From dca2552b06293c1f82a6af1c132e8a9c367162a8 Mon Sep 17 00:00:00 2001 From: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com> Date: Mon, 23 Sep 2024 15:14:54 -0700 Subject: [PATCH 1/4] set validation rule as "list like" --- modules/metabolomics/metaboliteType.csv | 82 ++++++++++++------------- 1 file changed, 41 insertions(+), 41 deletions(-) diff --git a/modules/metabolomics/metaboliteType.csv b/modules/metabolomics/metaboliteType.csv index 717d2fc..7bd5bae 100644 --- a/modules/metabolomics/metaboliteType.csv +++ b/modules/metabolomics/metaboliteType.csv @@ -1,41 +1,41 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module -metaboliteType,Class of metabolite.,"acylcarnitines, acylglycerols, amino acids, ApoA1, ApoE, bile acids, biogenic amines, carbohydrates, catecholamine, ceramides, cholesterol, cofactors and vitamins, drugs, eicosanoids, endocannabinoids, fatty acids, glycerides, glycerolipid, glycerophospholipid, ketones, lipids, lipoproteins, lysophosphatidylcholine, lysophospholipids, nucleotides, oxylipins, peptides, phosphatidylcholine, phosphatidylethonalamines, phospholipids, plasmalogens, sphingolipids, steroids, sterols, sugars, TCA cycle metabolites, triglycerides, untargeted metabolomics, xenobiotics",,,False,ManifestColumn,,sage.annotations-experimentalData.metaboliteType-0.0.5,,string,metabolomics -acylcarnitines,acylcarnitine,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/C116917,,string,metabolomics -acylglycerols,"Glycerides, more correctly known as acylglycerols, are esters formed from glycerol and fatty acids that are very hydrophobic. ",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D005989,,string,metabolomics -amino acids,Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D000596,,string,metabolomics -ApoA1,apolipoprotein A-I,,,,,metaboliteType,,http://purl.obolibrary.org/obo/OGG_3000000335,,string,metabolomics -ApoE,The protein-coding gene APOE (apolipoprotein E) located on the chromosome 19 mapped at 19q13.2.,,,,,metaboliteType,,http://identifiers.org/ncbigene/348,,string,metabolomics -bile acids,"Any member of a group of hydroxy-5beta-cholanic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration.",,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_3098,,string,metabolomics -biogenic amines,"A group of naturally occurring amines derived by enzymatic decarboxylation of the natural amino acids. Many have powerful physiological effects (e.g., histamine, serotonin, epinephrine, tyramine). Those derived from aromatic amino acids, and also their synthetic analogs (e.g., amphetamine), are of use in pharmacology.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D001679,,string,metabolomics -carbohydrates,"A class of organic compounds composed of carbon, hydrogen, and oxygen in a ratio of Cn(H2O)n.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D002241,,string,metabolomics -catecholamine,"4-(2-Aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution.",,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_33567,,string,metabolomics -ceramides,Members of the class of neutral glycosphingolipids. They are the basic units of SPHINGOLIPIDS.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D002518,,string,metabolomics -cholesterol,"A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group.",,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_16113,,string,metabolomics -cofactors and vitamins,"Those reactions involved in the synthesis, utilization and/or degradation of cofactors, vitamins and other nutrients.",,,,,metaboliteType,,http://bioportal.bioontology.org/ontologies/PW/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPW_0000135,,string,metabolomics -drugs,The pharmacokinetics and the pharmacodynamics pathway elicited by the administration of specific drugs.,,,,,metaboliteType,,http://bioportal.bioontology.org/ontologies/PW/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPW_0000754,,string,metabolomics -eicosanoids,"A class of compounds named after and generally derived from C20 fatty acids (EICOSANOIC ACIDS) that includes PROSTAGLANDINS; LEUKOTRIENES; THROMBOXANES, and HYDROXYEICOSATETRAENOIC ACIDS.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D015777,,string,metabolomics -endocannabinoids,Fatty acid derivatives that have specificity for CANNABINOID RECEPTORS. They are structurally distinct from CANNABINOIDS and were originally discovered as a group of endogenous CANNABINOID RECEPTOR AGONISTS.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D063388,,string,metabolomics -fatty acids,"Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D005227,,string,metabolomics -glycerides,GLYCEROL esterified with FATTY ACIDS.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D005989,,string,metabolomics -glycerolipid,Any member of the group of lipids containing a common glycerol backbone to which at least one fatty acid-derived group is attached.,,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_35741,,string,metabolomics -glycerophospholipid,Any glycerolipid having a phosphate group ester-linked to a terminal carbon of the glycerol backbone.,,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_37739,,string,metabolomics -ketones,Organic compounds containing a carbonyl group =C=O bonded to two hydrocarbon groups.