Index Fungorum: The Global Database for Fungal Nomenclature
The fungal kingdom is vast and incredibly diverse, making the task of accurately naming and classifying species a monumental scientific challenge. To manage this complexity, the scientific community relies on specialized databases to track the history and validity of names. One of the most critical resources in this field is Index Fungorum, an international project dedicated to indexing all formal scientific names within the fungus kingdom.
What is Index Fungorum?
Index Fungorum serves as a comprehensive registry for fungal names. As of 2015, the project is managed through a partnership between the Royal Botanic Gardens, Kew, Landcare Research, and the Institute of Microbiology at the Chinese Academy of Sciences. It functions similarly to the International Plant Names Index (IPNI), but with a key distinction: while IPNI focuses on plant names, Index Fungorum provides specific information regarding the status of a fungal name.
When searching the database, users can easily identify the standing of a name through a color-coded system. Currently correct names are displayed in green, while other names appear in blue. In some cases, aberrant usages of names are highlighted in red. Furthermore, all names are linked to detailed pages that provide the correct name along with a list of its synonyms (different names that refer to the same organism).
ไม่มีภาพประกอบKey Facts
- Purpose: To index all formal scientific names in the fungus kingdom.
- Partners: Royal Botanic Gardens (Kew), Landcare Research, and the Institute of Microbiology (Chinese Academy of Sciences).
- Scale: As of 2023, over one million fungal names have been linked to persistent identifiers across major databases.
- Official Status: It is one of three nomenclatural repositories recognized by the Nomenclature Committee for Fungi.
- Data Standards: Adheres to FAIR principles (Findable, Accessible, Interoperable, and Reusable).
History and Evolution of Fungal Indexing
The effort to catalog fungal names has evolved significantly since the early 19th century. Early milestones include Pier Andrea Saccardo’s Sylloge Fungorum (1882–1931), which attempted to compile all known fungal descriptions, and Franz Petrak’s Lists (1920–1939), which indexed new names and literature.
The modern Index Fungorum project has its roots in the Imperial Bureau of Mycology, established in 1920. This institution later became the Commonwealth Mycological Institute in 1948, then part of CAB International in 1986, before evolving into its current form. Today, the project is transitioning from simply indexing names after they are published to a pre-publication registration model. This shift, involving automated pipelines, helps streamline how new names and nomenclatural acts—the official actions taken to name or change a name—are recorded.
Since January 1, 2013, the International Code of Nomenclature for algae, fungi, and plants has mandated that all new fungal names must cite an identifier from a recognized repository prior to publication. This rule has made databases like Index Fungorum essential to modern mycological research.
Scope and Content: What Does the Database Cover?
Index Fungorum aims to be an exhaustive list of every fungal name that has ever been validly defined. This includes names that are currently in use, those that are conflicting, and those that are obsolete. The database covers a wide range of taxa (biological groups or units) at all ranks, from suprafamilial down to infraspecific levels. It also includes names for lichen-forming fungi and various types of typification—the process of designating a specific physical specimen (a "type") to serve as the permanent reference for a name.
Since 2019, the database has also registered new type designations for previously described taxa at or below the species rank, such as lectotypifications, neotypifications, and epitypifications. These acts must be registered to ensure scientific accuracy.
| Feature | Details |
|---|---|
| Site Type | Database |
| Owner | Index Fungorum Partnership |
| URL | IndexFungorum.org |
| Commercial Use | No |
| Registration | Not required |
Species Fungorum vs. Index Fungorum
While Index Fungorum is a massive repository of all historical names, it can sometimes include names that are no longer considered reliable for current use. To assist researchers, a closely related project called Species Fungorum exists. Based at the Royal Botanic Gardens, Kew, and supported by CABI, Species Fungorum provides a curated subset of names from the Index Fungorum database that are recommended as currently valid.
Users can search both databases separately. If an entry in Index Fungorum has a cross-reference to Species Fungorum, it is generally considered reliable for present-day scientific use. Names without such a reference are typically of historical interest only.
Modern Features and Data Standards
To support the global scientific community, Index Fungorum utilizes several advanced digital tools:
- Life Science Identifiers (LSIDs): Unique codes that allow fungal taxa to be identified and referenced consistently across different publications and databases.
- Machine-to-Machine Workflow: An XML-based system designed to work directly with publishers, allowing for efficient registration of names before they are published.
- SOAP Protocol Web Service: A technical service that allows researchers to search the database and retrieve records programmatically.
- FAIR Data Principles: The database is designed to be Findable, Accessible, Interoperable, and Reusable, ensuring high-quality data sharing.
Despite these advancements, challenges remain. One significant issue is the "long tail" problem, where many names are buried in small, obscure, or older publications, making complete coverage difficult. To combat this, Index Fungorum is working toward adopting the Taxon Concept Schema to standardize how new names and metadata—such as collection location, habitat, and substrate—are recorded.
Frequently Asked Questions
What is the difference between Index Fungorum and Species Fungorum?
Index Fungorum is a comprehensive database containing all validly defined fungal names, including obsolete or conflicting ones. Species Fungorum is a specialized subset that identifies which of those names are currently considered valid and recommended for use.
Why must new fungal names be registered in a repository?
According to the International Code of Nomenclature for algae, fungi, and plants, new names must cite an identifier from a recognized repository before they can be officially published. This ensures that every new name is uniquely recorded and easily findable by the scientific community.
What are the three recognized repositories for fungal names?
The Nomenclature Committee for Fungi recognizes three official repositories: Index Fungorum, MycoBank, and Fungal Names. These three systems synchronize their data monthly to maintain consistency.
How can I tell if a fungal name is currently correct in Index Fungorum?
Index Fungorum uses a color-coding system in its search results: names that are currently correct are indicated in green, while other names are shown in blue. A few aberrant name usages may appear in red.
What is the "long tail" problem in fungal indexing?
The "long tail" problem refers to the difficulty of capturing all fungal names because many are published in small, obscure, or older journals. This makes it challenging for databases to achieve 100% coverage of all existing mycological literature.