Question: What Is A Good Ontology For Experimental Results
9
gravatar for Dave Bridges
6.7 years ago by
Dave Bridges1.3k
Ann Arbor, MI
Dave Bridges1.3k wrote:

If i want to publish experimental results, preferably via RDFa using a standardized ontology what would be a good source to use. I am thinking of a triple such as:

Protein X --- Interacts with --- Protein Y

Where the ontology would spell out "Interacts with". Are there existing projects that mine the literature and generate triples like this?

ontology • 2.6k views
ADD COMMENTlink written 6.7 years ago by Dave Bridges1.3k

+1 for using RDF

ADD REPLYlink written 6.7 years ago by Pierre Lindenbaum98k

thanks to everyone for the great answers. As i was thinking about it some more, it would be nice for all experimental data to somehow be reproducibly put into the web of data. But i think for that one would require not just simple triples, but also some way to point directly to the result. I guess what I am getting at would be some way that you could represent claims/facts in a triple and then be able to add supporting/dissenting experiments to that claim with a second triple.

ADD REPLYlink written 6.7 years ago by Dave Bridges1.3k
7
gravatar for Casey Bergman
6.7 years ago by
Casey Bergman17k
Manchester, UK
Casey Bergman17k wrote:

I would recommend formatting your data using the IMEx (International Molecular Exchange Consortium) curation guidelines. This will allow you to submit your data easily to any of the participant databases (DIP, MINT, INTACT, etc). IMEx uses The PSI (Proteomics Standards Initiative) Molecular Interactions controlled vocabulary. There is a PSI-MI XML/CV validator here.

Yes, there are effort to mine protein-protein interactions and experiemntal methods from the literature, see the BioCreative PPI tasks. In particular, see the Biocreative 3 IMT (Interaction Method Task) which uses the PSI-MI.

ADD COMMENTlink written 6.7 years ago by Casey Bergman17k

this sounds great for protein interactions, but my question was meant more generally.

ADD REPLYlink written 6.7 years ago by Dave Bridges1.3k
5
gravatar for Nico Adams
6.7 years ago by
Nico Adams450
Cambridge
Nico Adams450 wrote:

To add to the answers here - if you want to broaden the understanding of "publishing experimental results" somewhat to "describing an experiment and the results of the experiment" then the Ontology for Biomedical Investigations is also worth considering. It has notions of experiments, planned outcomes of experiments, real outcomes etc. As an example, here are some axioms defining the term "assay" - which come close to experiment:

has_specified_input some 
    (material_entity
     and (has_role some 'evaluant role'))
has_specified_output only 'information content entity'
has_specified_output some 
    ('information content entity'
     and ('is about' some 
        (continuant
         and (has_role some 'evaluant role'))))
realizes some 'evaluant role'
realizes some (is_concretization_of some 
    ('plan specification'
     and (has_part some 'objective specification')))

There's almost everything there to define an experiment and experimental findings.

ADD COMMENTlink written 6.7 years ago by Nico Adams450

I agree, a broader view of different experiments is worth considering. Another more general experimental ontology is EXPO: http://expo.sourceforge.net/

ADD REPLYlink written 6.7 years ago by Casey Bergman17k
4
gravatar for Pierre Lindenbaum
6.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum98k wrote:

for an ontology describing the interaction, look at the BioPortal and search for a vocabulary. For example:

ADD COMMENTlink written 6.7 years ago by Pierre Lindenbaum98k
2
gravatar for Spitshine
6.7 years ago by
Spitshine620
Esch-sur-Alzette, Luxembourg
Spitshine620 wrote:

There's plenty of work by people maintaining the databases (see Casey Bergman's answer). If you want to start from scratch and not overly rely on complex schemes, do read the principal considerations by Lu et al. from Mark Gerstein's group, which suggests a plain and easy to implement ontology.

ADD COMMENTlink written 6.7 years ago by Spitshine620
2
gravatar for Tomasz
6.5 years ago by
Tomasz50
Milwaukee, WI
Tomasz50 wrote:

The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental factors in ArrayExpress. The ontology has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation, and to integrate external data.

The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps.

ADD COMMENTlink written 6.5 years ago by Tomasz50
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