Large language models (LLMs) have achieved remarkable success across a wide range of applications especially when augmented by external knowledge through retrieval-augmented generation (RAG). Despite their widespread adoption, recent studies have shown that LLMs often struggle to perform faithful reasoning when conflicting knowledge is retrieved. However, existing work primarily focuses on conflicts between external knowledge and the parametric knowledge of LLMs, leaving conflicts across external knowledge largely unexplored. Meanwhile, modern RAG systems increasingly emphasize the integration of unstructured text and (semi-)structured data like knowledge graphs (KGs) to improve knowledge completeness and reasoning faithfulness. To address this gap, we introduce ConflictQA, a novel benchmark that systematically instantiates conflicts between textual evidence and KG evidence. Extensive evaluations across representative LLMs reveal that, facing such cross-source conflicts, LLMs often fail to identify reliable evidence for correct reasoning. Instead, LLMs become more sensitive to prompting choices and tend to rely exclusively on either KG or textual evidence, resulting in incorrect responses. Based on these findings, we further propose XoT, a two-stage explanation-based thinking framework tailored for reasoning over heterogeneous conflicting evidence, and verify its effectiveness with extensive experiments.

Large Language Models (LLMs) have recently emerged as a powerful paradigm for Knowledge Graph Completion (KGC), offering strong reasoning and generalization capabilities beyond traditional embedding-based approaches. However, existing LLM-based methods often struggle to fully exploit structured semantic representations, as the continuous embedding space of pretrained KG models is fundamentally misaligned with the discrete token space of LLMs. This discrepancy hinders effective semantic transfer and limits their performance. To address this challenge, we propose ReaLM, a novel and effective framework that bridges the gap between KG embeddings and LLM tokenization through the mechanism of residual vector quantization. ReaLM discretizes pretrained KG embeddings into compact code sequences and integrates them as learnable tokens within the LLM vocabulary, enabling seamless fusion of symbolic and contextual knowledge. Furthermore, we incorporate ontology-guided class constraints to enforce semantic consistency, refining entity predictions based on class-level compatibility. Extensive experiments on two widely used benchmark datasets demonstrate that ReaLM achieves state-of-the-art performance, confirming its effectiveness in aligning structured knowledge with large-scale language models. The implementation is publicly available at https://github.com/xiumu-gg/ReaLM.

The ability of Large Language Models (LLMs) to perform reasoning tasks such as deduction has been widely investigated in recent years. Yet, their capacity to generate proofs—faithful, human-readable explanations of why conclusions follow—remains largely underexplored. In this work, we study proof generation in the context of OWL ontologies, which are widely adopted for representing and reasoning over complex knowledge, by developing an automated dataset construction and evaluation framework. Our evaluation encompassing three sequential tasks for complete proving: Extraction, Simplification, and Explanation, as well as an additional task of assessing Logic Completeness of the premise. Through extensive experiments on widely used reasoning LLMs, we achieve important findings including: (1) Some models achieve overall strong results but remain limited on complex cases; (2) Logical complexity, rather than representation format (formal logic language versus natural language), is the dominant factor shaping LLM performance; and (3) Noise and incompleteness in input data substantially diminish LLMs' performance. Together, these results underscore both the promise of LLMs for explanation with rigorous logics and the gap of supporting resilient reasoning under complex or imperfect conditions. Code and data are available at https://github.com/HuiYang1997/LLMOwlR.

Continual knowledge graph embedding (CKGE) has gained wide attention for managing dynamic knowledge graphs (KGs), which are continuously updated with new facts. Unlike traditional methods designed for static KGs, CKGE enables incremental updates to KG embeddings to accommodate new facts while retaining previously learned knowledge. Despite these advancements, current CKGE studies and benchmarks primarily focus on handling the increasing scale of data while overlooking changes in graph patterns. These changes, altering the graph structure of KGs, are referred to as pattern shifts in this paper. Pattern shifts frequently arise as new facts are added, introducing significant challenges to the stability and adaptability of CKGE methods. To address this gap, we introduce a suite of novel and challenging benchmarks, called PS-CKGE, specifically designed to evaluate CKGE methods under pattern shifts, where logic rules are utilized to capture and manage structural changes in dynamic KGs. Through these benchmarks, we comprehensively evaluate current CKGE methods in terms of their overall performance, resistance to catastrophic forgetting, and adaptability to new knowledge. The results show that pattern shifts not only exacerbate their risk of catastrophic forgetting but also impair their adaptability, usually with greater performance degradation over triples associated with more significant changes.

