[MOBY-l] ontology

[a.garcia at imb.uq.edu.au]

   About Mark's email regarding an ontology for analytical 
methods in bioinformatics. I am here presenting some 
comments, hope they are useful.

An ontology for analytical methods in bioinformatics 
    should ideally allow the discovery of web services 
from 
    the conceptual domain and not from the operational 
domain; 
    the same being true for those cases where users wish 
to 
    define workflows. Ideally the users should be able to 
    define an analysis, independently of whether this is a 
    single step or a workflow; a simple example would be 
    clustal/puzzle clustal/ednadist/ Eneigbor// Econsense 
    clustal/< > .These are three different cases of 
    estimating and realizing phylogenies by executing the 
    three main phylogenetic methods: distance, parsimony 
and 
    maximum likelihood. They may be semantically 
equivalent, 
    but are syntactically different. Some of the reasons 
for 
    having an ontology are explained at 
    http://protege.stanford.edu/publications/ontology_development/ontology101.pdf
    
    The role of the ontology should be to effectively 
identify 
    these kinds of scenarios. Bioinformatic analytical 
methods 
    should be classified according to their conceptual 
value. 
    Classes (concepts) are a part of the ontology, 
properties 
    for each concept describing various features and 
    attributes of the concepts (slots, sometimes called 
roles 
    or properties). A good example is given in the Protege 
    manual. In my view concepts are terms such as 
alignment, 
    from the properties (slots) the ontology should enable 
an 
    identification or at least provide guidance regarding 
    which alignment method to use depending on the case 
    (input). 
    
    Perhaps I misunderstand the structure presented in the 
    email, but following that structure may lead to an 
    ambiguous final result. Is it necessary to include 
    concepts such as: protein database (is-a)      + 
databases connecting other databases (is-a)? This ontology 
should be about analytical methods so is it necessary to 
include databases? Perhaps those are two different 
domains. Analytical methods are one thing and databases 
are another different thing, aren't they? This structure 
slightly resembles the taxonomy of analytical methods over 
which EMBOSS relies. But a taxonomy is not an ontology. 
    
    Analytical methods are always implementations aren't 
they? 
    I mean if they are not implemented then they are not 
    available as web services. Perhaps the case of 
multiple 
    implementations like BLAST (described by the author of 
the 
    email) may be resolved by using the concept of the 
    implementation as the class, for those cases where the 
    same implementation has several concepts slots should 
be 
    able to resolve the ambiguity. 
    
    I am/was working on an ontology for analytical 
methods, 
    I am working with Protegue, and basically I am using 
    bio-catalog as a starting point. The key issue here is 
    that biomoby requires an ontology for web services, 
which 
    is different from an ontology for analytical methods 
(I 
    guess). Well these were just some comments I hope you 
find 
    them useful.