Open Knowledgebase Research Articles

EnzChemRED, a rich enzyme chemistry relation extraction dataset

Expert curation is essential to capture knowledge of enzyme functions from the scientific literature in FAIR open knowledgebases but cannot keep pace with the rate of new discoveries and new publications. In this work we present EnzChemRED, for Enzyme Chemistry Relation Extraction Dataset, a new training and benchmarking dataset to support the development of Natural Language Processing (NLP) methods such as (large) language models that can assist enzyme curation. EnzChemRED consists of 1,210 expert curated PubMed abstracts where enzymes and the chemical reactions they catalyze are annotated using identifiers from the protein knowledgebase UniProtKB and the chemical ontology ChEBI. We show that fine-tuning language models with EnzChemRED significantly boosts their ability to identify proteins and chemicals in text (86.30% F1 score) and to extract the chemical conversions (86.66% F1 score) and the enzymes that catalyze those conversions (83.79% F1 score). We apply our methods to abstracts at PubMed scale to create a draft map of enzyme functions in literature to guide curation efforts in UniProtKB and the reaction knowledgebase Rhea.

Multi-level feature interaction for open knowledge base canonicalization

Open Information Extraction (OpenIE) aims to construct expansive open knowledge bases (OKBs) by extracting triples (noun phrase, relation phrase, noun phrase) from unstructured text. One critical problem in OKBs is the lack of canonicalization for noun phrases and relation phrases, leading to the storage of redundant and ambiguous facts. Consequently, open knowledge base canonicalization, which clusters synonymous phrases into the same group, has emerged as an active research area. Existing approaches either leverage fact triples or source context in isolation, or at best, interact them at the clustering level. However, these approaches lack explicit interaction or only loosely couple the two types of knowledge, resulting in the potential loss of valuable intermediate information. In this paper, we propose MuFIC, a novel unsupervised framework that interacts the fact triples and source context at the feature level to address these limitations. In order to capture and integrate fine-grained fact and context knowledge, we design three levels of feature interaction: low-level context-guided feature interaction, mid-level fact-guided feature interaction, and high-level gated fusion feature interaction. Furthermore, we introduce an additional objective function via contrastive learning to improve the quality of extracted features and reduce knowledge-specific noise. Finally, we design a bidirectional feedback mechanism to better guide the learning process of joint features by harnessing side information prototype learning, and to dynamically optimize side information based on the clustering results formed by joint features. Extensive experiments on three public benchmark datasets demonstrate the superiority of our proposed framework.

Open knowledge base canonicalization with multi-task learning

Open knowledge base canonicalization with multi-task learning

TracerDB: a crowdsourced fluorescent tracer database for target engagement analysis

Investigating ligand-protein complexes is essential in the areas of chemical biology and drug discovery. However, detailed information on key reagents such as fluorescent tracers and associated data for the development of widely used bioluminescence resonance energy transfer (BRET) assays including NanoBRET, time-resolved Förster resonance energy transfer (TR-FRET) and fluorescence polarization (FP) assays are not easily accessible to the research community. We created tracerDB, a curated database of validated tracers. This resource provides an open access knowledge base and a unified system for tracer and assay validation. The database is freely available at https://www.tracerdb.org/.

An ontology‐based semantic description model of ubiquitous map images

AbstractMap images with various themes and cartographic representations have become ubiquitous on the Internet. Such ubiquitously and openly accessible data, named ubiquitous map images in this study, are a potential resource for many geographic information applications such as cartographic design. However, there is a semantic gap between the simple physical form and the complex connotation of ubiquitous map images, which hinders their further applications. To mitigate such barrier, this article develops an ontology‐based semantic description model for ubiquitous map images. First, we discuss the design concerns and principles of the semantic description model of ubiquitous map images. Second, three semantic layers of the semantic description model are proposed, that is, image semantic description layer, cognitive tool layer, and information source layer, and detailed semantic description items are defined for each layer. Furthermore, a formalized semantic description model for ubiquitous map images is developed using ontology construction tools, which lays the foundation for automated and fine‐grained reasoning with the information embedded in map images. We construct a small test dataset consisting of weather maps, and use three types of constraints, namely “time‐topic,” “region‐topic,” and “map auxiliary elements” for the semantic retrieval experiments. The experiments show that the proposed semantic ontology model can enable complex semantic retrieval of ubiquitous map images. Finally, the scalability of the model is discussed from three perspectives: the depth of description, the combination with intelligent methods, and the integration with other open knowledge bases. The proposed model provides a semantic label system for applying data‐driven approaches to decode ubiquitous map images, which also paves the path to the development of cartographic theory in the era of information and communications technologies.

