[MOBY-l] ideas from the CRIB

[Chris Wroe]

Richard,

We've been working on using description logic based DAML+OIL to represent 
GO. The description logic folk have though a lot about what it is to be a 
relationship and many of those features have found their way into the 
DAML+OIL language. The is-a or subsumption relationship is central to 
logical inference and is considered separately from other relationships. 
All other relationships are confusingly called properties. They can be 
arranged into a taxonomy / DAG. They can have inverses (e.g. part-of / 
has-part), can be symmetrical, transitive (a part of a part of the whole is 
part of the whole), have valid subjects and values etc.
These features are useful if you want to start defining concepts in terms 
of their relationships to other concepts, as we are doing in our work. 
(e.g. carbohydrate metabolism -is a- metabolism which -acts on- carbohydrate)

Saying all that, from my experience using all this complexity from the 
start is not the way to go, especially for the intended use in BioMOBY. 
Much better to concentrate  early on getting consensus between the 
community of developers on what should go in and later on investigating the 
use of description logics to manage and deliver the ontology. I would be 
happy to help do the latter.

Chris


At 17:35 28/02/2003 -0800, Bruskiewich, Richard (IRRI) wrote:
>Heiko,
>
>It's interesting to see how thinking in the international community is
>converging upon a similar overall strategy. Chris Mungall at al. have a very
>similar view on how the GO consortium ontologies need to evolve, towards a
>more descriptive logic based approach. It would be interesting to exchange
>ideas with them on that.
>
>Richard
>
>-----Original Message-----
>From: Heiko Schoof [mailto:h.schoof at gsf.de]
>Sent: Saturday, March 01, 2003 1:18 AM
>To: Mark Wilkinson
>Cc: mobyl
>Subject: [MOBY-l] ideas from the CRIB
>
>
>Hi Mark,
>happy to see my ideas mirrored.
>
>To get some grip on the vastness of relationship space, I was
>immediately talking about an ontology... meaning, we can start with
>basic classes, and anyone who wants to get finegrained can go down the
>hierarchy forever if he wants, as long as toplevel users can still use
>the basic classes and get what they expect.
>
>To design an ontology, though, is a mindblaster of a problem, especially
>if it's to stand up to trial without having to be changed. For sure it'd
>need to make sure it doesn't integrate orthogonal ideas. I'm afraid that
>your "Primary" and "Secondary" reference thing already rings all alarm
>bells with me there: The concept of whether a relationship is firsthand
>or more cirmumstantial is, in my view, orthogonal (i.e. a different
>means of classification) from the type of relationship, e.g. isa, hasa.
>And should thus go into a separate ontology. To your concrete example:
>
>MyLiverCancerGene isReferredToIn PubMedCitation1
>MyLiverCancerGene isA TyrosineKinase
>MyLiverCancerGene has KeywordLiverCancer
>TyrosineKinase isReferredToIn PubMedCitation2
>LiverCancer isReferredToIn PubMedCitation3
>
>are all valid statements in my view. What I understand you are
>suggesting is to put in a CRIB:
>
>isReferredToIn (primaryReference) PubMedCitation1
>isA (primaryReference) TyrosineKinase
>has (primaryReference) KeywordLiverCancer
>isReferredToIn (secondaryReference) PubMedCitation2
>isReferredToIn (secondaryReference) PubMedCitation3
>
>Which I would strongly want to avoid, and I have already written the
>example in a way to show that the primary/secondary business is to my
>view separate from the relationship business. Instead, I'd put in the
>CRIB:
>
>isReferredToIn PubMedCitation1
>isA TyrosineKinase
>has KeywordLiverCancer
>
>And use MOBY to jump on from there, retrieving the TyrosineKinase object
>that contains in the CRIB:
>isReferredToIn PubMedCitation2
>
>and the KeywordLiverCancer object that contains:
>isReferredToIn PubMedCitation3
>
>What do we have Moby for, if not for following up those indirect
>relationships?
>
>For the relationship types, we need to sit down with an information
>theorist, I'd guess. I keep starting with basic things like isA, partOf,
>hasA, but I never know when I'm complete.
>
>isA: This contains all the identity, synonyms, heredity stuff. In Mark's
>terms: IdenticalTo, RelatedTo, FamiliarWith (except I don't agree about
>the individual exons, that's partOf. FamiliarWith in my reading means
>that I can move from one to the other object through some simple
>transformation, e.g. evolution, translation, and so on, but it's a
>one-on-one relationship (that doesn't exclude it occuring many times on
>one object))
>
>partOf: where one is more than the other, one is contained in the other,
>e.g. exons and introns are parts of a transcript, domains are parts of a
>protein, loci are parts of a chromosome.
>
>hasA: attachment, but not isA or partOf. This is all the annotation
>stuff, the references, keywords, GO terms, and so on.
>
>I'd be already very happy if we implemented just that very basic
>distinction, three base classes of relationships, with the option to
>refine them later. It'd immediately allow to differentiate between
>annotation and identity. Maybe a distinction in the isA part is
>valuable, identicalTo as an isA that is in the same scope and level
>(e.g. an EMBL acc and a SWISSPROT ID) and inheritsFrom as an isA on a
>different level (e.g. an enzyme that inheritsFrom an EC class or an
>organism that inheritsFrom a species that inheritsFrom a genus or a
>protein "TYRK" that inheritsFrom a gene "tyrk" that inheritsFrom a
>genefamily "Tyrosine Kinases" that inheritsFrom "Kinases" etc...)
>
>So, Mark, I even underbid your dozen types ;-)
>
>Best, Heiko
>
>------------------------------------
>Dr. Heiko Schoof
>Technische Universitaet Muenchen
>-Genome Oriented Bioinformatics-
>Wissenschaftszentrum Weihenstephan
>85350 Freising
>Germany
>
>Tel. +49 8161 71 5632
>Fax +49 8161 71 5629
>h.schoof at wzw.tum.de
>http://binfo.bio.wzw.tum.de
>
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