Merge pull request #458 from Peyman-N/chemicals

Molecular Entities needed for in depth

instances/molecularEntity/4-(2-Hydroxyethyl)-1-piperazineEthanesulfonicAcid.jsonld

@@ -0,0 +1,17 @@
+{
+  "@context": {
+    "@vocab": "https://openminds.ebrains.eu/vocab/"
+  },
+  "@id": "https://openminds.ebrains.eu/instances/molecularEntity/4-(2-Hydroxyethyl)-1-piperazineEthanesulfonicAcid",
+  "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+  "definition": "HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) is a zwitterionic sulfonic acid buffering agent; one of the twenty Good's buffers. [adapted from wikipedia (https://en.wikipedia.org/wiki/HEPES)]",
+  "description": null,
+  "interlexIdentifier": "http://uri.interlex.org/base/ilx_0484759",
+  "knowledgeSpaceLink": "https://knowledge-space.org/wiki/CHEBI:42334#2-4-2-hydroxyethyl-piperazin-1-yl-ethanesulfonic-acid",
+  "name": "4-(2-Hydroxyethyl)-1-piperazine ethanesulfonic acid",
+  "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_42334",
+  "synonym": [
+    "HEPES",
+    "2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid"
+  ]
+}

instances/molecularEntity/6,7-Dinitro-1,4-dihydroquinoxaline-2,3-dione.jsonld

@@ -0,0 +1,18 @@
+{
+  "@context": {
+    "@vocab": "https://openminds.ebrains.eu/vocab/"
+  },
+  "@id": "https://openminds.ebrains.eu/instances/molecularEntity/6,7-Dinitro-1,4-dihydroquinoxaline-2,3-dione",
+  "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+  "definition": "DNQX (6,7-dinitroquinoxaline-2,3-dione) is a competitive antagonist at AMPA and kainate receptors, two ionotropic glutamate receptor (iGluR) subfamilies. [adapted from wikipedia (https://en.wikipedia.org/wiki/DNQX)]",
+  "description": "DNQX (6,7-dinitroquinoxaline-2,3-dione) is used in a variety of molecular biology subfields, notably neurophysiology, to assist researchers in determining the properties of various types of ion channels and their potential applications in medicine. [adapted from wikipedia (https://en.wikipedia.org/wiki/DNQX)]",
+  "interlexIdentifier": "http://uri.interlex.org/base/ilx_0103368",
+  "knowledgeSpaceLink": null,
+  "name": "6,7-Dinitro-1,4-dihydroquinoxaline-2,3-dione",
+  "preferredOntologyIdentifier": "https://pubchem.ncbi.nlm.nih.gov/compound/3899541",
+  "synonym": [
+    "DNQX",
+    "6,7-dinitroquinoxaline-2,3-dione",
+    "6,7-Dinitro-1,4-dihydroquinoxaline-2,3-dione"
+  ]
+}

instances/molecularEntity/MagnesiumATP.jsonld

@@ -0,0 +1,16 @@
+{
+    "@context": {
+        "@vocab": "https://openminds.ebrains.eu/vocab/"
+    },
+    "@id": "https://openminds.ebrains.eu/instances/molecularEntity/MagnesiumATP",
+    "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+    "definition": "An ATP binded to magnesium ion (Mg2+) to compose biologically functional form, and most of intracellular ATP and Mg2+ assumed to form Mg-ATP complexes. [adapted from Yamanaka et al. Mitochondrial Mg(2+) homeostasis decides cellular energy metabolism and vulnerability to stress. Sci Rep. 2016 Jul 26;6:30027. doi: 10.1038/srep30027]",
+    "description": null,
+    "interlexIdentifier": null,
+    "knowledgeSpaceLink": null,
+    "name": "MagnesiumATP",
+    "preferredOntologyIdentifier": "https://pubchem.ncbi.nlm.nih.gov/compound/15126",
+    "synonym": [
+        "MgATP"
+    ]
+}