OWL (Web Ontology Language) ontologies, which are able to represent both relational and type facts as standard knowledge graphs and complex domain knowledge in Description Logic (DL) axioms, are widely adopted in domains such as healthcare and bioinformatics. Inspired by the success of knowledge graph embeddings, embedding OWL ontologies has gained significant attention in recent years. Current methods primarily focus on learning embeddings for atomic concepts and roles, enabling the evaluation based on normalized axioms through specially designed score functions. However, they often neglect the embedding of complex concepts, making it difficult to infer with more intricate axioms. This limitation reduces their effectiveness in advanced reasoning tasks, such as Ontology Learning and ontology-mediated Query Answering. In this paper, we propose EL++-closed ontology embeddings which are able to represent any logical expressions in DL EL++ via composition. Furthermore, we develop TransBox, an effective EL++ -closed ontology embedding method that can handle many-to-one, one-to-many and many-to-many relations. Our extensive experiments demonstrate that TransBox often achieves state-of-the-art performance across various real-world datasets for predicting complex axioms.

Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies can directly support are quite limited in learning, approximation and prediction. One straightforward solution is to integrate statistical analysis and machine learning. To this end, automatically learning vector representation for knowledge of an ontology i.e.,ontology embeddinghas been widely investigated. Numerous papers have been published on ontology embedding, but a lack of systematic reviews hinders researchers from gaining a comprehensive understanding of this field. To bridge this gap, we write this survey paper, which first introduces different kinds of semantics of ontologies and formally defines ontology embedding as well as its property of faithfulness. Based on this, it systematically categorizes and analyses a relatively complete set of over 80 papers, according to the ontologies they aim at and their technical solutions including geometric modeling, sequence modeling and graph propagation. This survey also introduces the applications of ontology embedding in ontology engineering, machine learning augmentation and life sciences, presents a new library mOWL and discusses the challenges and future directions.

Attributed Question Answering (AQA) aims to provide both a trustworthy answer and a reliable attribution report for a given question. Retrieval is a widely adopted approach, including two general paradigms: Retrieval-Then-Read (RTR) and post-hoc retrieval. Recently, Large Language Models (LLMs) have shown remarkable proficiency, prompting growing interest in AQA among researchers. However, RTR-based AQA often suffers from irrelevant knowledge and rapidly changing information, even when LLMs are adopted, while post-hoc retrievalbased AQA struggles with comprehending long-form answers with complex logic, and precisely identifying the content needing revision and preserving the original intent. To tackle these problems, this paper proposes an Atomic fact decompositionbased Retrieval and Editing (ARE) framework, which decomposes the generated long-form answers into molecular clauses and atomic facts by the instruction-tuned LLMs. Notably, the instruction-tuned LLMs are fine-tuned using a well-constructed dataset, generated from large scale Knowledge Graphs (KGs). This process involves extracting one-hop neighbors from a given set of entities and transforming the result into coherent long-form text. Subsequently, ARE leverages a search engine to retrieve evidences related to atomic facts, inputting these evidences into an LLM-based verifier to determine whether the facts require expansion for re-retrieval or editing. Furthermore, the edited facts are backtracked into the original answer, with evidence aggregated based on the relationship between molecular clauses and atomic facts. Extensive evaluations demonstrate the superior performance of our proposed method over the state-of-the-arts on several datasets, with an additionally proposed new metricAttrpfor evaluating the precision of evidence attribution.

Knowledge graph embedding (KGE) methods have achieved great success in handling various knowledge graph (KG) downstream tasks. However, KGE methods may learn biased representations on low-quality KGs that are prevalent in the real world. Some recent studies propose adversarial attacks to investigate the vulnerabilities of KGE methods, but their attackers are target-oriented with the KGE method and the target triples to predict are given in advance, which lacks practicability. In this work, we explore untargeted attacks with the aim of reducing the global performances of KGE methods over a set of unknown test triples and conducting systematic analyses on KGE robustness. Considering logic rules can effectively summarize the global structure of a KG, we develop rule-based attack strategies to enhance the attack efficiency. In particular, we consider adversarial deletion which learns rules, applying the rules to score triple importance and delete important triples, and adversarial addition which corrupts the learned rules and applies them for negative triples as perturbations. Extensive experiments on two datasets over three representative classes of KGE methods demonstrate the effectiveness of our proposed untargeted attacks in diminishing the link prediction results. And we also find that different KGE methods exhibit different robustness to untargeted attacks. For example, the robustness of methods engaged with graph neural networks and logic rules depends on the density of the graph. But rule-based methods like NCRL are easily affected by adversarial addition attacks to capture negative rules.