DegronMD: Leveraging Evolutionary and Structural Features for Deciphering Protein-Targeted Degradation, Mutations, and Drug Response to Degrons.

Protein-targeted degradation is an emerging and promising therapeutic approach. The specificity of degradation and the maintenance of cellular homeostasis are determined by the interactions between E3 ubiquitin ligase and degradation signals, known as degrons. The human genome encodes over 600 E3 ligases; however, only a small number of targeted degron instances have been identified so far. In this study, we introduced DegronMD, an open knowledgebase designed for the investigation of degrons, their associated dysfunctional events, and drug responses. We revealed that degrons are evolutionarily conserved and tend to occur near the sites of protein translational modifications, particularly in the regions of disordered structure and higher solvent accessibility. Through pattern recognition and machine learning techniques, we constructed the degrome landscape across the human proteome, yielding over 18,000 new degrons for targeted protein degradation. Furthermore, dysfunction of degrons disrupts the degradation process and leads to the abnormal accumulation of proteins; this process is associated with various types of human cancers. Based on the estimated phenotypic changes induced by somatic mutations, we systematically quantified and assessed the impact of mutations on degron function in pan-cancers; these results helped to build a global mutational map on human degrome, including 89,318 actionable mutations that may induce the dysfunction of degrons and disrupt protein degradation pathways. Multiomics integrative analysis unveiled over 400 drug resistance events associated with the mutations in functional degrons. DegronMD, accessible at https://bioinfo.uth.edu/degronmd, is a useful resource to explore the biological mechanisms, infer protein degradation, and assist with drug discovery and design on degrons.

A management knowledge graph approach for critical infrastructure protection: Ontology design, information extraction and relation prediction

Critical Infrastructures (CI) underpin the basic functioning of society and the economy. Proper governance of CI security management remains a crucial challenge. This study aims to construct a knowledge graph for modeling CI protection. While the previous research has focused on threat intelligence modeling and open knowledge bases, they miss considering the defense side. Accordingly, we propose a knowledge graph for critical infrastructure protection, CIPKG, that extends the management ontology to include the defense side. It addresses the cross-industry and cross-time information gaps that occur in the process of CI protection management, making it more comprehensive in structure than the existing knowledge graph. We employ simplified Structured Threat Information Expression as attack ontology and design a new ontology for the defense side, which could combine with the existing threat ontology to form the CI protection knowledge graph. To dynamically extract information from emerging knowledge, we employ a Bi-directional Long Short-Term Memory and Conditional Random Field model with pre-trained cybersecurity domain-specific Bidirectional Encoder Representations from Transformers to recognize the named entities from CI regulations and standards. To associate the threat part with the management portion of the knowledge graph, we adopt the Knowledge Graph Bidirectional Encoder Representations from Transformer model to capture the semantic information and predict the relationship between threat and management. After information extraction and relation prediction, we build a knowledge graph with 529,360 nodes and about 3,335,000 edges.

A semantic union model for open domain Chinese knowledge base question answering

In Open-domain Chinese Knowledge Base Question Answering (ODCKBQA), most common simple questions can be answered by a single relational fact in the knowledge base (KB). The abbreviations, aliases, and nesting of entities in Chinese question sentences, and the gap between them and the structured semantics in the knowledge base, make it difficult for the system to accurately return answers. This study proposes a semantic union model (SUM), which concatenates candidate entities and candidate relationships, using a contrastive learning algorithm to learn the semantic vector representation of question and candidate entity-relation pairs, and perform cosine similarity calculations to simultaneously complete entity disambiguation and relation matching tasks. It can provide information for entity disambiguation through the relationships between entities, avoid error propagation, and improve the system performance. The experimental results show that the system achieves a good average F1 of 85.94% on the dataset provided by the NLPCC-ICCPOL 2016 KBQA task.

