PubChem provides several ways for programmatic access to its data, including: Many researchers in the biomedical science community have a great interest in programmatic access to this vast amount of data because it presents new opportunities for data-driven research in a “big data” era. Overview of Programmatic Access to PubChemĬurrently PubChem 1, 2, 3 contains more than 235 million depositor-provided substance descriptions, 94 million unique chemical structures and 232 million biological test results from one million assays, covering more than 10 thousand unique protein target sequences. Programmatic Access to Web-Based Chemical Information – Examples.Some examples complied by the OLCC Cheminformatics Faculty are available at this URL: The present module focuses on accessing PubChem data, but many other public chemical information resources also provide programmatic access to their data. Programmatic Access to Data (by Jordi Cuadros).In addition, an introductory material about Web APIs (Application Programming Interfaces) is available at the OLCC web site (as a Special Topic Module). There are many online resources that help you learn computer programming and below are some of them. While this module does not require prior knowledge of computer programming, it is highly recommended that students with no or little programming background build some basic computer programming skills. Therefore, computer programming is an essential skill for future cheminformaticians. Cheminformaticians often write computer programs to process a large amount of chemical data and to automate some tasks that are routinely performed.
REST SYNONYM CHEMISTRY HOW TO
In this module, we will learn how to “programmatically” access PubChem and other public databases. Useful Resources for Students with no Programming Background Know how to access PubChem data from a python script.Know how to access PubChem data from a spread sheet (in Google Sheet).Know how to formulate a PUG-REST request URL.Accessing PubChem Data From a Spread Sheet Program.Getting a list of assays in which a compound was tested.Getting bioactivity data determined in an assay.Getting a list of compounds tested in an assay.Getting a list of AIDs for assays that target a given protein.Getting a list of CIDs for compounds with a given molecular formula.Getting a list of CIDs for compounds with a given substructure.Getting a list of CIDs for compounds identical to a query compound.Getting a list of CIDs whose synonym is or contains “atorvastatin”.Getting molecular properties of a set of compounds.
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