Taxon Constraint: Bone-related terms in Drosophila

[gocentral]

Hi,

Could you please put a never_in taxon constraint on bone-related terms for D.mel/Drosophila/Insecta?

I've tried to list terms that are parent terms or isolated child terms, but there may well be some redundancy.

Thanks

GO:0046849 bone remodeling GO:0060348 bone development GO:0048705 skeletal system morphogenesis GO:0030282 bone mineralization GO:0001503 ossification GO:0008147 structural constituent of bone GO:0071839 apoptotic process in bone marrow GO:0097241 hematopoietic stem cell migration to bone marrow GO:1901706 mesenchymal cell differentiation involved in bone development GO:0003433 chondrocyte development involved in endochondral bone morphogenesis GO:0035602 fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow GO:0035604 fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow GO:0060351 cartilage development involved in endochondral bone morphogenesis GO:0061592 phosphatidylserine exposure on osteoblast involved in bone mineralization GO:1900220 semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis

Reported by: hattrill

Original Ticket: geneontology/ontology-requests/10690

[gocentral]

thanks!

This list actually reveals a few issues with GO. I thought it would be sufficient to place a few high level constraints, e.g. to bone development. But because of missing links in GO, this would be insufficient to catch the errors. E.g. GO:1900220 semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis does not trace a path up to bone development (surprisingly).

What's the priority on this? Unless urgent I suggest we add these after we have completed https://www.ebi.ac.uk/panda/jira/browse/GO-267 (shortly after Texas, hopefully).

Note that in future we will get these constraints via inheritance from uberon, but this may be a few months in the future.

Original comment by: cmungall

[gocentral]

That sounds fine to me.

Thanks,

Helen

On 7 Mar 2014, at 16:35, Chris Mungall wrote:

thanks!

This list actually reveals a few issues with GO. I thought it would be sufficient to place a few high level constraints, e.g. to bone development. But because of missing links in GO, this would be insufficient to catch the errors. E.g. GO:1900220 semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis does not trace a path up to bone development (surprisingly).

What's the priority on this? Unless urgent I suggest we add these after we have completed https://www.ebi.ac.uk/panda/jira/browse/GO-267 (shortly after Texas, hopefully).

Note that in future we will get these constraints via inheritance from uberon, but this may be a few months in the future.

[ontology-requests:#10690] Taxon Constraint: Bone-related terms in Drosophila

Status: open Group: None Created: Thu Mar 06, 2014 01:24 PM UTC by Helen Attrill Last Updated: Thu Mar 06, 2014 01:24 PM UTC Owner: nobody

Hi,

Could you please put a never_in taxon constraint on bone-related terms for D.mel/Drosophila/Insecta?

I've tried to list terms that are parent terms or isolated child terms, but there may well be some redundancy.

Thanks

GO:0046849 bone remodeling GO:0060348 bone development GO:0048705 skeletal system morphogenesis GO:0030282 bone mineralization GO:0001503 ossification GO:0008147 structural constituent of bone GO:0071839 apoptotic process in bone marrow GO:0097241 hematopoietic stem cell migration to bone marrow GO:1901706 mesenchymal cell differentiation involved in bone development GO:0003433 chondrocyte development involved in endochondral bone morphogenesis GO:0035602 fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow GO:0035604 fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow GO:0060351 cartilage development involved in endochondral bone morphogenesis GO:0061592 phosphatidylserine exposure on osteoblast involved in bone mineralization GO:1900220 semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis

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Original comment by: hattrill

[gocentral]

• assigned_to: David Osumi-Sutherland

Original comment by: dosumis

[gocentral]

Adding these now as 'only in taxon' relationships to vertebrata + trying to add missing classifications in GO.

It would certainly be more efficient to simply relate the relevant processes to Uberon bone (or its subclasses). That way, we should be able to infer the missing classifications and inherit the relevant taxon restriction from uberon:bone.

Much or all of this already seems to be in place, e.g:

extensions/x-metazoan-anatomy-readonly.obo has

[Term] id: GO:0060348 ! bone development intersection_of: GO:0048856 ! anatomical structure development intersection_of: RO:0002296 UBERON:0001474 ! results in development of bone element

[Term] id: GO:0060350 ! endochondral bone morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: RO:0002298 UBERON:0002513 ! results in morphogenesis of endochondral bone

& http://purl.obolibrary.org/obo/uberon/ext.owl has taxon constraints on bone

e.g. 'bone element' subClassOf only_in_taxon some 'Vertebrata '

Chris: What's missing from the infrastructure to allow taxon constraint inference from Uberon to just work? Wondering whether I'm just adding assertions that will soon be redundant?

Original comment by: dosumis

[gocentral]

Related ticket: Is it safe to reduce the number of assertions we need to make by propagating over part_of ?

Original comment by: dosumis

[dosumis]

Import of taxon constraints from Uberon (pending) will fix this.