From bd2b2038b3d306f1c7bab527a0a3b4793e524596 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Tue, 30 May 2023 14:40:07 -0500 Subject: [PATCH 01/12] Update Uberon_imports.owl Committing after initial make imports --- .../OntoFox_outputs/Uberon_imports.owl | 33 +++++++++++++++---- 1 file changed, 27 insertions(+), 6 deletions(-) diff --git a/src/ontology/OntoFox_outputs/Uberon_imports.owl b/src/ontology/OntoFox_outputs/Uberon_imports.owl index ff7c76bf..623d3b65 100644 --- a/src/ontology/OntoFox_outputs/Uberon_imports.owl +++ b/src/ontology/OntoFox_outputs/Uberon_imports.owl @@ -120,6 +120,7 @@ + lymph node Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. @@ -180,6 +181,7 @@ + blood A fluid that is composed of blood plasma and erythrocytes. @@ -192,6 +194,7 @@ + breast The upper ventral region of the torso of an organism. @@ -217,6 +220,7 @@ + throat In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. @@ -279,7 +283,7 @@ anatomical cluster - Anatomical group that has its parts adjacent to one another. + Anatomical group whose component anatomical structures lie in close proximity to each other. anatomical cluster @@ -313,6 +317,7 @@ + epithelium Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. @@ -337,6 +342,7 @@ + aorta The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation. @@ -457,6 +463,7 @@ + adipose tissue Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. @@ -469,7 +476,6 @@ - strand of hair A filament, mostly protein, that grows from follicles found in the dermis[WP]. @@ -544,7 +550,6 @@ - diaphragm A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control. @@ -739,6 +744,7 @@ + cheek A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. @@ -751,7 +757,6 @@ - facial muscle A muscle innervated by a facial nerve. @@ -764,6 +769,7 @@ + coronary artery An artery that supplies the myocardium. @@ -776,6 +782,7 @@ + vein Any of the tubular branching vessels that carry blood from the capillaries toward the heart. @@ -836,6 +843,7 @@ + nasal cavity mucosa The mucous membrane that lines the nasal cavity[MP]. @@ -848,6 +856,7 @@ + minor salivary gland One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. @@ -896,6 +905,7 @@ + milk @@ -958,6 +968,7 @@ + areola Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple. @@ -1007,6 +1018,7 @@ + dermis The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. @@ -1019,6 +1031,7 @@ + hypodermis Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. @@ -1031,6 +1044,7 @@ + skin of body The organ covering the body that consists of the dermis and epidermis. @@ -1055,6 +1069,7 @@ + liver An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. @@ -1079,6 +1094,7 @@ + integument The dermis, epidermis and hypodermis. @@ -1091,6 +1107,7 @@ + peritoneum @@ -1141,7 +1158,6 @@ - forelimb zeugopod The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants. @@ -1203,6 +1219,7 @@ + esophagus mucosa A mucosa that is part of a esophagus [Automatically generated definition]. @@ -1239,6 +1256,7 @@ + trachea The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. @@ -1276,6 +1294,7 @@ + mucosa of nasopharynx A mucosa that is part of a nasopharynx [Automatically generated definition]. @@ -1288,6 +1307,7 @@ + mucosa of oropharynx A mucosa that is part of a oropharynx [Automatically generated definition]. @@ -1396,6 +1416,7 @@ + tibial artery The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot. @@ -1447,7 +1468,6 @@ - brachioradialis Brachioradialis is a muscle of the forearm that acts to flex the forearm at the elbow. It is also capable of both pronation and supination, depending on the position of the forearm. It is attached to the distal styloid process of the radius by way of the brachioradialis tendon, and to the lateral supracondylar ridge of the humerus. @@ -1508,6 +1528,7 @@ + suprapubic skin Area of skin in the hypoastric region of the abdomen. From 55806576cf10893369b216e4c6148f204a92df77 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Tue, 30 May 2023 14:46:19 -0500 Subject: [PATCH 02/12] Adding Uberon terms Added relevant Uberon anatomy terms --- src/ontology/OntoFox_inputs/Uberon_input.txt | 8 ++ .../OntoFox_outputs/Uberon_imports.owl | 102 ++++++++++++++++++ 2 files changed, 110 insertions(+) diff --git a/src/ontology/OntoFox_inputs/Uberon_input.txt b/src/ontology/OntoFox_inputs/Uberon_input.txt index c4340e35..f8d66599 100755 --- a/src/ontology/OntoFox_inputs/Uberon_input.txt +++ b/src/ontology/OntoFox_inputs/Uberon_input.txt @@ -130,6 +130,14 @@ http://purl.obolibrary.org/obo/UBERON_0013757 # capillary blood http://purl.obolibrary.org/obo/UBERON_0036149 http://purl.obolibrary.org/obo/UBERON_3000016 # anterior nasal wall http://purl.obolibrary.org/obo/UBERON_8470000 # placental blood +http://purl.obolibrary.org/obo/UBERON_0001811 # conjunctiva +http://purl.obolibrary.org/obo/UBERON_0000305 # amnion +http://purl.obolibrary.org/obo/UBERON_0001637 # artery +http://purl.obolibrary.org/obo/UBERON_0001893 # telencephalon +http://purl.obolibrary.org/obo/UBERON_0003128 # cranium +http://purl.obolibrary.org/obo/UBERON_0001003 # skin epidermis +http://purl.obolibrary.org/obo/UBERON_0002465 # lymphoid system +http://purl.obolibrary.org/obo/UBERON_0001530 # common carotid artery plus branches [Top level source term URIs and target direct superclass URIs] http://purl.obolibrary.org/obo/UBERON_0000465 # material anatomical entity diff --git a/src/ontology/OntoFox_outputs/Uberon_imports.owl b/src/ontology/OntoFox_outputs/Uberon_imports.owl index 623d3b65..74edfb3f 100644 --- a/src/ontology/OntoFox_outputs/Uberon_imports.owl +++ b/src/ontology/OntoFox_outputs/Uberon_imports.owl @@ -191,6 +191,19 @@ + + + + + + amnion + The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected. + + amnion + + + + @@ -448,6 +461,19 @@ + + + + + + skin epidermis + The outer epithelial layer of the skin that is superficial to the dermis. + + skin epidermis + + + + @@ -705,6 +731,18 @@ + + + + + common carotid artery plus branches + A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. + + common carotid artery plus branches + + + + @@ -771,6 +809,7 @@ + coronary artery An artery that supplies the myocardium. @@ -779,6 +818,19 @@ + + + + + + artery + An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. + + artery + + + + @@ -840,6 +892,18 @@ + + + + + conjunctiva + The mucous membrane that lines the inner surface of the eyelids and the front of the eyeball. + + conjunctiva + + + + @@ -902,6 +966,19 @@ + + + + + + telencephalon + Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. + + telencephalon + + + + @@ -1216,6 +1293,18 @@ + + + + + lymphoid system + The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. + + lymphoid system + + + + @@ -1266,6 +1355,18 @@ + + + + + cranium + Upper portion of the skull that excludes the mandible (when present in the organism). + + cranium + + + + @@ -1418,6 +1519,7 @@ + tibial artery The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot. From 5cba54856f35e4ffe3de1b19925c5f4c38358888 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Tue, 30 May 2023 15:23:50 -0500 Subject: [PATCH 03/12] Added anatomy terms and scratching process term. --- src/ontology/obi-edit.owl | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index b1f9264a..3f6cbe4b 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -22274,6 +22274,19 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + A process in which the target material entity is scraped by another material entity. + Sebastian Duesing + abrading + https://github.com/obi-ontology/obi/issues/1703 + scratching + + + + From 64e40f3bfdbd85ba26d6bfdd8884b8eee746ab8c Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 1 Jun 2023 16:29:07 -0500 Subject: [PATCH 04/12] Adding administration template Adds ROBOT template (administration.tsv) for administration of substance in vivo branch. --- Makefile | 3 +- src/ontology/catalog-v001.xml | 1 + src/ontology/modules/administration.owl | 1054 +++++++++++++++++++++ src/ontology/obi-edit.owl | 1 + src/ontology/templates/administration.tsv | 24 + 5 files changed, 1082 insertions(+), 1 deletion(-) create mode 100644 src/ontology/modules/administration.owl create mode 100644 src/ontology/templates/administration.tsv diff --git a/Makefile b/Makefile index 62939f32..48d477ea 100644 --- a/Makefile +++ b/Makefile @@ -101,7 +101,8 @@ src/ontology/modules/%.owl: src/ontology/templates/%.tsv | build/robot.jar # Update all modules. # NOTE: GNU Make will compare timestamps to see which updates are required. -MODULE_NAMES := assays\ +MODULE_NAMES := administration\ + assays\ biopsy\ biobank-specimens\ organizations\ diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index a32dd939..40b39d6b 100755 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -23,6 +23,7 @@ + diff --git a/src/ontology/modules/administration.owl b/src/ontology/modules/administration.owl new file mode 100644 index 00000000..7a249343 --- /dev/null +++ b/src/ontology/modules/administration.owl @@ -0,0 +1,1054 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the stomach of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intragastric administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the colon of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intracolonic administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the vagina of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + vaginal administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance onto the surface of the skin of an organism. + Sebastian Duesing + percutaneous administration + transcutaneous administration + https://github.com/obi-ontology/obi/issues/1703 + topical administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance to the cervix of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + cervical administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance to the conjunctiva of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + conjunctival administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the trachea of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intratracheal administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the amnion of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intra-amniotic administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the artery of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intra-arterial administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the cerebrum of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intracerebral administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the cranium of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intracranial administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the epidermis of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intraepidermal administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the lymphatic system of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intralymphatic administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An intralymphatic administration in which the substance is administered into a lymph node. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + lymph node administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the urethra of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + urethral administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An intraepidermal administration in which the skin is scratched before the substance is administered to the skin. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + skin scarification administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An adminstration of a substance into the uterus of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intrauteral administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An intra-arterial administration in which the substance is administered into the carotid artery. + Sebastian Duesing + i.c. + i.c. administration + https://github.com/obi-ontology/obi/issues/1703 + intracarotid administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance to the eye of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intraocular administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the placenta of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intraplacental administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the rectum of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intrarectal administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An administration of a substance into the spleen of an organism. