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Tool portal

Jim Kaput, 2009-11-03 13:13

It seems to me we should establish a "portal" immediately that provides a set of tools and links that eventually will be in or associated with the database and software suite for the dbNP. For example, Wishart's new paper on his metaboanalyst webserver (Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W652-60. Epub 2009 May 8.MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Xia J, Psychogios N, Young N, Wishart DS.) would be explained with links to that site.

We might also provide links to the new NIH 24hr dietary recall tool ( and perhaps the Viocare FFQ (

while these tools are not "linked" into dbNP nor connected (although Viocare FFQ can be used for a small fee per use, and data downloaded; the NIH 24hr will be free with the same ability to download data), they may provide a "vision" of what dbNP might do down the road.

Our group is also using SenseWear (acclerometer, galvanic skin response, heat flux from skin, near skin temp, with calculated values of calories out - - and these data would have to be uploaded.

Wasyl Malyj at UC Davis is doing heart rate variability for estimating calories out

These would be the "tool" section of dbNP.

One might also start developing the data capture modules (as I understand it - ISA-TAB, although I am using terms of tools I have not used).

As we develop the database, these links would become access into the dbNP suite.

Just some thoughts - comments?

Kees van Bochove, 2009-12-07 15:39

Hello Jim, thank you very much for your comments. I have not yet reacted on them, because we were still in the process of getting the core shape of dbNP together (see [dbNPFeatures]). But by now I can give a more informed reaction, and a proposal on how to implement this. I understand that [MetaboAnalyst] is a web service for the analysis of metabolomics data, and I described it on DbNPInspiration, which serves as a basic list of available omics tools and how dbNP relates to them. You are welcome to correct or add anything there!

Concerning MetaboAnalyst, from the website I can not learn anything about source or licensing, so integrating it (like we probably will do with GenePattern for transcriptomics data processing) is probably out of the question. Also, I could not find out if the MetaboAnalyst hosted site has a SOAP interface, so if we can walk that way is also unclear.

As I already said, at this moment, we are thinking of using a local GenePattern installation for the transcriptomics processing. When there is user interest for the features from MetaboAnalyst, we could use the underlying R procedures and re-package them as GenePattern modules. But for metabolomics, we also work together with NMC, and they are working on incorporating a private metabolomics data processing tool.

As for the NIH tool and SenseWare data, I think incorporating it into dbNP will be difficult indeed, but we could certainly store the resulting data and provide analysis links. We will need to add those requirements to the dbNP technical requirements specifcation at dbNPFeatures.

Greetings, Kees

Filtering ontologies

We asked the expert opinion of Tomasz Amadusiak, Ontocat developer, on the ontology relation filter topic.

Kees van Bochove, 2010-06-16 3:48:10 PM

Hello Tomasz, we are currently working with a project involving Ontocat. Our main next goal would be to be able to filter terms from ontologies using relations as a criteria. I described this topic briefly here: As far as I know, with the BioPortal REST service it is possible to explore relationships (e.g. get childs of a certain ontology), but it is not possible to search or query for a word and also having a relationship criterium. If you have any ideas on how to do this or if you plan on working on the same topic, please contact me. Regards, Kees van Bochove

Tomasz Amadusiak, 2010-06-16 4:20:00 PM

Hi Kees! I had a look at the specs. For the moment it could be done by trimming the search result list to terms that only contain a particular concept in the path to root, i.e. unit of measurement or species as in your example. As it requires a separate query for every term in the search result list it won't be particularly quick. However, we could multithread those requests behind the scenes to get there quicker. Would that work for you? This can only be done for the isa relationships though. To get a path to root along any other axis you would need to download the ontology and process the relationships locally as BioPortal does not support it at the moment. In any case I can email BioPortal guys and ask them when/how such a feature could be implemented on their side as well. Cheers, Tomasz

Kees van Bochove, 2010-06-16 4:29:36 PM

OK, Thanks very much for your reaction Tomasz! I tried to determine via the BioPortal ontology explorer whether for our use cases there are suitable is-a relationships for the NCBI species ontology and the Units of measurement ontologies, but unfortunately this does not seem to be the case. Anyway, thanks for your reaction and I would appreciate it very much if you could email the BioPortal people about this.

Tomasz Adamusiak to BioPortal support, 2010-06-16 6:28 PM

Would it be possible to add a feature (unless it's already possible) to limit a search query to a part of an ontology? Example search only children of Unit_of_Measure in NCI Thesaurus. At the moment the only way I think it could work would be to ask the root path for every term in the result list, which of course is not very effective...

Trish Whetzel 2010-06-16 6:28 PM

Hi Tomasz, Thanks for the feature request. There is a parameter to limit the search to a subtree. More documentation on the 'subtreerootconceptid' parameter is at: Does this meet your needs?

Tomasz Adamusiak, 2010-06-17 11:52 AM

Hi Kees, We'll have this implemented in Ontocat by end of next week. Hope that helps!