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D007659,,string,metabolomics -lipids,"A generic term for fats and lipoids, the alcohol-ether-soluble constituents of protoplasm, which are insoluble in water. They comprise the fats, fatty oils, essential oils, waxes, phospholipids, glycolipids, sulfolipids, aminolipids, chromolipids (lipochromes), and fatty acids. (Grant & Hackh's Chemical Dictionary, 5th ed)",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D008055,,string,metabolomics -lipoproteins,Lipid-protein complexes involved in the transportation and metabolism of lipids in the body. They are spherical particles consisting of a hydrophobic core of TRIGLYCERIDES and CHOLESTEROL ESTERS surrounded by a layer of hydrophilic free CHOLESTEROL; PHOSPHOLIPIDS; and APOLIPOPROTEINS.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D008074,,string,metabolomics -lysophosphatidylcholine,"An acylglycerophosphocholine resulting from partial hydrolysis of a phosphatidylcholine, which removes one of the fatty acyl groups. The structure is depicted in the image where R1 = acyl, R2 = H or where R1 = H, R2 = acyl.",,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_60479,,string,metabolomics -lysophospholipids,Derivatives of PHOSPHATIDIC ACIDS that lack one of its fatty acyl chains due to its hydrolytic removal.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D008246,,string,metabolomics -nucleotides,"The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D009711,,string,metabolomics -oxylipins,Eighteen-carbon cyclopentyl polyunsaturated fatty acids derived from ALPHA-LINOLENIC ACID via an oxidative pathway analogous to the EICOSANOIDS in animals.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D054883,,string,metabolomics -peptides,"Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D010455,,string,metabolomics -phosphatidylcholine,A glycerophosphocholine that is glycero-3-phosphocholine bearing two acyl substituents at positions 1 and 2.,,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_64482,,string,metabolomics -phosphatidylethonalamines,"Phosphatidylethanolamines (PE) are a class of phospholipids found in biological membranes.[1] They are synthesized by the addition of cytidine diphosphate-ethanolamine to diglycerides, releasing cytidine monophosphate.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/C483858,,string,metabolomics -phospholipids,"Lipids containing one or more phosphate groups, particularly those derived from either glycerol (phosphoglycerides see GLYCEROPHOSPHOLIPIDS) or sphingosine (SPHINGOLIPIDS).",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D010743,,string,metabolomics -plasmalogens,GLYCEROPHOSPHOLIPIDS in which one of the two acyl chains is attached to glycerol with an ether alkenyl linkage instead of an ester as with the other glycerophospholipids.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D010955,,string,metabolomics -sphingolipids,"A class of membrane lipids that have a polar head and two nonpolar tails. They are composed of one molecule of the long-chain amino alcohol sphingosine (4-sphingenine) or one of its derivatives, one molecule of a long-chain acid, a polar head alcohol and sometimes phosphoric acid in diester linkage at the polar head group. (Lehninger et al, Principles of Biochemistry, 2nd ed)",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D013107,,string,metabolomics -steroids,"A group of polycyclic compounds closely related biochemically to TERPENES. They include cholesterol, numerous hormones, precursors of certain vitamins, bile acids, alcohols (STEROLS), and certain natural drugs and poisons.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D013256,,string,metabolomics -sterols,Steroids with a hydroxyl group at C-3 and most of the skeleton of cholestane. Additional carbon atoms may be present in the side chain.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D013261,,string,metabolomics -sugars,Short chain carbohydrate molecules that have hydroxyl groups attached to each carbon atom unit with the exception of one carbon that has a doubly-bond aldehyde or ketone oxygen.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D000073893,,string,metabolomics -TCA cycle metabolites,TCA cycle metabolites,,,,,metaboliteType,,http://www.semanticweb.org/ADMO#TCACycle,,string,metabolomics -triglycerides,A triglyceride is an ester derived from glycerol and three fatty acids.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D014280,,string,metabolomics -untargeted metabolomics,"An untargeted metabolomics experiment registers all ions within a certain mass range, including ions belonging to structurally novel metabolites.",,,,,metaboliteType,,https://pubmed.ncbi.nlm.nih.gov/20373502/,,string,metabolomics -xenobiotics,"Chemical substances that are foreign to the biological system. They include naturally occurring compounds, drugs, environmental agents, carcinogens, insecticides, etc.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D015262,,string,metabolomics +Attribute ,Description ,Valid Values ,DependsOn ,Properties ,Required ,Parent ,DependsOn Component ,Source ,Validation Rules ,columnType ,module +metaboliteType ,Class of metabolite. ,"acylcarnitines, acylglycerols, amino acids, ApoA1, ApoE, bile acids, biogenic amines, carbohydrates, catecholamine, ceramides, cholesterol, cofactors and vitamins, drugs, eicosanoids, endocannabinoids, fatty acids, glycerides, glycerolipid, glycerophospholipid, ketones, lipids, lipoproteins, lysophosphatidylcholine, lysophospholipids, nucleotides, oxylipins, peptides, phosphatidylcholine, phosphatidylethonalamines, phospholipids, plasmalogens, sphingolipids, steroids, sterols, sugars, TCA cycle metabolites, triglycerides, untargeted metabolomics, xenobiotics" , , ,False ,ManifestColumn , ,sage.annotations-experimentalData.metaboliteType-0.0.5 ,list like error ,string ,metabolomics +acylcarnitines ,acylcarnitine , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/C116917 , ,string ,metabolomics +acylglycerols ,"Glycerides, more correctly known as acylglycerols, are esters formed from glycerol and fatty acids that are very hydrophobic. " , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D005989 , ,string ,metabolomics +amino acids ,Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D000596 , ,string ,metabolomics +ApoA1 ,apolipoprotein A-I , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/OGG_3000000335 , ,string ,metabolomics +ApoE ,The protein-coding gene APOE (apolipoprotein E) located on the chromosome 19 mapped at 19q13.2. , , , , ,metaboliteType , ,http://identifiers.org/ncbigene/348 , ,string ,metabolomics +bile acids ,"Any member of a group of hydroxy-5beta-cholanic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration." , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_3098 , ,string ,metabolomics +biogenic amines ,"A group of naturally occurring amines derived by enzymatic decarboxylation of the natural amino acids. Many have powerful physiological effects (e.g., histamine, serotonin, epinephrine, tyramine). Those derived from aromatic amino acids, and also their synthetic analogs (e.g., amphetamine), are of use in pharmacology." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D001679 , ,string ,metabolomics +carbohydrates ,"A class of organic compounds composed of carbon, hydrogen, and oxygen in a ratio of Cn(H2O)n." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D002241 , ,string ,metabolomics +catecholamine ,"4-(2-Aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution." , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_33567 , ,string ,metabolomics +ceramides ,Members of the class of neutral glycosphingolipids. They are the basic units of SPHINGOLIPIDS. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D002518 , ,string ,metabolomics +cholesterol ,"A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group." , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_16113 , ,string ,metabolomics +cofactors and vitamins ,"Those reactions involved in the synthesis, utilization and/or degradation of cofactors, vitamins and other nutrients." , , , , ,metaboliteType , ,http://bioportal.bioontology.org/ontologies/PW/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPW_0000135 , ,string ,metabolomics +drugs ,The pharmacokinetics and the pharmacodynamics pathway elicited by the administration of specific drugs. , , , , ,metaboliteType , ,http://bioportal.bioontology.org/ontologies/PW/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPW_0000754 , ,string ,metabolomics +eicosanoids ,"A class of compounds named after and generally derived from C20 fatty acids (EICOSANOIC ACIDS) that includes PROSTAGLANDINS; LEUKOTRIENES; THROMBOXANES, and HYDROXYEICOSATETRAENOIC ACIDS." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D015777 , ,string ,metabolomics +endocannabinoids ,Fatty acid derivatives that have specificity for CANNABINOID RECEPTORS. They are structurally distinct from CANNABINOIDS and were originally discovered as a group of endogenous CANNABINOID RECEPTOR AGONISTS. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D063388 , ,string ,metabolomics +fatty acids ,"Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)" , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D005227 , ,string ,metabolomics +glycerides ,GLYCEROL esterified with FATTY ACIDS. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D005989 , ,string ,metabolomics +glycerolipid ,Any member of the group of lipids containing a common glycerol backbone to which at least one fatty acid-derived group is attached. , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_35741 , ,string ,metabolomics +glycerophospholipid ,Any glycerolipid having a phosphate group ester-linked to a terminal carbon of the glycerol backbone. , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_37739 , ,string ,metabolomics +ketones ,Organic compounds containing a carbonyl group =C=O bonded to two hydrocarbon groups. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D007659 , ,string ,metabolomics +lipids ,"A generic term for fats and lipoids, the alcohol-ether-soluble constituents of protoplasm, which are insoluble in water. They comprise the fats, fatty oils, essential oils, waxes, phospholipids, glycolipids, sulfolipids, aminolipids, chromolipids (lipochromes), and fatty acids. (Grant & Hackh's Chemical Dictionary, 5th ed)" , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D008055 , ,string ,metabolomics +lipoproteins ,Lipid-protein complexes involved in the transportation and metabolism of lipids in the body. They are spherical particles consisting of a hydrophobic core of TRIGLYCERIDES and CHOLESTEROL ESTERS surrounded by a layer of hydrophilic free CHOLESTEROL; PHOSPHOLIPIDS; and APOLIPOPROTEINS. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D008074 , ,string ,metabolomics +lysophosphatidylcholine ,"An acylglycerophosphocholine resulting from partial hydrolysis of a phosphatidylcholine, which removes one of the fatty acyl groups. The structure is depicted in the image where R1 = acyl, R2 = H or where R1 = H, R2 = acyl." , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_60479 , ,string ,metabolomics +lysophospholipids ,Derivatives of PHOSPHATIDIC ACIDS that lack one of its fatty acyl chains due to its hydrolytic removal. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D008246 , ,string ,metabolomics +nucleotides ,"The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D009711 , ,string ,metabolomics +oxylipins ,Eighteen-carbon cyclopentyl polyunsaturated fatty acids derived from ALPHA-LINOLENIC ACID via an oxidative pathway analogous to the EICOSANOIDS in animals. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D054883 , ,string ,metabolomics +peptides ,"Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D010455 , ,string ,metabolomics +phosphatidylcholine ,A glycerophosphocholine that is glycero-3-phosphocholine bearing two acyl substituents at positions 1 and 2. , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_64482 , ,string ,metabolomics +phosphatidylethonalamines ,"Phosphatidylethanolamines (PE) are a class of phospholipids found in biological membranes.[1] They are synthesized by the addition of cytidine diphosphate-ethanolamine to diglycerides, releasing cytidine monophosphate." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/C483858 , ,string ,metabolomics +phospholipids ,"Lipids containing one or more phosphate groups, particularly those derived from either glycerol (phosphoglycerides see GLYCEROPHOSPHOLIPIDS) or sphingosine (SPHINGOLIPIDS)." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D010743 , ,string ,metabolomics +plasmalogens ,GLYCEROPHOSPHOLIPIDS in which one of the two acyl chains is attached to glycerol with an ether alkenyl linkage instead of an ester as with the other glycerophospholipids. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D010955 , ,string ,metabolomics +sphingolipids ,"A class of membrane lipids that have a polar head and two nonpolar tails. They are composed of one molecule of the long-chain amino alcohol sphingosine (4-sphingenine) or one of its derivatives, one molecule of a long-chain acid, a polar head alcohol and sometimes phosphoric acid in diester linkage at the polar head group. (Lehninger et al, Principles of Biochemistry, 2nd ed)" , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D013107 , ,string ,metabolomics +steroids ,"A group of polycyclic compounds closely related biochemically to TERPENES. They include cholesterol, numerous hormones, precursors of certain vitamins, bile acids, alcohols (STEROLS), and certain natural drugs and poisons." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D013256 , ,string ,metabolomics +sterols ,Steroids with a hydroxyl group at C-3 and most of the skeleton of cholestane. Additional carbon atoms may be present in the side chain. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D013261 , ,string ,metabolomics +sugars ,Short chain carbohydrate molecules that have hydroxyl groups attached to each carbon atom unit with the exception of one carbon that has a doubly-bond aldehyde or ketone oxygen. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D000073893 , ,string ,metabolomics +TCA cycle metabolites ,TCA cycle metabolites , , , , ,metaboliteType , ,http://www.semanticweb.org/ADMO#TCACycle , ,string ,metabolomics +triglycerides ,A triglyceride is an ester derived from glycerol and three fatty acids. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D014280 , ,string ,metabolomics +untargeted metabolomics ,"An untargeted metabolomics experiment registers all ions within a certain mass range, including ions belonging to structurally novel metabolites." , , , , ,metaboliteType , ,https://pubmed.ncbi.nlm.nih.gov/20373502/ , ,string ,metabolomics +xenobiotics ,"Chemical substances that are foreign to the biological system. They include naturally occurring compounds, drugs, environmental agents, carcinogens, insecticides, etc." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D015262 , ,string ,metabolomics From a1ac2a1a99b981beb92d2f7a294239f25e408c5d Mon Sep 17 00:00:00 2001 From: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com> Date: Mon, 23 Sep 2024 15:35:03 -0700 Subject: [PATCH 2/4] shrink rainbow csv column formatting before saving --- modules/metabolomics/metaboliteType.csv | 82 ++++++++++++------------- 1 file changed, 41 insertions(+), 41 deletions(-) diff --git a/modules/metabolomics/metaboliteType.csv b/modules/metabolomics/metaboliteType.csv index 7bd5bae..49229a0 100644 --- a/modules/metabolomics/metaboliteType.csv +++ b/modules/metabolomics/metaboliteType.csv @@ -1,41 +1,41 @@ -Attribute ,Description ,Valid Values ,DependsOn ,Properties ,Required ,Parent ,DependsOn Component ,Source ,Validation Rules ,columnType ,module -metaboliteType ,Class of metabolite. ,"acylcarnitines, acylglycerols, amino acids, ApoA1, ApoE, bile acids, biogenic amines, carbohydrates, catecholamine, ceramides, cholesterol, cofactors and vitamins, drugs, eicosanoids, endocannabinoids, fatty acids, glycerides, glycerolipid, glycerophospholipid, ketones, lipids, lipoproteins, lysophosphatidylcholine, lysophospholipids, nucleotides, oxylipins, peptides, phosphatidylcholine, phosphatidylethonalamines, phospholipids, plasmalogens, sphingolipids, steroids, sterols, sugars, TCA cycle metabolites, triglycerides, untargeted metabolomics, xenobiotics" , , ,False ,ManifestColumn , ,sage.annotations-experimentalData.metaboliteType-0.0.5 ,list like error ,string ,metabolomics -acylcarnitines ,acylcarnitine , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/C116917 , ,string ,metabolomics -acylglycerols ,"Glycerides, more correctly known as acylglycerols, are esters formed from glycerol and fatty acids that are very hydrophobic. " , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D005989 , ,string ,metabolomics -amino acids ,Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D000596 , ,string ,metabolomics -ApoA1 ,apolipoprotein A-I , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/OGG_3000000335 , ,string ,metabolomics -ApoE ,The protein-coding gene APOE (apolipoprotein E) located on the chromosome 19 mapped at 19q13.2. , , , , ,metaboliteType , ,http://identifiers.org/ncbigene/348 , ,string ,metabolomics -bile acids ,"Any member of a group of hydroxy-5beta-cholanic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration." , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_3098 , ,string ,metabolomics -biogenic amines ,"A group of naturally occurring amines derived by enzymatic decarboxylation of the natural amino acids. Many have powerful physiological effects (e.g., histamine, serotonin, epinephrine, tyramine). Those derived from aromatic amino acids, and also their synthetic analogs (e.g., amphetamine), are of use in pharmacology." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D001679 , ,string ,metabolomics -carbohydrates ,"A class of organic compounds composed of carbon, hydrogen, and oxygen in a ratio of Cn(H2O)n." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D002241 , ,string ,metabolomics -catecholamine ,"4-(2-Aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution." , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_33567 , ,string ,metabolomics -ceramides ,Members of the class of neutral glycosphingolipids. They are the basic units of SPHINGOLIPIDS. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D002518 , ,string ,metabolomics -cholesterol ,"A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group." , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_16113 , ,string ,metabolomics -cofactors and vitamins ,"Those reactions involved in the synthesis, utilization and/or degradation of cofactors, vitamins and other nutrients." , , , , ,metaboliteType , ,http://bioportal.bioontology.org/ontologies/PW/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPW_0000135 , ,string ,metabolomics -drugs ,The pharmacokinetics and the pharmacodynamics pathway elicited by the administration of specific drugs. , , , , ,metaboliteType , ,http://bioportal.bioontology.org/ontologies/PW/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPW_0000754 , ,string ,metabolomics -eicosanoids ,"A class of compounds named after and generally derived from C20 fatty acids (EICOSANOIC ACIDS) that includes PROSTAGLANDINS; LEUKOTRIENES; THROMBOXANES, and HYDROXYEICOSATETRAENOIC ACIDS." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D015777 , ,string ,metabolomics -endocannabinoids ,Fatty acid derivatives that have specificity for CANNABINOID RECEPTORS. They are structurally distinct from CANNABINOIDS and were originally discovered as a group of endogenous CANNABINOID RECEPTOR AGONISTS. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D063388 , ,string ,metabolomics -fatty acids ,"Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)" , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D005227 , ,string ,metabolomics -glycerides ,GLYCEROL esterified with FATTY ACIDS. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D005989 , ,string ,metabolomics -glycerolipid ,Any member of the group of lipids containing a common glycerol backbone to which at least one fatty acid-derived group is attached. , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_35741 , ,string ,metabolomics -glycerophospholipid ,Any glycerolipid having a phosphate group ester-linked to a terminal carbon of the glycerol backbone. , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_37739 , ,string ,metabolomics -ketones ,Organic compounds containing a carbonyl group =C=O bonded to two hydrocarbon groups. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D007659 , ,string ,metabolomics -lipids ,"A generic term for fats and lipoids, the alcohol-ether-soluble constituents of protoplasm, which are insoluble in water. They comprise the fats, fatty oils, essential oils, waxes, phospholipids, glycolipids, sulfolipids, aminolipids, chromolipids (lipochromes), and fatty acids. (Grant & Hackh's Chemical Dictionary, 5th ed)" , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D008055 , ,string ,metabolomics -lipoproteins ,Lipid-protein complexes involved in the transportation and metabolism of lipids in the body. They are spherical particles consisting of a hydrophobic core of TRIGLYCERIDES and CHOLESTEROL ESTERS surrounded by a layer of hydrophilic free CHOLESTEROL; PHOSPHOLIPIDS; and APOLIPOPROTEINS. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D008074 , ,string ,metabolomics -lysophosphatidylcholine ,"An acylglycerophosphocholine resulting from partial hydrolysis of a phosphatidylcholine, which removes one of the fatty acyl groups. The structure is depicted in the image where R1 = acyl, R2 = H or where R1 = H, R2 = acyl." , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_60479 , ,string ,metabolomics -lysophospholipids ,Derivatives of PHOSPHATIDIC ACIDS that lack one of its fatty acyl chains due to its hydrolytic removal. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D008246 , ,string ,metabolomics -nucleotides ,"The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D009711 , ,string ,metabolomics -oxylipins ,Eighteen-carbon cyclopentyl polyunsaturated fatty acids derived from ALPHA-LINOLENIC ACID via an oxidative pathway analogous to the EICOSANOIDS in animals. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D054883 , ,string ,metabolomics -peptides ,"Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D010455 , ,string ,metabolomics -phosphatidylcholine ,A glycerophosphocholine that is glycero-3-phosphocholine bearing two acyl substituents at positions 1 and 2. , , , , ,metaboliteType , ,http://purl.obolibrary.org/obo/CHEBI_64482 , ,string ,metabolomics -phosphatidylethonalamines ,"Phosphatidylethanolamines (PE) are a class of phospholipids found in biological membranes.[1] They are synthesized by the addition of cytidine diphosphate-ethanolamine to diglycerides, releasing cytidine monophosphate." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/C483858 , ,string ,metabolomics -phospholipids ,"Lipids containing one or more phosphate groups, particularly those derived from either glycerol (phosphoglycerides see GLYCEROPHOSPHOLIPIDS) or sphingosine (SPHINGOLIPIDS)." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D010743 , ,string ,metabolomics -plasmalogens ,GLYCEROPHOSPHOLIPIDS in which one of the two acyl chains is attached to glycerol with an ether alkenyl linkage instead of an ester as with the other glycerophospholipids. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D010955 , ,string ,metabolomics -sphingolipids ,"A class of membrane lipids that have a polar head and two nonpolar tails. They are composed of one molecule of the long-chain amino alcohol sphingosine (4-sphingenine) or one of its derivatives, one molecule of a long-chain acid, a polar head alcohol and sometimes phosphoric acid in diester linkage at the polar head group. (Lehninger et al, Principles of Biochemistry, 2nd ed)" , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D013107 , ,string ,metabolomics -steroids ,"A group of polycyclic compounds closely related biochemically to TERPENES. They include cholesterol, numerous hormones, precursors of certain vitamins, bile acids, alcohols (STEROLS), and certain natural drugs and poisons." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D013256 , ,string ,metabolomics -sterols ,Steroids with a hydroxyl group at C-3 and most of the skeleton of cholestane. Additional carbon atoms may be present in the side chain. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D013261 , ,string ,metabolomics -sugars ,Short chain carbohydrate molecules that have hydroxyl groups attached to each carbon atom unit with the exception of one carbon that has a doubly-bond aldehyde or ketone oxygen. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D000073893 , ,string ,metabolomics -TCA cycle metabolites ,TCA cycle metabolites , , , , ,metaboliteType , ,http://www.semanticweb.org/ADMO#TCACycle , ,string ,metabolomics -triglycerides ,A triglyceride is an ester derived from glycerol and three fatty acids. , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D014280 , ,string ,metabolomics -untargeted metabolomics ,"An untargeted metabolomics experiment registers all ions within a certain mass range, including ions belonging to structurally novel metabolites." , , , , ,metaboliteType , ,https://pubmed.ncbi.nlm.nih.gov/20373502/ , ,string ,metabolomics -xenobiotics ,"Chemical substances that are foreign to the biological system. They include naturally occurring compounds, drugs, environmental agents, carcinogens, insecticides, etc." , , , , ,metaboliteType , ,http://purl.bioontology.org/ontology/MESH/D015262 , ,string ,metabolomics +Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module +metaboliteType,Class of metabolite.,"acylcarnitines, acylglycerols, amino acids, ApoA1, ApoE, bile acids, biogenic amines, carbohydrates, catecholamine, ceramides, cholesterol, cofactors and vitamins, drugs, eicosanoids, endocannabinoids, fatty acids, glycerides, glycerolipid, glycerophospholipid, ketones, lipids, lipoproteins, lysophosphatidylcholine, lysophospholipids, nucleotides, oxylipins, peptides, phosphatidylcholine, phosphatidylethonalamines, phospholipids, plasmalogens, sphingolipids, steroids, sterols, sugars, TCA cycle metabolites, triglycerides, untargeted metabolomics, xenobiotics",,,False,ManifestColumn,,sage.annotations-experimentalData.metaboliteType-0.0.5,list like error,string,metabolomics +acylcarnitines,acylcarnitine,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/C116917,,string,metabolomics +acylglycerols,"Glycerides, more correctly known as acylglycerols, are esters formed from glycerol and fatty acids that are very hydrophobic. ",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D005989,,string,metabolomics +amino acids,Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D000596,,string,metabolomics +ApoA1,apolipoprotein A-I,,,,,metaboliteType,,http://purl.obolibrary.org/obo/OGG_3000000335,,string,metabolomics +ApoE,The protein-coding gene APOE (apolipoprotein E) located on the chromosome 19 mapped at 19q13.2.,,,,,metaboliteType,,http://identifiers.org/ncbigene/348,,string,metabolomics +bile acids,"Any member of a group of hydroxy-5beta-cholanic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration.",,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_3098,,string,metabolomics +biogenic amines,"A group of naturally occurring amines derived by enzymatic decarboxylation of the natural amino acids. Many have powerful physiological effects (e.g., histamine, serotonin, epinephrine, tyramine). Those derived from aromatic amino acids, and also their synthetic analogs (e.g., amphetamine), are of use in pharmacology.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D001679,,string,metabolomics +carbohydrates,"A class of organic compounds composed of carbon, hydrogen, and oxygen in a ratio of Cn(H2O)n.