Comments on: How to use ChemSpider webservices from Knime

By: Aileen Day

Aileen Day — Tue, 21 May 2013 16:16:29 +0000

Perhaps you could email me (chemspiderdec@rsc.org) with more details of what you’re trying to do. For example, if you could send screencaptures of how you’re configured the node, that might help us track down the problem…

By: Brian Masek

Brian Masek — Mon, 20 May 2013 17:57:08 +0000

Hi – I’ve configured a KNIME workflow as you suggest in your example, but the Generic Webservice Client node status is red (not executable). I can’t figure out what’s wrong. Any suggestions?

By: Aileen Day

Aileen Day — Fri, 21 Dec 2012 09:39:22 +0000

Great – glad you worked it out Robert!

By: Robert Mostyn

Robert Mostyn — Thu, 20 Dec 2012 22:03:56 +0000

I have answered my own question… register for a security token. Once I got my token everything started to work!

By: Robert Mostyn

Robert Mostyn — Thu, 20 Dec 2012 17:43:21 +0000

Hi. I am at the beginning of a research project that involves referencing specific chemical compounds. The project aims to track the throughput of all chemical compounds through industrial processes.

I am trying to work out whether ChemSpider will be use to this project. I am trying to test the web service and the only service call I get a result from is GetDatabases. Easy – it doesn’t require any parameters! But other service calls are difficult because I cannot provide valid parameters – probably because the parameters names are not intuitive and I am not providing valid values.

One success is SearchByFormula2… requires a Formula… I enter C9H8O4 and I get an array of numbers back. But I don’t know what to do with the numbers. Is there some documentation that describes the interface at a higher level than WSDLs?

By: Aileen Day

Aileen Day — Tue, 03 Jan 2012 17:03:56 +0000

I can log a feature request for the development team to consider adding a new web service which covers that functionality.
So just to clarify – would you be happy with a webservice into which you enter a CSID and data source type and returns the number of links for each corresponding data source? Or were you thinking of a webservice into which you enter the chemspider id a data source type and it returns the corresponding data sources? Or would either of these options work for you?
In the meantime (the development of a new web service is unlikely to happen immediately) if you email me at chemspiderdev@rsc.org so I have your email address, I could send you a list of all the data sources in ChemSpider with their corresponding data source type (“Contributor classification” in the corresponding Data Source page in ChemSpider). I think with this information and the existing CSID2ExtRefs web service you should have everything you need, even if it is via a longer route.

By: Peter Maas

Peter Maas — Tue, 03 Jan 2012 14:19:19 +0000

Hi Aileen,

I can see why you want to limit this. What I wanted to do is look for a big list of compounds what suppliers are available within ChemSpider. In that respect it would be nice feature to have type of suppliers here (Chemical Vendor, data aggregators, bioinfo, and so on). In that way you would not do a mass download, just the info one is looking for.
It’s just a suggestion. I managed to create a flow going through pubchem to do this task. However, some suppliers are included in chemspider but not in pubchem.

Thanks,

Peter

By: Aileen Day

Aileen Day — Tue, 03 Jan 2012 14:04:45 +0000

Hello,
Glad you’ve got it further with this.
The CSID2ExtRefs web service requires the entry of at least one datasource, and this is by design of the webservice itself (so that it can be of use to find links to specific data sources of interest, but to prevent the mass harvesting of links from ChemSpider) rather than a limitation of Knime.
So I’m afraid I can’t advise you of any way around this…
Regards,
Aileen

By: Peter Maas

Peter Maas — Fri, 30 Dec 2011 10:02:57 +0000

Hi Aileen,

I got this all up and running and it seems to be working OK.
However, I was trying to download all possible data sources for a certain entry using CSID2ExtRefs.
Within Knime this requires a string for .
When entering a datasource it does return the right information but I want all entries.
When leaving blank Knime gives me an error ordering me to fill this field.
Probably this is a limitation of knime.
Is there a way to get around it?

Thanks,

Peter