diff --git a/gecko.owl b/gecko.owl index 76829b7..8517df0 100644 --- a/gecko.owl +++ b/gecko.owl @@ -1406,7 +1406,7 @@ Written informed consent was obtained from the patient’s parents for publicati diseases - skin and subcutaneous tissue + skin and subcutaneous tissue diseases A disease involving the integumental system. MONDO:0045027 disease of integumental system @@ -1427,7 +1427,7 @@ Written informed consent was obtained from the patient’s parents for publicati diseases - musculoskeletal system + musculoskeletal system diseases A disease involving the musculoskeletal system. disease of musculoskeletal system disease or disorder of musculoskeletal system @@ -1443,6 +1443,46 @@ Written informed consent was obtained from the patient’s parents for publicati + + + + + diseases + urinary system diseases + A disease involving the renal system. + disease of renal system + disease or disorder of renal system + disorder of renal system + disorder of the urinary system + disorder of urinary system + non-neoplastic urinary tract disease + renal disease + renal system disease + renal system disease or disorder + urinary system disease + urinary tract disease + urinary tract disorder + urologic disorder + urological disorders + disease, urinary tract + disease, urologic + disease, urological + diseases, urinary tract + diseases, urologic + diseases, urological + disorder of renal system + urinary disease + urinary system disorder + urinary tract diseases + urologic disease + urological disease + urological diseases + urological disorder + urinary system disease + + + + @@ -1472,7 +1512,7 @@ Written informed consent was obtained from the patient’s parents for publicati diseases - digestive system + digestive system diseases A disease or disorder that involves the digestive system. alimentary system disease digestive disease @@ -1502,10 +1542,10 @@ Written informed consent was obtained from the patient’s parents for publicati diseases - oncological + cancer A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. CA - cancer + cancer cell type cancer malignancy malignant Growth @@ -1518,7 +1558,7 @@ Written informed consent was obtained from the patient’s parents for publicati organ system cancer primary cancer MT - cancer + cancer @@ -1528,7 +1568,7 @@ Written informed consent was obtained from the patient’s parents for publicati diseases - circulatory system + cardiovascular diseases A disease involving the cardiovascular system. cardiovascular disease cardiovascular disease (CVD) @@ -1546,12 +1586,34 @@ Written informed consent was obtained from the patient’s parents for publicati + + + + + diseases + immune system diseases + A disorder resulting from an abnormality in the immune system. + disease of immune system + disease or disorder of immune system + disorder of immune system + immune disease + immune disorder + immune dysfunction + immune system disease or disorder + immune system disorder + disorder of immune system + immune disorder, NOS + immune system disease + + + + diseases - nervous system + nervous system disorders A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves. disease of nervous system disease or disorder of nervous system @@ -1590,7 +1652,7 @@ Written informed consent was obtained from the patient’s parents for publicati diseases - respiratory system + respiratory system diseases A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma. disease of respiratory system disease or disorder of respiratory system @@ -1611,7 +1673,7 @@ Written informed consent was obtained from the patient’s parents for publicati diseases - endocrine/nutritional/metabolic disorders + endocrine system diseases A disease involving the endocrine system. disease of endocrine system disease or disorder of endocrine system @@ -1634,20 +1696,20 @@ Written informed consent was obtained from the patient’s parents for publicati diseases - infectious disease + infectious diseases A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact. ID clinical infection communicable disease infection infectious - infectious disease + infectious disease infectious diseases and manifestations infectious disorder transmissible disease disease by infectious agent Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself. - infectious disease + infectious disease @@ -1690,13 +1752,13 @@ Written informed consent was obtained from the patient’s parents for publicati diseases - injury + injuries Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. - injury + injury trauma traumatic injury wound - injury + injury @@ -1706,7 +1768,7 @@ Written informed consent was obtained from the patient’s parents for publicati diseases - visual system + visual system diseases A disease that involves the visual system. disease of visual system disease or disorder of visual system diff --git a/src/ontology/annotations.owl b/src/ontology/annotations.owl index 922bd80..8427af0 100644 --- a/src/ontology/annotations.owl +++ b/src/ontology/annotations.owl @@ -517,6 +517,42 @@ Written informed consent was obtained from the patient’s parents for publicati + + + + A disease involving the renal system. + disease of renal system + disease or disorder of renal system + disorder of