Overview
IKIMON's species list (taxonomy) fully complies with the GBIF Backbone Taxonomy managed by GBIF (Global Biodiversity Information Facility), the world's largest biodiversity data infrastructure. This is an ambitious technical choice that differs from the "proprietary lists" or "domestic-only lists (YList, etc.)" adopted by many conventional domestic apps.Why is GBIF Compliance Revolutionary?
1. Interoperability through International Standard ID (NubKey)
Each organism species in the GBIF Backbone is assigned a unique ID (NubKey). By adopting this as IKIMON's internal ID, the following benefits emerge:- Integration with Overseas Data: In the future, when importing data from or providing data to major overseas platforms like iNaturalist or eBird, instant data integration becomes possible on an ID basis.
- Absorbing Scientific Name "Fluctuations": Biological classification changes daily, and multiple scientific names (synonyms) exist for the same species in this chaotic world. The GBIF Backbone organizes these synonym relationships, automatically providing a mechanism where "searching with an old scientific name hits the current correct species."
2. From "Local Discovery" to "Global Science"
When using domestic proprietary classification codes, collected data tends to become "local data that only works domestically." IKIMON's data, built to GBIF standards from the start, is immediately in a format usable by researchers worldwide (Darwin Core compliant). The greatest value is being able to proudly tell users, "Your post is immediately in a state that can contribute to world science."Why Was This Difficult Until Now? (Technical and Operational Barriers)
There were clear reasons (barriers) why many services went with proprietary lists.
1. "Japanese Name" Coverage Problem
GBIF is an international organization, and its basic languages are "scientific names (Latin)" and "English." Japanese "Japanese names" are also registered, but there were many cases where they didn't completely match the standard Japanese names adopted by Japanese field guides and academic societies (missing, misspelled, or colloquial names mixed in). → IKIMON's Solution: A hybrid structure that uses GBIF as the master while overlaying Japan-specific "standard Japanese name lists (Japanese species catalogs, etc.)" as a sublayer.2. Taxonomic Conflicts
The taxonomic systems used by Japanese botanical societies often differ from the systems GBIF adopts (such as changed families). There's a risk of being told by users "This is different from my field guide!" so many operators chose to align with domestic field guides. → IKIMON's Solution: Cover this with UI design that balances data accuracy and user convenience, such as displaying notes like "Domestically sometimes classified as XX family."3. Performance Issues
GBIF's API is vast, and searches can take time. There was concern about compromising the app's responsiveness. → IKIMON's Solution: Periodically download the entire Backbone data and index it on a fast search server (Elasticsearch, etc.) to eliminate communication lag to zero.Implementation Policy: Utilizing the GBIF Backbone API
Basic Architecture
Rather than hitting GBIF's API in real-time, we build a "periodically synchronized proprietary mirror API."- Periodic Import: Obtain `backbone-current.zip` (all taxonomic data) and `VernacularName.tsv` (multilingual names) from GBIF.
- Filtering: Flag species inhabiting Japan (referencing JBIF lists, etc.) and raise search priority.
- Search API: When a user enters "カブトムシ" (Japanese rhinoceros beetle), first search the Japanese name index in our DB, identify the corresponding `NubKey`, and return the linked scientific names and hierarchical information.
Key API Endpoints to Use
(※For developer reference)- Match API (`/species/match`): Estimate species from strings. Strong for fuzzy search.
- Name Parser (`/parser/name`): Break down scientific name strings into genus, species epithet, etc.
- Search API (`/species/search`): Search with complex conditions (hierarchy, occurrence status, etc.).
Summary
Compliance with GBIF Backbone Taxonomy has high initial development costs (name matching and system construction), but in the long term brings immeasurable returns of "externalizing taxonomy maintenance costs (leaving it to GBIF)" and "maximizing the international value of data." This is an important technical foundation for the data IKIMON collects to be utilized as "reliable scientific data" rather than just hobby records.What IKIMON Aims For
The technical talk may sound difficult. But what we want to convey is simple.
"The single photo you take can contribute to world science."
A photo taken somewhere in Japan becomes data that researchers around the world can reference as-is. That's the system we're trying to build.
From local discovery to global knowledge. IKIMON is the data foundation that "connects Japan and the world."
References
- GBIF. The GBIF Backbone Taxonomy. https://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c
- iNaturalist. Managing Taxonomy. https://www.inaturalist.org/pages/curator+guide#taxonomy