OWL ontologies, whose formal semantics are rooted in Description Logic (DL), have been widely used for knowledge representation. Similar to Knowledge Graphs (KGs), ontologies are often incomplete, and maintaining and constructing them has proved challenging. While classical deductive reasoning algorithms use the precise formal semantics of an ontology to predict missing facts, recent years have witnessed growing interest in inductive reasoning techniques that can derive probable facts from an ontology. Similar to KGs, a promising approach is to learn ontology embeddings in a latent vector space, while additionally ensuring they adhere to the semantics of the underlying DL. While a variety of approaches have been proposed, current ontology embedding methods suffer from several shortcomings, especially that they all fail to faithfully model one-to-many, many-to-one, and many-to-many relations and role inclusion axioms. To address this problem and improve ontology completion performance, we propose a novel ontology embedding method named Box2EL for the DL EL++, which represents both concepts and roles as boxes (i.e., axis-aligned hyperrectangles), and models inter-concept relationships using a bumping mechanism. We theoretically prove the soundness of Box2EL and conduct an extensive experimental evaluation, achieving state-of-the-art results across a variety of datasets on the tasks of subsumption prediction, role assertion prediction, and approximating deductive reasoning.

\beginabstract High quality taxonomies play a critical role in various domains such as e-commerce, web search and ontology engineering. While there has been extensive work on expanding taxonomies from externally mined data, there has been less attention paid to enriching taxonomies by exploiting existing concepts and structure within the taxonomy. In this work, we show the usefulness of this kind of enrichment, and explore its viability with a new taxonomy completion system ICON (I mplicit CON cept Insertion). ICON generates new concepts by identifying implicit concepts based on the existing concept structure, generating names for such concepts and inserting them in appropriate positions within the taxonomy. ICON integrates techniques from entity retrieval, text summary, and subsumption prediction; this modular architecture offers high flexibility while achieving state-of-the-art performance. We have evaluated ICON on two e-commerce taxonomies, and the results show that it offers significant advantages over strong baselines including recent taxonomy completion models and the large language model, ChatGPT.

Knowledge graph (KG) completion aims to find out missing triples in a KG. Some tasks, such as link prediction and instance completion, have been proposed for KG completion. They are triple-level tasks with some elements in a missing triple given to predict the missing element of the triple. However, knowing some elements of the missing triple in advance is not always a realistic setting. In this paper, we propose a novel graph-level automatic KG completion task calledTriple Set Prediction (TSP)which assumes none of the elements in the missing triples is given. TSP is to predict a set of missing triples given a set of known triples. To properly and accurately evaluate this new task, we propose 4 evaluation metrics including 3 classification metrics and 1 ranking metric, considering both the partial-open-world and the closed-world assumptions. Furthermore, to tackle the huge candidate triples for prediction, we propose a novel and efficient subgraph-based method GPHT that can predict the triple set fast. To fairly compare the TSP results, we also propose two types of methods RuleTensor-TSP and KGE-TSP applying the existing rule- and embedding-based methods for TSP as baselines. During experiments, we evaluate the proposed methods on two datasets extracted from Wikidata following the relation-similarity partial-open-world assumption proposed by us, and also create a complete family data set to evaluate TSP results following the closed-world assumption. Results prove that the methods can successfully generate a set of missing triples and achieve reasonable scores on the new task, and GPHTperforms better than the baselines with significantly shorter prediction time.

Matching tabular data to a knowledge graph (KG) is critical for understanding the semantic column types, column relationships, and entities of a table. Existing matching approaches rely heavily on core columns that represent primary subject entities on which other columns in the table depend. However, discovering these core columns before understanding the table’s semantics is challenging. Most prior works use heuristic rules, such as the leftmost column, to discover a single core column, while an insightful discovery of the core column set that accurately captures the dependencies between columns is often overlooked. To address these challenges, we introduce Dependency-aware Core Column Set Discovery ( DaCo ), an iterative method that uses a novel rough matching strategy to identify both inter-column dependencies and the core column set. Additionally, DaCo can be seamlessly integrated with pre-trained language models, as proposed in the optimization module. Unlike other methods, DaCo does not require labeled data or contextual information, making it suitable for real-world scenarios. In addition, it can identify multiple core columns within a table, which is common in real-world tables. We conduct experiments on six datasets, including five datasets with single core columns and one dataset with multiple core columns. Our experimental results show that DaCo outperforms existing core column set detection methods, further improving the effectiveness of table understanding tasks.

Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a new concept is pre-discovered and cannot support out-of-KB mention discovery; (ii) only using the concept label as the input along with the KB and thus lacking the contexts of a concept label; and (iii) mostly focusing on concept placement w.r.t a taxonomy of atomic concepts, instead of complex concepts, i.e., with logical operators. To address these issues, we propose a new benchmark, adapting MedMentions dataset (PubMed abstracts) with SNOMED CT versions in 2014 and 2017 under the Diseases sub-category and the broader categories of Clinical finding, Procedure, and Pharmaceutical / biologic product. We provide usage on the evaluation with the dataset for out-of-KB mention discovery and concept placement, adapting recent Large Language Model based methods.

Discovering entity mentions that are out of a Knowledge Base (KB) from texts plays a critical role in KB maintenance, but has not yet been fully explored. The current methods are mostly limited to the simple threshold-based approach and feature-based classification, and the datasets for evaluation are relatively rare. We propose BLINKout, a new BERT-based Entity Linking (EL) method which can identify mentions that do not have corresponding KB entities by matching them to a special NIL entity. To better utilize BERT, we propose new techniques including NIL entity representation and classification, with synonym enhancement. We also apply KB Pruning and Versioning strategies to automatically construct out-of-KB datasets from common in-KB EL datasets. Results on five datasets of clinical notes, biomedical publications, and Wikipedia articles in various domains show the advantages of BLINKout over existing methods to identify out-of-KB mentions for the medical ontologies, UMLS, SNOMED CT, and the general KB, WikiData.

Business Knowledge Graphs (KGs) are important to many enterprises today, providing factual knowledge and structured data that steer many products and make them more intelligent. Despite their promising benefits, building business KG necessitates solving prohibitive issues of deficient structure and multiple modalities. In this paper, we advance the understanding of the practical challenges related to building KG in non-trivial real-world systems. We introduce the process of building an open business knowledge graph (OpenBG) derived from a well-known enterprise, Alibaba Group. Specifically, we define a core ontology to cover various abstract products and consumption demands, with fine-grained taxonomy and multimodal facts in deployed applications. OpenBG is an open business KG of unprecedented scale: 2.6 billion triples with more than 88 million entities covering over 1 million core classes/concepts and 2,681 types of relations. We release all the open resources (OpenBG benchmarks) derived from it for the community and report experimental results of KG-centric tasks. We also run up an online competition based on OpenBG benchmarks, and has attracted thousands of teams. We further pre-train OpenBG and apply it to many KG-enhanced downstream tasks in business scenarios, demonstrating the effectiveness of billion-scale multimodal knowledge for e-commerce. All the resources with codes have been released at https://github.com/OpenBGBenchmark/OpenBG.

In knowledge graph completion (KGC), predicting triples involving emerging entities and/or relations, which are unseen when the KG embeddings are learned, has become a critical challenge. Subgraph reasoning with message passing is a promising and popular solution. Some recent methods have achieved good performance, but they (i) usually can only predict triples involving unseen entities alone, failing to address more realistic fully inductive situations with both unseen entities and unseen relations, and (ii) often conduct message passing over the entities with the relation patterns not fully utilized. In this study, we propose a new method named RMPI which uses a novel Relational Message Passing network for fully Inductive KGC. It passes messages directly between relations to make full use of the relation patterns for subgraph reasoning with new techniques on graph transformation, graph pruning, relation-aware neighborhood attention, addressing empty subgraphs, etc., and can utilize the relation semantics defined in the KG’s ontological schema. Extensive evaluation on multiple benchmarks has shown the effectiveness of RMPI’s techniques and its better performance compared with the existing methods that support fully inductive KGC. RMPI is also comparable to the state-of-the-art partially inductive KGC methods with very promising results achieved. Our codes, data and some supplementary experiment results are available at https://github.com/zjukg/RMPI.

