All Notebooks | Help | Support | About
5th June 2013 @ 17:32

For CSSP

  • author roles to be included
  • change "compound being made" to "compound(s) being made"
  • when you save it the save button disappears because it goes under the toolbox
  • if email address for an author is blank then don't include (Peter Scott suggested)

ChemSpider

  • allow "assignment of peaks" to be new field for spectra uploaded to ChemSpider
  • Need corresponding (image?) field to be added to show molecule with atoms labelled so that peak assignments make sense
  • scale spectra images that are big (see 29211612)
  • external links id gets lost
  • deal with v3000 mol files
  • weird characters in depositions don't go

For LabTrove

  • define metadata dropdown in template Artifact 3614188
  • allow default values, dropdown lists, checkboxes and dates to be specified for fields in templatesArtifact 3614189 - ammended to add hyperlinks, links to blog posts and uploadfiles too
  • "upload" box is awful!
  • "Reason for edit" field is annoying
Linked Posts
3rd June 2013 @ 14:06

Find a reaction, put the compound(s) made in it into LabTrove using the ChemSpider compound and associated data template and into ChemSpider (if it's a pure compound - not a mixture) and the reaction that produced it into LabTrove using the ChemSpider SyntheticPages style reaction template and into ChemSpider SyntheticPages.

Example post for J Stec's thesis: 

JS Thesis 10_08.12.09 Final VI.pdf
, compound 4.82d, and the reaction that forms it:

Putting compound data into LabTrove and ChemSpider:

  • ChemSpider ID can be found by doing a search on ChemSpider on the page http://www.chemspider.com/Search.aspx. Try a search on name first, and then structure if not.
  • Input into LabTrove:
    • Use ChemSpider compound and associated data template (with help page
    • title of post is name of compound followed by reference number
    • all data needs to be for pure compound (not mixture)
    • Spectra files - if it's for the compound (not a mixture etc.) then store it here. If so need to track down each source file, save it as a jcamp files (jdx/dx) and as a pdf and then upload these files into the page and put a link into the table for spectra
    • paste peak assignment text into Comments box for each spectrum
  • Input into ChemSpider:
    • Will be more instructions about this in training by ChemSpider curators
    • Click on Deposit Structuresin Depositions menu
    • load mol to deposit
    • External ID: is title of page in LabTrove formatted e.g. like: "Characterisation of rac-3-Hexyl-2-methyltridec-4-yn-2-ol (4.82d)" LabTrove ELN post
    • External URL: is the link to the LabTrove post
    • Description and Tags are just copied from fields with same names in LabTrove template
    • Identifiers are copied from Chemical Name, Common Name and Synonyms fields in LabTrove template

Putting reactions into LabTrove and ChemSpider/CSSP:

  • Input into LabTrove:
    • Submissions page is: http://cssp.chemspider.com/ArticleImport.aspx
    • Use ChemSpider SyntheticPages style reaction template (with help page
    • Author2 is whoever wrote the thesis
    • "Procedure or transformation" you’ll have to put together yourself – find nearest subtitle for inspiration, and include name of product to make it unique. Make it be the same as the title of this LabTrove post.
    • "Compound being made" – see if you can get it from the contents, or list of compounds at end, or failing all else use a structure to name generator once it has been drawn out. Mark it up as link to compound page in LabTrove.
    • "Chemicals used" from description of reaction, contents, list of compounds or name to structure generator (are supplier, concentration or purity available in lab notebook)? Do a ChemSpider search for each one and mark them up as a link to ChemSpider if so (with format e.g. http://www.chemspider.com/Chemical-Structure.28605365.html). If the compound is in chemspider but the name isn't there or approved then add it as a synonym. If the compound isn't in ChemSpider then add it.
    • "Procedure" copy from end section
    • "Authors Comments" from lab notebook?
    • "Lead reference" is thesis title unless it's been published somewhere 
    • "Data" - just put in types of spectra that characterised product
    • "Data file 1"etc. – for spectra for pure compounds (already loaded in compound characterisation page) then just put in links to data files already loaded up. If they haven't been loaded (for mixtures etc.) then upload the jdx file into this page and put a link to it in the boxes here. The 
    • Also pdf any relevant pages in the thesis and upload the files to the labtrove post (just at the end of it, no need to link in it)
    • watch out for weird symbols when pasted in (check how it looks once published)
    • to make the "Scheme" structure and image file, copy and paste the reaction from the thesis into ChemDraw CSSP template (
      CSSP.cds
      ), take out intermediates. Will be more instructions about this in training by ChemSpider curators
  • Input into CSSP: 
    • copy and paste from LabTrove post above into CSSP article import page
    • Some extra fields to manually make for now are:
    • Author1 is you
    • Abstracted submission field - original url will be to LabTrove post, and ID with be e.g. "Whitby group ELN LabTrove post ID 42193" (post ID viewable in url of post)
    • leave embargo field blank
    • Will be more instructions about this in training by ChemSpider curators

If you have any feature requests for CSSP, ChemSpider, or LabTrove add them to here: Feature requests

Attached Files