instances/molecularEntity/calciumChloride.jsonld

@@ -0,0 +1,19 @@
+{
+  "@context": {
+    "@vocab": "https://openminds.ebrains.eu/vocab/"
+  },
+  "@id": "https://openminds.ebrains.eu/instances/molecularEntity/calciumChloride",
+  "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+  "definition": "Calcium chloride is an inorganic compound, a salt with the chemical formula CaCl2. [adapted from wikipedia (https://en.wikipedia.org/wiki/Calcium_chloride)]",
+  "description": "CaCl2 is a white crystalline solid at room temperature, and it is highly soluble in water. It can be created by neutralising hydrochloric acid with calcium hydroxide. Calcium chloride is commonly encountered as a hydrated solid with generic formula CaCl2·nH2O, where n = 0, 1, 2, 4, and 6. These compounds are mainly used for de-icing and dust control. Because the anhydrous salt is hygroscopic and deliquescent, it is used as a desiccant. [adapted from wikipedia (https://en.wikipedia.org/wiki/Calcium_chloride)]",
+  "interlexIdentifier": "http://uri.interlex.org/base/ilx_0101566",
+  "knowledgeSpaceLink": "https://knowledge-space.org/wiki/CHEBI:3312#calcium-dichloride",
+  "name": "Calcium chloride",
+  "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_3312",
+  "synonym": [
+    "CaCl2",
+    "calcium(II) chloride",
+    "calcium dichloride (1:2)",
+    "E509"
+  ]
+}

instances/molecularEntity/carbonDioxide.jsonld

@@ -0,0 +1,22 @@
+{
+  "@context": {
+    "@vocab": "https://openminds.ebrains.eu/vocab/"
+  },
+  "@id": "https://openminds.ebrains.eu/instances/molecularEntity/carbonDioxide",
+  "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+  "definition": "A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. [adapted from ChEBI (https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16526)]",
+  "description": "Carbon dioxide is a chemical compound with the chemical formula CO2. It is made up of molecules that each have one carbon atom covalently double bonded to two oxygen atoms. It is found in the gas state at room temperature, and as the source of available carbon in the carbon cycle, atmospheric CO2 is the primary carbon source for life on Earth. In the air, carbon dioxide is transparent to visible light but absorbs infrared radiation, acting as a greenhouse gas. Carbon dioxide is soluble in water and is found in groundwater, lakes, ice caps, and seawater. [adapted from ChEBI (https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16526)]",
+  "interlexIdentifier": "http://uri.interlex.org/base/ilx_0780969",
+  "knowledgeSpaceLink": "https://knowledge-space.org/wiki/CHEBI:16526#carbon-dioxide",
+  "name": "Carbon dioxide",
+  "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_16526",
+  "synonym": [
+    "CO2",
+    "Carbonic acid gas",
+    "Carbonic anhydride",
+    "Carbonic dioxide",
+    "Dry ice",
+    "Carbonic oxide",
+    "E290"
+  ]
+}

instances/molecularEntity/choline.jsonld

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+{
+  "@context": {
+    "@vocab": "https://openminds.ebrains.eu/vocab/"
+  },
+  "@id": "https://openminds.ebrains.eu/instances/molecularEntity/choline",
+  "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+  "definition": "Choline is a cation with the chemical formula [(CH3)3NCH2CH2OH]+. Choline forms various salts, for example choline chloride and choline bitartrate. [adapted from wikipedia (https://en.wikipedia.org/wiki/Choline)]",
+  "description": null,
+  "interlexIdentifier": "http://uri.interlex.org/base/ilx_0102128",
+  "knowledgeSpaceLink": "https://knowledge-space.org/wiki/CHEBI:15354#choline",
+  "name": "Choline",
+  "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_15354",
+  "synonym": [
+    "(2-Hydroxyethyl)trimethylammonium",
+    "2-Hydroxy-N,N,N-trimethylethanaminium",
+    "Bilineurine",
+    "Choline cation",
+    "Choline ion"
+  ]
+}

instances/molecularEntity/diboronTrioxide.jsonld

@@ -0,0 +1,21 @@
+{
+  "@context": {
+    "@vocab": "https://openminds.ebrains.eu/vocab/"
+  },
+  "@id": "https://openminds.ebrains.eu/instances/molecularEntity/diboronTrioxide",
+  "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+  "definition": "Diboron trioxide or boron trioxide is the oxide of boron with the formula B2O3. [adapted from wikipedia (https://en.wikipedia.org/wiki/Boron_trioxide)]",
+  "description": " Diboron trioxide is a colorless transparent solid, almost always glassy (amorphous), which can be crystallized only with great difficulty. It is also called boric oxide or boria. It has many important industrial applications, chiefly in ceramics as a flux for glazes and enamels and in the production of glasses. [adapted from wikipedia (https://en.wikipedia.org/wiki/Boron_trioxide)]",
+  "interlexIdentifier": null,
+  "knowledgeSpaceLink": null,
+  "name": "Diboron trioxide",
+  "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_30163",
+  "synonym": [
+    "Boron trioxide",
+    "Boron oxide",
+    "Boron sesquioxide",
+    "Boric oxide",
+    "Boria",
+    "Boric anhydride"
+  ]
+}