Knowledge Graph (KG) and its variant of ontology have been widely used for knowledge representation, and have shown to be quite effective in augmenting Zero-shot Learning (ZSL). However, existing ZSL methods that utilize KGs all neglect the intrinsic complexity of inter-class relationships represented in KGs. One typical feature is that a class is often related to other classes in different semantic aspects. In this paper, we focus on ontologies for augmenting ZSL, and propose to learn disentangled ontology embeddings guided by ontology properties to capture and utilize more fine-grained class relationships in different aspects. We also contribute a new ZSL framework named DOZSL, which contains two new ZSL solutions based on generative models and graph propagation models, respectively, for effectively utilizing the disentangled ontology embeddings. Extensive evaluations have been conducted on five benchmarks across zero-shot image classification (ZS-IMGC) and zero-shot KG completion (ZS-KGC). DOZSL often achieves better performance than the state-of-the-art, and its components have been verified by ablation studies and case studies. Our codes and datasets are available at https://github.com/zjukg/DOZSL.

Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation of OM systems, it still suffers from several limitations including limited evaluation of subsumption mappings, suboptimal reference mappings, and limited support for the evaluation of ML-based systems. To tackle these limitations, we introduce five new biomedical OM tasks involving ontologies extracted from Mondo and UMLS. Each task includes both equivalence and subsumption matching; the quality of reference mappings is ensured by human curation, ontology pruning, etc.; and a comprehensive evaluation framework is proposed to measure OM performance from various perspectives for both ML-based and non-ML-based OM systems. We report evaluation results for OM systems of different types to demonstrate the usage of these resources, all of which are publicly available as part of the new Bio-ML track at OAEI 2022. Resource type: Ontology Matching Dataset License: CC BY 4.0 International DOI: https://doi.org/10.5281/zenodo.6510086 Documentation: https://krr-oxford.github.io/DeepOnto/#/om_resources OAEI track: https://www.cs.ox.ac.uk/isg/projects/ConCur/oaei/

Knowledge Graph (KG) alignment aims at finding equivalent entities and relations (i.e., mappings) between two KGs. The existing approaches utilize either reasoning-based or semantic embedding-based techniques, but few studies explore their combination. In this demonstration, we present PRASEMap, an unsupervised KG alignment system that iteratively computes the Mappings with both Probabilistic Reasoning (PR) And Semantic Embedding (SE) techniques. PRASEMap can support various embedding-based KG alignment approaches as the SE module, and it also enables easy human computer interaction that additionally provides an option for users to feed the mapping annotations back to the system for better results. The demonstration showcases these features via a stand-alone Web application with user friendly interfaces. The demo is available at https://prasemap.qizhy.com.

Zero-shot Learning (ZSL), which aims to predict for those classes that have never appeared in the training data, has arisen hot research interests. The key of implementing ZSL is to leverage the prior knowledge of classes which builds the semantic relationship between classes and enables the transfer of the learned models (e.g., features) from training classes (i.e., seen classes) to unseen classes. However, the priors adopted by the existing methods are relatively limited with incomplete semantics. In this paper, we explore richer and more competitive prior knowledge to model the inter-class relationship for ZSL via ontology-based knowledge representation and semantic embedding. Meanwhile, to address the data imbalance between seen classes and unseen classes, we developed a generative ZSL framework with Generative Adversarial Networks (GANs).

The usefulness and usability of knowledge bases (KBs) is often limited by quality issues. One common issue is the presence of erroneous assertions, often caused by lexical or semantic confusion. We study the problem of correcting such assertions, and present a general correction framework which combines lexical matching, semantic embedding, soft constraint mining and semantic consistency checking. The framework is evaluated using DBpedia and an enterprise medical KB.

Knowledge Graph Completion (KGC) has been proposed to improve Knowledge Graphs by filling in missing connections via link prediction or relation extraction. One of the main difficulties for KGC is a low resource problem. Previous approaches assume sufficient training triples to learn versatile vectors for entities and relations, or a satisfactory number of labeled sentences to train a competent relation extraction model. However, low resource relations are very common in KGs, and those newly added relations often do not have many known samples for training. In this work, we aim at predicting new facts under a challenging setting where only limited training instances are available. We propose a general framework called Weighted Relation Adversarial Network, which utilizes an adversarial procedure to help adapt knowledge/features learned from high resource relations to different but related low resource relations. Specifically, the framework takes advantage of a relation discriminator to distinguish between samples from different relations, and help learn relation-invariant features more transferable from source relations to target relations. Experimental results show that the proposed approach outperforms previous methods regarding low resource settings for both link prediction and relation extraction.

