[MOBY-l] ideas from the CRIB

Mon Mar 3 15:43:19 UTC 2003

chris just committed a relationship ontology to the GO cvs
repository I believe last week sometime. its pretty rudimentary,
but its structured and provides a seeding mechanism to
build from.

-s

On Friday, February 28, 2003, at 07:00 PM, David Block wrote:

> Hi moby-ites!
> I'm attempting to surface for a moment, then go back to lurking.
>
> I've been wanting to see a relationship ontology ever since our 
> SymGene project started, and indeed, I spoke with Michael Ashburner 
> about developing one, and he said that he had also started in on such 
> an ontology.
>
> I got to a similar place and set it aside, but since Singapore is 
> bringing ontology support to BioSQL, it may be just about time to pick 
> it up again, for us.  We want to track the metadata that connects two 
> biological entities within our data warehouse, so we need something 
> like RO.
>
> I was told to use the tools developed for GO to build an ontology, 
> then submit it.  So maybe I will, but for sure it needs to be a group 
> effort.  Of course, an unambiguous starting point would be nice, but 
> then it needs to be grown carefully, with some central authority 
> pruning down community contributions into a logical, non-redundant 
> system.
>
> Sounds like it needs another mailing list :-)
>
> If this is off-topic, respond off-list.  But I'm very interested in 
> whatever develops here.
>
> Dave
> GNF
> dblock at gnf.org
> waiting for a new hard drive for my beloved, but battered laptop
>
>> -----Original Message-----
>> From: Heiko Schoof [mailto:h.schoof at gsf.de]
>> Sent: Friday, February 28, 2003 9:18 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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