping the community of internet savvy chemists a breasted on some of the latest and coolest research (http://wiki.cubic.uni-koeln.de/cb/index.php). But, unless you have a huge audience and build a faithful readership, no one will ever know your views and it can be rather difficult to have an intellectual conversation with just yourself.

With all this in mind, I set out to create a website that would overcome these historic limitations to academic communication. I created a new website called ChemRank: http://www.chemrank.com Screen Shot shown Below

At ChemRank you can add a paper to the database and then vote whether you find it a good or bad paper. You can also leave comments critiquing the yield or congratulating the authors on a job well done. Most importantly, there is a public record of your views! Your pain does not need to be repeated if you point out the problematic reaction or the incorrect eqn in the comments section.

An other cool feature of ChemRank is the building of a database that knows the good chemical literature from the bad chemical literature. Currently, there is no database to my knowledge, except your own brain or PI’s brain, that tracks this information. Although, Noel’s experiments with Connotea is a step in the right direction.

There is even something for the already established pioneers in online chemical literature discussions (aka chemical bloggers) too. For each paper added to the database a script, behind the scenes, will generate a little code snippet to allow voting on the literature your discussing on your blog too. For example, if you are discussing the recent paper “Atomic Structure of Graphene on SiO2” you can generate the following from copy/pasting a code snippet. Assuming you’ve already added the paper to the database and clicked the link: “add to your blog

This by no means is a completed project, there is still much more to do.

  • Make links that show the papers posted last 7days, 1month, 1 year, all time
  • Make users register before posting.
  • Add the ability to tag the articles with relevant keywords
  • Make a pipe’s rss feed of the author’s most recent papers, on the fly and behind the scenes, display in the description as well.
  • Make an api so others can access the database and use it for cool-new mashups.
  • Add a search feature, but that is kind of pointless while the database has less than 10 papers in it.

All of the above can be done in time, but it depends on the feedback from the community and the popularity of the website. As with all projects, I don’t necessarily expect it to catch on right away if at all. A lot of times I code, simply to show how to do it, and how to do it well. Allowing public comment on the current literature is something the chemical publishers should be doing anyways, now we no longer have to wait for them…

Mitch

By May 29, 2007 0 comments chem 2.0

Chem 2.0 – Search ACS, Nature, APS, Science, RSC, Springer Simultaneously

I’ve discussed yahoo pipes previously,1,2 and now I’ve created a new pipe far more powerful than the previous two. I added a pipe that will allow you to search all of the ACS’s, Nature’s, APS’s, Science’s, RSC’s rss feeds simultaneously and it also searches in all of the Springer chemical publications too.

This isn’t limited to just searching, you can also syndicate the search results in rss format and then plug that feed into the rss reader of your choice. The reader will then notify you whenever a new publication containing what you searched for was published. That includes searches for authors, topics or whatever tickles your fancy. The url to the pipe is below:
http://pipes.yahoo.com/pipes/pipe.info?_id=XHBpdITV2xGyLtzzy6ky6g

A few suggestions to the Net people at major publication houses:

  • Suggestion 1: It would be nice if all of you allowed the ability to syndicate an rss from a search result. Only Springer currently lets you do this. Without this capacity, I had to make the work around of searching in the rss files only. Since this involved incorporating a huge batch of RSS feeds I wasn’t able to also include the chemical relevant journals of Wiley. But for those of you that also want to be plugged into the Wiley publications here is the pipe I created for you:
    http://pipes.yahoo.com/pipes/pipe.info?_id=wjTp78fV2xGqkWjOBx2yXQ
  • Suggestion 2: Let me know if you do or plan to do suggestion 1. Wink

Below is a list of the huge assortment of journals that are searched and syndicated with the above two pipes.

