Fwd: Testing Spectral Upload
Jean-Claude Bradley
---------- Forwarded message ----------
From: Antony Williams
Date: Aug 6, 2007 9:52 PM
Subject: Testing Spectral Upload
To: Jean-Claude Bradley <jeanclaud...@gmail.com>
Bob…we are ready to accept spectra on ChemSpider…can you or your students help us test?
Process to Associate Spectra with a Structure
1) In order to be able to submit spectra to the database you must first be a registered user. Visit http://www.chemspider.com/RegForm.aspx and register. This process will include using a received email to confirm registration.
2) Once you have registered please login and update your information on the profile page at http://www.chemspider.com/UserProfile.aspx . This must be updated to complete your registration.
3) For now please do NOT use any of the deposition features…these are being debugged at present. What we want to test is the Spectrum Updating.
4) In order to associate a spectrum (you must login first) simply search for the appropriate structure using the usual approach (via SMILES, InChI or structure drawing). When you have found the correct structure to associate the spectrum then look for ADD SPECTRUM at the top right hand side. PLEASE UPDATE APPROPRIATE SPECTRA – IF YOU ARE UPDATING "FAKE SPECTRA' NOT MATCHING THE STRUCTURE PLEASE SEND THE ID TO US SO WE CAN REMOVE THEM LATER.
5) Clicking on "Add Spectrum" gives the following components on the screen
6) In order to add a new spectrum simply choose from the drop down list and select the type of spectrum you want to upload. Browse to the JCAMP spectrum on your hard drive and select it. Add any comments you would like to see in the text box. This can include details about the sample preparation, observations about the spectrum etc.
7) Click Add Spectrum
8) A few seconds later you should be able to see the Spectrum at the bottom of the screen associated with the record.
KNOWN ISSUES
1) There appear to be issues with the Spectrum Applet under certain versions of Java Plugin (>= v1.6)
2) Sometimes the spectrum cannot be seen even though the spectrum has been uploaded. Please CONTINUE to upload a series of example spectra even if you cannot see them
REQUESTS
1) Please let us know what spectrum types we should add to the drop down list
2) Please send us a list of and PROBLEMS you see
3) Please send us a list of any suggested enhancements you have.
--
Jean-Claude Bradley, Ph. D.
E-Learning Coordinator for the College of Arts and Sciences
Associate Professor of Chemistry
Drexel University
http://drexel-coas-elearning.blogspot.com
http://drexel-coas-talks-mp3-podcast.blogspot.com/
http://usefulchem.blogspot.com
Khalid Mirza
I have uploaded a couple of NMR spectra on chemspider...(Benzaldehyde: http://www.chemspider.com/RecordView.aspx?id=235 ) and others.
Problem: When I uploaded the HNMR of Propionaldehyde, I forgot to select the type of spectrum it was, it was set to -ve ion mass spectrum as default. I reloaded the spectrum with correct choice.
Now the same spectrum appears twice. I hope you can fix it. Thanks.
Khalid - can you try to upload some of our starting material NMRs?
---------- Forwarded message ----------
From: Antony Williams
Date: Aug 6, 2007 9:52 PM
Subject: Testing Spectral Upload
To: Jean-Claude Bradley <jeanclaud...@gmail.com>
Bob...we are ready to accept spectra on ChemSpider...can you or your students help us test?
Process to Associate Spectra with a Structure
1) In order to be able to submit spectra to the database you must first be a registered user. Visit http://www.chemspider.com/RegForm.aspx and register. This process will include using a received email to confirm registration.
2) Once you have registered please login and update your information on the profile page at http://www.chemspider.com/UserProfile.aspx . This must be updated to complete your registration.
3) For now please do NOT use any of the deposition features...these are being debugged at present. What we want to test is the Spectrum Updating.
4) In order to associate a spectrum (you must login first) simply search for the appropriate structure using the usual approach (via SMILES, InChI or structure drawing). When you have found the correct structure to associate the spectrum then look for ADD SPECTRUM at the top right hand side. PLEASE UPDATE APPROPRIATE SPECTRA - IF YOU ARE UPDATING "FAKE SPECTRA' NOT MATCHING THE STRUCTURE PLEASE SEND THE ID TO US SO WE CAN REMOVE THEM LATER.