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1703 + intrasplenic administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 3f6cbe4b..942bea34 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -38,6 +38,7 @@ + diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv new file mode 100644 index 00000000..a53e6d83 --- /dev/null +++ b/src/ontology/templates/administration.tsv @@ -0,0 +1,24 @@ +ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class target of administration material administered administration technique +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C (('realizes' some 'material to be added role') and ('realizes' some ('target of material addition role' and ('role of' some %)))) SPLIT=| C (('realizes' some ('material to be added role' and (‘role of’ some %))) and ('realizes' some 'target of material addition role')) SPLIT=| C ('has part' some %) SPLIT=| +OBI:0003553 intragastric administration An administration of a substance into the stomach of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo stomach +OBI:0003554 intracolonic administration An administration of a substance into the colon of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo colon +OBI:0003555 vaginal administration An administration of a substance into the vagina of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo vagina +OBI:0003556 topical administration percutaneous administration|transcutaneous administration An administration of a substance onto the surface of the skin of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo skin of body +OBI:0003557 cervical administration An administration of a substance to the cervix of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo uterine cervix +OBI:0003558 conjunctival administration An administration of a substance to the conjunctiva of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo conjunctiva +OBI:0003559 intratracheal administration An administration of a substance into the trachea of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo trachea +OBI:0003560 intra-amniotic administration An administration of a substance into the amnion of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo amnion +OBI:0003561 intra-arterial administration An administration of a substance into the artery of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo artery +OBI:0003562 intracerebral administration An administration of a substance into the cerebrum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo telencephalon +OBI:0003563 intracranial administration An administration of a substance into the cranium of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo cranium +OBI:0003564 intraepidermal administration An administration of a substance into the epidermis of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo skin epidermis +OBI:0003565 intralymphatic administration An administration of a substance into the lymphatic system of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo ('part of' some 'lymphoid system') +OBI:0003566 lymph node administration An intralymphatic administration in which the substance is administered into a lymph node. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intralymphatic administration lymph node +OBI:0003567 urethral administration An administration of a substance into the urethra of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo urethra +OBI:0003568 skin scarification administration An intraepidermal administration in which the skin is scratched before the substance is administered to the skin. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intraepidermal administration skin epidermis scratching +OBI:0003569 intrauteral administration An adminstration of a substance into the uterus of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo uterus +OBI:0003570 intracarotid administration i.c.|i.c. administration An intra-arterial administration in which the substance is administered into the carotid artery. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intra-arterial administration common carotid artery plus branches +OBI:0003571 intraocular administration An administration of a substance to the eye of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo eye +OBI:0003572 intraplacental administration An administration of a substance into the placenta of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo placenta +OBI:0003573 intrarectal administration An administration of a substance into the rectum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo rectum +OBI:0003574 intrasplenic administration An administration of a substance into the spleen of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo spleen From 95e425642810a7dfe230e9a3495fcd1b87465dab Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Mon, 12 Jun 2023 16:21:38 -0500 Subject: [PATCH 05/12] Simplifying axioms as discussed Simplified the logical axioms of administration.tsv as per conversation on 06.05.2023 OBI dev call. --- src/ontology/modules/administration.owl | 808 +++++++++------------- src/ontology/templates/administration.tsv | 2 +- 2 files changed, 314 insertions(+), 496 deletions(-) diff --git a/src/ontology/modules/administration.owl b/src/ontology/modules/administration.owl index 7a249343..5af8f454 100644 --- a/src/ontology/modules/administration.owl +++ b/src/ontology/modules/administration.owl @@ -92,12 +92,6 @@ - - - - - - @@ -109,28 +103,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the stomach of an organism. Sebastian Duesing @@ -145,28 +131,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the colon of an organism. Sebastian Duesing @@ -181,28 +159,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the vagina of an organism. Sebastian Duesing @@ -217,28 +187,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance onto the surface of the skin of an organism. Sebastian Duesing @@ -255,28 +217,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance to the cervix of an organism. Sebastian Duesing @@ -291,28 +245,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance to the conjunctiva of an organism. Sebastian Duesing @@ -327,28 +273,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the trachea of an organism. Sebastian Duesing @@ -363,28 +301,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the amnion of an organism. Sebastian Duesing @@ -399,28 +329,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the artery of an organism. Sebastian Duesing @@ -435,28 +357,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the cerebrum of an organism. Sebastian Duesing @@ -471,28 +385,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the cranium of an organism. Sebastian Duesing @@ -507,28 +413,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the epidermis of an organism. Sebastian Duesing @@ -543,33 +441,25 @@ - - - - - - - - - - - - + + + + + + + + + - - - - - - - + + - - - - - - + + + + + + An administration of a substance into the lymphatic system of an organism. Sebastian Duesing @@ -584,28 +474,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An intralymphatic administration in which the substance is administered into a lymph node. Sebastian Duesing @@ -620,28 +502,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the urethra of an organism. Sebastian Duesing @@ -655,36 +529,28 @@ - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + An intraepidermal administration in which the skin is scratched before the substance is administered to the skin. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 @@ -698,28 +564,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An adminstration of a substance into the uterus of an organism. Sebastian Duesing @@ -734,28 +592,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An intra-arterial administration in which the substance is administered into the carotid artery. Sebastian Duesing @@ -772,28 +622,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance to the eye of an organism. Sebastian Duesing @@ -808,28 +650,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the placenta of an organism. Sebastian Duesing @@ -844,28 +678,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the rectum of an organism. Sebastian Duesing @@ -880,28 +706,20 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + An administration of a substance into the spleen of an organism. Sebastian Duesing diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv index a53e6d83..a6567e16 100644 --- a/src/ontology/templates/administration.tsv +++ b/src/ontology/templates/administration.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class target of administration material administered administration technique -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C (('realizes' some 'material to be added role') and ('realizes' some ('target of material addition role' and ('role of' some %)))) SPLIT=| C (('realizes' some ('material to be added role' and (‘role of’ some %))) and ('realizes' some 'target of material addition role')) SPLIT=| C ('has part' some %) SPLIT=| +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and (‘role of’ some %)) SPLIT=| C 'has part' some % SPLIT=| OBI:0003553 intragastric administration An administration of a substance into the stomach of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo stomach OBI:0003554 intracolonic administration An administration of a substance into the colon of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo colon OBI:0003555 vaginal administration An administration of a substance into the vagina of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo vagina From 52401a1150fec8dc51a032726ece0c2a6a52c1b0 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Wed, 5 Jul 2023 14:42:43 -0500 Subject: [PATCH 06/12] Importing HP:'neoplasm' Added for use for intratumoral administration NTR --- src/ontology/OntoFox_inputs/HP_input.txt | 4 +++- src/ontology/OntoFox_outputs/HP_imports.owl | 18 ++++++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/src/ontology/OntoFox_inputs/HP_input.txt b/src/ontology/OntoFox_inputs/HP_input.txt index a56b9fcc..950dae1f 100644 --- a/src/ontology/OntoFox_inputs/HP_input.txt +++ b/src/ontology/OntoFox_inputs/HP_input.txt @@ -7,11 +7,13 @@ HP [Low level source term URIs] http://purl.obolibrary.org/obo/HP_0000855 +http://purl.obolibrary.org/obo/HP_0002664 #neoplasm [Top level source term URIs and target direct superclass URIs] http://purl.obolibrary.org/obo/HP_0000855 subClassOf http://purl.obolibrary.org/obo/BFO_0000016 - +http://purl.obolibrary.org/obo/HP_0002664 #neoplasm +subClassOf http://purl.obolibrary.org/obo/UBERON_0000465 [Source term retrieval setting] includeNoIntermediates diff --git a/src/ontology/OntoFox_outputs/HP_imports.owl b/src/ontology/OntoFox_outputs/HP_imports.owl index b5497dd6..7510a0e6 100644 --- a/src/ontology/OntoFox_outputs/HP_imports.owl +++ b/src/ontology/OntoFox_outputs/HP_imports.owl @@ -77,6 +77,24 @@ Insulin resistance + + + + + + + + Neoplasm + An organ or organ-system abnormality that consists of uncontrolled autonomous cell-proliferation which can occur in any part of the body as a benign or malignant neoplasm (tumor). + + Neoplasm + + + + + + + From 5c10c1e1779a51a7b261416d6bc7c21b38fe6e6f Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Wed, 5 Jul 2023 15:45:46 -0500 Subject: [PATCH 07/12] Adding intratumoral administration term for IEDB --- src/ontology/modules/administration.owl | 33 +++++++++++++++++++++++ src/ontology/templates/administration.tsv | 1 + 2 files changed, 34 insertions(+) diff --git a/src/ontology/modules/administration.owl b/src/ontology/modules/administration.owl index 5af8f454..a39b21e3 100644 --- a/src/ontology/modules/administration.owl +++ b/src/ontology/modules/administration.owl @@ -92,6 +92,12 @@ + + + + + + @@ -735,6 +741,33 @@ + + + + + + + + + + + + + + + + + + + + + An administration of a substance into a tumor of an organism. + Sebastian Duesing + intratumoral administration + + + + diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv index a6567e16..163ebc00 100644 --- a/src/ontology/templates/administration.tsv +++ b/src/ontology/templates/administration.tsv @@ -22,3 +22,4 @@ OBI:0003571 intraocular administration An administration of a substance to th OBI:0003572 intraplacental administration An administration of a substance into the placenta of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo placenta OBI:0003573 intrarectal administration An administration of a substance into the rectum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo rectum OBI:0003574 intrasplenic administration An administration of a substance into the spleen of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo spleen +OBI:0003603 intratumoral administration An administration of a substance into a tumor of an organism. Sebastian Duesing subclass administering substance in vivo Neoplasm From 2c2e9fa8f5129d6c00de11e0036f2b369ec2e93b Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 20 Jul 2023 14:14:36 -0500 Subject: [PATCH 08/12] Moving some terms from obi-edit into administration.tsv --- src/ontology/modules/administration.owl | 151 ++++++++++++++++++++++ src/ontology/obi-edit.owl | 120 ----------------- src/ontology/templates/administration.tsv | 54 ++++---- 3 files changed, 180 insertions(+), 145 deletions(-) diff --git a/src/ontology/modules/administration.owl b/src/ontology/modules/administration.owl index a39b21e3..a20cd8a0 100644 --- a/src/ontology/modules/administration.owl +++ b/src/ontology/modules/administration.owl @@ -22,6 +22,18 @@ + + + + + + + + + + + + @@ -40,6 +52,12 @@ + + + + + + @@ -98,12 +116,133 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intraperitoneal administration + Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h + The administration of a substance into the peritoneum of an organism + Person:Bjoern Peters + intraperitoneal administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intranasal mucosal administration + The administration of a substance into the intranasal mucosis of an organism + Melanie Courtot + intranasal mucosal administration + + + + + + + + + + + + + + + + + + + + + + + + + antibiotic administration process + Administering substance in vivo where an antibiotic substance is adminstered to a living organism. + Chris Stoeckert + Cristian Cocos + Jie Zheng + Penn Group + antibiotic administration process + + + + + + + + + in vivo challenge + The administration of a challenge to a live host. + Hector Guzman-Orozco + IEDB + in vivo challenge + + + + @@ -882,6 +1021,12 @@ + + + + + + @@ -897,6 +1042,12 @@ + + + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 942bea34..2062092e 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -6731,48 +6731,6 @@ that has_part some material entity is a material entity. If we add as equivalent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - intraperitoneal administration - Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h - - The administration of a substance into the peritoneum of an organism - Person:Bjoern Peters - intraperitoneal administration - - @@ -11983,47 +11941,6 @@ In the examples above, a reagent is an operational component of a device, but th - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - intranasal mucosal administration - - The administration of a substance into the intranasal mucosis of an organism - PERSON: Melanie Courtot - intranasal mucosal administration - - @@ -21152,34 +21069,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - Administering substance in vivo where an antibiotic substance is administered to a living organism. - Chris Stoeckert - Cristian Cocos - Jie Zheng - Penn Group - antibiotic administration process - - @@ -22222,15 +22111,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - The administration of a challenge to a live host. - Hector Guzman-Orozco - IEDB - in vivo challenge - diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv index 163ebc00..b7a92c07 100644 --- a/src/ontology/templates/administration.tsv +++ b/src/ontology/templates/administration.tsv @@ -1,25 +1,29 @@ -ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class target of administration material administered administration technique -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and (‘role of’ some %)) SPLIT=| C 'has part' some % SPLIT=| -OBI:0003553 intragastric administration An administration of a substance into the stomach of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo stomach -OBI:0003554 intracolonic administration An administration of a substance into the colon of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo colon -OBI:0003555 vaginal administration An administration of a substance into the vagina of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo vagina -OBI:0003556 topical administration percutaneous administration|transcutaneous administration An administration of a substance onto the surface of the skin of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo skin of body -OBI:0003557 cervical administration An administration of a substance to the cervix of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo uterine cervix -OBI:0003558 conjunctival administration An administration of a substance to the conjunctiva of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo conjunctiva -OBI:0003559 intratracheal administration An administration of a substance into the trachea of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo trachea -OBI:0003560 intra-amniotic administration An administration of a substance into the amnion of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo amnion -OBI:0003561 intra-arterial administration An administration of a substance into the artery of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo artery -OBI:0003562 intracerebral administration An administration of a substance into the cerebrum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo telencephalon -OBI:0003563 intracranial administration An administration of a substance into the cranium of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo cranium -OBI:0003564 intraepidermal administration An administration of a substance into the epidermis of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo skin epidermis -OBI:0003565 intralymphatic administration An administration of a substance into the lymphatic system of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo ('part of' some 'lymphoid system') -OBI:0003566 lymph node administration An intralymphatic administration in which the substance is administered into a lymph node. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intralymphatic administration lymph node -OBI:0003567 urethral administration An administration of a substance into the urethra of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo urethra -OBI:0003568 skin scarification administration An intraepidermal administration in which the skin is scratched before the substance is administered to the skin. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intraepidermal administration skin epidermis scratching -OBI:0003569 intrauteral administration An adminstration of a substance into the uterus of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo uterus -OBI:0003570 intracarotid administration i.c.|i.c. administration An intra-arterial administration in which the substance is administered into the carotid artery. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intra-arterial administration common carotid artery plus branches -OBI:0003571 intraocular administration An administration of a substance to the eye of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo eye -OBI:0003572 intraplacental administration An administration of a substance into the placenta of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo placenta -OBI:0003573 intrarectal administration An administration of a substance into the rectum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo rectum -OBI:0003574 intrasplenic administration An administration of a substance into the spleen of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo spleen -OBI:0003603 intratumoral administration An administration of a substance into a tumor of an organism. Sebastian Duesing subclass administering substance in vivo Neoplasm +ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class target of administration material administered administration technique associated axiom +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and ('role of' some %)) SPLIT=| C 'has part' some % SPLIT=| C % +OBI:0000429 intraperitoneal administration intraperitoneal administration The administration of a substance into the peritoneum of an organism Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h Person:Bjoern Peters equivalent administering substance in vivo peritoneum +OBI:0000983 intranasal mucosal administration intranasal mucosal administration The administration of a substance into the intranasal mucosis of an organism Melanie Courtot equivalent administering substance in vivo mucosa of nasopharynx +OBI:0003057 antibiotic administration process antibiotic administration process Administering substance in vivo where an antibiotic substance is adminstered to a living organism. Penn Group Chris Stoeckert|Cristian Cocos|Jie Zheng subclass administering substance in vivo antibacterial +OBI:0003456 in vivo challenge in vivo challenge The administration of a challenge to a live host. IEDB Hector Guzman-Orozco subclass administering substance in vivo +OBI:0003553 intragastric administration An administration of a substance into the stomach of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo stomach +OBI:0003554 intracolonic administration An administration of a substance into the colon of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo colon +OBI:0003555 vaginal administration An administration of a substance into the vagina of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo vagina +OBI:0003556 topical administration percutaneous administration|transcutaneous administration An administration of a substance onto the surface of the skin of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo skin of body +OBI:0003557 cervical administration An administration of a substance to the cervix of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo uterine cervix +OBI:0003558 conjunctival administration An administration of a substance to the conjunctiva of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo conjunctiva +OBI:0003559 intratracheal administration An administration of a substance into the trachea of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo trachea +OBI:0003560 intra-amniotic administration An administration of a substance into the amnion of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo amnion +OBI:0003561 intra-arterial administration An administration of a substance into the artery of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo artery +OBI:0003562 intracerebral administration An administration of a substance into the cerebrum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo telencephalon +OBI:0003563 intracranial administration An administration of a substance into the cranium of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo cranium +OBI:0003564 intraepidermal administration An administration of a substance into the epidermis of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo skin epidermis +OBI:0003565 intralymphatic administration An administration of a substance into the lymphatic system of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo ('part of' some 'lymphoid system') +OBI:0003566 lymph node administration An intralymphatic administration in which the substance is administered into a lymph node. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intralymphatic administration lymph node +OBI:0003567 urethral administration An administration of a substance into the urethra of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo urethra +OBI:0003568 skin scarification administration An intraepidermal administration in which the skin is scratched before the substance is administered to the skin. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intraepidermal administration skin epidermis scratching +OBI:0003569 intrauteral administration An adminstration of a substance into the uterus of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo uterus +OBI:0003570 intracarotid administration i.c.|i.c. administration An intra-arterial administration in which the substance is administered into the carotid artery. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intra-arterial administration common carotid artery plus branches +OBI:0003571 intraocular administration An administration of a substance to the eye of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo eye +OBI:0003572 intraplacental administration An administration of a substance into the placenta of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo placenta +OBI:0003573 intrarectal administration An administration of a substance into the rectum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo rectum +OBI:0003574 intrasplenic administration An administration of a substance into the spleen of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo spleen +OBI:0003603 intratumoral administration An administration of a substance into a tumor of an organism. Sebastian Duesing subclass administering substance in vivo Neoplasm From 20c1aade14ae991d555a681337cd355a6a8a7a2e Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Tue, 25 Jul 2023 13:40:04 -0500 Subject: [PATCH 09/12] Moving more terms from obi-edit to administration.tsv --- src/ontology/modules/administration.owl | 449 +++++++++++++++++++++- src/ontology/obi-edit.owl | 444 +-------------------- src/ontology/templates/administration.tsv | 15 +- 3 files changed, 462 insertions(+), 446 deletions(-) diff --git a/src/ontology/modules/administration.owl b/src/ontology/modules/administration.owl index a20cd8a0..11d83fe4 100644 --- a/src/ontology/modules/administration.owl +++ b/src/ontology/modules/administration.owl @@ -58,6 +58,12 @@ + + + + + + @@ -93,6 +99,18 @@ + + + + + + + + + + + + @@ -110,6 +128,12 @@ + + + + + + @@ -122,12 +146,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + intraperitoneal injection + is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe + BP + intraperitoneal injection + + + + + + + + + + @@ -167,6 +229,224 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oral ingestion of pill + An adding a material entity to target with the entity is a pill and the target is the mouth + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + oral ingestion of pill + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intramuscular injection + is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe + intramuscular injection + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intradermal injection + is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe + PERSON: Melanie Courtot + intradermal injection + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oral administration + An administering substance in vivo into the mouth of an organism + PERSON: Melanie Courtot + oral administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subcutaneous injection + is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe + PERSON: Melanie Courtot + subcutaneous injection + + + + @@ -193,12 +473,88 @@ intranasal mucosal administration The administration of a substance into the intranasal mucosis of an organism - Melanie Courtot + PERSON: Melanie Courtot intranasal mucosal administration + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intravenous injection + is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe + PERSON: Melanie Courtot + intravenous injection + + + + + + + + + + + + + + + + + + + + + + + + + passive immunization + Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another. + The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. + PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum + adoptive transfer + passive immunization + + + + @@ -220,7 +576,7 @@ antibiotic administration process - Administering substance in vivo where an antibiotic substance is adminstered to a living organism. + Administering substance in vivo where an antibiotic substance is administered to a living organism. Chris Stoeckert Cristian Cocos Jie Zheng @@ -230,6 +586,30 @@ + + + + + An administration of substance in vivo with the intention to induce disease in the organism. + IEDB + IEDB + administering substance in vivo to cause disease + + + + + + + + + An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. + IEDB + IEDB + administering substance in vivo to reduce or prevent disease + + + + @@ -913,6 +1293,41 @@ + + + + + + + + + + + + + + + + + + + + + administration in vivo with infectious agent + is an administration of an infectious agent to a host organism + IEDB + IEDB + administration in vivo with infectious agent + + + + + + + + + + @@ -931,6 +1346,12 @@ + + + + + + @@ -973,6 +1394,12 @@ + + + + + + @@ -991,6 +1418,12 @@ + + + + + + @@ -1009,6 +1442,18 @@ + + + + + + + + + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 2062092e..26bf36ea 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -5542,60 +5542,6 @@ for now. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - intraperitoneal injection - - is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe - BP - intraperitoneal injection - @@ -6635,8 +6581,7 @@ activity) - - + @@ -6677,8 +6622,8 @@ activity) OBI Biomaterial injection - + @@ -9860,56 +9805,6 @@ http://en.wikipedia.org/wiki/Survival_rate - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - oral ingestion of pill - - An adding a material entity to target with the entity is a pill and the target is the mouth - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - oral ingestion of pill - - @@ -11139,61 +11034,6 @@ Added duirng Mar 1, 2010 dev call - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - intramuscular injection - - is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe - intramuscular injection - - - @@ -11263,62 +11103,6 @@ Added duirng Mar 1, 2010 dev call - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - intradermal injection - - is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe - PERSON: Melanie Courtot - intradermal injection - - - @@ -11471,44 +11255,6 @@ Biochimie. 2010 Feb 18. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - oral administration - - An administering substance in vivo into the mouth of an organism - PERSON: Melanie Courtot - oral administration - - @@ -11535,61 +11281,6 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - subcutaneous injection - - is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe - PERSON: Melanie Courtot - subcutaneous injection - - @@ -12034,61 +11725,6 @@ In the examples above, a reagent is an operational component of a device, but th - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - intravenous injection - - is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe - PERSON: Melanie Courtot - intravenous injection - - @@ -13004,36 +12640,6 @@ All subtype will be defined by textual definition now. - - - - - - - - - - - - - - - - - - - - - passive immunization - Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. -Transferring epitope specific T cells from one mouse into another. - - The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. - PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum - adoptive transfer - passive immunization - - @@ -22006,27 +21612,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - An administration of substance in vivo with the intention to induce disease in the organism. - IEDB - IEDB - administering substance in vivo to cause disease - - - - - - - - An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. - IEDB - IEDB - administering substance in vivo to reduce or prevent disease - @@ -29964,33 +29551,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - - - - - - - - - - - - - - - - - - - - - administration in vivo with infectious agent - - is an administration of an infectious agent to a host organism - IEDB - IEDB - administration in vivo with infectious agent - diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv index b7a92c07..22ad8e68 100644 --- a/src/ontology/templates/administration.tsv +++ b/src/ontology/templates/administration.tsv @@ -1,8 +1,18 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class target of administration material administered administration technique associated axiom ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and ('role of' some %)) SPLIT=| C 'has part' some % SPLIT=| C % +OBI:0000281 intraperitoneal injection intraperitoneal injection is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe BP equivalent intraperitoneal administration ('realizes' some ('function' and ('inheres in' some 'syringe'))) OBI:0000429 intraperitoneal administration intraperitoneal administration The administration of a substance into the peritoneum of an organism Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h Person:Bjoern Peters equivalent administering substance in vivo peritoneum -OBI:0000983 intranasal mucosal administration intranasal mucosal administration The administration of a substance into the intranasal mucosis of an organism Melanie Courtot equivalent administering substance in vivo mucosa of nasopharynx -OBI:0003057 antibiotic administration process antibiotic administration process Administering substance in vivo where an antibiotic substance is adminstered to a living organism. Penn Group Chris Stoeckert|Cristian Cocos|Jie Zheng subclass administering substance in vivo antibacterial +OBI:0000837 oral ingestion of pill oral ingestion of pill An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case equivalent oral administration pill ('has_specified_input' some 'pill') +OBI:0000934 intramuscular injection intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe equivalent administering substance in vivo skeletal muscle tissue ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0000942 intradermal injection intradermal injection is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo dermis ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0000952 oral administration oral administration An administering substance in vivo into the mouth of an organism PERSON: Melanie Courtot equivalent administering substance in vivo mouth +OBI:0000954 subcutaneous injection subcutaneous injection is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo hypodermis ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0000983 intranasal mucosal administration intranasal mucosal administration The administration of a substance into the intranasal mucosis of an organism PERSON: Melanie Courtot equivalent administering substance in vivo mucosa of nasopharynx +OBI:0000994 intravenous injection intravenous injection is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo vein ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0001174 passive immunization passive immunization adoptive transfer The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum subclass administering substance in vivo adaptive immune receptor +OBI:0003057 antibiotic administration process antibiotic administration process Administering substance in vivo where an antibiotic substance is administered to a living organism. Penn Group Chris Stoeckert|Cristian Cocos|Jie Zheng subclass administering substance in vivo antibacterial +OBI:0003413 administering substance in vivo to cause disease An administration of substance in vivo with the intention to induce disease in the organism. IEDB IEDB subclass administering substance in vivo +OBI:0003414 administering substance in vivo to reduce or prevent disease