How do the Object and Description table and JSON Output of Drugbank pharmacology API function?
In this article, I will provide a clear understanding of the object table and JSON output of Drugbank pharmacology API. As a programmer, you are likely to encounter these two data structures when working with Drugbank's pharmacology API. The object table is a tabular representation of the data, where each row represents a unique record, and each column represents a different attribute of the record. On the other hand, JSON (JavaScript Object Notation) is a lightweight data interchange format that is easy to read and write. I will explain the structure and components of both the object table and JSON, providing examples and illustrations to help you better understand how to work with these data structures.
API Table
Objects | Description |
|---|---|
pharmacology | |
indication | The approved conditions, diseases, or states for which a drug can safely and effectively be used. An indication is considered to be FDA-approved when it has any of the following designations: NDA, ANDA, BLA, or OTC. May also include indications in other countries, such as Canada (through Health Canada) or in Europe (through the European Medicines Agency). |
pharmacodynamics | A description of how the drug modifies or affects the organism it is being used in. May include effects in the body that are desired (enzyme or protein targets for example) and undesired (also known as “side effects”). This is in contrast to pharmacokinetics, which describes how the body modifies the drug being used. |
mechanism_of_action | A component of pharmacodynamics that describes the biochemical interaction through which a drug produces its intended effect. May include the exact molecular protein or enzyme targets and/or a description of the physiological effects produced. |
absorption | A description of the movement of the drug from the site of administration into the bloodstream or target tissue. Common pharmacokinetic metrics used to evaluate absorption include Area Under the Curve (AUC), bioavailability (F), maximum concentration (Cmax), and time to maximum concentration (Tmax). |
toxicity | Any adverse reaction, or side effect, that may or may not occur with use of the drug. May be attributed to a number of effects including: an enhanced therapeutic effect, rare anaphylactic reactions, interactions with other medications, or unanticipated binding of the molecule at different sites within the body. |
protein_binding | A description of the drug’s affinity for plama proteins and the proportion of the drug that is bound to them when in circulation within the body. |
metabolism | A description of the chemical degradation of the drug molecule within the body; most commonly by enzymes from the Cytochrome P450 (CYP) system in the liver. |
half_life | The period of time it takes for the amount of drug in the body to be reduced by one half. Provides a description of how quickly the drug is being eliminated and how much is available in the bloodstream. |
route_of_elimination | A description of the pathway that is used to excrete the drug from the body. Common pharmacokinetic parameters used to evaluate excretion include elemination half life, renal clearance, and tracking of radiolabelled compounds through the renal and GI system. |
volume_of_distribution | The Vd of a drug represents the degree to which it is distributed into body tissue compared to the plasma. |
clearance | A pharmacokinetic measurement of the rate of removal of the drug from plasma, expressed as mL/min; reflects the rate of elimination of the drug. |
structured_indications |
pharmacology - This object contains general information about the drug, such as its name, brand name, and drug type.
indication - This object describes the approved conditions, diseases, or states for which a drug can safely and effectively be used. It may also include indications in other countries.
pharmacodynamics - This object provides a description of how the drug modifies or affects the organism it is being used in. It includes the effects in the body that are desired (enzyme or protein targets, for example) and undesired (also known as "side effects").
mechanism_of_action - This object describes the biochemical interaction through which a drug produces its intended effect. It may include the exact molecular protein or enzyme targets and/or a description of the physiological effects produced.
absorption - This object describes the movement of the drug from the site of administration into the bloodstream or target tissue. It includes common pharmacokinetic metrics used to evaluate absorption such as Area Under the Curve (AUC), bioavailability (F), maximum concentration (Cmax), and time to maximum concentration (Tmax).
toxicity - This object describes any adverse reaction, or side effect, that may or may not occur with the use of the drug. It may be attributed to a number of effects, including an enhanced therapeutic effect, rare anaphylactic reactions, interactions with other medications, or unanticipated binding of the molecule at different sites within the body.
protein_binding - This object describes the drug's affinity for plasma proteins and the proportion of the drug that is bound to them when in circulation within the body.
metabolism - This object describes the chemical degradation of the drug molecule within the body, most commonly by enzymes from the Cytochrome P450 (CYP) system in the liver.
half_life - This object provides the period of time it takes for the amount of drug in the body to be reduced by one half. It provides a description of how quickly the drug is being eliminated and how much is available in the bloodstream.
route_of_elimination - This object describes the pathway that is used to excrete the drug from the body. Common pharmacokinetic parameters used to evaluate excretion include elimination half-life, renal clearance, and tracking of radiolabeled compounds through the renal and GI system.
volume_of_distribution - This object provides the degree to which a drug is distributed into body tissue compared to the plasma.
clearance - This object provides a pharmacokinetic measurement of the rate of removal of the drug from plasma, expressed as mL/min. It reflects the rate of elimination of the drug.
The information provided in the table is useful for individuals and organizations in the pharmaceutical industry. It enables them to gain a comprehensive understanding of the drug and its effects on the body. This information is essential in drug development, clinical trials, and drug regulation, as it helps in determining the safety and efficacy of the drug. The table provides detailed information on various pharmacokinetic and pharmacodynamic parameters, such as absorption, metabolism, half-life, and route of elimination, which can be used to optimize drug dosages, reduce side effects, and improve patient outcomes. In summary, having access to this information allows researchers, healthcare providers, and regulatory agencies to make informed decisions regarding the use of drugs in treating various conditions.
