Notes
Oct 21, 2024 - This repository has recently been transferred from The University of Alabama Libraries Web Services GitHub to The University of Alabama Libraries Research Data Services GitHub organization. All GitHub related hyperlinks should automatically redirect to the new GitHub location, but if you notice anything that is not working correctly, please let us know.
This repository contains Entrez Direct (EDirect, an NCBI tool) Unix scripts for programmatically obtaining data from various NCBI databases. Other EDirect resources and guides exist (referenced below). This EDirectChemInfo repository differs in that the focus is on teaching how to obtain chemical information, cheminformatics data, and chemical structure <--> bioassay <--> document relationship links. There are not many PubChem EDirect examples available, so hopefully this repository proves useful. I have also added some tips, step-wise directions, and code output examples to help you get started.
Please note that this EDirectChemInfo repository is not affiliated with NCBI. You should contact NCBI for specific questions related to EDirect. This repository was created to accompany library instruction at The University of Alabama. With that in mind, please feel free to open a GitHub Issue or contact me directly with comments/questions if you think there is something I can help you with. In addition, if this repository has been a useful resource for you, please do let me know as this type of feedback can help prioritize my time.
Vincent Scalfani
Science and Engineering Librarian
The University of Alabama
UA Libraries Directory
- What is EDirect?
- Available Databases, Data Fields, and Data Structures
- PubChem <--> PubChem BioAssay <--> PubMed EDirect Recipes
- PubChem EDirect Recipes
- PubMed EDirect Recipes
- Combining EDirect Results with Chemical Depiction and Plotting
These are the main references I used to learn about NCBI E-Utilities, the EDirect syntax, Unix commands/scripts, and the importance of linked chemical data. Many thanks to the authors for their work.
- NCBI Documentation for Entrez Direct: E-utilities on the UNIX Command Line
- NIH NLM The Insider's Guide to Accessing NLM Data
- NCBI EDirect Cookbook
- Computational Genomics Manual: NCBI EDirect
- Entrez Link Descriptions
- Software Carpentry: The Unix Shell
- Opening up connectivity between documents, structures and bioactivity by Christopher Southan
Code in this repository is licensed under the MIT License. Some of the chemical depiction demonstrations from EDirect output use proprietary software, such as ChemAxon Marvin, which is not included under this license. Users must have valid licenses for any required proprietary software to run these portions of the code.
Code output (e.g., reference/molecular data snippets) retrieved from NCBI via their EDirect utility is shown for code demonstration purposes only and is credited to NCBI and NLM. Please see the NCBI Website and Data Usage Policies and Disclaimers for more information regarding the data.