MeLinDa: an interlinking framework for the web of data

The web of data consists of data published on the web in such a way that they can be interpreted and connected together. It is thus critical to establish links between these data, both for the web of data and for the semantic web that it contributes to feed. We consider here the various techniques developed for that purpose and analyze their commonalities and differences. We propose a general framework and show how the diverse techniques fit in the framework. From this framework we consider the relation between data interlinking and ontology matching. Although, they can be considered similar at a certain level (they both relate formal entities), they serve different purposes, but would find a mutual benefit at collaborating. We thus present a scheme under which it is possible for data linking tools to take advantage of ontology alignments.Comment: N° RR-7691 (2011

CESI: Canonicalizing Open Knowledge Bases using Embeddings and Side Information

Open Information Extraction (OpenIE) methods extract (noun phrase, relation phrase, noun phrase) triples from text, resulting in the construction of large Open Knowledge Bases (Open KBs). The noun phrases (NPs) and relation phrases in such Open KBs are not canonicalized, leading to the storage of redundant and ambiguous facts. Recent research has posed canonicalization of Open KBs as clustering over manuallydefined feature spaces. Manual feature engineering is expensive and often sub-optimal. In order to overcome this challenge, we propose Canonicalization using Embeddings and Side Information (CESI) - a novel approach which performs canonicalization over learned embeddings of Open KBs. CESI extends recent advances in KB embedding by incorporating relevant NP and relation phrase side information in a principled manner. Through extensive experiments on multiple real-world datasets, we demonstrate CESI's effectiveness.Comment: Accepted at WWW 201

LODE: Linking Digital Humanities Content to the Web of Data

Numerous digital humanities projects maintain their data collections in the form of text, images, and metadata. While data may be stored in many formats, from plain text to XML to relational databases, the use of the resource description framework (RDF) as a standardized representation has gained considerable traction during the last five years. Almost every digital humanities meeting has at least one session concerned with the topic of digital humanities, RDF, and linked data. While most existing work in linked data has focused on improving algorithms for entity matching, the aim of the LinkedHumanities project is to build digital humanities tools that work "out of the box," enabling their use by humanities scholars, computer scientists, librarians, and information scientists alike. With this paper, we report on the Linked Open Data Enhancer (LODE) framework developed as part of the LinkedHumanities project. With LODE we support non-technical users to enrich a local RDF repository with high-quality data from the Linked Open Data cloud. LODE links and enhances the local RDF repository without compromising the quality of the data. In particular, LODE supports the user in the enhancement and linking process by providing intuitive user-interfaces and by suggesting high-quality linking candidates using tailored matching algorithms. We hope that the LODE framework will be useful to digital humanities scholars complementing other digital humanities tools

A Practical Entity Linking System for Tables in Scientific Literature

Entity linking is an important step towards constructing knowledge graphs that facilitate advanced question answering over scientific documents, including the retrieval of relevant information included in tables within these documents. This paper introduces a general-purpose system for linking entities to items in the Wikidata knowledge base. It describes how we adapt this system for linking domain-specific entities, especially for those entities embedded within tables drawn from COVID-19-related scientific literature. We describe the setup of an efficient offline instance of the system that enables our entity-linking approach to be more feasible in practice. As part of a broader approach to infer the semantic meaning of scientific tables, we leverage the structural and semantic characteristics of the tables to improve overall entity linking performance

Linking named entities to Wikipedia

Natural language is fraught with problems of ambiguity, including name reference. A name in text can refer to multiple entities just as an entity can be known by different names. This thesis examines how a mention in text can be linked to an external knowledge base (KB), in our case, Wikipedia. The named entity linking (NEL) task requires systems to identify the KB entry, or Wikipedia article, that a mention refers to; or, if the KB does not contain the correct entry, return NIL. Entity linking systems can be complex and we present a framework for analysing their different components, which we use to analyse three seminal systems which are evaluated on a common dataset and we show the importance of precise search for linking. The Text Analysis Conference (TAC) is a major venue for NEL research. We report on our submissions to the entity linking shared task in 2010, 2011 and 2012. The information required to disambiguate entities is often found in the text, close to the mention. We explore apposition, a common way for authors to provide information about entities. We model syntactic and semantic restrictions with a joint model that achieves state-of-the-art apposition extraction performance. We generalise from apposition to examine local descriptions specified close to the mention. We add local description to our state-of-the-art linker by using patterns to extract the descriptions and matching against this restricted context. Not only does this make for a more precise match, we are also able to model failure to match. Local descriptions help disambiguate entities, further improving our state-of-the-art linker. The work in this thesis seeks to link textual entity mentions to knowledge bases. Linking is important for any task where external world knowledge is used and resolving ambiguity is fundamental to advancing research into these problems

Revised fission yeast gene and allele nomenclature guidelines for machine readability

Standardized nomenclature for genes, gene products, and isoforms is crucial to prevent ambiguity and enable clear communication of scientific data, facilitating efficient biocuration and data sharing. Standardized genotype nomenclature, which describes alleles present in a specific strain that differ from those in the wild-type reference strain, is equally essential to maximize research impact and ensure that results linking genotypes to phenotypes are Findable, Accessible, Interoperable, and Reusable (FAIR). In this publication, we extend the fission yeast clade gene nomenclature guidelines to support the curation efforts at PomBase (www.pombase.org), the Schizosaccharomyces pombe Model Organism Database. This update introduces nomenclature guidelines for noncoding RNA genes, following those set forth by the Human Genome Organisation Gene Nomenclature Committee. Additionally, we provide a significant update to the allele and genotype nomenclature guidelines originally published in 1987, to standardize the diverse range of genetic modifications enabled by the fission yeast genetic toolbox. These updated guidelines reflect a community consensus between numerous fission yeast researchers. Adoption of these rules will improve consistency in gene and genotype nomenclature, and facilitate machine-readability and automated entity recognition of fission yeast genes and alleles in publications or datasets. In conclusion, our updated guidelines provide a valuable resource for the fission yeast research community, promoting consistency, clarity, and FAIRness in genetic data sharing and interpretation

Aligning Large Language Models to a Domain-specific Graph Database

Graph Databases (Graph DB) are widely applied in various fields, including finance, social networks, and medicine. However, translating Natural Language (NL) into the Graph Query Language (GQL), commonly known as NL2GQL, proves to be challenging due to its inherent complexity and specialized nature. Some approaches have sought to utilize Large Language Models (LLMs) to address analogous tasks like text2SQL. Nevertheless, when it comes to NL2GQL taskson a particular domain, the absence of domain-specific NL-GQL data pairs makes it difficult to establish alignment between LLMs and the graph DB. To address this challenge, we propose a well-defined pipeline. Specifically, we utilize ChatGPT to create NL-GQL data pairs based on the given graph DB with self-instruct. Then, we use the created data to fine-tune LLMs, thereby achieving alignment between LLMs and the graph DB. Additionally, during inference, we propose a method that extracts relevant schema to the queried NL as the input context to guide LLMs for generating accurate GQLs.We evaluate our method on two constructed datasets deriving from graph DBs in finance domain and medicine domain, namely FinGQL and MediGQL. Experimental results demonstrate that our method significantly outperforms a set of baseline methods, with improvements of 5.90 and 6.36 absolute points on EM, and 6.00 and 7.09 absolute points on EX, respectively.Comment: 13 pages,2 figure