instances/molecularEntity/dimethylSulfoxide.jsonld

@@ -0,0 +1,49 @@
+{
+  "@context": {
+    "@vocab": "https://openminds.ebrains.eu/vocab/"
+  },
+  "@id": "https://openminds.ebrains.eu/instances/molecularEntity/dimethylSulfoxide",
+  "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+  "definition": "Dimethyl sulfoxide (DMSO) is an organosulfur compound with the formula (CH3)2SO. [adapted from wikipedia (https://en.wikipedia.org/wiki/Dimethyl_sulfoxide)]",
+  "description": "A highly polar organic liquid, that is used widely as a chemical solvent. Because of its ability to penetrate biological membranes, it is used as a vehicle for topical application of pharmaceuticals. It is also used to protect tissue during cryopreservation. Dimethyl sulfoxide shows a range of pharmacological activity including analgesia and anti-inflammation. (PubChem) Pharmacology: Dimethyl Sulfoxide may have anti-inflammatory, antioxidant and analgesic activities. Dimethyl Sulfoxide also readily penetrates cellular membranes. The membrane-penetrating ability of dimethyl sulfoxide may enhance diffusion of other substances through the skin. For this reason, mixtures of idoxuridine and dimethyl sulfoxide have been used for topical treatment of herpes zoster in the United Kingdom. Mechanism of action: The mechanism of dimethyl sulfoxide's actions is not well understood. Dimethyl sulfoxide has demonstrated antioxidant activity in certain biological settings. For example, the cardiovascular protective effect of dimethyl sulfoxide in copper-deficient rats is thought to occur by an antioxidant mechanism. It is also thought that dimethyl sulfoxide's possible anti-inflammatory activity is due to antioxidant action. [adapted from wikipedia (https://en.wikipedia.org/wiki/Dimethyl_sulfoxide)]",
+  "interlexIdentifier": "http://uri.interlex.org/base/ilx_0103278",
+  "knowledgeSpaceLink": "https://knowledge-space.org/wiki/CHEBI:28262#dimethyl-sulfoxide",
+  "name": "Dimethyl sulfoxide",
+  "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_28262",
+  "synonym": [
+    "DMSO",
+    "Diemthyl sulfoxide",
+    "Dimethyl sulfoxide BP",
+    "Dimethyl sulfur oxide",
+    "Dimethyl sulphoxide",
+    "Dimethyl sulpoxide",
+    "Dimexidum",
+    "Methyl sulfoxide",
+    "Methylsulfinylmethane",
+    "Sulfinylbis-methane",
+    "Sulfinylbismethane",
+    "Sulfinyldimethane",
+    "Decap",
+    "Deltan",
+    "Demasorb",
+    "Demavet",
+    "Demeso",
+    "Demsodrox",
+    "Dermasorb",
+    "Dimexide",
+    "Dipirartril-tropico",
+    "Dolicur",
+    "Doligur",
+    "Domoso",
+    "Dromisol",
+    "Durasorb",
+    "Gamasol 90",
+    "Hyadur",
+    "Infiltrina",
+    "Kemsol",
+    "Rimso 50",
+    "Sclerosol",
+    "Somipront",
+    "Syntexan"
+  ]
+}

instances/molecularEntity/dinitrogen.jsonld

@@ -0,0 +1,18 @@
+{
+  "@context": {
+    "@vocab": "https://openminds.ebrains.eu/vocab/"
+  },
+  "@id": "https://openminds.ebrains.eu/instances/molecularEntity/dinitrogen",
+  "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+  "definition": "An elemental molecule consisting of two trivalently-bonded nitrogen atoms. [adapted from ChEBI (https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17997)]",
+  "description": "At standard temperature and pressure, two atoms of the element nitrogen bond to form N2, a colorless and odorless diatomic gas. N2 forms about 78% of Earth's atmosphere, making it the most abundant uncombined element in air. Because of the volatility of nitrogen compounds, nitrogen is relatively rare in the solid parts of the Earth. [adapted from wikipedia (https://en.wikipedia.org/wiki/Nitrogen)]",
+  "interlexIdentifier": null,
+  "knowledgeSpaceLink": null,
+  "name": "Dinitrogen",
+  "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_17997",
+  "synonym": [
+    "N2",
+    "Nitrogen",
+    "N≡N"
+  ]
+}

