Vincent Emonet

J. Harry Caufield, Harshad Hegde, Vincent Emonet et al. · berkeley

Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrary complex nested knowledge schemas. Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against GPT-3+ to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for all matched elements. We present examples of use of SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease causation graphs. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction (RE) methods, but has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. SPIRES is available as part of the open source OntoGPT package: https://github.com/ monarch-initiative/ontogpt.

Panayiotis Smeros, Vincent Emonet, Ruijie Wang et al.

The advent of large language models is contributing to the emergence of novel approaches that promise to better tackle the challenge of generating structured queries, such as SPARQL queries, from natural language. However, these new approaches mostly focus on response accuracy over a single source while ignoring other evaluation criteria, such as federated query capability over distributed data stores, as well as runtime and cost to generate SPARQL queries. Consequently, they are often not production-ready or easy to deploy over (potentially federated) knowledge graphs with good accuracy. To mitigate these issues, in this paper, we extend our previous work and describe and systematically evaluate SPARQL-LLM, an open-source and triplestore-agnostic approach, powered by lightweight metadata, that generates SPARQL queries from natural language text. First, we describe its architecture, which consists of dedicated components for metadata indexing, prompt building, and query generation and execution. Then, we evaluate it based on a state-of-the-art challenge with multilingual questions, and a collection of questions from three of the most prevalent knowledge graphs within the field of bioinformatics. Our results demonstrate a substantial increase of 24% in the F1 Score on the state-of-the-art challenge, adaptability to high-resource languages such as English and Spanish, as well as ability to form complex and federated bioinformatics queries. Furthermore, we show that SPARQL-LLM is up to 36x faster than other systems participating in the challenge, while costing a maximum of $0.01 per question, making it suitable for real-time, low-cost text-to-SPARQL applications. One such application deployed over real-world decentralized knowledge graphs can be found at https://www.expasy.org/chat.

Nacira Abbas, Kholoud Alghamdi, Mortaza Alinam et al.

One of the grand challenges discussed during the Dagstuhl Seminar "Knowledge Graphs: New Directions for Knowledge Representation on the Semantic Web" and described in its report is that of a: "Public FAIR Knowledge Graph of Everything: We increasingly see the creation of knowledge graphs that capture information about the entirety of a class of entities. [...] This grand challenge extends this further by asking if we can create a knowledge graph of "everything" ranging from common sense concepts to location based entities. This knowledge graph should be "open to the public" in a FAIR manner democratizing this mass amount of knowledge." Although linked open data (LOD) is one knowledge graph, it is the closest realisation (and probably the only one) to a public FAIR Knowledge Graph (KG) of everything. Surely, LOD provides a unique testbed for experimenting and evaluating research hypotheses on open and FAIR KG. One of the most neglected FAIR issues about KGs is their ongoing evolution and long term preservation. We want to investigate this problem, that is to understand what preserving and supporting the evolution of KGs means and how these problems can be addressed. Clearly, the problem can be approached from different perspectives and may require the development of different approaches, including new theories, ontologies, metrics, strategies, procedures, etc. This document reports a collaborative effort performed by 9 teams of students, each guided by a senior researcher as their mentor, attending the International Semantic Web Research School (ISWS 2019). Each team provides a different perspective to the problem of knowledge graph evolution substantiated by a set of research questions as the main subject of their investigation. In addition, they provide their working definition for KG preservation and evolution.