Ontology meeting 2023-09-18
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- Group members: Pascale, Raymond, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul
- Present: Pascale, Raymond, David, Jim, Kimberly, Edith, Chris (Val, Paul, Peter, later)
- Regrets:
Precompute inferred taxon constraints and add to ontology release
See https://github.com/geneontology/go-ontology/issues/19759
Odd parent - child relationships for binding MF terms
Edith
Following up on Cell cell-signaling terms
Request was to
- Replace "epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification GO:0060802, with epiblast cell-extraembryonic ectoderm cell signaling
- Single EXP to PMID:14511481
- Replace "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation GO:0021937, with: cerebellar Purkinje cell-granule cell precursor cell signaling (def: Any process that mediates the transfer of information from Purkinje cells to granule cell precursors.)
- Chris's slides: Decomposition of macro biological processes in GO
- Following up on last week's discussion, can we propose guidelines for signaling pathways that require that they are described molecularily, and not just at the level of the cell? ie either:
- x receptor signaling pathway
- x (intracellular molecule) signal transduction for cassettes?
If we agree on this, it would make the 2 above terms out of scope. Other similar terms:
- regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling
- neuron-glial cell signaling
- epithelial-mesenchymal cell signaling
- mesenchymal-epithelial cell signaling
- visceral mesoderm-endoderm interaction involved in midgut development
- astrocyte-dopaminergic neuron signaling
- cell-cell signaling involved in cardiac conduction
- epithelial-mesenchymal signaling involved in prostate gland development
- cell-cell signaling involved in mammary gland development
- ectoderm and mesoderm interaction
- mesenchymal-epithelial cell signaling involved in prostate gland development
- mesodermal-endodermal cell signaling
- cell-cell signaling via exosome
- epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification
- glial cell-neuron signaling
- mesenchymal smoothened signaling pathway involved in prostate gland development
- mesenchymal-epithelial cell signaling involved in lung development
- regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling
- stromal-epithelial cell signaling involved in prostate gland development
- positive regulation of dentin-containing tooth bud formation by mesenchymal-epithelial signaling
- regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling
- stromal-epithelial cell signaling involved in prostate gland development
Has_part guidelines
Reaction participants from RHEA
- Is there any documentation describing how this is generated?
- also, how are participants updated when RHEA mappings are updated? See https://github.com/geneontology/go-ontology/commit/8e3fc671c6cb01157304643730795cf344fd792f#commitcomment-126664552 for GO_0033771:
- Def: Catalysis of the reaction: a flavanone + O2 + reduced [NADPH--hemoprotein reductase] = a 2-hydroxyflavanone + H+ + H2O + oxidized [NADPH--hemoprotein reductase].
- This is OK
Removed flavanone 2-hydroxylase activity SubClassOf has participant some licodione(1-) flavanone 2-hydroxylase activity SubClassOf has participant some liquiritigenin.
Added flavanone 2-hydroxylase activity SubClassOf has participant some 2-hydroxyflavanones
- Expected addition of flavanone and removal of: FMN(3-) and FMNH2(2-)
- Non-chebi entities are not handled? reduced [NADPH--hemoprotein reductase] and oxidized [NADPH--hemoprotein reductase] >> is this right? this means we dont have *all* reaction participants?
Tickets to discuss
Input versus direct input
https://github.com/oborel/obo-relations/issues/740
BP refactoring- development - GitHub Project
- NTR animal/ plant gross anatomical part developmental process - Raymond
- remove link between reproductive structure development and uberon reproductive structure - Jim
- missing children of post-embryonic animal organ development