JSON output
The given JSON output provides pharmacological information on Gadobenate Dimeglumine, an MRI contrast agent. The "indication" object describes the primary use of the drug for MR imaging of the liver and also its usage for MRI of the heart and central nervous system in adults to visualize lesions with abnormal brain vascularity or abnormalities in the blood brain barrier, the brain, spine, or other associated tissues. The "pharmacodynamics" object explains that Gadobenate dimeglumine shares pharmacokinetic properties of the ECF contrast agent gadopentetate dimeglumine but is selectively taken up by hepatocytes and excreted via bile. The "toxicity" object suggests that Gadolinium-based radiocontrast agents like Gadobenate dimeglumine are cytotoxic to renal cells, and the toxic effects include apoptosis, cellular energy failure, disruption of calcium homeostasis, and disturbance of tubular cell polarity, and are thought to be linked to oxidative stress. Additionally, the "half-life" object reveals that the elimination half-life of Gadobenate Dimeglumine is approximately one hour, and it is not metabolized. The "route_of_elimination" object describes that Gadobenate ion is eliminated predominately via the kidneys, with 78% to 96% of an administered dose recovered in the urine. The "clearance" object provides a pharmacokinetic measurement of the rate of removal of the drug from plasma, expressed as L/hr/kg. Finally, the "structured_indications" object is an empty list.
{
"pharmacology": {
"indication": "Gadobenate Dimeglumine is an MRI contrast agent used primarily for MR imaging of the liver. It can also be used for MRI of the heart, as well as and central nervous system in adults to visualize lesions with abnormal brain vascularity or abnormalities in the blood brain barrier, the brain, spine, or other associated tissues.",
"pharmacodynamics": "Gadobenate dimeglumine shares the pharmacokinetic properties of the ECF contrast agent gadopentetate dimeglumine; however, gadobenate differs in that is also selectively taken-up by hepatocytes and excreted via the bile (up to 5% of dose). The elimination half-life of gadobenate dimeglumine is approximately 1 hour. It is not metabolized.",
"mechanism_of_action": "Based on the behavior of protons when placed in a strong magnetic field, which is interpreted and transformed into images by magnetic resonance (MR) instruments. Paramagnetic agents have unpaired electrons that generate a magnetic field about 700 times larger than the proton's field, thus disturbing the proton's local magnetic field. When the local magnetic field around a proton is disturbed, its relaxation process is altered. MR images are based on proton density and proton relaxation dynamics. MR instruments can record 2 different relaxation processes, the T1 (spin-lattice or longitudinal relaxation time) and the T2 (spin-spin or transverse relaxation time). In magnetic resonance imaging (MRI), visualization of normal and pathological brain tissue depends in part on variations in the radiofrequency signal intensity that occur with changes in proton density, alteration of the T1, and variation in the T2. When placed in a magnetic field, Gadobenate Dimeglumine shortens both the T1 and the T2 relaxation times in tissues where it accumulates. At clinical doses, Gadobenate Dimeglumine primarily affects the T1 relaxation time, thus producing an increase in signal intensity. Gadobenate Dimeglumine does not cross the intact blood-brain barrier; therefore, it does not accumulate in normal brain tissue or in central nervous system (CNS) lesions that have not caused an abnormal blood-brain barrier (e.g., cysts, mature post-operative scars).",
"absorption": "",
"toxicity": "Gadolinium-based radiocontrast agents like gadobenate dimeglumine are cytotoxic to renal cells. The toxic effects include apoptosis, cellular energy failure, disruption of calcium homeostasis, and disturbance of tubular cell polarity, and are thought to be linked to oxidative stress.",
"protein_binding": "Plasma protein binding is low, weak, and transient.",
"metabolism": "Not metabolized.",
"half_life": "1 hour",
"route_of_elimination": "Gadobenate ion is eliminated predominately via the kidneys, with 78% to 96% of an administered dose recovered in the urine.",
"volume_of_distribution": "",
"clearance": "* 0.093 +/- 0.010 L/hr/kg [healthy male subjects receiving 3 single-dose IV administration with doses from 0.005-0.4 mmol/kg]",
"structured_indications": [ ]
}
}
Closing up
In this article, we discussed an object table and JSON output related to the Drugbank pharmacology API. The table contained various pharmacokinetic and pharmacodynamic parameters, while the JSON output provided detailed pharmacological information on a specific drug. The information in both the table and JSON output is valuable for researchers, healthcare providers, and regulatory agencies, as it enables them to make informed decisions regarding drug development, clinical trials, drug regulation, and patient treatment. Understanding these parameters and the pharmacological properties of drugs is crucial for optimizing dosages, reducing side effects, and improving patient outcomes. Overall, this conversation emphasizes the importance of pharmacological knowledge in the pharmaceutical industry and its significance in advancing medical research and patient care.
Reference
It is possible to request access to the Drugbank pharmacology API through the third-party data marketplace of Worldindata. Worldindata is a platform that provides various datasets for researchers and analysts to use in their work. To request access to the Drugbank pharmacology API, one must create an account on Worldindata and then navigate to the "Data Marketplace" section. In the marketplace, you can search for "Drugbank API" and select the dataset. Once selected, you will be prompted to submit a request to the data provider for access. After approval, you can access the Drugbank pharmacology API through the Worldindata platform. This process ensures that users can access the data securely and with the necessary permissions.