Welcome to Biorels! We're excited to introduce you to a dynamic platform designed to empower you with the best resources from the scientific community in biological sciences. Our mission is to make it easy for you to access a wealth of data from scientific publications, patents, clinical trials, and various databases. Biorels is not just about simplifying data access; it’s about fostering collaboration and innovation by creating a shared space for scientists to build upon existing knowledge.
Our platform consists of two main components: a flexible backend infrastructure and a user-friendly website. The backend allows you to select amond the 30 data sources below and store only the data you need, giving you the freedom to develop your projects privately. Meanwhile, our website is modular and visually intuitive, making it easy to explore and analyze data. We also offer different levels of security and access to cater to enterprise needs. Join us in transforming the way we connect with and utilize biological data!
The list of data sources with the license and release frequency are provided below to the best of our knowledge:
| Data type | Data Source | Release frequency | License |
|---|---|---|---|
| Taxonomy | NCBI Taxonomy | Daily | NCBI Policy |
| Gene | NCBI Gene | Daily | NCBI Policy |
| Ensembl | Bi-Weekly | No restrictions | |
| Orthologs | NCBI Orthologs | Daily | NCBI Policy |
| HCOP | |||
| Variant/Mutation | dbSNP | No schedule | NCBI Policy |
| Small molecule | ChEMBL | No schedule | CC BY-SA 3.0 |
| Clinical variant | Clinvar | Weekly | NCBI Policy |
| RNA Expression | GTEX | Version 8 | GTEx License |
| Protein domain | InterPro | 1-3 Months | CC 0 |
| Drug | DrugBank | Weekly | DrugBank license |
| Disease | MONDO | Bi-Monthly | CC BY 4.0 |
| Anatomy | UBERON | Bi-Monthly | CC BY 3.0 |
| Small molecule/Lipid | SwissLipids | Weekly | CC BY 4.0 |
| Small molecule/Patent | SureChEMBL | No schedule | CC BY-SA 3.0 |
| Cell Lines | Cellosaurus | No schedule | CC BY 4.0 |
| Disease/Drug/Clinical trials | Open Target | Bi-Monthly | CC 0 |
| Disease Ontology | EFO | Monthly | Apache 2.0 |
| Sequence Ontology | SO | No schedule | CC BY-SA 4.0 |
| Evidence Ontology | ECO | Monthly | CC0 1.0 Public domain |
| BioAssay Ontology | BAO | No schedule | CC BY 4.0 |
| Protein information | UniProt | Quarterly | CC BY 4.0 |
| Publication | PubMed | Daily | NCBI Policy |
| Pathway | Reactome | Bi-monthly | CC 0 |
| Gene Ontology | GO | Monthly | CC BY 4.0 |
| Gene/DNA/RNA | RefSeq | No schedule | NCBI Policy |
| Ensembl | No restrictions | ||
| Clinical Trials | US Clinical trials | Daily | US CT.gov Terms of use |
| Disease/Gene information | OMIM | Daily | OMIM License |
| Gene information | Gene Reviews® | Frequently | Gene Reviews Copyright |
| Liver Toxicity | LiverTox | Frequently | Freely available |
| PubMed Central (PMC) | PMC | Daily | CC Only |
If you're wondering where to start, we recommend diving into our documentation to get familiar with the project and its goals:
The documentation has everything you need to set things up.
You are not sure yet if you want to dig in the whole process? Fair enough, we've got you covered. If you want to evaluate BioRels with the minimal amount of configuration, please go to QUICKSTART
We warmly welcome contributors to our code repository! Whether you're a seasoned developer or just starting out, your contributions can make a real difference. To get involved, check out our issues list—it's a great way to find tasks that match your skills and interests. We are also looking to grow the number of data sources covered in BioRels! Every contribution, big or small, helps us improve and grow, and we’re excited to see what you bring to the table and add you to the list below! Don’t hesitate to reach out to the community or use the contact information below for guidance or clarification; we’re here to help. Once you’ve found a task, fork the repository, make your changes, and submit a pull request. Your contributions are valued, and we can’t wait to see what you’ll create! So join us in building something amazing together!
For any questions, please contact desaphy_jeremy[@]lilly.com
Please use the following citation:
BioRels' data infrastructure: A Scientific Schema and Exchange Standard to transform and enhance biological data sciences
Jibo Wang, Bruno dos Santos, Amanda Turney, Lauren Murray, Andrew M Craven, Patty Bragger-Wilkinson, Jaroslav Martasek, Jeremy Desaphy
Nucleic Acids Research - 2024 - In review
We want to thank all the contributors of BioRels:
- Jibo Wang
- Bruno dos Santos,
- Amanda Turney
- Lauren Murray
- Andrew M Craven
- Patty Bragger-Wilkinson
- Jaroslav Martasek
- Jeremy Desaphy
GPL V3
Copyright (c) 2024 Eli Lilly and Company All rights reserved. All source files is subject to the license and copyright provided in this repository.
- We make no warranties regarding the correctness of the data, and disclaim liability for damages resulting from its use.
- We do not provided unrestricted permission regarding the use of the data, as some data may be covered by patents, other rights or licenses.
- User is responsible for complying with the legal terms for BioRels, any data source and packages used in BioRels