5) Clicking on "Add Spectrum" gives the following components on the screen
6) In order to add a new spectrum simply choose from the drop down list and select the type of spectrum you want to upload. Browse to the JCAMP spectrum on your hard drive and select it. Add any comments you would like to see in the text box. This can include details about the sample preparation, observations about the spectrum etc.
7) Click Add Spectrum
8) A few seconds later you should be able to see the Spectrum at the bottom of the screen associated with the record.
KNOWN ISSUES
1) There appear to be issues with the Spectrum Applet under certain versions of Java Plugin (>= v1.6)
2) Sometimes the spectrum cannot be seen even though the spectrum has been uploaded. Please CONTINUE to upload a series of example spectra even if you cannot see them
REQUESTS
1) Please let us know what spectrum types we should add to the drop down list
2) Please send us a list of and PROBLEMS you see
3) Please send us a list of any suggested enhancements you have.
--
Jean-Claude Bradley, Ph. D.
E-Learning Coordinator for the College of Arts and Sciences
Associate Professor of Chemistry
Drexel University
http://drexel-coas-elearning.blogspot.com
http://drexel-coas-talks-mp3-podcast.blogspot.com/
http://usefulchem.blogspot.com
--
Khalid Mirza
Graduate Student
The Bradley Research Group
Department of Chemistry
Drexel University
usefulchem.wikispaces.com
Jean-Claude Bradley
Tony at ChemSpider
DEFAULT needs to be "Please Select Type of Spectrum". In this case
it's not an error but an opportunity for improvement so THANKS!
On Aug 8, 1:46 pm, "Khalid Mirza" <khalidsmi...@gmail.com> wrote:
> Tony
> I have uploaded a couple of NMR spectra on chemspider...(Benzaldehyde:http://www.chemspider.com/RecordView.aspx?id=235) and others.
>
> Problem: When I uploaded the HNMR of Propionaldehyde, I forgot to select the
> type of spectrum it was, it was set to -ve ion mass spectrum as default. I
> reloaded the spectrum with correct choice.
> Now the same spectrum appears twice. I hope you can fix it. Thanks.
>
> On 8/7/07, Jean-Claude Bradley <jeanclaude.brad...@gmail.com> wrote:
>
>
>
>
>
>
>
> > Khalid - can you try to upload some of our starting material NMRs?
>
> > ---------- Forwarded message ----------
> > From: Antony Williams
> > Date: Aug 6, 2007 9:52 PM
> > Subject: Testing Spectral Upload
> > To: Jean-Claude Bradley <jeanclaude.brad...@gmail.com>
>
> > Bob...we are ready to accept spectra on ChemSpider...can you or your
> > students help us test?
>
> > *Process to Associate Spectra with a Structure*
>
> > 1) In order to be able to submit spectra to the database you must
> > first be a registered user. Visithttp://www.chemspider.com/RegForm.aspxandregister. This process will include using a received email to confirm
> > registration.
>
> > 2) Once you have registered please login and update your information
> > on the profile page athttp://www.chemspider.com/UserProfile.aspx. This
> > must be updated to complete your registration.
>
> > 3) For now please do *NOT* use any of the deposition features...these
> > are being debugged at present. What we want to test is the Spectrum
> > Updating.
>
> > *4) *In order to associate a spectrum (you must login first) simply
> > search for the appropriate structure using the usual approach (via SMILES,
> > InChI or structure drawing). When you have found the correct structure to
> > associate the spectrum then look for ADD SPECTRUM at the top right hand
> > side. *PLEASE UPDATE APPROPRIATE SPECTRA - IF YOU ARE UPDATING "FAKE
> > SPECTRA' NOT MATCHING THE STRUCTURE PLEASE SEND THE ID TO US SO WE CAN
> > REMOVE THEM LATER.*
>
> > 5) Clicking on "Add Spectrum" gives the following components on the
> > screen
>
> > 6) In order to add a new spectrum simply choose from the drop down
> > list and select the type of spectrum you want to upload. Browse to the *
> > JCAMP* spectrum on your hard drive and select it. Add any comments you
> > would like to see in the text box. This can include details about the sample
> > preparation, observations about the spectrum etc.