renal system + disorder of the urinary system + disorder of urinary system + non-neoplastic urinary tract disease + renal disease + renal system disease + renal system disease or disorder + urinary system disease + urinary tract disease + urinary tract disorder + urologic disorder + urological disorders + disease, urinary tract + disease, urologic + disease, urological + diseases, urinary tract + diseases, urologic + diseases, urological + disorder of renal system + urinary disease + urinary system disorder + urinary tract diseases + urologic disease + urological disease + urological diseases + urological disorder + + + + @@ -604,6 +640,24 @@ Written informed consent was obtained from the patient’s parents for publicati + + + + A disorder resulting from an abnormality in the immune system. + disease of immune system + disease or disorder of immune system + disorder of immune system + immune disease + immune disorder + immune dysfunction + immune system disease or disorder + immune system disorder + disorder of immune system + immune disorder, NOS + + + + diff --git a/src/ontology/templates/external.tsv b/src/ontology/templates/external.tsv index 492c7eb..dd44c0b 100644 --- a/src/ontology/templates/external.tsv +++ b/src/ontology/templates/external.tsv @@ -11,8 +11,8 @@ blood pressure measurement data item blood pressure cardiovascular measurement d body height data item height body morphological measurement data item anthropometry Replaces GECKO 'height' body morphological measurement data item anthropometry clinical measurement data item physiological measurements Replaces GECKO 'anthropometry' body weight data item weight body morphological measurement data item anthropometry Replaces GECKO 'weight' -cancer oncological disease or disorder diseases Replaces GECKO 'oncological' -cardiovascular disease circulatory system disease or disorder diseases Replaces GECKO 'circulatory system' +cancer cancer disease or disorder diseases Replaces GECKO 'oncological' +cardiovascular disease cardiovascular diseases disease or disorder diseases Replaces GECKO 'circulatory system' cardiovascular measurement data item circulation and respiration clinical measurement data item physiological measurements Replaces GECKO 'circulation and respiration' cause of participant death cause of death information content entity other questionnaire/survey data clinical history information content entity @@ -24,15 +24,15 @@ copy number variation profiling assay Sequence variants (CNV, SNP arrays) genomi count measurement datum data item information content entity date date and time-related information measurement datum survey administration Replaces GECKO 'date and time-related information' -digestive system disease digestive system disease or disorder diseases Replaces GECKO 'digestive system' +digestive system disease digestive system diseases disease or disorder diseases Replaces GECKO 'digestive system' directive information entity information content entity -disease of visual system visual system disease or disorder diseases +disease of visual system visual system diseases disease or disorder diseases disease or disorder diseases disposition questionnaire/survey data Replaces GECKO 'diseases' disposition realizable entity document information content entity drug administration specification administration directive information entity medication Replaces GECKO 'administration' drug prescription prescription document medication Replaces GECKO 'prescription' -endocrine system disease endocrine/nutritional/metabolic disorders disease or disorder diseases Replaces GECKO 'endocrine/nutritional/metabolic disorders' +endocrine system disease endocrine system diseases disease or disorder diseases Replaces GECKO 'endocrine/nutritional/metabolic disorders' environment associated with human dwelling physical environment material entity questionnaire/survey data epigenetic modification assay Epigenetics genomic assay genomics Replaces GECKO 'Epigenetics' exome sequencing assay WES genomic assay genomics Replaces GECKO 'WES' @@ -44,20 +44,21 @@ hematologic disease blood-related disorders disease or disorder diseases Replace hospitalization information hospitalizations information content entity healthcare information identifier information content entity immaterial entity +immune system disease immune system diseases disease or disorder diseases inclusion criterion criteria for enrollment and recruitment procedures directive information entity population data Replaces GECKO 'criteria for enrollment and recruitment procedures' income data income and possessions data item socio-demographic and economic characteristics -infectious disease infectious disease disease or disorder diseases +infectious disease infectious diseases disease or disorder diseases information content entity -injury injury disease or disorder diseases -integumentary system disease skin and subcutaneous tissue disease or disorder diseases +injury injuries disease or disorder diseases +integumentary system disease skin and subcutaneous tissue diseases disease or disorder diseases life cycle stage life stage/time point process other questionnaire/survey data marital status marital status