Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2409.13906

A Change Language for Ontologies and Knowledge Graphs

Harshad Hegde·Jennifer Vendetti·Damien Goutte-Gattat·J Harry Caufield·John B Graybeal·Nomi L Harris·Naouel Karam·Christian Kindermann·Nicolas Matentzoglu·James A Overton·Mark A Musen·Christopher J Mungall
View original source ↗Read source document ↗Export metadata ↓

Abstract

Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users, and providing mechanisms to make it easier for multiple stakeholders to contribute. To fill that need, we have created KGCL, the Knowledge Graph Change Language, a standard data model for describing changes to KGs and ontologies at a high level, and an accompanying human-readable controlled natural language. This language serves two purposes: a curator can use it to request desired changes, and it can also be used to describe changes that have already happened, corresponding to the concepts of "apply patch" and "diff" commonly used for managing changes in text documents and computer programs. Another key feature of KGCL is that descriptions are at a high enough level to be useful and understood by a variety of stakeholders--for example, ontology edits can be specified by commands like "add synonym 'arm' to 'forelimb'" or "move 'Parkinson disease' under 'neurodegenerative disease'". We have also built a suite of tools for managing ontology changes. These include an automated agent that integrates with and monitors GitHub ontology repositories and applies any requested changes, and a new component in the BioPortal ontology resource that allows users to make change requests directly from within the BioPortal user interface. Overall, the KGCL data model, its controlled natural language, and associated tooling allow for easier management and processing of changes associated with the development of ontologies and KGs.

Explore related subjects

cs.DB

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Harshad Hegde, Jennifer Vendetti, Damien Goutte-Gattat, J Harry Caufield, John B Graybeal, Nomi L Harris, Naouel Karam, Christian Kindermann, Nicolas Matentzoglu, James A Overton, Mark A Musen, Christopher J Mungall. 2024-09-20. A Change Language for Ontologies and Knowledge Graphs. https://doi.org/10.1093/database%2Fbaae133

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

VectorMaton: Efficient Vector Search with Pattern Constraints via an Enhanced Suffix Automaton

Approximate nearest neighbor search (ANNS) has become a cornerstone in modern vector database systems. Given a query vector, ANNS retrieves the closest vectors from a set of base vectors. In real-world applications, vectors are often accompanied by additional information, such as sequences or structured attributes, motivating the need for fine-grained vector search with constraints on this auxiliary data. Existing methods support attribute-based filtering or range-based filtering on categorical and numerical attributes, but they do not support pattern predicates over sequence attributes. In relational databases, predicates such as LIKE and CONTAINS are fundamental operators for filtering records based on substring patterns. As vector databases increasingly adopt SQL-style query interfaces, enabling pattern predicates over sequence attributes (e.g., texts and biological sequences) alongside vector similarity search becomes essential. In this paper, we formulate a novel problem: given a set of vectors each associated with a sequence, retrieve the nearest vectors whose sequences contain a given query pattern. To address this challenge, we propose VectorMaton, an automaton-based index that integrates pattern filtering with efficient vector search, while maintaining an index size comparable to the dataset size. Extensive experiments on real-world datasets demonstrate that VectorMaton consistently outperforms all baselines, achieving up to 10x higher query throughput at the same accuracy and up to 18x reduction in index size.

cs.DB↗
arXiv2026

Efficient K-generalizable Learned Search

Learned top-K search improves the accuracy-latency trade-off of graph-based vector search, but existing methods are designed for a fixed K: serving production workloads with varying K values requires preprocessing cost proportional to the number of distinct Ks served - prohibitive in practice. This paper shows that learned search can support arbitrary K with the preprocessing cost of a single top-1 model. The key idea is to reduce top-K learned search to repeated masked top-1 refinement, which works because the distance-reduction trajectory for discovering the next top-1 vector is largely invariant to the number of results already found. We therefore train the model on trajectory features that remain effective under masking. To make repeated refinement robust and efficient, OMEGA counters error accumulation across iterations with rank-wise confidence allocation, and skips unnecessary model invocations with a statistical forecast of recall from partial results. Across nine dataset-scale configurations, OMEGA meets the 0.95 recall target with one K-independent model. Under the lowest-preprocessing configuration of each learned baseline,it reduces mean latency by 7-36% versus DARTH, 3-25% versus MultiK-DARTH, and 8-21% versus LAET on BIGANN, BIGANN-1B, DEEP, and three production workloads. On GIST, Text2Image, and MS MARCO, its latency remains within 9% of DARTH and MultiK-DARTH. On production traces, OMEGA further reduces total serving and preprocessing computation by up to 28%.

cs.DB↗
arXiv2026

Samyama: A Unified Graph-Vector Database with In-Database Optimization, Agentic Enrichment, and Hardware Acceleration

Modern data architectures fragment across graph databases, vector stores, analytics engines and optimization solvers, forcing ETL between them. We present Samyama, a graph-vector database in Rust that unifies these workloads in one engine: a RocksDB-backed store with MVCC, a vectorized executor, a cost-based planner, a CSR analytics engine, RDF and SPARQL, 22 metaheuristic solvers callable from the query language, HNSW vector indexing, and agentic enrichment that expands a graph via LLMs. It has been run to billion-edge scale: 74.3M nodes and 1.07B edges from four biomedical sources on one machine for $2.50 of spot compute. This version re-measures the system at release v1.8.0 on rented Linux hosts a reader can boot, replacing earlier figures taken on a Mac Mini that nobody could re-run. On a 16-vCPU cloud instance, ingestion reaches 123K-152K nodes/s and PageRank costs 6.7 ms per iteration at ten thousand nodes and 236 ms at a million. The previously reported 8.2x GPU speedup is withdrawn; in its place we measure the CUDA path, which no earlier version measured at all, on a rented NVIDIA A16: parity with the CPU at ten thousand nodes, 1.62x at a hundred thousand and 2.70x at a million, with 1.1-1.35 s of context initialisation on the first call. The earlier Cypher-throughput figure, its claim of near-constant index-driven scaling, and a vector-search figure are withdrawn as unreproducible. openCypher conformance, once estimated at ~90%, is now measured at 99.9% of evaluated TCK scenarios. Against Neo4j 5 and FalkorDB on one host over an identical SF10 extract, 14 of 14 SNB complex reads land within 5x of the best competitor and 7 of 14 are faster.

cs.DB↗