ACS
Accounts of Chemical Research
ACS Chemical Biology
Analytical Chemistry
Biochemistry
Bioconjugate Chemistry
Biomacromolecules
Biotechnology Progress
Chemical & Engineering News
Nanofocus
Chemical Research in Toxicology
Chemical Reviews
Chemistry of Materials
Crystal Growth & Design
Energy & Fuels
Environmental Science & Technology
Industrial & Engineering Chemistry Research
Inorganic Chemistry
Journal of Agricultural and Food Chemistry
Journal of the American Chemical Society
Journal of Chemical & Engineering Data
Journal of Chemical Information and Modeling
Journal of Chemical Theory and Computation
Journal of Combinatorial Chemistry
Journal of Medicinal Chemistry
Journal of Natural Products
The Journal of Organic Chemistry
The Journal of Physical Chemistry A
The Journal of Physical Chemistry B
The Journal of Physical Chemistry C
Journal of Proteome Research
Langmuir
Macromolecules
Molecular Pharmaceutics
Nano Letters
Organic Letters
Organic Process Research & Development
Organometallics

Nature
Nature – issue
Nature – AOP
Nature China
Nature Japanese Highlights
Nature Digest
Nature Biotechnology
Nature Cell Biology
Nature Chemical Biology – issue
Nature Chemical Biology – AOP
Nature Genetics
Nature Immunology
Nature Medicine
Nature Methods
Nature Nanotechnology
Nature Neuroscience
Nature Photonics
Nature Physics – issue
Nature Physics – AOP
Nature Protocols
Nature Structural & Molecular Biology
Nature Reviews: Cancer
Nature Reviews: Drug Discovery
Nature Reviews: Genetics
Nature Reviews: Immunology
Nature Reviews: Microbiology
Nature Reviews: Molecular Cell Biology
Nature Reviews: Neuroscience
Nature Clinical Practice Cardiovascular Medicine
Nature Clinical Practice Endocrinology & Metabolism
Nature Clinical Practice Gastroenterology & Hepatology
Nature Clinical Practice Nephrology
Nature Clinical Practice Neurology
Nature Clinical Practice Oncology
Nature Clinical Practice Rheumatology
Nature Clinical Practice Urology
Bone Marrow Transplantation – AOP
British Dental Journal
British Journal of Cancer – AOP
British Journal of Pharmacology – AOP
Cancer Gene Therapy – AOP
Cell Death and Differentiation – AOP
Cell Research – AOP
Clinical Pharmacology & Therapeutics
The EMBO Journal – AOP
EMBO Reports – AOP
European Journal of Clinical Nutrition – AOP
European Journal of Human Genetics – AOP
Eye – AOP
Gene Therapy – AOP
Genes and Immunity – AOP
Heredity – AOP
Immunology and Cell Biology – AOP
International Journal of Impotence Research – AOP
International Journal of Obesity – AOP
Journal of Cerebral Blood Flow & Metabolism – AOP
Journal of Exposure Science and Environmental Epidemiology – AOP
Journal of Human Hypertension – AOP
Journal of Investigative Dermatology – AOP
Journal of Perinatology – AOP
Kidney International – AOP
Laboratory Investigation – AOP
Leukemia – AOP
Modern Pathology – AOP
Molecular Psychiatry – AOP
Molecular Systems Biology
Molecular Therapy – issue
Molecular Therapy – AOP
Neuropsychopharmacology – AOP
Oncogene – AOP
The Pharmacogenomics Journal – AOP
Prostate Cancer and Prostatic Diseases – AOP
Spinal Cord – AOP
Naturejobs: Biological Sciences
Naturejobs: Editorial
Naturejobs: General
Naturejobs: Physical Sciences
Cell Migration Gateway
Dissect Medicine
Functional Glycomics Gateway
News@Nature.com
Nature Materials Update
Nature Web Focus: Access to the literature: the debate continues
Neuroscience Gateway
Omics Gateway
Pathway Interaction Database
Signaling Gateway Update
The Librarian Gateway – What’s New?