information content entity socio-demographic and economic characteristics material entity material processing planned process measurement datum data item mental disorder mental and behaviour disorders disease or disorder diseases Replaces GECKO 'mental and behaviour disorders' -musculoskeletal system disease musculoskeletal system disease or disorder diseases -nervous system disorder nervous system disease or disorder diseases Replaces GECKO 'nervous system' +musculoskeletal system disease musculoskeletal system diseases disease or disorder diseases +nervous system disorder nervous system disorders disease or disorder diseases Replaces GECKO 'nervous system' objective specification aims and objectives directive information entity basic cohort attributes Replaces GECKO 'aims and objectives' occupation occupation information content entity socio-demographic and economic characteristics organism identification assay microbiology assay laboratory measures Replaces GECKO 'microbiology' @@ -71,7 +72,7 @@ process pulse data item heart rate (HR) cardiovascular measurement data item circulation and respiration Replaces GECKO 'heart rate (HR)' quality realizable entity -respiratory system disease respiratory system disease or disorder diseases Replaces GECKO 'respiratory system' +respiratory system disease respiratory system diseases disease or disorder diseases Replaces GECKO 'respiratory system' RNA-seq assay RNAseq/gene expression genomic assay genomics Replaces GECKO 'RNAseq/gene expression' saliva saliva organism substance sample type Replaces GECKO 'saliva' site immaterial entity @@ -81,5 +82,6 @@ study design study design plan specification basic cohort attributes Replaces GE symptom signs and symptoms quality other questionnaire/survey data Replaces GECKO 'signs and symptoms' textual entity information content entity urine urine organism substance sample type Replaces GECKO 'urine' +urinary system disease urinary system diseases disease or disorder diseases whole genome sequencing assay WGS genomic assay genomics Replaces GECKO 'WGS' whole metagenome sequencing assay Metagenomics genomic assay genomics Replaces GECKO 'Metagenomics' diff --git a/src/ontology/templates/index.tsv b/src/ontology/templates/index.tsv index d10da62..73af4c7 100644 --- a/src/ontology/templates/index.tsv +++ b/src/ontology/templates/index.tsv @@ -95,10 +95,12 @@ MF:0000041 belief MONDO:0000001 disease or disorder MONDO:0002051 integumentary system disease MONDO:0002081 musculoskeletal system disease +MONDO:0002118 urinary system disease MONDO:0003900 connective tissue disease MONDO:0004335 digestive system disease MONDO:0004992 cancer MONDO:0004995 cardiovascular disease +MONDO:0005046 immune system disease MONDO:0005071 nervous system disorder MONDO:0005084 mental disorder MONDO:0005087 respiratory system disease diff --git a/views/ihcc-gecko.csv b/views/ihcc-gecko.csv index 6ff28a1..0c8a176 100644 --- a/views/ihcc-gecko.csv +++ b/views/ihcc-gecko.csv @@ -99,20 +99,22 @@ cognitive functioning,GECKO:0000135,MMSE,A cognitive measurement that is an outp cognitive and psychological measurements,GECKO:0000120,personality,"A psychological measurement of a person's individual sets of behaviours, cognitions, and emotional patterns." cognitive and psychological measurements,GECKO:0000121,psychological distress and emotions,A biological process that results from neurophysiological changes in response to internal and external events. questionnaire/survey data,MONDO:0000001,diseases,A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. -diseases,MONDO:0002051,skin and subcutaneous tissue,A disease involving the integumental system. -diseases,MONDO:0002081,musculoskeletal system,A disease involving the musculoskeletal system. +diseases,MONDO:0002051,skin and subcutaneous tissue diseases,A disease involving the integumental system. +diseases,MONDO:0002081,musculoskeletal system diseases,A disease involving the musculoskeletal system. +diseases,MONDO:0002118,urinary system diseases,A disease involving the renal system. diseases,MONDO:0003900,connective tissue,A disease involving the connective tissue. -diseases,MONDO:0004335,digestive system,A disease or disorder that involves the digestive system. -diseases,MONDO:0004992,oncological,"A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas." -diseases,MONDO:0004995,circulatory system,A disease involving the cardiovascular system. -diseases,MONDO:0005071,nervous system,"A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves." +diseases,MONDO:0004335,digestive system diseases,A disease or disorder that involves the digestive system. +diseases,MONDO:0004992,cancer,"A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas." +diseases,MONDO:0004995,cardiovascular diseases,A disease involving the cardiovascular system. +diseases,MONDO:0005046,immune system diseases,A disorder resulting from an abnormality in the immune system. +diseases,MONDO:0005071,nervous system disorders,"A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves." diseases,MONDO:0005084,mental and behaviour disorders,A disease that has its basis in the disruption of mental process. -diseases,MONDO:0005087,respiratory