An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. IEDB IEDB subclass administering substance in vivo OBI:0003456 in vivo challenge in vivo challenge The administration of a challenge to a live host. IEDB Hector Guzman-Orozco subclass administering substance in vivo OBI:0003553 intragastric administration An administration of a substance into the stomach of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo stomach OBI:0003554 intracolonic administration An administration of a substance into the colon of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo colon @@ -27,3 +37,4 @@ OBI:0003572 intraplacental administration An administration of a substance in OBI:0003573 intrarectal administration An administration of a substance into the rectum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo rectum OBI:0003574 intrasplenic administration An administration of a substance into the spleen of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo spleen OBI:0003603 intratumoral administration An administration of a substance into a tumor of an organism. Sebastian Duesing subclass administering substance in vivo Neoplasm +OBI:1110007 administration in vivo with infectious agent administration in vivo with infectious agent is an administration of an infectious agent to a host organism IEDB IEDB subclass administering substance in vivo infectious agent From 3c22e78b26a03476f155390a767c23a5dc05b30a Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Mon, 16 Oct 2023 10:40:09 -0500 Subject: [PATCH 10/12] Add column for objective --- src/ontology/templates/administration.tsv | 80 +++++++++++------------ 1 file changed, 40 insertions(+), 40 deletions(-) diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv index 22ad8e68..bdb6e1c4 100644 --- a/src/ontology/templates/administration.tsv +++ b/src/ontology/templates/administration.tsv @@ -1,40 +1,40 @@ -ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class target of administration material administered administration technique associated axiom -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and ('role of' some %)) SPLIT=| C 'has part' some % SPLIT=| C % -OBI:0000281 intraperitoneal injection intraperitoneal injection is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe BP equivalent intraperitoneal administration ('realizes' some ('function' and ('inheres in' some 'syringe'))) -OBI:0000429 intraperitoneal administration intraperitoneal administration The administration of a substance into the peritoneum of an organism Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h Person:Bjoern Peters equivalent administering substance in vivo peritoneum -OBI:0000837 oral ingestion of pill oral ingestion of pill An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case equivalent oral administration pill ('has_specified_input' some 'pill') -OBI:0000934 intramuscular injection intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe equivalent administering substance in vivo skeletal muscle tissue ('realizes' some ('function' and ('inheres in' some 'syringe'))) -OBI:0000942 intradermal injection intradermal injection is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo dermis ('realizes' some ('function' and ('inheres in' some 'syringe'))) -OBI:0000952 oral administration oral administration An administering substance in vivo into the mouth of an organism PERSON: Melanie Courtot equivalent administering substance in vivo mouth -OBI:0000954 subcutaneous injection subcutaneous injection is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo hypodermis ('realizes' some ('function' and ('inheres in' some 'syringe'))) -OBI:0000983 intranasal mucosal administration intranasal mucosal administration The administration of a substance into the intranasal mucosis of an organism PERSON: Melanie Courtot equivalent administering substance in vivo mucosa of nasopharynx -OBI:0000994 intravenous injection intravenous injection is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo vein ('realizes' some ('function' and ('inheres in' some 'syringe'))) -OBI:0001174 passive immunization passive immunization adoptive transfer The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum subclass administering substance in vivo adaptive immune receptor -OBI:0003057 antibiotic administration process antibiotic administration process Administering substance in vivo where an antibiotic substance is administered to a living organism. Penn Group Chris Stoeckert|Cristian Cocos|Jie Zheng subclass administering substance in vivo antibacterial -OBI:0003413 administering substance in vivo to cause disease An administration of substance in vivo with the intention to induce disease in the organism. IEDB IEDB subclass administering substance in vivo -OBI:0003414 administering substance in vivo to reduce or prevent disease An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. IEDB IEDB subclass administering substance in vivo -OBI:0003456 in vivo challenge in vivo challenge The administration of a challenge to a live host. IEDB Hector Guzman-Orozco subclass administering substance in vivo -OBI:0003553 intragastric administration An administration of a substance into the stomach of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo stomach -OBI:0003554 intracolonic administration An administration of a substance into the colon of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo colon -OBI:0003555 vaginal administration An administration of a substance into the vagina of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo vagina -OBI:0003556 topical administration percutaneous administration|transcutaneous administration An administration of a substance onto the surface of the skin of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo skin of body -OBI:0003557 cervical administration An administration of a substance to the cervix of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo uterine cervix -OBI:0003558 conjunctival administration An administration of a substance to the conjunctiva of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo conjunctiva -OBI:0003559 intratracheal administration An administration of a substance into the trachea of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo trachea -OBI:0003560 intra-amniotic administration An administration of a substance into the amnion of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo amnion -OBI:0003561 intra-arterial administration An administration of a substance into the artery of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo artery -OBI:0003562 intracerebral administration An administration of a substance into the cerebrum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo telencephalon -OBI:0003563 intracranial administration An administration of a substance into the cranium of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo cranium -OBI:0003564 intraepidermal administration An administration of a substance into the epidermis of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo skin epidermis -OBI:0003565 intralymphatic administration An administration of a substance into the lymphatic system of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo ('part of' some 'lymphoid system') -OBI:0003566 lymph node administration An intralymphatic administration in which the substance is administered into a lymph node. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intralymphatic administration lymph node -OBI:0003567 urethral administration An administration of a substance into the urethra of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo urethra -OBI:0003568 skin scarification administration An intraepidermal administration in which the skin is scratched before the substance is administered to the skin. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intraepidermal administration skin epidermis scratching -OBI:0003569 intrauteral administration An adminstration of a substance into the uterus of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo uterus -OBI:0003570 intracarotid administration i.c.|i.c. administration An intra-arterial administration in which the substance is administered into the carotid artery. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intra-arterial administration common carotid artery plus branches -OBI:0003571 intraocular administration An administration of a substance to the eye of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo eye -OBI:0003572 intraplacental administration An administration of a substance into the placenta of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo placenta -OBI:0003573 intrarectal administration An administration of a substance into the rectum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo rectum -OBI:0003574 intrasplenic administration An administration of a substance into the spleen of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo spleen -OBI:0003603 intratumoral administration An administration of a substance into a tumor of an organism. Sebastian Duesing subclass administering substance in vivo Neoplasm -OBI:1110007 administration in vivo with infectious agent administration in vivo with infectious agent is an administration of an infectious agent to a host organism IEDB IEDB subclass administering substance in vivo infectious agent +ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class target of administration material administered administration technique objective associated axiom +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and ('role of' some %)) SPLIT=| C 'has part' some % SPLIT=| C achieves_planned_objective some % C % +OBI:0000281 intraperitoneal injection intraperitoneal injection is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe BP equivalent intraperitoneal administration ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0000429 intraperitoneal administration intraperitoneal administration The administration of a substance into the peritoneum of an organism Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h Person:Bjoern Peters equivalent administering substance in vivo peritoneum +OBI:0000837 oral ingestion of pill oral ingestion of pill An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case equivalent oral administration pill ('has_specified_input' some 'pill') +OBI:0000934 intramuscular injection intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe equivalent administering substance in vivo skeletal muscle tissue ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0000942 intradermal injection intradermal injection is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo dermis ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0000952 oral administration oral administration An administering substance in vivo into the mouth of an organism PERSON: Melanie Courtot equivalent administering substance in vivo mouth +OBI:0000954 subcutaneous injection subcutaneous injection is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo hypodermis ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0000983 intranasal mucosal administration intranasal mucosal administration The administration of a substance into the intranasal mucosis of an organism PERSON: Melanie Courtot equivalent administering substance in vivo mucosa of nasopharynx +OBI:0000994 intravenous injection intravenous injection is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo vein ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0001174 passive immunization passive immunization adoptive transfer The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum subclass administering substance in vivo adaptive immune receptor +OBI:0003057 antibiotic administration process antibiotic administration process Administering substance in vivo where an antibiotic substance is administered to a living organism. Penn Group Chris Stoeckert|Cristian Cocos|Jie Zheng subclass administering substance in vivo antibacterial +OBI:0003413 administering substance in vivo to cause disease An administration of substance in vivo with the intention to induce disease in the organism. IEDB IEDB subclass administering