The sense of smell, reimagined through data
What if it were possible to discover the evolutionary history of smell—how organisms in thousands of species use their olfactory genes to sense and meaningfully navigate their world? While comprehensive analysis of olfactory systems across species was previously challenging due to scattered data, CORD provides a centralized resource for such studies. CORD (Chordata Olfactory Receptor Database), launched in 2024 by researchers at ShanghaiTech University, is the first general and searchable database of olfactory receptor (OR) genes for the entire phylum Chordata. This article will discuss what makes CORD significant, how it functions, and its value for researchers in genetics, neuroscience, evolutionary biology and bioinformatics.
If you are a scientist seeking answers to fundamental questions about the origins of sensory systems, or if you are a data scientist interested in studying gene family evolution, CORD offers a new perspective on how organisms perceive the world.
What is the Chordata Olfactory Receptor Database?
The Chordata olfactory receptor database is a curated, interactive database of olfactory receptor genes in over 150 chordate species (including mammals, birds, reptiles, amphibians, and fish) and allows scientists to compare olfactory receptor genes, and in turn how a variety of organisms sense odors, in detail across many species. The goal is to provide a uniform standard for classifying OR genes at multiple taxonomic and molecular classifications (Protein & Cell, 2024).
Developed by a team at the iHuman Institute, ShanghaiTech University, CORD fills a critical gap in comparative genomics. While olfactory receptors are the largest gene family in vertebrates, comprehensive datasets spanning species have been scarce—until now.
The design of the database reflects practical needs in the lab. From intuitive search tools to visual diagrams and sequence networks, it supports both hypothesis generation and validation.
Key Features and Structure of the Chordata Olfactory Receptor Database
CORD is not just a static database; it’s a interactive database. Let’s break down what makes it powerful:
1. Searchable by Keywords
Users can search through a gene name (like OR52E1), organism name (like Homo sapiens, Pan troglodytes) or custom identifiers such as CO1.1, as this is incredibly versatile for general exploration or specific querying.
2. Core Data Fields
Each database entry includes:
- Entry: Unique OR gene identifier
- Gene Name: Standardized gene classification
- Organism: Verified species name
- Length: Amino acid count of the protein sequence
- UniProt ID: Cross-linked protein identifier
- External Name: Corresponding name in UniProt
- Func./Pseudo: Indicates whether gene is functional or a pseudogene
- Gene Family/Subfamily: Internal classification hierarchy
3. Filtering Options
Refine your search using filters like:
- Popular Organisms
- Taxonomy
- Gene
- Functional vs Pseudogene
- Sequence Length
- Number of ORs in Species
- Match Score
- Odor (when applicable)
This allows researchers to quickly extract subsets of data relevant to their hypotheses.
4. Interactive Entry Pages
Clicking any OR entry reveals:
- Basic Info (taxonomy, gene family, amino acid length, functional status)
- Sequences
- Snake Diagrams
- 3D Structures
- Sequence Similarity Networks
- Ligand Associations
These visualization tools bridge raw data and biological meaning.
5. Advanced Search
Researchers can run searches using Gene Name, Taxonomy ID, or other filters.
Practical Use Cases of the Chordata Olfactory Receptor Database
Comparative Genomics
CORD enables alignment of OR gene families across species. For example, a researcher can analyze the functional OR repertoire in primates versus rodents to infer evolutionary adaptations to terrestrial vs arboreal environments.
Functional Annotation
Each OR gene is linked to UniProt entries, making it easier to integrate CORD data with protein-level annotations.
Evolutionary Neuroscience
By exploring the number and diversity of OR genes, scientists can estimate the complexity of olfactory perception in extinct or poorly studied species.
This kind of insight has implications for understanding not just evolution, but also sensory disorders and how species interact with their environments.
Data Tools and Analysis Modules in the Chordata Olfactory Receptor Database
The CORD portal also offers a suite of analytical tools:
- Statistics Dashboard: Summary metrics on species, families, pseudogene ratios.
- Analysis Tool: Enables comparative charts and plots.
- Sequence Similarity Network: Visualize relationships between OR genes.
- PSSM Profile Generator: For motif and domain analysis.
- WebLogo Viewer: Generates sequence logos for OR families.
- BLAST Tool: Compare custom sequences against the full CORD database.
Each tool is engineered to make data interpretation smoother for both biologists and data scientists.
Why the Chordata Olfactory Receptor Database Matters
A New Frontier for Olfaction Research
The breadth and usability of CORD allows for questions that were previously out of reach. For instance, how do aquatic mammals like dolphins adapt their OR repertoire compared to terrestrial ones? Or why do some reptiles have far more pseudogenes than birds?
These aren’t just academic questions—they relate to real-world adaptation, biodiversity, and ecological pressures. CORD gives us a framework to answer them.
Open Access, Peer-Reviewed Science
CORD is free to use and maintained by a reputable academic institution. It is peer-reviewed and supported by detailed documentation (CORD Help Guide).
Future-Proofed
Given its modular structure, CORD can easily integrate more data as new genomes are sequenced, ensuring long-term relevance.
The more complete our genome assemblies become, the more valuable this kind of centralized, standardized database becomes to the global scientific community.
Limitations and Considerations of the Chordata Olfactory Receptor Database
While CORD offers valuable resources, users should be aware of: – Data quality depends on the underlying genome assemblies – Update frequency varies by species – Some taxonomic groups may have better coverage than others – Functional annotations rely on computational predictions that may require experimental validation
Final Thoughts
The Chordata Olfactory Receptor Database is not just a database, it’s a comprehensive database. Through advanced tools, expert curation, and large species representation, it provides a critical link in our understanding of evolutionary genetics, molecular biology, and neuroinformatics. For any researcher who wants to plunge into the science of smell, CORD is now an indispensable tool.
Its future potential lies in interdisciplinary collaboration—from artificial intelligence to pharmacology. Wherever there’s a need to understand how living beings perceive chemical signals, CORD is ready to provide the molecular map.
For researchers working across molecular disciplines, the Organic Spectral Database offers a complementary perspective—focusing on the structural signatures of organic compounds through spectroscopy. Used together with genetic tools like the Chordata Olfactory Receptor Database, it helps paint a more complete picture of how molecules function and interact across biological systems.