Reasoning is essential for the development of large knowledge graphs, especially for completion, which aims to infer new triples based on existing ones. Both rules and embeddings can be used for knowledge graph reasoning and they have their own advantages and difficulties. Rule-based reasoning is accurate and explainable but rule learning with searching over the graph always suffers from efficiency due to huge search space. Embedding-based reasoning is more scalable and efficient as the reasoning is conducted via computation between embeddings, but it has difficulty learning good representations for sparse entities because a good embedding relies heavily on data richness. Based on this observation, in this paper we explore how embedding and rule learning can be combined together and complement each other's difficulties with their advantages. We propose a novel framework IterE iteratively learning embeddings and rules, in which rules are learned from embeddings with proper pruning strategy and embeddings are learned from existing triples and new triples inferred by rules. Evaluations on embedding qualities of IterE show that rules help improve the quality of sparse entity embeddings and their link prediction results. We also evaluate the efficiency of rule learning and quality of rules from IterE compared with AMIE+, showing that IterE is capable of generating high quality rules more efficiently. Experiments show that iteratively learning embeddings and rules benefit each other during learning and prediction.

Smog disaster is a type of air pollution event that negatively affects people's life and health. Forecasting smog disasters may largely reduce potential loss that they may cause. However, it is a great challenge since smog disasters are often caused by many complex factors. With the availability of huge amounts of data from the social web and physical sensors, covering information of air quality, meteorology, social event, human mobility, people's opinion, etc., it becomes possible to utilize such big data to forecast smog disasters. Especially, we can investigate the effect of social activities in smog disaster forecasting with the help of social web, which is ignored in traditional studies. In this paper, we propose a big data approach named B-Smog for smog disaster forecasting. It mainly has two components: 1) features extraction from multiple data sources to model the factors that indicate the appearance or disappearance of a smog disaster like traffic condition, human mobility, weather condition and air pollution transportation; 2) learning and predicting with heterogeneous features in multiple views. For the second component, we propose a prediction model based on an ensemble learning framework and artificial neural networks (ANNs), which achieves high accuracy in this application and can also be applied to other similar problems. We present the effectiveness of B-Smog through two cases studies in Beijing and Shanghai, and evaluate the accuracy of the prediction model through comparing it with some baselines. Moreover, the empirical findings of our study can also support decision making in smog disaster management.

Chaos of data is the total unpredictability of all the data elements, and can by quantified by Shannon entropy. In this paper, we firstly propose an entropy based theoretic framework for machine learning, which states that chaos in sample data will decrease and rule will advance as learning progresses. However, it is usually time consuming to apply the theoretic framework because groups of rule need to be trained iteratively and data chaos will be recalculated during each iteration. To implement the theoretic framework for scalable learning, we propose a MapReduce based distributed computational framework. In a case study of classification, the framework parallelly trains multiple classifiers and calculats chaos of the sample set during each iteration, and then resamples a small sample subset with the highest entropy for training of the next iteration, reducing chaos in sample data as quickly as possible. With typical classification benchmarks, our experiment presents entropy in sample data, and proves that the theoretic framework is rational and can help improve the accuracy of machine learning. Meanwhile, the computational framework shows high performance including high efficiency and scalability for large scale learning on hadoop cluster.

Recently, the emerging accumulation of biomedical data on the Web (e.g. vast amounts of protein sequences, genes, gene products, drugs, diseases and chemical compounds, etc.) has shaped a big network of isolated professional knowledge. Embedded with domain knowledge from different disciplines all regarding to human biological systems, the decentralized data repositories are implicitly connected by human expert knowledge. Lots of biomedical data sources are published separately in the form of semantic ontologies represented by Web Ontology Language (OWL) syntax, which is naturally based on linked graphs. When we are faced with such massive, disparate and interlinked data, biomedical data analysis becomes a challenge. In this paper, we present a general OWL reasoning framework for the analysis of big biomedical data and implement a MapReduce-based property chain reasoning prototype system. OWL reasoning method is ideally suitable for problems involved complex semantic associations because it is able to infer logical consequences based on a set of asserted rules or axioms. MapReduce framework is used to solve the problem of scalability. In our experiment, we focus on the discovery of associations between Traditional Chinese Medicine (TCM) and Western Medicine (WM). The results show the system achieves high performance, accuracy and scalability.