[MOBY-l] ideas from the CRIB

Sat Mar 1 00:00:53 UTC 2003

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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