Knowledge Base Reuse With Frame Representation In Artificial Intelligence Applications

The creation and upkeep of knowledge bases have emerged as the primary issue in artificial intelligence development. The knowledge domain is expanding, and application interoperability is urgently demanded. To accommodate this modification, the knowledge base, which serves as the foundation of the artificial intelligence architecture, must be updated. XML (extensible markup language), RDF (resources description framework), DAML (DARPA agent markup language), OIL (ontology inference layer), and OKBC are just a few of the standards that have been introduced as a result of the development of the internet (Open Knowledge-Base Connectivity). One type of knowledge representation that can store information and facts about a subject is frame-based representation. The OKBC, which can help with knowledge base interoperability, supports this approach. In this work, the main issues covered are the comprehension and fundamentals of knowledge base creation with frame representation. To better understand how frame representation functions as a reusable component, a case study from a news publication were used as an example.

Investigating the potential of the semantic web for education: Exploring Wikidata as a learning platform.

Wikidata is a free, multilingual, open knowledge-base that stores structured, linked data. It has grown rapidly and as of December 2022 contains over 100 million items and millions of statements, making it the largest semantic knowledge-base in existence. Changing the interaction between people and knowledge, Wikidata offers various learning opportunities, leading to new applications in sciences, technology and cultures. These learning opportunities stem in part from the ability to query this data and ask questions that were difficult to answer in the past. They also stem from the ability to visualize query results, for example on a timeline or a map, which, in turn, helps users make sense of the data and draw additional insights from it. Research on the semantic web as learning platform and on Wikidata in the context of education is almost non-existent, and we are just beginning to understand how to utilize it for educational purposes. This research investigates the Semantic Web as a learning platform, focusing on Wikidata as a prime example. To that end, a methodology of multiple case studies was adopted, demonstrating Wikidata uses by early adopters. Seven semi-structured, in-depth interviews were conducted, out of which 10 distinct projects were extracted. A thematic analysis approach was deployed, revealing eight main uses, as well as benefits and challenges to engaging with the platform. The results shed light on Wikidata's potential as a lifelong learning process, enabling opportunities for improved Data Literacy and a worldwide social impact.

Automated determination of grain boundary energy and potential-dependence using the OpenKIM framework

We present a systematic methodology, built within the Open Knowledgebase of Interatomic Models (OpenKIM) framework (https://openkim.org), for quantifying properties of grain boundaries (GBs) for arbitrary interatomic potentials (IPs), GB character, and lattice structure and species. The framework currently generates results for symmetric tilt GBs in cubic materials, but can be readily extended to other types of boundaries. In this paper, GB energy data are presented that were generated automatically for Al, Ni, Cu, Fe, and Mo with 225 IPs; the system is installed on openkim.org and will continue to generate results for all new IPs uploaded to OpenKIM. The results from the atomistic calculations are compared to the lattice matching model, which is a semi-analytic geometric model for approximating GB energy. It is determined that the energy predicted by all IPs (that are stable for the given boundary type) correlate closely with the energy from the model, up to a multiplicative factor. It thus is concluded that the qualitative form of the GB energy versus tilt angle is dominated more by geometry than the choice of IP, but that the IP can strongly affect the energy level. The spread in GB energy predictions across the ensemble of IPs in OpenKIM provides a measure of uncertainty for GB energy predictions by classical IPs.

Development of a university’s intellectual capital within “ontologisation”

This article introduces the concept of Networked Self-Developing Education System (NSDES). Such a system could be considered a modern university with a triple network structure where network team interactions between representatives of science, education and production are developed. A new model to explain NSDES intellectual capital development management is described. The model includes four interrelated parts (intellectual property, human, organisation and consumer types of capital). An important NSDES function is to provide conditions for lifelong self-development of scholars and students’ mastery of the scientific method. This is especially important for interdisciplinary natural sciences (biophysics, etc.). The NSDES has its integrative resource potential to meet this challenge. Such potential is accumulated in the open knowledge base and can be transferred to the education process provided knowledge is standardised in an ontology format. To build a course ontology to study the bioluminescent enzyme technology, the experience of developing ontology-based education solutions for railway universities which are evolving into “knowledge factories” is useful. Thus, “ontologisation” is proved to be a trend in the digital transformation of NSDES. The model’s implementation through ontology-based education solutions will create a foundation for the development of students’ research competences to solve urgent problems in sciences and industries.

