[Ontology-editors] help wanted getting CL and GO consistent

Chris Mungall cjm at berkeleybop.org
Mon Oct 6 19:39:57 PDT 2008 

The formatting on the sourceforge page makes the report hard to read.  
Here is the same information, with terms listed underneath their  
proposed is_a parents:

** GO:0055001 muscle cell development **
GO:0055013 cardiac muscle cell development

** GO:0048103 somatic stem cell division **
GO:0055057 neuroblast division

** GO:0002262 myeloid cell homeostasis **
GO:0034101 erythrocyte homeostasis

** GO:0048666 neuron development **
GO:0042461 photoreceptor cell development
GO:0060117 auditory receptor cell development

** GO:0048864 stem cell development **
GO:0014019 neuroblast development

** GO:0048468 cell development" [GO:0048468]
GO:0030097 hemopoiesis
GO:0048477 oogenesis            CURRENTLY: part_of

** GO:0043373 CD4-positive, alpha-beta T cell lineage commitment **
GO:0002295 T-helper cell lineage commitment
GO:0002362 CD4-positive, CD25-positive, alpha-beta regulatory T cell  
lineage commitment

** GO:0035315 hair cell differentiation **
GO:0048886 neuromast hair cell differentiation

** GO:0030154 cell differentiation **
GO:0002268 follicular dendritic cell differentiation

** GO:0048665 neuron fate specification **
GO:0042667 auditory receptor cell fate specification
GO:0043704 photoreceptor cell fate specification

** GO:0007281 germ cell development **
GO:0007286 spermatid development
GO:0009554 megasporogenesis
GO:0009556 microsporogenesis

** GO:0042491 auditory receptor cell differentiation **
GO:0060114 vestibular receptor cell differentiation

** GO:0001764 neuron migration **
GO:0021852 pyramidal neuron migration

** GO:0048663 neuron fate commitment **
GO:0009912 auditory receptor cell fate commitment
GO:0046552 photoreceptor cell fate commitment

** GO:0048866 stem cell fate specification **
GO:0010056 atrichoblast fate specification
GO:0010057 trichoblast fate specification
GO:0014018 neuroblast fate specification

** GO:0048646 anatomical structure formation **
GO:0001410 chlamydospore formation
GO:0006949 syncytium formation
GO:0007279 pole cell formation
GO:0030220 platelet formation
GO:0030437 ascospore formation
GO:0034295 basidiospore formation
GO:0034296 zygospore formation
GO:0034300 sporangiospore formation
GO:0034301 endospore formation

** GO:0042387 plasmatocyte differentiation **
GO:0035171 lamellocyte differentiation

** GO:0002295 T-helper cell lineage commitment **
GO:0002296 T-helper 1 cell lineage commitment
GO:0002297 T-helper 2 cell lineage commitment

** GO:0060088 auditory receptor cell stereocilium organization and  
biogenesis **
GO:0060121 vestibular receptor cell stereocilium organization and  
biogenesis

** GO:0002443 leukocyte mediated immunity **
GO:0001909 leukocyte mediated cytotoxicity
GO:0002371 dendritic cell cytokine production

** GO:0010444 guard mother cell differentiation **
GO:0010052 guard cell differentiation

** GO:0048760 parenchymal cell differentiation **
GO:0048758 companion cell differentiation

** GO:0014016 neuroblast differentiation **
GO:0060019 radial glial cell differentiation

** GO:0002363 alpha-beta T cell lineage commitment **
GO:0002364 NK T cell lineage commitment
GO:0043373 CD4-positive, alpha-beta T cell lineage commitment
GO:0043375 CD8-positive, alpha-beta T cell lineage commitment

** GO:0048867 stem cell fate determination **
GO:0007400 neuroblast fate determination
GO:0007402 ganglion mother cell fate determination