Science
News Summaries — The week’s news highlights, from Science Magazine
This Week in Science — Brief summaries of new research papers published in Science
Editors’ Choice — Highlights of the recent literature
ScienceNOW daily headlines

APS
Physical Review Letters
Physical Review A
Physical Review B
Physical Review C
Physical Review D
Physical Review E
Physical Review ST Accel. and Beams
Physical Review ST Phys. Educ. Res.
Reviews of Modern Physics

RSC
RSC News
Chemistry World | Latest News
RSC Journals
The Analyst
Annual Reports A: Inorganic Chemistry
Annual Reports B: Organic Chemistry
Annual Reports C: Physical Chemistry
Chemical Biology Research Articles
Chemical Communications
CrystEngComm
Chemical Society Reviews
Dalton Transactions
Faraday Discussions
Green Chemistry
JAAS
Journal of Environmental Monitoring
Journal of Materials Chemistry
Lab on a Chip
Molecular BioSystems
New Journal of Chemistry
Natural Product Reports
Organic & Biomolecular Chemistry
PCCP
Photochemical & Photobiological Sciences
Soft Matter

Springer
Accreditation and Quality Assurance
Advanced Composite Materials
Amino Acids · The Forum for Amino A…
Analytical and Bioanalytical Chemistry
Applied Composite Materials · An In…
Applied Magnetic Resonance
Applied Mathematics and Optimization
Applied Microbiology and Biotechnology
Applied Physics A · Materials Scien…
Applied Physics B · Lasers and Optics
Archive for History of Exact Sciences
Archives of Environmental Contamination an…
Biogerontology
Biometals
Bioprocess and Biosystems Engineering
Bulletin of Environmental Contamination an…
Catalysis Letters
Catalysis Surveys from Asia
Cellulose
Central European Journal of Chemistry
Chemical and Petroleum Engineering
Chemical Papers
Chemistry and Technology of Fuels and Oils
Chemistry of Heterocyclic Compounds
Chemistry of Natural Compounds
Chinese Science Bulletin
Chromatographia · An International …
Coke and Chemistry
Colloid and Polymer Science · Kollo…
Colloid Journal
Composite Interfaces
Computing and Visualization in Science
Contributions to Mineralogy and Petrology
Crystallography Reports
Designed Monomers and Polymers
Doklady Chemistry
Doklady Physical Chemistry
Environmental Chemistry Letters
Environmental Management
European Food Research and Technology
The European Physical Journal D
The European Physical Journal E
Fibre Chemistry
Foundations of Chemistry
Frontiers of Chemistry in China
Geochemistry International
High Energy Chemistry
Inorganic Materials
International Journal of Peptide Research …
Ionics
Journal of the American Oil Chemists&#…
Journal of Analytical Chemistry
Journal of Applied Electrochemistry
Journal of Applied Spectroscopy
Journal of Bioenergetics and Biomembranes
JBIC Journal of Biological Inorganic Chemi…
Journal of Biological Physics
Journal of Biomaterials Science, Polymer E…
Journal of Biomolecular NMR
Journal of Chemical Crystallography
Journal of Chemical Sciences
Journal of Chemical Ecology
Journal of Cluster Science
Journal of ComputerAided Molecular Design
Journal of Inclusion Phenomena and Macrocy…
Journal of Industrial Microbiology & Biote…
Journal of Inorganic and Organometallic Po…
Journal of Materials Science
Journal of Mathematical Chemistry
Journal of Molecular Modeling
Journal of Polymers and the Environment
Journal of Radioanalytical and Nuclear Che…
Journal of Solid State Electrochemistry
Journal of Solution Chemistry
Journal of Structural Chemistry
Journal of Surfactants and Detergents
Journal of Thermal Analysis
Journal of Zehjiang Univesity B
Kinetics and Catalysis
Lipids
Microchimica Acta · An Internationa…
Microfluidics and Nanofluidics
Molecular Diversity
Monatshefte für ChemieChemical Monthly
Moscow University Chemistry Bulletin
Petroleum Chemistry
Pharmaceutical Chemistry Journal
Phytochemistry Reviews · Proceeding…
Plasmas and Polymers
Plasma Chemistry and Plasma Processing
Polymer Bulletin
Polymer Science Series A · Chemistr…
Polymer Science Series B · Rapid Co…
Protection of Metals
Polymer Science Series C · Chemistr…
Radiochemistry
Reaction Kinetics and Catalysis Letters
Rheologica Acta
Russian Chemical Bulletin
Russian Journal of Applied Chemistry
Russian Journal of Bioorganic Chemistry
Russian Journal of Coordination Chemistry
Russian Journal of Electrochemistry
Russian Journal of General Chemistry
Russian Journal of Inorganic Chemistry
Russian Journal of Organic Chemistry
Russian Journal of Physical Chemistry
Science in China Series B: Chemistry
Silicon Chemistry
Structural Chemistry
Theoretical Chemistry Accounts
Theoretical and Experimental Chemistry
Theoretical Foundations of Chemical Engine…
Transition Metal Chemistry