>
> > 7) Click Add Spectrum
>
> > 8) A few seconds later you should be able to see the Spectrum at the
> > bottom of the screen associated with the record.
>
> > *KNOWN ISSUES*
>
> > 1) There appear to be issues with the Spectrum Applet under certain
> > versions of Java Plugin (>= v1.6)
>
> > 2) Sometimes the spectrum cannot be seen even though the spectrum has
> > been uploaded. Please CONTINUE to upload a series of example spectra even if
> > you cannot see them
>
> > *REQUESTS*
>
> > 1) Please let us know what spectrum types we should add to the drop
> > down list
>
> > 2) Please send us a list of and PROBLEMS you see
>
> > 3) Please send us a list of any suggested enhancements you have.
>
> > --
> > Jean-Claude Bradley, Ph. D.
> > E-Learning Coordinator for the College of Arts and Sciences
> > Associate Professor of Chemistry
> > Drexel University
>
> >http://drexel-coas-elearning.blogspot.com
> >http://drexel-coas-talks-mp3-podcast.blogspot.com/
> >http://usefulchem.blogspot.com
>
> --
> Khalid Mirza
> Graduate Student
> The Bradley Research Group
> Department of Chemistry
> Drexel University
> usefulchem.wikispaces.com
>
> image002.jpg
> 16KViewDownload
>
> image001.jpg
> 12KViewDownload- Hide quoted text -
>
> - Show quoted text -
Tony at ChemSpider
Just to confirm what you want...you want us to make sure that there is
a link BACK to the originating source... i.e back to your webpage or
wiki or....
If this is what you mean then there is a place for Comments to be
entered when the spectrum is uploaded and what we still need to do is
DISPLAY the entered comments for you to read what the data source is.
Does this suffice?
On Aug 8, 3:59 pm, "Jean-Claude Bradley"
<jeanclaude.brad...@gmail.com> wrote:
> Tony,
> I saw how nicely the spectra expand. Is there a way to add a hyperlink to
> the spectrum source?
>
> On 8/8/07, Khalid Mirza <khalidsmi...@gmail.com> wrote:
>
>
>
>
>
>
>
> > Tony
> > I have uploaded a couple of NMR spectra on chemspider...(Benzaldehyde:
> >http://www.chemspider.com/RecordView.aspx?id=235) and others.
>
> > Problem: When I uploaded the HNMR of Propionaldehyde, I forgot to select
> > the type of spectrum it was, it was set to -ve ion mass spectrum as
> > default. I reloaded the spectrum with correct choice.
> > Now the same spectrum appears twice. I hope you can fix it. Thanks.
>
> > On 8/7/07, Jean-Claude Bradley < jeanclaude.brad...@gmail.com> wrote:
>
> > > Khalid - can you try to upload some of our starting material NMRs?
>
> > > ---------- Forwarded message ----------
> > > From: Antony Williams
> > > Date: Aug 6, 2007 9:52 PM
> > > Subject: Testing Spectral Upload
> > > To: Jean-Claude Bradley <jeanclaude.brad...@gmail.com>
>
> > > Bob...we are ready to accept spectra on ChemSpider...can you or your
> > > students help us test?
>
> > > *Process to Associate Spectra with a Structure*
>
> > > 1) In order to be able to submit spectra to the database you must
> > > first be a registered user. Visithttp://www.chemspider.com/RegForm.aspxandregister. This process will include using a received email to confirm
> > > registration.
>
> > > 2) Once you have registered please login and update your
> > > information on the profile page athttp://www.chemspider
> > > .com/UserProfile.aspx . This must be updated to complete your
> > > registration.
>
> > > 3) For now please do *NOT* use any of the deposition
> > > features...these are being debugged at present. What we want to test is the
> > > Spectrum Updating.