instances/molecularEntity/dioxygen.jsonld

@@ -0,0 +1,21 @@
+{
+  "@context": {
+    "@vocab": "https://openminds.ebrains.eu/vocab/"
+  },
+  "@id": "https://openminds.ebrains.eu/instances/molecularEntity/dioxygen",
+  "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+  "definition": "The common allotrope of elemental oxygen on Earth, O2, is generally known as oxygen. [adapted from wikipedia (https://en.wikipedia.org/wiki/Allotropes_of_oxygen)]",
+  "description": null,
+  "interlexIdentifier": "http://uri.interlex.org/base/ilx_0398707",
+  "knowledgeSpaceLink": "https://knowledge-space.org/wiki/CHEBI:15379#dioxygen",
+  "name": "Dioxygen",
+  "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_15379",
+  "synonym": [
+    "Oxygen",
+    "O2",
+    "Diatomic oxygen",
+    "Molecular oxygen",
+    "dioxidene",
+    "Oxygen gas"
+  ]
+}

instances/molecularEntity/edeticAcid.jsonld

@@ -0,0 +1,31 @@
+{
+    "@context": {
+        "@vocab": "https://openminds.ebrains.eu/vocab/"
+    },
+    "@id": "https://openminds.ebrains.eu/instances/molecularEntity/edeticAcid",
+    "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+    "definition": "Edetic Acid (Ethylenediaminetetraacetic acid, EDTA), also called edetic acid after its own abbreviation, is an aminopolycarboxylic acid with the formula [CH2N(CH2CO2H)2]2. [adapted from wikipedia (https://en.wikipedia.org/wiki/Ethylenediaminetetraacetic_acid)]",
+    "description": "This white, water-soluble solid is widely used to bind to iron (Fe2+/Fe3+) and calcium ions (Ca2+), forming water-soluble complexes even at neutral pH. It is thus used to dissolve Fe- and Ca-containing scale as well as to deliver iron ions under conditions where its oxides are insoluble. EDTA is available as several salts, notably disodium EDTA, sodium calcium edetate, and tetrasodium EDTA, but these all function similarly. [adapted from wikipedia (https://en.wikipedia.org/wiki/Ethylenediaminetetraacetic_acid)]",
+    "interlexIdentifier": null,
+    "knowledgeSpaceLink": "https://knowledge-space.org/wiki/CHEBI:4735#ethylene-glycol-bis-2-aminoethyl-tetraacetic-acid",
+    "name": "Edetic acid",
+    "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_4735",
+    "synonym": [
+        "EGTA",
+        "Edetic acid",
+        "(ethylenedinitrilo)tetraacetic acid",
+        "2,2',2'',2'''-(ethane-1,2-diylbis(azanetriyl))tetraacetic acid",
+        "2,2',2'',2'''-(ethane-1,2-diyldinitrilo)tetraacetic acid",
+        "2-([2-[bis(carboxymethyl)amino]ethyl](carboxymethyl)amino)acetic acid",
+        "edathamil",
+        "EDTA (chelating agent)",
+        "ethylene-N,N'-biscarboxymethyl-N,N'-diglycine",
+        "ethylenediamine-N,N,N',N'-tetraacetic acid",
+        "ethylenediaminetetraacetic acid",
+        "ethylenedinitrilotetraacetic acid",
+        "H4edta",
+        "N,N'-1,2-Ethane diylbis-(N-(carboxymethyl)glycine)",
+        "N,N'-1,2-ethanediylbis[N-(carboxymethyl)glycine]",
+        "{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC"
+    ]
+}