FDup: a framework for general-purpose and efficient entity deduplication of record collections.

Deduplication is a technique aiming at identifying and resolving duplicate metadata records in a collection. This article describes FDup (Flat Collections Deduper), a general-purpose software framework supporting a complete deduplication workflow to manage big data record collections: metadata record data model definition, identification of candidate duplicates, identification of duplicates. FDup brings two main innovations: first, it delivers a full deduplication framework in a single easy-to-use software package based on Apache Spark Hadoop framework, where developers can customize the optimal and parallel workflow steps of blocking, sliding windows, and similarity matching function via an intuitive configuration file; second, it introduces a novel approach to improve performance, beyond the known techniques of “blocking” and “sliding window”, by introducing a smart similarity matching function T-match. T-match is engineered as a decision tree that drives the comparisons of the fields of two records as branches of predicates and allows for successful or unsuccessful early-exit strategies. The efficacy of the approach is proved by experiments performed over big data collections of metadata records in the OpenAIRE Research Graph, a known open access knowledge base in Scholarly communication.

Transforming Closed Silos into Shared Resources: Opening up data on historical collection agents affiliated with the Museum für Naturkunde Berlin

Many natural science collections (NSCs) and museums keep information about collectors and other collection agents affiliated with their specimens and respective institution in internal catalogues, databases or wikis. Despite the fact that people data are crucial for linking collection objects, expeditions, publications, archival material, correspondence, etc. (Page 2016, Groom et al. 2020), such data are often only available internally, with limited or no access for external users. In the past, collectors have often been active in multiple fields, gathering e.g., zoological and botanical as well as ethnological or anthropological objects. This transdisciplinary collecting practice, in addition to the tradition of exchanging duplicates between institutions, results in a large overlap of people affiliated with different collections. Opening up available data will improve data quality in collection databases, support the disambiguation of collection agents (Dillen et al. 2021) and allow cross-disciplinary reuse of the data. Within a pilot study conducted at the Museum für Naturkunde Berlin (MfN), the information kept in an internal “MfN collector wiki” is made available via Wikidata. Wikidata is a free and open knowledge base that is collaborative and multilingual, and can be edited by anyone in the world. Wikidata stores structured data that are both human and machine readable, and it serves as a hub/broker for other identifiers (Vrandečić and Krötzsch 2014). An innovative open participatory approach is taken using edit-a-thons, involving MfN staff (collection manager, scientific heads of collections, scientists, etc.) to add and update information ‘passively’ available within the institution, and the wider public, e.g., citizen scientists and other interested parties. MfN staff (collection manager, scientific heads of collections, scientists, etc.) to add and update information ‘passively’ available within the institution, and the wider public, e.g., citizen scientists and other interested parties. Wikidata items are newly created or updated and enriched with additional information, also linking to collections, archives, and libraries. In this talk we will present the method and preliminary results of our study. One focus will be ‘hidden champions’ such as women scientists and local collectors, to make their contribution to global natural heritage visible. Another focus will be on collections from the era of European colonial expansion until the beginning of the 20th century, especially the former German colony, Cameroon. The number of institutions openly sharing data is increasing. However, following the TDWG 2022 conference motto “Stronger together”, we call for others to join in sharing data using persistent (people) identifiers and standards.

Ethical Considerations of Including Personal Demographic Information in Open Knowledge Platforms