>
> > > *4) *In order to associate a spectrum (you must login first) simply
> > > search for the appropriate structure using the usual approach (via SMILES,
> > > InChI or structure drawing). When you have found the correct structure to
> > > associate the spectrum then look for ADD SPECTRUM at the top right hand
> > > side. *PLEASE UPDATE APPROPRIATE SPECTRA - IF YOU ARE UPDATING "FAKE
> > > SPECTRA' NOT MATCHING THE STRUCTURE PLEASE SEND THE ID TO US SO WE CAN
> > > REMOVE THEM LATER.*
>
> > > 5) Clicking on "Add Spectrum" gives the following components on the
> > > screen
>
> > > 6) In order to add a new spectrum simply choose from the drop down
> > > list and select the type of spectrum you want to upload. Browse to the *
> > > JCAMP* spectrum on your hard drive and select it. Add any comments you
> > > would like to see in the text box. This can include details about the sample
> > > preparation, observations about the spectrum etc.
>
> > > 7) Click Add Spectrum
>
> > > 8) A few seconds later you should be able to see the Spectrum at
> > > the bottom of the screen associated with the record.
>
> > > *KNOWN ISSUES*
>
> > > 1) There appear to be issues with the Spectrum Applet under certain
> > > versions of Java Plugin (>= v1.6)
>
> > > 2) Sometimes the spectrum cannot be seen even though the spectrum
> > > has been uploaded. Please CONTINUE to upload a series of example spectra
> > > even if you cannot see them
>
> > > *REQUESTS*
Jean-Claude Bradley
in...@chemspider.com
the comments field will be enabled as you requested. Watch this space.
On Aug 8, 5:20 pm, "Jean-Claude Bradley"
<jeanclaude.brad...@gmail.com> wrote:
> Tony,
> Yes a hyperlink to the original source would be best. If it is a starting
> material the link will be to an experiment page on the wiki where the
> compound was used. If it is a product the link will be to an experiment
> page with the details of the synthesis.
>
> We could put it in the general comments but a separate field that is an
> active hyperlink would make it easier than copying and pasting a url from
> the comments. (Or better enable the comments to handle hyperlinks)
>
> >http://drexel-coas-elearning.blogspot.comhttp://drexel-coas-talks-mp3...
>
> > > image002.jpg
> > > 16KViewDownload
>
> > > image001.jpg
> > > 12KViewDownload- Hide quoted text -
>
> > > - Show quoted text -
>
> --
> Jean-Claude Bradley, Ph. D.
> E-Learning Coordinator for the College of Arts and Sciences
> Associate Professor of Chemistry
> Drexel University
>
> http://drexel-coas-elearning.blogspot.comhttp://drexel-coas-talks-mp3-podcast.blogspot.com/http://usefulchem.blogspot.com- Hide quoted text -
Jean-Claude Bradley
Understood....already discussed internally and the Hyperlink within
the comments field will be enabled as you requested. Watch this space.
Val at ChemSpider
1. Spectrum type is mandatory with default to nothing.
2. Optional Associated Hyperlink field is added. Anything entered here
will be considered as hyperlink. Remember to put full qualified URL
here.
3. All URL-like strings in Comments field will be automatically
converted into URLs on record view page, so don't wrap URL into anchor
tags.
Hope this is what's required.
Egon Willighagen
On 8/9/07, Val at ChemSpider <va...@chemspider.com> wrote:
>
> Spectrum upload form's changed.
>
> 1. Spectrum type is mandatory with default to nothing.
I recommend to do some validation, as I expect people to pick to wrong
type from time to time... you could simply look at the x range and
values to do some validation, if nothing more useful is present in the
uploaded data (can I upload CMLSpect files?)... it's not fool -proof,
just a useful backup, I think.
Egon
Val at ChemSpider
Makes sense... we already have ESP files submitted. Actually you can
submit whatever JSpecView digests. For now intention is to curate
spectra manually as 1) there are few of them and 2) it's difficult to
filter out junk without human intervention. But as fool-proof some
simple checks would suffice. Thanks for suggestion!
Regards
Val
-----Original Message-----
From: usefu...@googlegroups.com [mailto:usefu...@googlegroups.com]
On Behalf Of Egon Willighagen
Sent: Thursday, August 09, 2007 2:04 AM
To: usefu...@googlegroups.com
Subject: [UsefulChem] Re: Fwd: Testing Spectral Upload