** GO:0002066 columnar/cuboidal epithelial cell development **
GO:0007438 oenocyte development

** GO:0030225 macrophage differentiation **
GO:0014004 microglia differentiation

** GO:0060117 auditory receptor cell development **
GO:0060118 vestibular receptor cell development

** GO:0002093 auditory receptor cell morphogenesis **
GO:0060116 vestibular receptor cell morphogenesis

** GO:0002444 myeloid leukocyte mediated immunity **
GO:0002372 myeloid dendritic cell cytokine production

** GO:0030097 hemopoiesis **
GO:0048821 erythrocyte development

** GO:0009912 auditory receptor cell fate commitment **
GO:0060115 vestibular receptor cell fate commitment

** GO:0048865 stem cell fate commitment **
GO:0014017 neuroblast fate commitment

** GO:0030182 neuron differentiation **
GO:0021755 eurydendroid cell differentiation
GO:0035315 hair cell differentiation
GO:0046530 photoreceptor cell differentiation

** GO:0010631 epithelial cell migration **
GO:0007298 border follicle cell migration
GO:0043534 blood vessel endothelial cell migration
GO:0060269 centripetally migrating follicle cell migration

** GO:0002065 columnar/cuboidal epithelial cell differentiation **
GO:0001742 oenocyte differentiation
GO:0031149 sorocarp stalk cell differentiation

** GO:0048863 stem cell differentiation **
GO:0010054 trichoblast differentiation
GO:0010055 atrichoblast differentiation
GO:0014016 neuroblast differentiation

** GO:0048664 neuron fate determination **
GO:0042668 auditory receptor cell fate determination
GO:0043703 photoreceptor cell fate determination

** GO:0048708 astrocyte differentiation **
GO:0060020 Bergmann glial cell differentiation

** GO:0007309 oocyte axis determination" [GO:0007309]
GO:0007310 oocyte dorsal/ventral axis determination   CURRENTLY: part_of

** GO:0021781 glial cell fate commitment **
GO:0060018 astrocyte fate commitment

** GO:0030855 epithelial cell differentiation **
GO:0009913 epidermal cell differentiation



On Oct 6, 2008, at 2:39 PM, Chris Mungall wrote:

>
> We have a set of computable cross-product definitions for a subset  
> of GO-biological process terms referencing cell types. See:
>
> 	http://wiki.geneontology.org/index.php/XP:biological_process_xp_cell
>
> Using the OBO-Edit reasoner we can find implied links in GO. The  
> policy in GO is to redundantly assert links that can be implied by  
> the reasoner through xp defs.
>
> For example, CL says:
>
> * oenocyte is columnar/cuboidal epithelial cell
>
> The xp defs say:
>
> * oenocyte differentiation = cell differentiation that  
> results_in_acquisition_of_features_of oenocyte
> * columnar/cuboidal epithelial cell differentiation = cell  
> differentiation that results_in_acquisition_of_features_of columnar/ 
> cuboidal epithelial cell
>
> Given this, a reasoner will infer:
>
> * oenocyte differentiation is_a columnar/cuboidal epithelial cell  
> differentiation
>
> This link is not present in GO
>
> There is a summary of these results here:
>
> https://sourceforge.net/tracker/index.php?func=detail&aid=1940574&group_id=36855&atid=440764
>
> - Many of these pertain to immunology; Alex suggested waiting on CL  
> revisions based on recent immunology work. This seems reasonable -  
> provided this is reasonably imminent. If not, I think we should just  
> go in and make things consistent.
>
> - The non-immunology ones seem fairly straightforward cases of one  
> ontology being right and the other being wrong.
>
> - David S : can you comment on oenocyte?
>
> I volunteer to make required changes to CL - just send me a list of  
> what needs fixed
>
> I also volunteer to fix GO too (I can check in directly or just send  
> someone an updated file to check in). There's no reason to do this  
> by hand when it can be done with a few clicks in OE. I can also give  
> another demo of how this can be done in OE if people are interested.
>
> Cheers
> Chris
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>

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