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D002241,,string,metabolomics +catecholamine,"4-(2-Aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution.",,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_33567,,string,metabolomics +ceramides,Members of the class of neutral glycosphingolipids. They are the basic units of SPHINGOLIPIDS.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D002518,,string,metabolomics +cholesterol,"A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group.",,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_16113,,string,metabolomics +cofactors and vitamins,"Those reactions involved in the synthesis, utilization and/or degradation of cofactors, vitamins and other nutrients.",,,,,metaboliteType,,http://bioportal.bioontology.org/ontologies/PW/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPW_0000135,,string,metabolomics +drugs,The pharmacokinetics and the pharmacodynamics pathway elicited by the administration of specific drugs.,,,,,metaboliteType,,http://bioportal.bioontology.org/ontologies/PW/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPW_0000754,,string,metabolomics +eicosanoids,"A class of compounds named after and generally derived from C20 fatty acids (EICOSANOIC ACIDS) that includes PROSTAGLANDINS; LEUKOTRIENES; THROMBOXANES, and HYDROXYEICOSATETRAENOIC ACIDS.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D015777,,string,metabolomics +endocannabinoids,Fatty acid derivatives that have specificity for CANNABINOID RECEPTORS. They are structurally distinct from CANNABINOIDS and were originally discovered as a group of endogenous CANNABINOID RECEPTOR AGONISTS.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D063388,,string,metabolomics +fatty acids,"Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D005227,,string,metabolomics +glycerides,GLYCEROL esterified with FATTY ACIDS.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D005989,,string,metabolomics +glycerolipid,Any member of the group of lipids containing a common glycerol backbone to which at least one fatty acid-derived group is attached.,,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_35741,,string,metabolomics +glycerophospholipid,Any glycerolipid having a phosphate group ester-linked to a terminal carbon of the glycerol backbone.,,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_37739,,string,metabolomics +ketones,Organic compounds containing a carbonyl group =C=O bonded to two hydrocarbon groups.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D007659,,string,metabolomics +lipids,"A generic term for fats and lipoids, the alcohol-ether-soluble constituents of protoplasm, which are insoluble in water. They comprise the fats, fatty oils, essential oils, waxes, phospholipids, glycolipids, sulfolipids, aminolipids, chromolipids (lipochromes), and fatty acids. (Grant & Hackh's Chemical Dictionary, 5th ed)",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D008055,,string,metabolomics +lipoproteins,Lipid-protein complexes involved in the transportation and metabolism of lipids in the body. They are spherical particles consisting of a hydrophobic core of TRIGLYCERIDES and CHOLESTEROL ESTERS surrounded by a layer of hydrophilic free CHOLESTEROL; PHOSPHOLIPIDS; and APOLIPOPROTEINS.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D008074,,string,metabolomics +lysophosphatidylcholine,"An acylglycerophosphocholine resulting from partial hydrolysis of a phosphatidylcholine, which removes one of the fatty acyl groups. The structure is depicted in the image where R1 = acyl, R2 = H or where R1 = H, R2 = acyl.",,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_60479,,string,metabolomics +lysophospholipids,Derivatives of PHOSPHATIDIC ACIDS that lack one of its fatty acyl chains due to its hydrolytic removal.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D008246,,string,metabolomics +nucleotides,"The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D009711,,string,metabolomics +oxylipins,Eighteen-carbon cyclopentyl polyunsaturated fatty acids derived from ALPHA-LINOLENIC ACID via an oxidative pathway analogous to the EICOSANOIDS in animals.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D054883,,string,metabolomics +peptides,"Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D010455,,string,metabolomics +phosphatidylcholine,A glycerophosphocholine that is glycero-3-phosphocholine bearing two acyl substituents at positions 1 and 2.,,,,,metaboliteType,,http://purl.obolibrary.org/obo/CHEBI_64482,,string,metabolomics +phosphatidylethonalamines,"Phosphatidylethanolamines (PE) are a class of phospholipids found in biological membranes.[1] They are synthesized by the addition of cytidine diphosphate-ethanolamine to diglycerides, releasing cytidine monophosphate.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/C483858,,string,metabolomics +phospholipids,"Lipids containing one or more phosphate groups, particularly those derived from either glycerol (phosphoglycerides see GLYCEROPHOSPHOLIPIDS) or sphingosine (SPHINGOLIPIDS).",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D010743,,string,metabolomics +plasmalogens,GLYCEROPHOSPHOLIPIDS in which one of the two acyl chains is attached to glycerol with an ether alkenyl linkage instead of an ester as with the other glycerophospholipids.