From 07ba792b657eecdd9112231c0725113b7ca9dea1 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Mon, 17 Jul 2023 14:38:58 -0500 Subject: [PATCH 1/5] Updates from initial make imports --- src/ontology/OntoFox_outputs/OGMS_imports.owl | 11 +++++-- .../OntoFox_outputs/Uberon_imports.owl | 33 +++++++++++++++---- src/ontology/modules/physical-examination.owl | 4 +-- 3 files changed, 37 insertions(+), 11 deletions(-) diff --git a/src/ontology/OntoFox_outputs/OGMS_imports.owl b/src/ontology/OntoFox_outputs/OGMS_imports.owl index e6bf2277..3f11e906 100644 --- a/src/ontology/OntoFox_outputs/OGMS_imports.owl +++ b/src/ontology/OntoFox_outputs/OGMS_imports.owl @@ -24,15 +24,20 @@ - + + editor preferred term + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + editor preferred term + - definition - definition + definition + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + definition 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. diff --git a/src/ontology/modules/physical-examination.owl b/src/ontology/modules/physical-examination.owl index 8ed00973..c07186b4 100644 --- a/src/ontology/modules/physical-examination.owl +++ b/src/ontology/modules/physical-examination.owl @@ -156,7 +156,7 @@ - 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 @@ -1172,7 +1172,7 @@ - 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 From 0acaa7fd6dab93131ec1c7490802a123396a7f49 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Mon, 17 Jul 2023 15:18:38 -0500 Subject: [PATCH 2/5] Adding OGMS:clinical data item --- src/ontology/OntoFox_inputs/OGMS_input.txt | 2 +- src/ontology/OntoFox_outputs/OGMS_imports.owl | 27 +++++++++++++++++-- 2 files changed, 26 insertions(+), 3 deletions(-) diff --git a/src/ontology/OntoFox_inputs/OGMS_input.txt b/src/ontology/OntoFox_inputs/OGMS_input.txt index ab848402..c39d9f03 100644 --- a/src/ontology/OntoFox_inputs/OGMS_input.txt +++ b/src/ontology/OntoFox_inputs/OGMS_input.txt @@ -12,7 +12,7 @@ http://purl.obolibrary.org/obo/OGMS_0000063 http://purl.obolibrary.org/obo/OGMS_0000090 http://purl.obolibrary.org/obo/OGMS_0000031 # disease http://purl.obolibrary.org/obo/OGMS_0000073 # diagnosis - +http://purl.obolibrary.org/obo/OGMS_0000123 # clinical data item [Top level source term URIs and target direct superclass URIs] http://purl.obolibrary.org/obo/OGMS_0000015 diff --git a/src/ontology/OntoFox_outputs/OGMS_imports.owl b/src/ontology/OntoFox_outputs/OGMS_imports.owl index 3f11e906..8f62c639 100644 --- a/src/ontology/OntoFox_outputs/OGMS_imports.owl +++ b/src/ontology/OntoFox_outputs/OGMS_imports.owl @@ -81,13 +81,24 @@ - + + + data item + An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + + data item + - + + information content entity + A generically dependent continuant that is about some thing. + + information content entity + @@ -166,6 +177,18 @@ treatment + + + + + + + + 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 + From effeabc1a7a00619b83a168e54931e9f2fe01b86 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Mon, 17 Jul 2023 15:55:05 -0500 Subject: [PATCH 3/5] Adding nasal lavage fluid term --- src/ontology/modules/biobank-specimens.owl | 43 ++++++++++++++++++++ src/ontology/templates/biobank-specimens.tsv | 1 + 2 files changed, 44 insertions(+) diff --git a/src/ontology/modules/biobank-specimens.owl b/src/ontology/modules/biobank-specimens.owl index 1b29fe27..96023e8c 100644 --- a/src/ontology/modules/biobank-specimens.owl +++ b/src/ontology/modules/biobank-specimens.owl @@ -3912,6 +3912,49 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + diff --git a/src/ontology/templates/biobank-specimens.tsv b/src/ontology/templates/biobank-specimens.tsv index e544b0cd..88f34c48 100644 --- a/src/ontology/templates/biobank-specimens.tsv +++ b/src/ontology/templates/biobank-specimens.tsv @@ -82,6 +82,7 @@ OBI:0003380 placental blood specimen A specimen that is derived from placenta OBI:0003415 peripheral blood mononuclear cell specimen PBMC specimen A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell Jie Zheng|Chris Stoeckert subclass collecting specimen from organism peripheral blood mononuclear cell CL_2000001 OBI:0003482 lymph specimen A specimen that is derived from a portion of lymph collected from an organism. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 collecting specimen from organism (tissue and ('part of' some lymph)) UBERON_0002391 OBI:0003483 digestive tract specimen A specimen that is derived from part of a digestive tract. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 collecting specimen from organism (tissue and ('part of' some 'digestive tract')) UBERON_0001555 +OBI:0003595 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. Sebastian Duesing|Randi Vita subclass collecting specimen from organism nasal cavity mucosa UBERON_0001826 OBI:2000000 uterine cervix specimen A specimen that is derived from some uterine cervix Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some 'uterine cervix')) UBERON_0000002 OBI:2000001 urethra specimen A specimen that is derived from some urethra Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some urethra)) UBERON_0000057 OBI:2000002 cervical mucus specimen A specimen that is derived from some cervical mucus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism cervical mucus UBERON_0000316 From ca762da54f6dc41b3e69c8fe34662ce34ab54637 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Tue, 18 Jul 2023 15:42:54 -0500 Subject: [PATCH 4/5] Adding 3 assay terms --- src/ontology/modules/assays.owl | 166 ++++++++++++++++++++++++++++++ src/ontology/templates/assays.tsv | 3 + 2 files changed, 169 insertions(+) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 7d087776..68f68ce1 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -26250,6 +26250,172 @@ + + + + + + + + + + + + + + + An assay that has cell culture as an input. + Randi Vita + Sebastian Duesing + cell culture 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A CMV antibody assay that has serum as an input. + Randi Vita + Sebastian Duesing + CMV + serum anti-cytomegalovirus antibody level assay + + + + diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 48831ee1..1871f8d9 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -648,6 +648,9 @@ OBI:0003580 nasal aspirate microbiology assay An organism detection assay tha OBI:0003582 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 equivalent cell proliferation assay carboxyfluorescein succinimidyl ester staining OBI:0003583 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 equivalent cytometry assay viability OBI:0003584 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 equivalent cell viability assay Annexin V staining +OBI:0003587 cell culture assay An assay that has cell culture as an input. Sebastian Duesing|Randi Vita equivalent assay cultured cell population +OBI:0003589 serum anti-Epstein-Barr virus antibody level assay EBV An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. Sebastian Duesing|Randi Vita equivalent antigen specific antibodies assay blood serum specimen ('immunoglobulin complex' and ('has disposition to bind' some 'Human gammaherpesvirus 4')) +OBI:0003590 serum anti-cytomegalovirus antibody level assay CMV A CMV antibody assay that has serum as an input. Sebastian Duesing|Randi Vita equivalent CMV antibody assay blood serum specimen OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course From 820d29b94f4c28e131139c60392dbd40bd7051fc Mon Sep 17 00:00:00 2001 From: Sebastian Duesing Date: Tue, 18 Jul 2023 16:45:46 -0500 Subject: [PATCH 5/5] Adding clinical data item terms --- src/ontology/obi-edit.owl | 67 +++++++++++++++++++++++++++++++++++++-- 1 file changed, 64 insertions(+), 3 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 1ec79429..ce1f73a4 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -22298,6 +22298,67 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + + + + @@ -22656,7 +22717,7 @@ 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) @@ -22669,7 +22730,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from PERSON:Matthew Brush primary cultured cell population - + 0 @@ -22677,7 +22738,7 @@ 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.