OBO-Edit Working Group, Tuesday November 17th, 2009 8.30 a.m. PDT
Conference call details:
Outside US: 1-719-867-3417
Action items carried over
I (Terry Meehan, MGI) am generating cross-product definitions in the Cell Ontology. To do this, I load the Cell ontology (CL), the three GO ontologies, PR0 and the Uberon ontology. I accidentally generated a cyclical relationship between the two terms after reasoning (see pictures). I *think* this resulted from using two related GO processes in the cross-product definition but am not sure due to some buggy issues.
- The "Explanation" feature both in the graph editor and in the Assert Implied links panel fail to explain reasoning. This is an issue Amina and Chris are aware of.
- Perhaps related... the Parent editor fails to show implied links, even when the checkbox is checked.
- Tree editor fails to show any relationship between the two terms.
- Should have the verification manager prevented this cyclical relationship from occurring? The reasoner stopped running checks due to the number of errors (>200). Most of these errors are miss-spellings in Uberon.
[Term] id: CL:0000840 name: immature myeloid dendritic cell namespace: cell def: "An immature cell of the myeloid dendritic cell lineage, characterized by high levels of antigen uptake via endocytosis, macropinocytosis, and phagocytosis, and typically found resident in the tissues." [GOC:add, PMID:9521319] is_a: CL:0000782 ! myeloid dendritic cell intersection_of: CL:0000782 ! myeloid dendritic cell intersection_of: capable_of GO:0006897 ! endocytosis relationship: develops_from CL:0000576 ! monocyte
[Term] id: CL:0000841 name: mature myeloid dendritic cell namespace: cell def: "A mature cell of the myeloid dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node." [GOC:add, GOC:tfm, PMID:9521319] is_a: CL:0000782 ! myeloid dendritic cell intersection_of: CL:0000782 ! myeloid dendritic cell intersection_of: capable_of GO:0019882 ! antigen processing and presentation relationship: develops_from CL:0000840 ! immature myeloid dendritic cell