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D010955,,string,metabolomics +sphingolipids,"A class of membrane lipids that have a polar head and two nonpolar tails. They are composed of one molecule of the long-chain amino alcohol sphingosine (4-sphingenine) or one of its derivatives, one molecule of a long-chain acid, a polar head alcohol and sometimes phosphoric acid in diester linkage at the polar head group. (Lehninger et al, Principles of Biochemistry, 2nd ed)",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D013107,,string,metabolomics +steroids,"A group of polycyclic compounds closely related biochemically to TERPENES. They include cholesterol, numerous hormones, precursors of certain vitamins, bile acids, alcohols (STEROLS), and certain natural drugs and poisons.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D013256,,string,metabolomics +sterols,Steroids with a hydroxyl group at C-3 and most of the skeleton of cholestane. Additional carbon atoms may be present in the side chain.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D013261,,string,metabolomics +sugars,Short chain carbohydrate molecules that have hydroxyl groups attached to each carbon atom unit with the exception of one carbon that has a doubly-bond aldehyde or ketone oxygen.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D000073893,,string,metabolomics +TCA cycle metabolites,TCA cycle metabolites,,,,,metaboliteType,,http://www.semanticweb.org/ADMO#TCACycle,,string,metabolomics +triglycerides,A triglyceride is an ester derived from glycerol and three fatty acids.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D014280,,string,metabolomics +untargeted metabolomics,"An untargeted metabolomics experiment registers all ions within a certain mass range, including ions belonging to structurally novel metabolites.",,,,,metaboliteType,,https://pubmed.ncbi.nlm.nih.gov/20373502/,,string,metabolomics +xenobiotics,"Chemical substances that are foreign to the biological system. They include naturally occurring compounds, drugs, environmental agents, carcinogens, insecticides, etc.",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D015262,,string,metabolomics From cfed51d991a4caef92a0b7c1f297658bdfc5d6cb Mon Sep 17 00:00:00 2001 From: avanlinden Date: Mon, 23 Sep 2024 22:36:17 +0000 Subject: [PATCH 3/4] GitHub Action: assemble *.model.csv from modules directory --- AD.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AD.model.csv b/AD.model.csv index 8e3bca7..ebd0403 100644 --- a/AD.model.csv +++ b/AD.model.csv @@ -924,7 +924,7 @@ meanCoverage,Total number of bases covered by ATAC-seq reads/size of genome,,,,F meanGCContent,Mean GC content per sample,,,,False,ManifestColumn,,sage.annotations-qc.meanGCContent-0.0.2,,number,sequencing medianGenes,The median number of genes detected (with nonzero UMI counts) across all cell-associated barcodes,,,,False,ManifestColumn,,sage.annotations-qc.medianGenes-0.0.2,,number,sequencing medianUMIs,The median number of total Unique Molecular Identifier (UMI) counts across all cell-associated barcodes,,,,False,ManifestColumn,,sage.annotations-qc.medianUMIs-0.0.2,,number,sequencing -metaboliteType,Class of metabolite.,"acylcarnitines, acylglycerols, amino acids, ApoA1, ApoE, bile acids, biogenic amines, carbohydrates, catecholamine, ceramides, cholesterol, cofactors and vitamins, drugs, eicosanoids, endocannabinoids, fatty acids, glycerides, glycerolipid, glycerophospholipid, ketones, lipids, lipoproteins, lysophosphatidylcholine, lysophospholipids, nucleotides, oxylipins, peptides, phosphatidylcholine, phosphatidylethonalamines, phospholipids, plasmalogens, sphingolipids, steroids, sterols, sugars, TCA cycle metabolites, triglycerides, untargeted metabolomics, xenobiotics",,,False,ManifestColumn,,sage.annotations-experimentalData.metaboliteType-0.0.5,,string,metabolomics +metaboliteType,Class of metabolite.,"acylcarnitines, acylglycerols, amino acids, ApoA1, ApoE, bile acids, biogenic amines, carbohydrates, catecholamine, ceramides, cholesterol, cofactors and vitamins, drugs, eicosanoids, endocannabinoids, fatty acids, glycerides, glycerolipid, glycerophospholipid, ketones, lipids, lipoproteins, lysophosphatidylcholine, lysophospholipids, nucleotides, oxylipins, peptides, phosphatidylcholine, phosphatidylethonalamines, phospholipids, plasmalogens, sphingolipids, steroids, sterols, sugars, TCA cycle metabolites, triglycerides, untargeted metabolomics, xenobiotics",,,False,ManifestColumn,,sage.annotations-experimentalData.metaboliteType-0.0.5,list like error,string,metabolomics metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file.","analytical covariates, assay metadata, biospecimen, data dictionary, ID mapping, individual, manifest, protocol",,,False,ManifestColumn,,sage.annotations-experimentalData.metadataType-0.0.4,,string,ADKP MICR,Microinfarcts,"No, Yes, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.MICR-0.0.2,string,,clinical microchipID,Identifying string of p-chip implanted in the animal being studied,,,,False,ManifestColumn,,sage.annotations-neuro.microchipID-0.0.1,,string,MODEL-AD From 70e4fe8ca5e31932d43f707af6698b82a0f40f14 Mon Sep 17 00:00:00 2001 From: avanlinden Date: Mon, 23 Sep 2024 22:36:33 +0000 Subject: [PATCH 4/4] GitHub Action: convert *.model.csv to *.model.jsonld --- AD.model.jsonld | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/AD.model.jsonld b/AD.model.jsonld index 99d2773..5d70162 100644 --- a/AD.model.jsonld +++ b/AD.model.jsonld @@ -19684,7 +19684,9 @@ ], "sms:displayName": "metaboliteType", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "list like error" + ] }, { "@id": "bts:Acylcarnitines",