lab

 

In the develop of ChAMP it will be necessary to develop controlled vocabularies for some important metadata fields.  As these are identified, they will be added to this page and links to ongoing development in the forums will be added.

Below are presentations related to the ChAMP project

  • Poster presented at the Dial-a-Molecule Annual Meeting in Birmingham, England - July 2014 (PDF)
  • Paper presented at the 248th ACS Meeting in San Francisco, CA - August 2014 (Slideshare)
  • Status update presentation - December 2014 (Screencast)
  • Paper presented at Pittcon 2015 in New Orleans, LA - March 2015 (PDF)
  • Presentation given at NLM, Bethesda, MD - March 2015 (PDF)
  • Paper presented at the 249th ACS Meeting in Denver, CO - March 2015 (Slideshare)

Here is a list of the ontologies important to ChAMP

  • Chemical Entities of Biological Interest (ChEBI)
  • Chemical Information Ontology (CHEMINF)
    See also: Michel Dumontier. "The chemical information ontology: Provenance and disambiguation for chemical data on the biological semantic web. PLoS ONE 6, e25513+ (2011) doi:10.1371/journal.pone.0025513
  • Eagle-i resource ontology (ERO)
  • Ontology for Biomedical Investigations (CHMO or CMO)
  • Chemical Methods Ontology (CHMO or CMO)

And then there are the vocabularies...

They say that necessity is the mother of invention.  Whoever 'they' are, it seems to be a true statement.  I wanted to do something useful, creative, and well, publishable ( :) ) during my sabbatical.  And so, when I was lucky enough to strike up a conversation with Tony Williams at the 246th ACS meeting in Indianapolis, I suggested that we work a project together.  Then I had to come with something, and fast...

Being an analytical chemist turned cheminformatician made the scope of any proposed project at the same time limited and obvious.  Tony and his team are working on the RSC's data repository, the next big project since ChemSpider (https://www.chemspider.com) and so, after some discussion, we came up with 'Data Standards for Representation and Annotation of Analysis Information'.  This project proposal outlined the idea of developing ChAMP as the basis by which the RSC could text mine its archive of over 300,000 research papers for any reported analytical methodology.

I guess it goes without saying that the proposal was funded as you would not be reading this if it weren't.  In the six months since then I have had many ideas that continue to reinforce that this idea is a really good one.  I have been fortunate enough in my academic career to work on a number of projects that contribute to my perspective on the fundamental need for ChAMP such as:

So, the scope of ChAMP is broad with many user communities, perspectives, and needs.  The nice thing is this is not a standards project.  Even though the original proposal has 'Standards' in the title (and in some way we are going to 'standardize' some things), the platform will not be a monolithic mandate to the masses about how to annotate a chemical analysis.  It will be a platform that describes metadata elements, controlled vocabularies, ontologies, and datatype specifications such that:

  1. Standards can be built from the platform to fit the need of particular fields/application areas (e.g. pharmaceuticals, environmental)
  2. Educators can teach chemical analysis using defined vocabulary terms (and potentially create teaching material linked to those terms)
  3. Publishers/authors can annotate papers as they are accepted, making comparison to existing research easier
  4. Analysts can move toward consensus about the 'Minimal Amount of Information' needed to characterize different analytical techniques (see MIAME)
  5. Integration of chemical analysis information into the semantic web is easy

It is obvious that this project is going to take time, certainly longer than my sabbatical. So, my job is to gather data on what's been done, identify the needs of the community (help me!), write first drafts of metadata/vocabularies/ontologies/best practices, catalyze discussion around this topic and encourage participation.  To me this sounds like fun and I am 'ChAMPing' at the bit - as it were. SJC.