Comments on: How Mass Spectrometrists Might Use ChemSpider

By: Chris Singleton

Chris Singleton — Thu, 25 Sep 2008 16:28:12 +0000

I suppose my expectations would be that we can include moeties in a search as we do other physical properties. Such as MW 370, logP from 1-3, with an -NH2 group, like Ilmari suggests. If we could put it into general search terms I think it would be useful for not only for mass spectrocopists, but also the Chemspider community as a whole. Perhaps we could just add qualifiers to the existing substructure search? For example, when you search for a substructure you can have it filter on other properties, like logP or MW as mentioned above.

By: Ilmari Krebs

Ilmari Krebs — Mon, 22 Sep 2008 11:55:02 +0000

A similiar question was on the tip of my tongue last week already. I was wondering if Chemspider offers searching by screen numbers as CAS uses for restricting its substructure searches. From MS point of view one would derive certain functional groups from the spectroscopic data. Searching for a certain formula and filtering the data for existance of these observed functional groups would narrow down the possiblities, hopefully.

By: Antony Williams

Antony Williams — Mon, 22 Sep 2008 05:14:51 +0000

Thanks for the acknowledgment re. the presentation. It’s certainly only showing some of the capabilities. It is NOT yet possible to exclude moeities as well as elements but we are considering doing exactly that. It would be good to align your expectations with our overall development plan so if you could outline your expectations for us that would be great.
We “could” pull out the entire experimental part but I am concerned about overwhelming records. We have expanded the schema to include documents and this will make the connections much better if we do this moving forward.

By: Chris Singleton

Chris Singleton — Sat, 20 Sep 2008 03:09:39 +0000

I love the presentation, it really shows the capability of Chemspider when it comes to analytical searching. Is it possible to include/exclude moeities as well as elements? That was I can select for a particular group for a certain MS mode (carboxylic acid for negative mode for Atmospheric Pressure Ionization, for example)?
Only thing about extracting the experimental approach, is the text mining pretty reliable? Perhaps it would be easier to include the experimental section of the paper in its entirety, rather than pull out the relevant parts for that particular experiment. I know it’s not as elegant, but I’m just wondering about how much effort we’ll need to do in manual curation (if any) if we try to extract only the relevant parts.