Wiley
Acta hydrochimica et hydrobiologica
Advanced Functional Materials
Advanced Materials
Advanced Synthesis & Catalysis
Advances in Polymer Technology
AIChE
Angewandte Chemie
Angewandte Chemie International Edition
Annali di Chimica
Applied Organometallic Chemistry
Archiv der Pharmazie
Archives of Insect Biochemistry and Physiology
Asia-Pacific Journal of Chemical Engineering
Berichte zur Wissenschaftsgeschichte
Biomedical Chromatography
Biopharmaceutics & Drug Disposition
Biopolymers
Biotechnology and Bioengineering
Biotechnology
ChemBioChem
Chemical Engineering & Technology
The Chemical Record
Chemical Vapor Deposition
Chemie in unserer Zeit
Chemie Ingenieur Technik – CIT
ChemInform
Chemistry – A European
Chemistry – An Asian
Chemistry & Biodiversity
CHEMKON
ChemMedChem
ChemPhysChem
Chinese Journal of Chemistry
Chirality
CLEAN – Soil, Air, Water
Color Research & Application
Concepts in Magnetic Resonance Part A
Concepts in Magnetic Resonance Part B: Magnetic Resonance Engineering
Contrast Media & Molecular Imaging
Electroanalysis
ELECTROPHORESIS
Engineering in Life Sciences
Environmental Progress
European Journal of Inorganic Chemistry
European Journal of Lipid Science and Technology
European Journal of Organic Chemistry
Flavour and Fragrance
Fuel Cells
Helvetica Chimica Acta
Heteroatom Chemistry
International Journal of Chemical Kinetics
International Journal of Quantum Chemistry
Journal of Applied Toxicology
Journal of Basic Microbiology
Journal of Biochemical Toxicology
Journal of Cellular Biochemistry
Journal of Chemical Technology & Biotechnology
Journal of Chemometrics
Journal of Computational Chemistry
Journal of Labelled Compounds and Radiopharmaceuticals
Journal of Mass Spectrometry
Journal of Molecular Recognition
Journal of Peptide Science
Journal of Pharmaceutical Sciences
Journal of Physical Organic Chemistry
Journal of Raman Spectroscopy
Journal of Separation Science
Journal of the Science of Food and Agriculture
Laser Physics Letters
Lipid Technology
Luminescence
Macromolecular Reaction Engineering
Macromolecular Symposia
Magnetic Resonance in Chemistry
Mass Spectrometry Reviews
Materials and Corrosion
Materialwissenschaft und Werkstofftechnik
Medicinal Research Reviews
Molecular Nutrition & Food Research
Particle & Particle Systems Characterization
Pest Management Science
Pesticide Science
Pharmazie in unserer Zeit
Phytochemical Analysis
Phytotherapy Research
Process Safety Progress
Propellants, Explosives, Pyrotechnics
Proteins: Structure, Function, and Bioinformatics
PROTEOMICS
QSAR & Combinatorial Science
Rapid Communications in Mass Spectrometry
Single Molecules
Starch – Stärke
Surface and Interface Analysis
Vakuum in Forschung und Praxis
X-Ray Spectrometry
Zeitschrift für anorganische und allgemeine Chemie

Note 1: Although, I’m aware that Web of Science will also let you syndicate a search string, they tend to be a bit slower in updating their database for the journals I’m interested in(anywhere from 1-6months. So, if you want to seriously stay on top of a topic, I would recommend using the above two yahoo pipes.

