PhiBabs935
commented
3 years ago An important additional note.
There is an issue that I noticed, but I didn't address in the OWL file associated with this pull request.
GO: 'establishment of localization' has the OWL definition <'preceded by' SOME 'pathogen transmission process'>. This axiom should be removed, as 'establishment of localization' is far more inclusive than pathogen establishment. It need not involve pathogens at all. This axiom should only be added to the subclass 'establishment of localization in host'.
Terms imported in my recent IDO Core update (in addition to changes made from last pull request, which this succeeds). These terms are also added to the other ontologies.
Note that other previous changes I made to the OWL files are documented in the Updates Google docs for reference
Vector-borne transmission was missing from the last IDO file. I put this back in. Also added more subclasses -added ‘or acellular structure’ to definition of GO:entry into host Added missing axioms for imported ‘directive information content’ entities, including Apollo-SV classes.
Was in VIDO but not IDO, so I added the following to IDO: epitope, antigen, antigen role, epitope role, epitope site. These can also apply to bacteria and eukaryotic pathogens. -In line with this, I updated epitope site so that it has an IDO rather than VIDO namespace
Added OBI:investigation [this is the parent for my ‘surveillance process’ class that was added to OBI.
Immune response-related terms added to all the ontologies:
OBI:adaptive immune receptor, GO:immunoglobulin complex, circulating (synonymous with ‘antibody’), immunoglobulin complex (human), GO:MHC protein complex, MHC class I protein complex, MHC class II protein complex, type I interferon receptor complex
Uberon:anatomical system, immune system NCIT:complement (relabeled as ‘complement system’)
RO:system, ENVO:enviromental system, ecosystem, biome; to serve as superclasses for import of OHMI:microbiome -RO relations for axioms: capable of produces
GO:immune system process; GO:antigen processing and presentation and its subclasses GO:B cell antigen processing and presentation and GO:T cell antigen processing and presentation, dendritic cell antigen processing and presentation, monocyte antigen processing and presentation, macrophage antigen processing and presentation, antigen binding (as well as superclasses molecular_function and binding)
GO:defense response, inflammatory response
GO:primary adaptive immune response, primary adaptive immune response involving T cells and B cells, adaptive immune memory response, adaptive immune memory response involving T cells and B cells, adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains, B cell mediated immunity, immunoglobulin mediated immune response, T cell mediated immunity, T cell mediated cytotoxicity, natural killer mediated immunity GO:cytokine production, cytokine production involved in immune response, T cell cytokine production, B cell cytokine production, chemokine production, type I interferon production, interferon-alpha production, interferon-beta production, interferon-gamma production, interleukin production (various types)
GO:evasion of host immune response, antigenic variation
GO: cellular process, cell motility, vesicle-mediated transport, phagocytosis
PR:CD4 molecule OBI:CD8 receptor NCIT:cytokine, NCIT:chemokine
ERO:antibody reagent. ERO:monoclonal antibody reagent
OBI:immunogen, OBI:immunogen role
Immune response relevant cell classes from Cell Ontology: native cell, leukocyte, myeloid leukocyte, lymphocyte, lymphocyte of B lineage, B cell, mature B cell, Be cell, T cell, mature T cell, effector T cell, cytotoxic T cell, helper T cell, memory T cell, memory B cell, antibody secreting cell, plasma cell (as well as various subclasses and the corresponding GO immunoglobulin antibodies they secrete), dendretic cell, monocyte, phagocyte, macrophage, alveolar macrophages, granulocyte, neutrophil, mature neutrophil,
Protein components of the immune system, from PR: type I interferon, interferon alpha, interferon beta, type II interferon, interferon gamma, class 2 cytokine, IL-10 type, type III interferon, interferon lambda Various PRO terms for interleukins, toll-like receptor GO:Interleukin-12 complex