instances/molecularEntity/egtazicAcid.jsonld

@@ -0,0 +1,22 @@
+{
+    "@context": {
+        "@vocab": "https://openminds.ebrains.eu/vocab/"
+    },
+    "@id": "https://openminds.ebrains.eu/instances/molecularEntity/EgtazicAcid",
+    "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+    "definition": "EGTA (ethylene glycol-bis(β-aminoethyl ether)-N,N,N',N'-tetraacetic acid), also known as egtazic acid (INN, USAN), is an aminopolycarboxylic acid, a chelating agent. [adapted from wikipedia (https://en.wikipedia.org/wiki/EGTA_(chemical))]",
+    "description": "EGTA is a white solid that is related to the better known EDTA. Compared to EDTA, it has a lower affinity for magnesium, making it more selective for calcium ions. It is useful in buffer solutions that resemble the environment in living cells where calcium ions are usually at least a thousandfold less concentrated than magnesium. [adapted from wikipedia (https://en.wikipedia.org/wiki/EGTA_(chemical))]",
+    "interlexIdentifier": null,
+    "knowledgeSpaceLink": "https://knowledge-space.org/wiki/CHEBI:30740#ethylene-glycol-bis-2-aminoethyl-tetraacetic-acid",
+    "name": "Egtazic acid",
+    "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_30740",
+    "synonym": [
+        "3,12-bis(carboxymethyl)-6,9-dioxa-3,12-diazatetradecanedioic acid",
+        "[ethylenebis(oxyethylenenitrilo)]tetraacetic acid",
+        "EGTA",
+        "Egtazic acid",
+        "ethylene glycol bis(β-aminoethyl ether)-N,N,N',N'-tetraacetic acid",
+        "ethylene glycol-O,O'-bis(2-aminoethyl)-N,N,N',N'-tetraacetic acid",
+        "H4egta"
+    ]
+}

instances/molecularEntity/ethanol.jsonld

@@ -0,0 +1,28 @@
+{
+  "@context": {
+    "@vocab": "https://openminds.ebrains.eu/vocab/"
+  },
+  "@id": "https://openminds.ebrains.eu/instances/molecularEntity/ethanol",
+  "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+  "definition": "Ethanol (also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound with the chemical formula CH3CH2OH. [adapted from wikipedia (https://en.wikipedia.org/wiki/Ethanol)]",
+  "description": "Ethanol is an alcohol, with its formula also written as C2H5OH, C2H6O or EtOH, where Et stands for ethyl. Ethanol is a volatile, flammable, colorless liquid with a characteristic wine-like odor and pungent taste. It is a psychoactive recreational drug, and the active ingredient in alcoholic drinks. [adapted from wikipedia (https://en.wikipedia.org/wiki/Ethanol)]",
+  "interlexIdentifier": "http://uri.interlex.org/base/ilx_0103948",
+  "knowledgeSpaceLink": "https://knowledge-space.org/wiki/CHEBI:16236#ethanol",
+  "name": "Ethanol",
+  "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_16236",
+  "synonym": [
+    "Absolute alcohol",
+    "Alcohol",
+    "Cologne spirit",
+    "Drinking alcohol",
+    "Ethylic alcohol",
+    "EtOH",
+    "Ethyl alcohol",
+    "Ethyl hydroxide",
+    "Ethylene hydrate",
+    "Ethylol",
+    "Grain alcohol",
+    "Hydroxyethane",
+    "Methylcarbinol"
+  ]
+}

instances/molecularEntity/formaldehyde.jsonld

@@ -0,0 +1,24 @@
+{
+  "@context": {
+    "@vocab": "https://openminds.ebrains.eu/vocab/"
+  },
+  "@id": "https://openminds.ebrains.eu/instances/molecularEntity/formaldehyde",
+  "@type": "https://openminds.ebrains.eu/controlledTerms/MolecularEntity",
+  "definition": "Formaldehyde is an organic compound with the formula CH2O and structure H-CHO. [adapted from wikipedia (https://en.wikipedia.org/wiki/Formaldehyde)]",
+  "description": "Formaldehyde is a pungent, colourless gas that polymerises spontaneously into paraformaldehyde . It is stored as aqueous solutions (formalin), which consists mainly of the hydrate CH2(OH)2. It is the simplest of the aldehydes (R-CHO). It is produced commercially as a precursor to many other materials and chemical compounds. In 2006, the global production rate of formaldehyde was estimated at 12 million tons per year. It is mainly used in the production of industrial resins, e.g., for particle board and coatings. Small amounts also occur naturally. [adapted from wikipedia (https://en.wikipedia.org/wiki/Formaldehyde)]",
+  "interlexIdentifier": null,
+  "knowledgeSpaceLink": "https://knowledge-space.org/wiki/CHEBI:16842#formaldehyde",
+  "name": "Formaldehyde",
+  "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/CHEBI_16842",
+  "synonym": [
+    "Methyl aldehyde",
+    "Methylene glycol",
+    "Methylene oxide",
+    "Formalin (aqueous solution)",
+    "Formol",
+    "Carbonyl hydride",
+    "Methanone",
+    "Oxomethane",
+    "Methanal"
+  ]
+}