In recent years, galleries, libraries, archives, and museums (GLAMs) have sought to leverage open knowledge platforms such as Wikidata to highlight or provide more visibility for traditionally marginalized groups and their work, collections, or contributions. Efforts like Art + Feminism, local edit-a-thons, and, more recently, GLAM institution-led projects have promoted open knowledge initiatives to a broader audience of participants. One such open knowledge project, the Program for Cooperative Cataloging (PCC) Wikidata Pilot, has brought together over seventy GLAM organizations to contribute linked open data for individuals associated with their institutions, collections, or archives. However, these projects have brought up ethical concerns around including potentially sensitive personal demographic information, such as gender identity, sexual orientation, race, and ethnicity, in entries in an open knowledge base about living persons. GLAM institutions are thus in a position of balancing open access with ethical cataloging, which should include adhering to the personal preferences of the individuals whose data is being shared. People working in libraries and archives have been increasingly focusing their energies on issues of diversity, equity, and inclusion in their descriptive practices, including remediating legacy data and addressing biased language. Moving this work into a more public sphere and scaling up in volume creates potential risks to the individuals being described. While adding demographic information on living people to open knowledge bases has the potential to enhance, highlight, and celebrate diversity, it could also potentially be used to the detriment of the subjects through surveillance and targeting activities. In this article we seek to investigate the changing role of metadata and open knowledge in addressing, or not addressing, issues of under- and misrepresentation, especially as they pertain to gender identity as described in the sex or gender property in Wikidata. We report findings from a survey investigating how organizations participating in open knowledge projects are addressing ethical concerns around including personal demographic information as part of their projects, including what, if any, policies they have implemented and what implications these activities may have for the living people being described.

A Question Answering Framework Based on Hybridization of Deep Learning and Semantic Web Techniques

The question answering (QA) system has been existing for several years. QA systems are divided into different processes such as question processing, document processing, paragraph extraction, answer extraction, question analysis, phrase mapping, disambiguation, query construction, querying the Knowledge Base (KB), and result ordering on user response respectively. Based on these processes, many models have been developed using approaches ranging from linguistic, statistical, and pattern matching. Popular models are Feedback, Refinement and Extended VocabularY Aggregation (FREyA), PowerAqua, SemSek, Semantic Interpretation of User Queries for QA on Interlinked Data (SINA), DEep Answers for maNy Naturally Asked questions (DEANNA), gAnswer, SemGraph, OKBQA (Open Knowledge Base and Question Answering) and Semantic Question Answering (SQA), for performance evaluation, these mostly focus on higher precision, recall, and/or F-measure. However, most of these models are constrained in the following operations: the combination of knowledge bases from different sources, formalism for knowledge representation to support interoperability, optimization of query construction and generation, ranking of responses, and support for set operations (union, sorting, comparison, and aggregation on user query) during query generation. This research proposes a hybrid of recurrent neural network and semantic-web-based question answering as the (RNNSQA) framework that combines heterogeneous knowledge sources and improves on state-of-the-art query generation mechanisms to allow for integration of comprehensive question-type operations, and set-based operations listed above. First, there would be a combination of techniques that is Natural Language Processing (NLP) and Recurrent Neural Network (RNN) techniques in classifying questions into types. Secondly, the semantic web technique is then employed in generating (SPARQL Protocol and RDF (Resource Description Framework) Query Language) SPARQL-based candidate queries. The result of this study is an enhanced QA framework with improved query translation and construction capability.

Expanding clinical actionability in individual patient profiles with the Molecular Oncology Almanac.

3015 Background: The clinical care of oncology patients is routinely informed by tumor and inherited genetic profiles. This is accomplished by molecular pathologists synthesizing the growing body of clinical guidelines and scientific evidence that associates cancer genome alterations and therapeutic response, and applying that knowledge during case reviews. Many academic medical centers formalize this process in the form of molecular tumor boards. As the number of cases for review and literature continue to increase, there is opportunity to leverage clinical interpretation algorithms to computationally prioritize molecular features and both enhance and automate the sample contextualization process. Here, we present the Molecular Oncology Almanac (MOAlmanac) to enable the rapid assessment of tumor actionability. Methods: Molecular Oncology Almanac is an open source clinical interpretation algorithm and paired knowledge base for precision cancer medicine. It is used to rapidly characterize and identify genomic features related to therapeutic sensitivity and resistance and of prognostic relevance. This is performed by assessing not only individual genomic features (e.g. somatic variants, copy number alterations, germline variants, and fusions) but also interactions between these events as well as secondary features such as mutational burden, mutational signatures, MSI status, and aneuploidy. MOAlmanac summarizes all clinically relevant findings into a web-based actionability report. The underlying knowledge base can be accessed through our API endpoints and web browser, and entries may be recommended through either Github or our browser extension. In addition, we developed a cloud-based web portal on top of the Terra framework to increase accessibility. Results: A total of 32,108 samples from 30,607 patients across 66 cancer types received targeted sequencing to characterize somatic variants, copy number alterations, and fusions from PROFILE’s Oncopanel and were evaluated with MOAlmanac. Based on Oncopanel’s tier 1 and tier 2 criteria for clinical actionability, we observed that 8,285 samples (26%, 0 - 69% by cancer type) of patients harbored at least one alteration suggesting therapeutic sensitivity based on FDA approvals or clinical guidelines. Actionability increases to 18,117 samples (56%, 0 - 85% by cancer type) when considering an expanded set of evidence to include relationships captured from clinical trials, clinical, preclinical, and inferential evidence; consequently providing at least one therapeutic hypothesis to otherwise variant-negative patients. Conclusions: Clinical actionability of molecular tumor data was increased in individual patients by expanding the set of evidence considered. Source code and a web portal for this project are available at moalmanac.org .

