- chemweb - imperial.ac.uk

Results of data needs survey
by Gary Wiggins 23 Jan '97

23 Jan '97

This is being sent to CHMINF-L, CHEMWEB, and CHEMIND-L. (It's long.) ------------> Data Needs of Academic Research on the Internet Gary Wiggins Indiana University Chemistry Library wiggins(a)indiana.edu Data on the Web "All in all, the chemical data now available on the web is in a different class from the data found in refereed journals, critical reviews and books from reputable publishers. - David Lide (CHMINF-L, 30 October 1996) The above response was one of several received in response to questions sent to three chemically-oriented discussion lists in the fall of 1996. This was in preparation for a lecture and demonstration delivered at the National Institute of Standards and Technology on December 4, 1996. Most of the information in this paper was included in that presentation. Questions were sent to CHMINF-L, CHEMWEB, & CHEMIND-L in late October 1996. They were designed to: - Gauge the extent of inaccurate data in Web databases - Define the characteristics of data on the Web >> Sources of data >> Need for standardization of data formats - Determine the best guides to data. Respondents to the survey noted these problems with the accuracy of data on the Web: - Units are frequently omitted - Transcription errors are often encountered - This leads to a need to find redundant data - Very few sources have quality assurance statements - Few of the Web data sites give the source of the data - If they do, data are likely to be copied from outdated sources. Other Survey Results Several people commented on efforts or practices that will likely improve the quality of data on the Internet, including: - Standardization efforts: >> CLIC, Chemical MIME, CML >> Roles for IUPAC, CODATA: certification? (One person, however, questioned whether standardization efforts were worthwhile.) - Efforts to share data or to cooperatively compile data sources >> Open Molecule Foundation >> Molecule of the Month >> Reciprocal Net >> Structure and Reactivity Across the Periodic Table - Provision of a minimal level of auxiliary information (metadata) >> authorship >> units >> conditions of measurement >> references to primary and secondary sources of data - Use of standard symbols and terminology - Guidelines on how to handle special characters. General Comments on Data on the Web "While some might argue that the Internet is designed to make information in a single location accessible to users around the world, the large number of mirrored sites already in existence points out the Net's inadequacy." - Byte, December 1996 There are a number of steps needed to improve the quality of data found on the Web. Among them are: - Mechanisms to synchronize changes made at multiple sites - Faster access to resources - More secure transactions - Progress on chemical metadata standards - Interoperability of chemical plug-in programs. Some Goals for Improving Data on the Web - Assemble the most reliable data available - Arrange data for easy retrieval - Provide a "SuperIndex" of available data sources - Establish criteria for evaluation of data sources: >> descriptions of physical theories on which data are based >> full references to literature >> format of the database >> search capabilities How to Find Data Now A second part of the NIST presentation was a look at how to find data on the Web today. One person pointed me toward Alexander Lebedev's "Best Search Engines for Finding Scientific Information in the Web" (http://www.chem.msu.su/eng/comparison.html) He searched 11 Web search engines and concluded: - Excite retrieves a comparable number of documents to Altavista - Metacrawler is the most powerful search engine for SATI - Two of the search engines are not being updated. Lebedev also compared the Web searches to INSPEC results for 1994 & 1995 on the same topics. He found: - Only 5-10 % of relevant information is on the net - The Web is particularly good for supplemental information: >> on authors >> on their work and research projects >> on foundations supporting them. Besides using search engines, these are some other ways to find data using the Internet: - Submit the question to a knowledgeable source - Consult lists of sources (guides) - Try known sources - Try comprehensive chemistry guides. Lists of Sources (Guides) CIS-IU (Chemical Information Sources from Indiana University) http://www.indiana.edu/~cheminfo/ca_accc.html http://www.indiana.edu/~cheminfo/ca_ppi.html Databases for Atomic and Plasma Physics http://plasma-gate.weizmann.ac.il/DBfAPP.html IOP's Software and Data Page http://www.iop.org/Physics/Resources/phsoft.html Known Sources NIST Physics Laboratory http://physics.nist.gov/PhysRefData/contents.html Sheffield ChemPuter http://www.shef.ac.uk/~chem/chemputer/ Biocatalysis/Biodegradation Database http://dragon.labmed.umn.edu/~lynda/index.html Comprehensive Chemistry Guides Chemfinder http://chemfinder.camsoft.com WWW Chemical Structures Database http://schiele.organik.uni-erlangen.de/services/webmol.html SpaceCrunch http://www.tripos.com/spacecrunch/ Other Examples University of Texas's ThermoDex http://www.lib.utexas.edu/Libs/Chem/info/thermodex/ Table of the Properties of 200 Linear Macromolecules and Small Molecules http://funnelweb.utcc.utk.edu/~athas/databank/intro.html Chemical errors found on WWW sites; A discussion of problems encountered while creating the ChemFinder WebServer database http://www.camsoft.com/chemfinder/errorsfound.html Internet Demos at NIST CIS-IU ca_accc.html Go to Anal Chem page, then to MS Links at SIS, then Dave's Math Tables www.sisweb.com/math/tables.htm NMR Information Server at U of Florida micro.ifas.ufl.edu/ playing Happy Birthday to You on an NMR Spectrometer Dababase of Core-Edge (Inner-Shell) Excitation Spectra of Gas Phase Atoms and Molecules xray.uu.se/hypertext/corexdb.html SEARCH naphthalene Spin trap Data Base alfred.niehs.nih.gov/LMB/stdb ENTER THE DATABASE doesn't work, but HIPPO does Electron Paramagnetic Resonance at Bristol emrs.chm.bris.ac.uk/ Beautiful background! In "About the Database" in the Introduction, Spectra examples, Show the example Cu(II) (nothing else works!) Look at IU Molecular Structure Center's Reciprocal Net www.cica.indiana.edu/~recip/ www.indiana.edu/ReciprocalNet.html Molecules R Us molbio.info.nih.gov/cgi-bin/pdb Search dehalogenase (E.C.3.8.1.5) NIST Chemistry WebBook webbook.nist.gov/chemistry Look for 91-56-5 AIRSITE ozone.sph.unc.edu Has "Environmental Data, but it's "under construction" THERMODEX www.lib.utexas.edu/Libs/Chem/info/thermodex/ Search Gibbs Free Energy and organic Chemfinder chemfinder.camsoft.com Search MEK WWW Chemical Structures Database schiele.organik.uni-erlangen.de/services/webmol.html Search MEK, then 2-butanone SpaceCrunch www.tripos.com/spacecrunch/ Molecule of the Month www.bris.ac.uk/MOTM/motm.html ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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IUPAC stereochemistry, Atomic Wts etc
by G.P.Moss 21 Jan '97

