On Friday 04 May 2007, Bob Hanson wrote: > Egon Willighagen wrote: > >for those who use PDB files: > > > >http://cszamudio.spaces.live.com/Blog/cns!9BCF6F9D6772B8F5!1566.entry > > interesting. What does "ontologically incorrect" mean?
An ontology is a set of well defined terms which can be used to describe domain knowledge with. In that sense it is like a 'dictionary' or 'thesaurus' with are sort-of special cases. Where an ontology can have relations between any two terms, a language dictionary restricts itself to 'synonymous' or 'is-like' relations. A thesaurus, like the Gene Ontology, uses a tree like organization as classification. Many things can go wrong in 'ontologies', that is, it is difficult to design them properly, so that anyone actually can interpret 'knowledge' expressed using ontologies. Things that can go wrong are inaccurate or circular definitions, ambiguities, etc. The article refers with "ontologically incorrect" to problems that there are definitions for terms which hint at closely related terms, which have not been defined. It gives the example of "_chem_comp.mon_nstd_class" which is "a description of the class of a nonstandard monomer if nonstandard monomer represents a modification of a standard monomer". There is not a term for non standard monomers which are not modifications of a standard monomer. Apparently, such cases do exist, so the ontology can onlt partly describe the data which it is supposed to cover. Moreover, it uses other terms, like 'modification' which likely is missing from the ontology too; that is, I am sure they do not define how many atoms you may remove/replace/add to get a 'modified monomer' instead of a completely new monomer :) Those who ever worked on a PDB reader, like I did for Jmol, recognizes the first point in the list of problems: the PDB format and the reengeneered mmCIF they used later, has certain bits of information split up over different tables, which makes reading it into an internal representation or a relational DB a nightmare. Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