Bayesian, frequentist, and information geometric approaches to parametric uncertainty quantification of classical empirical interatomic potentials

In this paper, we consider the problem of quantifying parametric uncertainty in classical empirical interatomic potentials (IPs) using both Bayesian (Markov Chain Monte Carlo) and frequentist (profile likelihood) methods. We interface these tools with the Open Knowledgebase of Interatomic Models and study three models based on the Lennard-Jones, Morse, and Stillinger-Weber potentials. We confirm that IPs are typically sloppy, i.e., insensitive to coordinated changes in some parameter combinations. Because the inverse problem in such models is ill-conditioned, parameters are unidentifiable. This presents challenges for traditional statistical methods, as we demonstrate and interpret within both Bayesian and frequentist frameworks. We use information geometry to illuminate the underlying cause of this phenomenon and show that IPs have global properties similar to those of sloppy models from fields, such as systems biology, power systems, and critical phenomena. IPs correspond to bounded manifolds with a hierarchy of widths, leading to low effective dimensionality in the model. We show how information geometry can motivate new, natural parameterizations that improve the stability and interpretation of uncertainty quantification analysis and further suggest simplified, less-sloppy models.

TECHNOLOGY FOR CREATING A DOMAIN KNOWLEDGE BASE OF QUESTION-ANSWERING SYSTEM BASED ON A LARGE-SCALE UNIVERSAL KNOWLEDGE BASE

Usage of question-answering systems has become a popular way to access knowledge bases that contain a large number of facts from different domains. Large-scale universal knowledge bases with open access, such as Wikidata, contain huge collections of facts. Although those bases cover the most significant part of the accumulated humankind knowledge, there are a number of reasons why their direct usage in question-answering systems can be less preferable than the creation of specialized domain knowledge bases based on them. This paper presents a technology for building a domain knowledge base for a dialogue system based on domain boundaries detection from an open large-scale universal knowledge base. It is based on a multi-step process of analyzing a large number of free-form questions on a given subject area that were collected using a crowdsourcing platform. The technology includes the correction of the original knowledge base ontological structure and its filling with additional content. The proposed technology is invariant to the original knowledge base and the modeling subject area. We tested it on the Wikidata knowledge base and six subject areas.

Representing COVID-19 information in collaborative knowledge graphs: The case of Wikidata

Information related to the COVID-19 pandemic ranges from biological to bibliographic, from geographical to genetic and beyond. The structure of the raw data is highly complex, so converting it to meaningful insight requires data curation, integration, extraction and visualization, the global crowdsourcing of which provides both additional challenges and opportunities. Wikidata is an interdisciplinary, multilingual, open collaborative knowledge base of more than 90 million entities connected by well over a billion relationships. It acts as a web-scale platform for broader computer-supported cooperative work and linked open data, since it can be written to and queried in multiple ways in near real time by specialists, automated tools and the public. The main query language, SPARQL, is a semantic language used to retrieve and process information from databases saved in Resource Description Framework (RDF) format. Here, we introduce four aspects of Wikidata that enable it to serve as a knowledge base for general information on the COVID-19 pandemic: its flexible data model, its multilingual features, its alignment to multiple external databases, and its multidisciplinary organization. The rich knowledge graph created for COVID-19 in Wikidata can be visualized, explored, and analyzed for purposes like decision support as well as educational and scholarly research.