21 Jan '97

Apologies for duplicate posting. If you visit my IUPAC Nomenclature Web site (see below) site you will find I have recently added Basic Terminology of Stereochemistry (IUPAC Recommendations 1996) identical to the version published in Pure Appl. Chem. 68, 2193-2222 (1996). In addition I have added the 1995 IUPAC values for atomic weights published in Pure Appl. Chem., 1996, 68, 2339-2359. Some of the changes were added earlier last year but the details of all the changes and additions are now available. If you are interested in Enzyme Nomenclature I have added all of category EC 3.4 The Proteases. Details are provided of 270 enzymes which cleave proteins and peptides. Please note that the URL of this site was changed last November to that given below. For the moment the old address will work - but not for ever ! If you are interested in receiving direct information on changes to this data base send a message to g.p.moss(a)qmw.ac.uk requesting update information and giving your e-mail address and name. This mail list is only used by me for this purpose. Gerry Moss ___________________________________________________________________ Dr GP Moss Telephone: +44 171 775 3262 Department of Chemistry Queen Mary & Westfield College Facsimile: +44 181 981 8745 Mile End Road London E1 4NS, United Kingdom E-mail: g.p.moss(a)qmw.ac.uk World Wide Web server: http://www.chem.qmw.ac.uk/ IUPAC data base: http://www.chem.qmw.ac.uk/iupac/ ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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ChemDraw
by Terry M. Gray 20 Jan '97

20 Jan '97

Here's yet another alternative that I've used. Adobe PageMill, WYSIWYG HTML editor, will automatically convert a PICT image to a GIF when you drag a PICT from another document (ChemDraw or a word processor, if you images are already out of ChemDraw). It takes me about 5 minutes to convert a WordPerfect test with several ChemDraw images into HTML. First I save the WP document as HTML. Open it with PageMill, then drag the graphics into the PageMill document and they get automatically converted to GIF. TG _____________________________________________________________ Terry M. Gray, Ph.D. Department of Chemistry and Biochemistry Calvin College 3201 Burton SE Grand Rapids, MI 40546 Office: (616) 957-7187 FAX: (616) 957-6501 Email: grayt(a)calvin.edu http://www.calvin.edu/~grayt *This mission critical message was written on a Macintosh with Eudora Pro* A special message for Macintosh naysayers: http://www.macworld.com/pages/july.96/Column.2204.html ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Internet 2
by Jan Labanowski 19 Jan '97