Note 2: Due to the high volume of journals searched it can take upwards to 15-20 seconds to generate your feed. I have not seen it take longer than that. For whatever reason, the pipe sometimes doesn’t spit out any search results even though there are publications dealing with your search query–if you do the search again, it will return results the second time round. I have never had to do a search more than 2-times to get it to generate a feed with results.

Note 3: In case you are too lazy to scroll back up, here are the two URLs:
ACS + Nature + APS + Science + RSC + Springer
http://pipes.yahoo.com/pipes/pipe.info?_id=XHBpdITV2xGyLtzzy6ky6g
Wiley
http://pipes.yahoo.com/pipes/pipe.info?_id=wjTp78fV2xGqkWjOBx2yXQ

Note 4: Feedback is very much welcomed, please tell me how you like it.

Mitch
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By March 19, 2007 7 comments chem 2.0

Chem 2.0 – ACS Alerts Your Way

There should be a way to have ACS notify you when a paper is published about a topic you are interested in. For instance, if you were an aromatic freak, there should be a way to have ACS tell you when a paper regarding aromaticity comes out. Now there is! The following is the url for an RSS feed for the term “Aromatic”:

TM

http://pipes.yahoo.com/pipes/pipe.run?_id=vOrZbmnT2xGwr12mJhOy0Q&pubssearch=aromatic&_render=rss

The rss feed will automatically update itself when a new article with the term aromatic is published. The only catch is that the word aromatic has to be found in the title. The above url could be placed into the reader of your choice and you will always be kept up to date. But that isn’t all, who isn’t a fan of James Tour’s nanopeople? If you want to be kept up to speed every time Tour sneezes you can follow his exploits with the following feed:
http://pipes.yahoo.com/pipes/pipe.run?_id=vOrZbmnT2xGwr12mJhOy0Q&pubssearch=Tour&_render=rss

Like Gabor Somorjai? Stalk him with this feed:
http://pipes.yahoo.com/pipes/pipe.run?_id=vOrZbmnT2xGwr12mJhOy0Q&pubssearch=Somorjai&_render=rss

Want to make your own personal feeds. Here is the link:
http://pipes.yahoo.com/pipes/pipe.info?_id=vOrZbmnT2xGwr12mJhOy0Q

This was all accomplished with the wonderful Yahoo Pipes.

Yahoo Pipes is the latest product of the new semi-autonomous business unit, Yahoo Brickhouse, of Yahoo!. Speaking of which, Salim Ismail, the co-founder of Flickr, is now running the show at the Brickhouse. http://www.techcrunch.com/2007/03/14/salim-ismail-to-head-yahoo-brickhouse/

I will continue to expand the chemical possibilities of yahoo pipes, so expect more. In the mean time, I will be having some insane fun with this new “research-tool”. Feel free to go nuts!

Mitch

By March 15, 2007 2 comments chem 2.0

Chem 2.0 – Stalking Commenters

Ever do something so incredibly cool it is hard to know where to begin describing it? Here is the gist of what I did using the simplest English as I can. I easily created a tool that lets you search the comments that people have made in the various popular chemistry blogs. Not only does this tool let you search various chemistry blogs’ comment sections quickly, but you can syndicate the results in an rss format. Meaning, you can take the rss that you generated from that search and incorporate it into your favorite reader of choice, and when future commenters write about what you searched, the new results will be displayed in that rss feed. Now that is cool! The tool was made with Yahoo Pipes.

To check out the tool I mentioned above goto this url: http://pipes.yahoo.com/pipes/pipe.info?_id=MhgRd3zO2xGtSroDmLokhQ

The default search is “Mitch”, and it’ll let you track all of my recent comments across the blogosphere. IT also lets you track who was talking about me or to me in the blogosphere as well. You could also use this tool to track the comments of other people you are interested in or see if anyone has been talking about a particular topic. It would be trivial at this stage to also include an other tool that would let you search the main content of the blog posts, and I’ll probably work on it tonight.

I hope you enjoy this new Chem 2.0 tool, I know I will. Stalking just became so much easier…

Mitch

By March 9, 2007 0 comments chem 2.0