substance in vivo +OBI:0003414 administering substance in vivo to reduce or prevent disease An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. IEDB IEDB subclass administering substance in vivo +OBI:0003456 in vivo challenge in vivo challenge The administration of a challenge to a live host. IEDB Hector Guzman-Orozco subclass administering substance in vivo +OBI:0003553 intragastric administration An administration of a substance into the stomach of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo stomach +OBI:0003554 intracolonic administration An administration of a substance into the colon of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo colon +OBI:0003555 vaginal administration An administration of a substance into the vagina of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo vagina +OBI:0003556 topical administration percutaneous administration|transcutaneous administration An administration of a substance onto the surface of the skin of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo skin of body +OBI:0003557 cervical administration An administration of a substance to the cervix of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo uterine cervix +OBI:0003558 conjunctival administration An administration of a substance to the conjunctiva of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo conjunctiva +OBI:0003559 intratracheal administration An administration of a substance into the trachea of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo trachea +OBI:0003560 intra-amniotic administration An administration of a substance into the amnion of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo amnion +OBI:0003561 intra-arterial administration An administration of a substance into the artery of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo artery +OBI:0003562 intracerebral administration An administration of a substance into the cerebrum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo telencephalon +OBI:0003563 intracranial administration An administration of a substance into the cranium of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo cranium +OBI:0003564 intraepidermal administration An administration of a substance into the epidermis of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo skin epidermis +OBI:0003565 intralymphatic administration An administration of a substance into the lymphatic system of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo ('part of' some 'lymphoid system') +OBI:0003566 lymph node administration An intralymphatic administration in which the substance is administered into a lymph node. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intralymphatic administration lymph node +OBI:0003567 urethral administration An administration of a substance into the urethra of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo urethra +OBI:0003568 skin scarification administration An intraepidermal administration in which the skin is scratched before the substance is administered to the skin. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intraepidermal administration skin epidermis scratching +OBI:0003569 intrauteral administration An adminstration of a substance into the uterus of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo uterus +OBI:0003570 intracarotid administration i.c.|i.c. administration An intra-arterial administration in which the substance is administered into the carotid artery. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass intra-arterial administration common carotid artery plus branches +OBI:0003571 intraocular administration An administration of a substance to the eye of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo eye +OBI:0003572 intraplacental administration An administration of a substance into the placenta of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo placenta +OBI:0003573 intrarectal administration An administration of a substance into the rectum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo rectum +OBI:0003574 intrasplenic administration An administration of a substance into the spleen of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo spleen +OBI:0003603 intratumoral administration An administration of a substance into a tumor of an organism. Sebastian Duesing subclass administering substance in vivo Neoplasm +OBI:1110007 administration in vivo with infectious agent administration in vivo with infectious agent is an administration of an infectious agent to a host organism IEDB IEDB subclass administering substance in vivo infectious agent From 480b578f06bb4a19905e4db89995c0d7e9d7e0ba Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Tue, 7 Nov 2023 14:25:43 -0600 Subject: [PATCH 11/12] Updating obi.owl to merge changes from master --- obi.owl | 1484 +++++++++++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 1342 insertions(+), 142 deletions(-) diff --git a/obi.owl b/obi.owl index f154e236..5495774f 100755 --- a/obi.owl +++ b/obi.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -80,7 +80,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2023-03-29 + 2023-09-20 @@ -1750,14 +1750,7 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - - - - - - - - + is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) @@ -3376,6 +3369,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ spatial region + + + + (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] + + + + + + (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] + + @@ -3395,18 +3400,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - @@ -6058,7 +6051,14 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series. LC-MS-MS LC-MS/MS @@ -6098,7 +6098,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cell line cell cell line cell 细胞系细胞 @@ -6113,14 +6113,14 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ cell line cell 细胞系细胞 - + - + 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. @@ -9317,6 +9317,7 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data + data item @@ -9375,6 +9376,7 @@ JAR: A data item is an approximately justified approximately true approximate be Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 + information content entity @@ -13929,7 +13931,7 @@ objectives is a planned process. waiting - not actively doing anything to a material for a duration of time. + A planned process where an agent does not take any new actions towards a particular objective for a period of time until a set of conditions is met. PERSON:Alan Ruttenberg OBI branch derived BP: I have doubts about the utility of this. @@ -14425,8 +14427,9 @@ editor = PRS assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. - A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. + A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. + Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683. PlanAndPlannedProcess Branch measuring scientific observation @@ -16148,7 +16151,7 @@ An individual or juridicial or other body authorized under applicable law to con antigen role - Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response + A role of a material entity that is being recognized in whole or in part by receptors of the immune system such as antibodies or T cell receptors. An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens Role Branch OBI @@ -16338,7 +16341,7 @@ for now. - + DNA extraction @@ -19110,7 +19113,8 @@ that has_part some material entity is a material entity. If we add as equivalent manufacturing - Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process + A planned process with the objective to produce a processed material which will have a function for future use. + A person or organization (having manufacturer role) is a participant in this process Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters @@ -24401,9 +24405,9 @@ http://sourceforge.net/p/obi/obi-terms/716/ vaccine preparation The production of B. pertussis vaccine. - vaccine preparation is a planned process with specified output a vaccine + A planned process with the objective to create a vaccine. OBI - vaccine preparation + vaccine production @@ -25906,8 +25910,9 @@ http://en.wikipedia.org/wiki/Survival_rate informing investigator of subject study arm + Informing the investigator whether a patient is receiving a placebo or a treatment with an investigational compound. - A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. + A planned process with the objective to make the investigator aware of which study arm a patient is participating in. 09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case @@ -25985,7 +25990,7 @@ http://en.wikipedia.org/wiki/Survival_rate presentation of stimulus The presentation of a flashing light to a monkey during reward training - a planned process in which an organism is exposed to some stimulus with the intent to invoke an action + A planned process with the objective to expose an organism to a stimulus. Helen Parkinson, Jessica Turner, Dirk Derom stimulation of organism Helen Parkinson, Jessica Turner, Dirk Derom @@ -26076,7 +26081,7 @@ http://en.wikipedia.org/wiki/Survival_rate informed consent process - A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. + A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate. 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed @@ -26606,7 +26611,7 @@ http://en.wikipedia.org/wiki/Survival_rate manufacturer - A person or organization that has a manufacturer role + A person or organization that has a manufacturer role. manufacturer @@ -26698,7 +26703,7 @@ http://en.wikipedia.org/wiki/Survival_rate material maintenance - a process with that achieves the objective to maintain some or all of the characteristics of an input material over time + A planned process with the objective to maintain some or all of the characteristics of an input material over time. material maintenance @@ -26752,7 +26757,7 @@ placeholder unblinding process - The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials + A planned process that is the part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials. Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case unblinding process @@ -26772,7 +26777,7 @@ placeholder subject agrees they understand informed consent document - A process in which a subject receives an informed consent document and agrees that they have understood it + A planned process in which a subject receives an informed consent document and agrees that they have understood it. 09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case @@ -26805,8 +26810,9 @@ placeholder informing subject of study arm + Informing participants whether they are receiving a placebo or a treatment with an investigational compound. - A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. + A planned process with the objective to make the subject aware of which study arm they are participating in. 09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case @@ -27840,38 +27846,6 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -28248,6 +28222,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. + in vitro cell killing assay Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. @@ -28263,6 +28238,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. + @@ -28356,8 +28332,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t supplying Jackson Labs supplies mouse strains. - The planned process of providing material entities -to be used in an investigation. + A planned process with the objective to provide material entities to be used in an investigation. Jennifer Fostel Jennifer Fostel 5/31/2012: A supplying process implies that there is an acquisition process. These may need to be tied together, so that modeling either way is reciprocal. @@ -29211,7 +29186,7 @@ Added duirng Mar 1, 2010 dev call study intervention - the part of the execution of an intervention design study which is varied between two or more subjects in the study + A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study. PERSON: Bjoern Peters GROUP: OBI study intervention @@ -53244,7 +53219,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + @@ -64153,7 +64128,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. - A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. + A planned process with the objective to create a group of entities by applying a predefined criteria to a larger group of entities. this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary) Person: Philippe Rocca-Serra selection process @@ -64762,7 +64737,7 @@ PMID: 23587118. freezing - A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities. + A planned process with the objective to bring some material entity to a temperature below its freezing point. Person: Mathias Brochhausen, Jie Zheng Mathias Brochhausen freezing @@ -70063,24 +70038,22 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - - - + + + + + + + + + + + + carboxyfluorescein succinimidyl ester staining assay Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division. - a assay detecting a molecular label assay where the amount of carboxyfluorescein succinimidyl ester is measured using fluorescence detection. + An assay using carboxyfluorescein succinimidyl ester staining. IEDB CFSE assay IEDB @@ -74527,10 +74500,10 @@ https://www.doi.org/ - physical examination of individual + physical examination of an organism - An assay that produces a description of the qualities of an entity that has not been transformed, through observation and physical, non-invasive techniques. - physical examination of individual + An assay that produces a description of the qualities of an organism that has not been transformed, through observation and physical, non-invasive techniques. + physical examination of an organism @@ -78873,7 +78846,7 @@ https://www.doi.org/ machine learning - A planned process in which statistical techniques are used to give computers the ability to learn about patterns in data, without being explicitly programmed. Learning is defined in this case as progressively improving performance on a specific task. + A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. Mark A. Miller https://en.wikipedia.org/wiki/Machine_learning https://github.com/TrisSN @@ -86003,7 +85976,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre specimen collection device - A container used to collect a specimen. + A device used to collect a specimen. https://orcid.org/0000-0002-8844-9165 specimen collection device @@ -88023,6 +87996,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. Rebecca Jackson TCR repertoire sequencing assay + bulk TCR assay doi:10.1186/s12896-017-0379-9 https://github.com/obi-ontology/obi/issues/1307 T cell receptor repertoire sequencing assay @@ -88040,6 +88014,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Rebecca Jackson Antibody repertoire sequencing assay BCR repertoire sequencing assay + bulk BCR assay doi:10.1186/s12896-017-0379-9 https://github.com/obi-ontology/obi/issues/1307 B cell receptor repertoire sequencing assay @@ -89093,7 +89068,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre coma severity assay Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale. - A physical examination of individual that has the objective to determine the severity of coma in a patient. + A physical examination of an organism that has the objective to determine the severity of coma in a patient. John Judkins https://github.com/obi-ontology/obi/issues/1357 John Judkins @@ -90660,31 +90635,18 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + + - - - - - - - - - - - - - - - - + + - + + liquid chromatography mass spectrometry assay A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance. @@ -96664,6 +96626,101 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + + computed image data set + The production of JPEG file by a digital camera. + + An image data set that is the output of an image data set analysis. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-1604-3078 "Alan Ruttenberg" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://github.com/obi-ontology/obi/issues/1481 + computed image data set + + + + + + + + + + + + + + + + + + + + + reconstructed magnetic resonance image data set + The product of a mathematical transformation of raw "k-space" data produced by an MRI machine into a form that represents the anatomical structure of the brain. + + An image data set that is the direct output of a raw magnetic resonance image data set reconstruction or a transformation of another MR image data set. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://github.com/obi-ontology/obi/issues/1481 + reconstructed magnetic resonance image data set + + + + + + + + + + + + + + + + + + + + + + + + + raw magnetic resonance image data set + The untransformed ("k-space") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. + + An image data set that is the direct output of an magnetic resonance imaging assay and whose values encode spatial frequencies produced by the NMR or MRI instrument. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://github.com/obi-ontology/obi/issues/1481 + raw magnetic resonance image data set + + + + @@ -96689,6 +96746,42 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + + + + + + + raw magnetic resonance image data set reconstruction + A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined. + + A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://github.com/obi-ontology/obi/issues/1481 + raw magnetic resonance image data set reconstruction + + + + @@ -96727,7 +96820,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre organism diagnostic process - A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has a disease, disorder, or syndrome of a certain type, or none of these as output. + A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has or had a disease, disorder, or syndrome of a certain type, or none of these as output. Jie Zheng https://github.com/obi-ontology/obi/issues/1505 organism diagnostic process @@ -100437,7 +100530,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre functional assessment of individual - A physical examination of an individual's ability to perform functional activities. + A physical examination of an organism's ability to perform functional activities. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -101523,7 +101616,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre observational assessment of individual - A physical examination of an individual through visual assesment. + A physical examination of an organism through visual assesment. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -101995,6 +102088,1100 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + liquid chromatography + + A preparative chromatography in which material components are separated in a liquid solution. + Hector Guzman-Orozco + OBI + https://github.com/obi-ontology/obi/issues/1685 + liquid chromatography + + + + + + + + + upper limit of detection + + A value specification that specifies the largest concentration/amount of a substance that can be quantified in an analyte assay. + Bjoern Peters + Hector Guzman-Orozco + OBI + https://github.com/obi-ontology/obi/issues/1485 + upper limit of detection + + + + + + + + + lower limit of detection + + A value specification that specifies the smallest concentration/amount of a substance that can be detected in an analyte assay. + Bjoern Peters + Hector Guzman-Orozco + OBI + https://github.com/obi-ontology/obi/issues/1485 + lower limit of detection + + + + + + + + + odor baited CDC light trap + + A CDC light trap that uses odorous gas from a human being as an attractant, by pumping it from the room where the human being sleeps into the trap. + John Judkins ORCID:0000-0001-6595-0902 + human odour baited light trap + VEuPathDB + https://github.com/obi-ontology/obi/issues/1654 + odor baited CDC light trap + + + + + + + + + resting clay pot trap + + A resting arthropod trap that consists of a container composed primarily of clay. + John Judkins ORCID:0000-0001-6595-0902 + resting clay pot catch + https://github.com/obi-ontology/obi/issues/1651 + resting clay pot trap + + + + + + + + + proximity ligation-assisted ChIP-seq + + A chromosome conformation capture assay in which proximity ligation is conducted in nuclei prior to chromatin shearing and immunoprecipitation. Immunopreciptation with an antibody that targets a transcription factor or histone modification allows for selection and enrichment of specific genomic regions for investigation of long-range chromosomal interactions. + Hector Guzman-Orozco + PLAC-seq + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5143423/ + https://github.com/obi-ontology/obi/issues/1145 + proximity ligation-assisted ChIP-seq + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + skin of body microbiology assay + + An organism detection assay that detects microorganisms in a skin of body specimen. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1680 + skin of body microbiology assay + + + + + + + + + + + + + + + + + + + + skin of body microbiology datum + + An organism detection datum that is the specified output of a skin of body microbiology assay. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1680 + skin of body microbiology datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bone marrow microbiology assay + + An organism detection assay that detects microorganisms in a bone marrow specimen. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1680 + bone marrow microbiology assay + + + + + + + + + + + + + + + + + + + + bone marrow microbiology datum + + An organism detection datum that is the specified output of a bone marrow microbiology assay. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1680 + bone marrow microbiology datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nasal aspirate microbiology assay + + An organism detection assay that detects microorganisms in a nasal aspirate specimen. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1680 + nasal aspirate microbiology assay + + + + + + + + + + + + + + + + + + + + nasal aspirate microbiology datum + + An organism detection datum that is the specified output of a nasal aspirate microbiology assay. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1680 + nasal aspirate microbiology datum + + + + + + + + + + + + + + + + + + + + + cell proliferation assay using carboxyfluorescein succinimidyl ester staining + + A cell proliferation assay that uses carboxyfluorescein succinimidyl ester staining to detect cell division. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1007 + cell proliferation assay using carboxyfluorescein succinimidyl ester staining + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay + + A cytometry assay which measures the number of living cells in a population. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1007 + cell viability assay + + + + + + + + + + + + + + + + + + + + cell viability assay using Annexin V staining + + A cell viability assay that uses Annexin V staining to detect apoptotic cells. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1007 + cell viability assay using Annexin V staining + + + + + + + + + carboxyfluorescein succinimidyl ester staining + + Staining using carboxyfluorescein succinimidyl ester. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1007 + carboxyfluorescein succinimidyl ester staining + + + + + + + + + Annexin V staining + + Staining using Annexin V to detect apoptotic cells. + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1007 + Annexin V staining + + + + + + + + + + + + + + + + + + + + cell culture assay + + An assay that has cell culture as an input. + Randi Vita + Sebastian Duesing + cell culture assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + serum anti-Epstein-Barr virus antibody level assay + + An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. + Randi Vita + Sebastian Duesing + EBV + serum anti-Epstein-Barr virus antibody level assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + serum anti-cytomegalovirus antibody level assay + + A CMV antibody assay that has serum as an input. + Randi Vita + Sebastian Duesing + CMV + serum anti-cytomegalovirus antibody level assay + + + + + + + + + + + + + + + chronic allograft damage index score + + A clinical data item that quantifies the degree of tissue damage in biopsies taken from transplanted kidneys. + Sebastian Duesing + CADI + chronic allograft damage index score + + + + + + + + + sequential organ failure assessment score + + A clinical data item that quantifies the degree of function of a critically ill patient's organs. + Sebastian Duesing + SOFA score + https://en.wikipedia.org/wiki/SOFA_score + sequential organ failure assessment score + + + + + + + + + + + + + + + physician's global assessment of disease activity + + A clinical data item that quantifies a physician's judgement of the overall activity of some specific disease in a patient. + Sebastian Duesing + MD global, PGA + physician's global assessment of disease activity + + + + + + + + + human leukocyte antigen mismatch count + + A genetic characteristics information that is about the number of dissimilarities in the human leukocyte antigen gene complexes of two humans. + Sebastian Duesing + HLA mismatch count, HLA mismatch + human leukocyte antigen mismatch count + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nasal lavage fluid + + A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. + Randi Vita + Sebastian Duesing + nasal lavage fluid + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + single cell B cell receptor repertoire sequencing assay + + A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin. + Randi Vita + Sebastian Duesing + single-cell BCR assay + single cell B cell receptor repertoire sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + single cell T cell receptor repertoire sequencing assay + + A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin. + Randi Vita + Sebastian Duesing + single-cell TCR assay + single cell T cell receptor repertoire sequencing assay + + + + + + + + + hypertension grade + + A categorical value specification that indicates the severity of hypertension. + Bjoern Peters + Randi Vita + Sebastian Duesing + hypertension grade + + + + + + + + + quartz crystal microbalance assay + + An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. + Bjoern Peters + Randi Vita + Sebastian Duesing + QCM + http://www.ncbi.nlm.nih.gov/pubmed/23504432 + https://en.wikipedia.org/wiki/Quartz_crystal_microbalance + quartz crystal microbalance assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + quartz crystal microbalance measuring the dissociation constant [KD] of a B cell epitope:antibody complex + + A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + Bjoern Peters + Randi Vita + Sebastian Duesing + QCM measuring KD + IEDB + dissociation constant KD|quartz crystal microbalance|nM + quartz crystal microbalance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + + + + + + + + + multiplexed error-robust fluorescence in situ hybridization assay + + A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. + Sebastian Duesing + MERFISH + https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH + https://github.com/obi-ontology/obi/issues/1724 + Brain Image Library + multiplexed error-robust fluorescence in situ hybridization assay + + + + + + + + + single molecule fluorescence in situ hybridization + + A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. + Sebastian Duesing + smFISH + https://doi.org/10.21769/BioProtoc.3070 + https://github.com/obi-ontology/obi/issues/1725 + Brain Image Library + single molecule fluorescence in situ hybridization + + + + + + + + + + + + + + + Illumina NextSeq 1000 + + A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + Sebastian Duesing + NextSeq 1000 + https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html + https://github.com/obi-ontology/obi/issues/1711 + GENEPIO + Illumina NextSeq 1000 + + + + @@ -102442,7 +103629,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - + primary cultured cell population Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) @@ -102455,7 +103642,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from PERSON:Matthew Brush primary cultured cell population - + 0 @@ -102463,7 +103650,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - + consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. @@ -104910,7 +106097,7 @@ In this equation b0 is the regression coefficient for the intercept and the bi v data visualization Generation of a heatmap from a microarray dataset - An planned process that creates images, diagrams or animations from the input data. + A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations. Elisabetta Manduchi James Malone Melanie Courtot @@ -107510,13 +108697,13 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - irradiation + planned irradiation PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370. - irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves + A planned process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays, X-rays, charged particles or neutrons) or non-ionizing radiation (such as UV light or microwaves) Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) - irradiation + planned irradiation @@ -107626,7 +108813,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. - A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability + A planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment. Philippe Rocca-Serra OBI-Branch storage @@ -111336,7 +112523,7 @@ https://sourceforge.net/p/obi/obi-terms/738/ acquisition Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. - the planned process of gaining possession of a continuant. + A planned process with the objective of gaining possession of an entity. 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria @@ -111835,7 +113022,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ maintaining cell culture When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture - a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing + A planned process with the objective to keep cells alive in a defined environment outside of an organism. PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture @@ -112036,6 +113223,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ + @@ -113121,7 +114309,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + RNA extraction @@ -113156,7 +114344,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + nucleic acid extraction @@ -113411,7 +114599,7 @@ Possible ecological risks of transgenic organism release when transgenes affect epitope - a material entity bearing the epitope role + A material entity with the disposition to be bound by an adaptive immune receptor. IEDB IEDB epitope @@ -113830,7 +115018,7 @@ Possible ecological risks of transgenic organism release when transgenes affect Immunization in vitro - Process of administering an object playing the role of immunogen to a cell culture + A planned process with the objective to administer an object playing the role of immunogen to a cell culture. IEDB IEDB Immunization in vitro @@ -114095,13 +115283,13 @@ Possible ecological risks of transgenic organism release when transgenes affect - + antigen - is a material entity that has the antigen role + A material entity that has the antigen role. IEDB IEDB antigen @@ -114750,7 +115938,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it immunogen role - any entity capable of eliciting an immune response when introduced to components of the immune system + A role of a material entity that is realized when the material elicits an immune response targeting itself in whole or in part. IEDB IEDB immunogen role @@ -114880,7 +116068,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it donor role IEDB Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. - donor + donor role @@ -115256,7 +116444,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -115265,7 +116453,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it assay antigen role - Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively with 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. see OBI_1110120 below + An antigen role that is realized as part of an assay, where immune recognition of the material with the assay antigen role is being detected as part of the assay. IEDB IEDB assay antigen role @@ -144794,6 +145982,18 @@ realizes some 'host of immune response role' + + + + + clinical data item + A data item that is about a patient and is the specified output of a health care process assay or diagnostic process + + clinical data item + + + + @@ -146601,7 +147801,7 @@ realizes some 'host of immune response role' anatomical cluster - Anatomical group that has its parts adjacent to one another. + Anatomical group whose component anatomical structures lie in close proximity to each other. anatomical cluster From e809a75a681f1965c3e1f0dc186d49f0f703faea Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Thu, 9 Nov 2023 11:47:54 -0600 Subject: [PATCH 12/12] Adds disease-related objectives Adds "disease causation objective," "disease prevalence reduction objective," "disease severity reduction objective," and "disease prevention objective" to the objective column of relevant terms. --- src/ontology/modules/administration.owl | 50 +++++++++++++++++++++++ src/ontology/templates/administration.tsv | 4 +- 2 files changed, 52 insertions(+), 2 deletions(-) diff --git a/src/ontology/modules/administration.owl b/src/ontology/modules/administration.owl index 11d83fe4..c0141b5e 100644 --- a/src/ontology/modules/administration.owl +++ b/src/ontology/modules/administration.owl @@ -105,6 +105,12 @@ + + + + + + @@ -590,6 +596,12 @@ + + + + + + An administration of substance in vivo with the intention to induce disease in the organism. IEDB IEDB @@ -602,6 +614,20 @@ + + + + + + + + + + + + + + An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. IEDB IEDB @@ -1287,6 +1313,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv index bdb6e1c4..cc5b8e9d 100644 --- a/src/ontology/templates/administration.tsv +++ b/src/ontology/templates/administration.tsv @@ -11,8 +11,8 @@ OBI:0000983 intranasal mucosal administration intranasal mucosal administration OBI:0000994 intravenous injection intravenous injection is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo vein ('realizes' some ('function' and ('inheres in' some 'syringe'))) OBI:0001174 passive immunization passive immunization adoptive transfer The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum subclass administering substance in vivo adaptive immune receptor OBI:0003057 antibiotic administration process antibiotic administration process Administering substance in vivo where an antibiotic substance is administered to a living organism. Penn Group Chris Stoeckert|Cristian Cocos|Jie Zheng subclass administering substance in vivo antibacterial -OBI:0003413 administering substance in vivo to cause disease An administration of substance in vivo with the intention to induce disease in the organism. IEDB IEDB subclass administering substance in vivo -OBI:0003414 administering substance in vivo to reduce or prevent disease An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. IEDB IEDB subclass administering substance in vivo +OBI:0003413 administering substance in vivo to cause disease An administration of substance in vivo with the intention to induce disease in the organism. IEDB IEDB subclass administering substance in vivo disease causation objective +OBI:0003414 administering substance in vivo to reduce or prevent disease An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. IEDB IEDB subclass administering substance in vivo ('disease prevalence reduction objective' or 'disease severity reduction objective' or 'disease prevention objective') OBI:0003456 in vivo challenge in vivo challenge The administration of a challenge to a live host. IEDB Hector Guzman-Orozco subclass administering substance in vivo OBI:0003553 intragastric administration An administration of a substance into the stomach of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo stomach OBI:0003554 intracolonic administration An administration of a substance into the colon of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 subclass administering substance in vivo colon