19 Jan '97

Dear, You may want to visit http://www.internet2.edu to see how some universities, who can afford it, work on ensuring their leadership in the use of Internet in providing cutting edge "distance teaching" capability. Jan Labanowski jkl(a)osc.edu ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Best on the web (Chemistry)
by Jeffrey J Gosper 17 Jan '97

17 Jan '97

Does anyone who the URL containing the summary of the Chemsitry: Best on the Web survey? /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper(a)brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Powder Diffraction Program 'Dragon' on the PDPL suite (Daresbury
by M Cole 17 Jan '97

17 Jan '97

Hi there, I am trying to run the program 'DRAGON' on the PDPL suite (Powder Diffraction) at Daresbury but I am unable to gain access to it. I can use all the other programs on the PDPL suite with the exception of dragon. This suite of programs is accessed via the xrdsv1 server at Daresbury Labs. Has anyone-else encountered such problems ? Mike Cole Chemistry Department Manchester Metropolitan University Manchester. M1 5GD. Tel. (0161) 247 1427 ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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URL required
by Jeffrey J Gosper 14 Jan '97

14 Jan '97

Could someone provide the URL for the results of the Chemistry on the Internet: The best of the Web 1996 exercise. Thanks /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper(a)brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Re: Chemdraw images
by GRIFFITHSJ＠rsc.org 13 Jan '97

13 Jan '97

Subject: Re: Chemdraw images Author: a.k.hughes(a)durham.ac.uk at INTERNET Date: 13/01/97 11:49 >I have a number of structures created in Chemdraw, and would like to include >these in my web pages. The program does not offer a .gif extension file >type. Could anyone suggest how I might do this please? > There are several ways to achieve this. You could open the files using a free program aptly named "ChemWeb". This is available from www.softshell.com (certainly for PCs it is). This allows you to open chemdraw files and directly export them as gif files. However, I've found the quality of the gif files to be a little ropy ... My preferred method is to use the screen capture method available in several of the graphic packages. I believe Paint Shop Pro (free?) has this facility. With PSP, there are various capture options (e.g. application screen, working area, etc) and this just grabs the image you desire and creates a bitmap file within PSP. Using the SaveAs facility generates the desired gif image. Hope this helps Griff ---------- Dr Jonathan Griffiths 1) The CLIC Consortium - http://chemcomm.clic.ac.uk/ 2) NewMedia, The Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge, United Kingdom Tel/Fax: +44 (0)1223 432136/420247, http://chemistry.rsc.org/rsc/ ---------- ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Re: Chemdraw images
by jsb2＠camsoft.com 13 Jan '97

13 Jan '97

>I have a number of structures created in Chemdraw, and would like to include >these in my web pages. The program does not offer a .gif extension file >type. Could anyone suggest how I might do this please? If you're on Windows, the simplest solution would be update to ChemDraw 4.0, which *does* support GIF. If you're on Mac, wait about 2-3 weeks then do the same thing. (The Windows version made it through production first, with the Mac version trailing behind somewhat). More information on ChemDraw 4.0 is available at our WWW site, http://www.camsoft.com If you need an immediate Macintosh solution, I would also recommend clip2gif, which has already been strongly endorsed by others on this list. Jonathan Brecher CambridgeSoft Corporation jsb(a)camsoft.com ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Re: ChemDraw structures
by Mitch Miller - MDL Information Systems, Inc. 13 Jan '97

13 Jan '97

I see there have been a number of responses, but please permit me to offer one more. I believe the current version of ChemDraw allows one to save a structure as a molfile or pdb file. Using either of these formats, it's advantageous to encorporate the structure in a Web page using the format <embed src="filename.pdb" height=200 width=200 ...> so that the structure can be viewed with a Chemical MIME plug-in, such as Chemscape Chime. This offers the viewer of the page the opportunity to rotate the structure, resize, change several viewing options and even save to disk. The structure remains a 'live' chemical object, rather than simply a graphic. My two cents worth. Mitch Miller >I have a number of structures created in Chemdraw, and would like to include >these in my web pages. The program does not offer a .gif extension file >type. Could anyone suggest how I might do this please? >---------------------------------------------------------------------------- >M.R.Danson E mail: M.Danson(a)lboro.ac.uk >Teaching Support Officer Phone: 01509 222561 >Chemistry Department >Loughborough University >Loughborough >Leicestershire >LE11 3TU Mitchell Miller, Ph.D. e-mail: mitch(a)mdli.com MDL Information Systems (801) 569-1390 "It is better to die on your feet than live on your knees." - Dolores Ibarruri ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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