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Author Topic: Chem 2.0 - Search ACS, Nature, APS, Science, RSC, Springer Simultaneously  (Read 19725 times)

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Mitch

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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. ;)

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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« Last Edit: May 08, 2007, 06:16:48 PM by Mitch »
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Maz

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wow, i totally got trumped. 

Now that is working (when I tested it earlier, it timed out), it is an amazingly useful tool.  Well done!
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Ψ×Ψ

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WOW that's useful.  THANKS!!!
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skoch

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I will give your method a try and believe it will give hits from the absolute most recent literature.  But I find Web of science search are quicker than 1-6 months.  I looked at some of my searches alerts that I received last week and they are giving journal articles that have March publication dates.
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skoch

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I sent a link to your Yahoo Pipes literature searching methods to  The Chemical Information Listserv, which is a listserv for ~ 2000 chemical information specialists.
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mmitch1628

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Very Nice, Mitch.  Now please spend some time working on incorporating Boolean logic into your searching to allow more comprehensive fine tuning of the results and you'll REALLY have one heck of an aggregator!  I'll certainly stay tuned for ongoing developments in this area.   Thanks skoch for sending to the CHMINF list.   Also, if we can see dog pictures in the PIPES example on the yahoo documenation page, I'm sure that the feeds should be able to deliver chemical structures.    I'd love to see a short citation with the structures from relevant abstracts when available.     
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Mitch

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Thanks skoch! That would explain the second huge traffic *Ignore me, I am impatient* today.

mmitch1628: Pipes is definitely amenable for incorporating boolean logic into the actual pipes code, it would be rather problematic to try to incorporate that kind of logic into the search query box on the pipes page. A possible work around would be, for me to build the back end boolean logic for the search query here at chemicalforums and then feed that into yahoo pipes on the fly and behind the scenes. I'll add it to my todo list.

David Bradley also had a very nice piece on it as well: http://www.sciencebase.com/science-blog/

Below is a graph of the traffic only to this one forum + blog.
« Last Edit: March 21, 2007, 10:08:57 PM by Mitch »
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mmitch1628

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As an alternative to formal Boolean search strategies, if you could take advantage of Yahoo Advanced Search logic, ie "all of these words"  "exact phrase"  "None of these words" "any of these words," that would be a powerful alternative.   Do you have the flexibility of utilizing the Yahoo Advanced Search algorithms with the PIPES programing?   Perhaps I'm talking apples and oranges.   I'll admit that I don't know how the programs work.
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shy_ysh

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It is very useful! Thanks!!
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Equi

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I don't get it. Aren't there portals, like NCBI for biologists, for chemists available as well?
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Mitch

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Never heard of one. What would you be looking for in a portal?
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Most Common Suggestions I Make on the Forums.
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2. Don't confuse thermodynamic stability with chemical reactivity.
3. Forum Supports LaTex

Equi

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Never heard of one. What would you be looking for in a portal?
http://www.ncbi.nlm.nih.gov/
All I need. Though I recently had to recognise that NCBI does not search JCAS publications, very much to my disliking as an important GFP paper was published there and it took me ages to find it via our ejournal library pages - grrr.
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you mean JACS?
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Equi

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Mitch

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What features make the portal most useful for you?
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2. Don't confuse thermodynamic stability with chemical reactivity.
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