From ec60b6314626667c6ec2650210e874d2e84c592e Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 27 Aug 2024 16:01:18 -0500 Subject: [PATCH] Fix almost all unsatisfiability issues --- src/ontology/OntoFox_inputs/GO_input.txt | 7 ++-- src/ontology/OntoFox_outputs/GO_imports.owl | 35 ++++++++--------- src/ontology/modules/assays.owl | 18 ++++----- src/ontology/modules/obsolete.owl | 24 ++++++++++++ src/ontology/obi-edit.owl | 42 +++++++-------------- src/ontology/templates/obsolete.tsv | 1 + 6 files changed, 66 insertions(+), 61 deletions(-) diff --git a/src/ontology/OntoFox_inputs/GO_input.txt b/src/ontology/OntoFox_inputs/GO_input.txt index 8a413b0a..829ce0e5 100755 --- a/src/ontology/OntoFox_inputs/GO_input.txt +++ b/src/ontology/OntoFox_inputs/GO_input.txt @@ -41,6 +41,7 @@ http://purl.obolibrary.org/obo/GO_0004448 # isocitrate dehydrogenase [NAD(P)+] a http://purl.obolibrary.org/obo/GO_0004457 # lactate dehydrogenase activity http://purl.obolibrary.org/obo/GO_0004540 # ribonuclease activity http://purl.obolibrary.org/obo/GO_0005216 +http://purl.obolibrary.org/obo/GO_0005488 # binding http://purl.obolibrary.org/obo/GO_0005575 http://purl.obolibrary.org/obo/GO_0005577 # fibrinogen complex http://purl.obolibrary.org/obo/GO_0005694 @@ -179,8 +180,6 @@ http://purl.obolibrary.org/obo/GO_0140730 # amphiregulin production http://purl.obolibrary.org/obo/GO_0140779 # XCL1 production [Top level source term URIs and target direct superclass URIs] -http://purl.obolibrary.org/obo/GO_0001047 # core promoter binding -subClassOf http://purl.obolibrary.org/obo/OBI_0001588 # binding http://purl.obolibrary.org/obo/GO_0001788 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0001806 @@ -264,7 +263,7 @@ subClassOf http://purl.obolibrary.org/obo/GO_0032991 http://purl.obolibrary.org/obo/GO_0019882 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0019904 -subClassOf http://purl.obolibrary.org/obo/OBI_0001588 +subClassOf http://purl.obolibrary.org/obo/GO_0005488 http://purl.obolibrary.org/obo/GO_0030041 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0030097 @@ -394,7 +393,7 @@ subClassOf http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/GO_0043316 subClassOf http://purl.obolibrary.org/obo/GO_0001906 http://purl.obolibrary.org/obo/GO_0043565 -subClassOf http://purl.obolibrary.org/obo/OBI_0001588 +subClassOf http://purl.obolibrary.org/obo/GO_0005488 http://purl.obolibrary.org/obo/GO_0048869 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0050896 diff --git a/src/ontology/OntoFox_outputs/GO_imports.owl b/src/ontology/OntoFox_outputs/GO_imports.owl index 014e607f..7e04ef73 100644 --- a/src/ontology/OntoFox_outputs/GO_imports.owl +++ b/src/ontology/OntoFox_outputs/GO_imports.owl @@ -89,7 +89,7 @@ - + core promoter sequence-specific DNA binding Binding to a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon. @@ -99,15 +99,6 @@ - - - - - - - - - @@ -313,7 +304,7 @@ - + antigen binding Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. Antigen binding by an MHC protein complex allows the antigen to be displayed to a T cell or NK cell. @@ -514,6 +505,18 @@ + + + + + binding + The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. + + binding + + + + @@ -853,7 +856,7 @@ - + protein domain specific binding Binding to a specific domain of a protein. @@ -1657,7 +1660,7 @@ - + sequence-specific DNA binding Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. @@ -2143,12 +2146,6 @@ XCL1 production - - - - - - diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 729ca80d..f02130ed 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -1040,6 +1040,12 @@ + + + + + + @@ -5443,7 +5449,7 @@ - + @@ -7055,7 +7061,7 @@ - + @@ -8445,12 +8451,6 @@ - - - - - - @@ -8765,7 +8765,7 @@ - + diff --git a/src/ontology/modules/obsolete.owl b/src/ontology/modules/obsolete.owl index bcced89c..46ce6ac3 100644 --- a/src/ontology/modules/obsolete.owl +++ b/src/ontology/modules/obsolete.owl @@ -40,6 +40,12 @@ + + + + + + @@ -834,6 +840,24 @@ + + + + + A peptide binding to an MHC molecule to form a complex. + + The process of material entities forming complexes. + 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. + PERSON: Bjoern Peters, Randi Vita + IEDB + + + obsolete_binding + true + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 4d9c6359..598b8f6c 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -12581,7 +12581,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -14118,11 +14118,11 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + @@ -14840,7 +14840,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -14932,7 +14932,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -14961,7 +14961,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -14979,22 +14979,6 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - binding - A peptide binding to an MHC molecule to form a complex. - - The process of material entities forming complexes. - 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. - PERSON: Bjoern Peters, Randi Vita - IEDB - binding - - - - @@ -15044,7 +15028,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -15073,7 +15057,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -15582,7 +15566,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -21100,7 +21084,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -21128,7 +21112,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -29844,7 +29828,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + epitope binding by adaptive immune receptor is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding. @@ -30716,7 +30700,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + diff --git a/src/ontology/templates/obsolete.tsv b/src/ontology/templates/obsolete.tsv index 46d45302..60fdfb0e 100755 --- a/src/ontology/templates/obsolete.tsv +++ b/src/ontology/templates/obsolete.tsv @@ -48,6 +48,7 @@ OBI:0001572 obsolete cell bound MHC binding constant determination assay metada OBI:0001574 obsolete cell lysate MHC competitive binding assay using radioactivity detection ready for release cell lysate MHC competitive binding using radioactivity competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000227 OBI:0001544 OBI:0001576 obsolete purified MHC binding constant determination assay metadata complete An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant. IEDB PERSON: Bjoern Peters subclass Obsolete Class true IAO:0000103 OBI:0001582 obsolete cell bound MHC direct binding assay ready for release cell bound MHC direct binding direct binding assay measuring MHC ligand binding using MHC derived from a cell IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000103 +OBI:0001588 obsolete_binding metadata complete The process of material entities forming complexes. IEDB A peptide binding to an MHC molecule to form a complex. PERSON: Bjoern Peters, Randi Vita 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. subclass Obsolete Class true IAO:0000228 GO:0005488 OBI:0001611 obsolete purified MHC direct binding assay ready for release purified MHC direct binding direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000103 OBI:0001712 obsolete B cell epitope direct binding assay ready for release direct binding assay A direct binding assay using a assay IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000103 OBI:0001715 obsolete B cell epitope competitive binding assay ready for release competitive binding assay A competitive inhibition of binding assay using a assay IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000103