system,"A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma." -diseases,MONDO:0005151,endocrine/nutritional/metabolic disorders,A disease involving the endocrine system. -diseases,MONDO:0005550,infectious disease,"A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact." +diseases,MONDO:0005087,respiratory system diseases,"A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma." +diseases,MONDO:0005151,endocrine system diseases,A disease involving the endocrine system. +diseases,MONDO:0005550,infectious diseases,"A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact." diseases,MONDO:0005570,blood-related disorders,A disease involving the hematopoietic system. -diseases,MONDO:0021178,injury,"Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity." -diseases,MONDO:0024458,visual system,A disease that involves the visual system. +diseases,MONDO:0021178,injuries,"Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity." +diseases,MONDO:0024458,visual system diseases,A disease that involves the visual system. diseases,MONDO:0024623,"diseases of the ear, nose, and/or throat","Pathological processes of the ear, the nose, and the throat, also known as the ENT diseases." diseases,MONDO:0029000,poisoning,"A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent." questionnaire/survey data,PATO:0001995,socio-demographic and economic characteristics,A quality that inheres in an entire organism or part of an organism. diff --git a/views/ihcc-gecko.owl b/views/ihcc-gecko.owl index 127fab2..ea6084a 100644 --- a/views/ihcc-gecko.owl +++ b/views/ihcc-gecko.owl @@ -1058,7 +1058,7 @@ Written informed consent was obtained from the patient’s parents for publicati integumentary system disease disorder of integument disorder of integumental system - skin and subcutaneous tissue + skin and subcutaneous tissue diseases @@ -1077,7 +1077,45 @@ Written informed consent was obtained from the patient’s parents for publicati musculoskeletal system disorder disorder of musculoskeletal system musculoskeletal disorder - musculoskeletal system + musculoskeletal system diseases + + + + + + + + + A disease involving the renal system. + disease of renal system + disease or disorder of renal system + disorder of renal system + disorder of the urinary system + disorder of urinary system + non-neoplastic urinary tract disease + renal disease + renal system disease + renal system disease or disorder + urinary system disease + urinary tract disease + urinary tract disorder + urologic disorder + urological disorders + disease, urinary tract + disease, urologic + disease, urological + diseases, urinary tract + diseases, urologic + diseases, urological + disorder of renal system + urinary disease + urinary system disorder + urinary tract diseases + urologic disease + urological disease + urological diseases + urological disorder + urinary system diseases @@ -1127,7 +1165,7 @@ Written informed consent was obtained from the patient’s parents for publicati git disease stomach or intestinal disorder disorder of digestive system - digestive system + digestive system diseases @@ -1151,7 +1189,7 @@ Written informed consent was obtained from the patient’s parents for publicati organ system cancer primary cancer MT - oncological + cancer @@ -1172,7 +1210,28 @@ Written informed consent was obtained from the patient’s parents for publicati disorder of cardiovascular system circulatory system disease disorder of cardiovascular system - circulatory system + cardiovascular diseases + + + + + + + + + A disorder resulting from an abnormality in the immune system. + disease of immune system + disease or disorder of immune system + disorder of immune system + immune disease + immune disorder + immune dysfunction + immune system disease + immune system disease or disorder + immune system disorder + disorder of immune system + immune disorder, NOS + immune system diseases @@ -1193,7 +1252,7 @@ Written informed consent was obtained from the patient’s parents for publicati neurological disease neurological disorder disorder of nervous system - nervous system + nervous system disorders @@ -1227,7 +1286,7 @@ Written informed consent was obtained from the patient’s parents for publicati respiratory system disease or disorder respiratory system disorder disorder of respiratory system - respiratory system + respiratory system diseases @@ -1248,7 +1307,7 @@ Written informed consent was obtained from the patient’s parents for publicati endocrinopathy thyroid or other glandular disorders disorder of endocrine system - endocrine/nutritional/metabolic disorders + endocrine system diseases @@ -1269,7 +1328,7 @@ Written informed consent was obtained from the patient’s parents for publicati transmissible disease disease by infectious agent Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself. - infectious disease + infectious diseases @@ -1315,7 +1374,7 @@ Written informed consent was obtained from the patient’s parents for publicati trauma traumatic injury wound - injury + injuries @@ -1332,7 +1391,7 @@ Written informed consent was obtained from the patient’s parents for publicati visual system disease or disorder visual system disorder disorder of visual system - visual system + visual system diseases