[Obo-discuss] Re: Vol 1 #33 - 4 msgs - cell ontology etc comment

[Jonathan B. <jb...@st...>]

From Jonathan Bard


> It seems most of the development ontologies have been subsumed into the
> anatomical ontologies, with the exception of worm, medaka and cereals. Is
> there any plan to do the same for these organisms?

True; but much of development is assayed via temporal changes in anatomy and the
ontologies can also incorporate lineage data and cell-type data (planned)

> Message: 3
> Date: Tue, 4 May 2004 16:50:31 -0700 (PDT)
> From: Chris Mungall <cj...@fr...>
> To: <Obo...@li...>
> Below is a list of redundant relationships in the cell types ontology
>
> Most of these are of the form
>
>   X is_a Y
>   X is_a Z
>   Z is_a+ Y
>
> (where is_a+ is possibly transitive)
>
> One involves develops_from:
>
>   fibrocyte @develops_from@ fibroblast
>   fibrocyte @develops_from@ fibroblast_neural_crest_derived
>   fibroblast_neural_crest_derived @is_a@ fibroblast

This handles the problem that there are 2 sorts of fibroblasts who are
morphologically the same but have different lineages: they can derive from
mesenchyme and from neural crest

> Here's the full list; redundant relationships don't really cause any harm
> but it's nice to keep the ontology free of redundancies

thanks for the analysis

Jonathan


--

Jonathan Bard
Bioinformatics,  Medical School
University of Edinburgh, EH8 9XD, UK
T:  44/0-131-650-3107