The popularity of XML has exacerbated the need for an easy-to-use, high precision query interface for XML data. When traditional document-oriented keyword search techniques do not suffice, natural language interfaces and keyword search techniques that take advantage of XML structure make it very easy for ordinary users to query XML databases. Unfortunately, current approaches to processing these queries rely heavily on heuristics that are intuitively appealing but ultimately ad hoc. These approaches often retrieve false positive answers, overlook correct answers, and cannot rank answers appropriately. To address these problems for data-centric XML, we propose coherency ranking (CR), a domain- and database design-independent ranking method for XML keyword queries that is based on an extension of the concepts of data dependencies and mutual information. With coherency ranking, the results of a keyword query are invariant under a class of equivalency-preserving schema reorganizations. We analyze the way in which previous approaches to XML keyword search approximate coherency ranking, and present efficient algorithms to process queries and rank their answers using coherency ranking. Our empirical evaluation with two real-world XML data sets shows that coherency ranking has better precision and recall and provides better ranking than all previous approaches.

It is well established that extracting and annotating occurrences of entities in a collection of unstructured text documents with their concepts improve the effectiveness of answering queries over the collection. However, it is very resource intensive to create and maintain large annotated collections. Since the available resources of an enterprise are limited and/or its users may have urgent information needs, it may have to select only a subset of relevant concepts for extraction and annotation. We call this subset a conceptual design for the annotated collection. In this paper, we introduce the problem of cost effective conceptual design, where given a collection, a set of relevant concepts, and a fixed budget, one likes to find a conceptual design that improves the effectiveness of answering queries over the collection the most. We prove that the problem is generally NP-hard in the number of relevant concepts and propose two efficient approximation algorithms to solve the problem: Approximate Popularity Maximization (APM for short) and Approximate Annotation-benefit Maximization (AAM for short). We show that if there is not any constraints regrading the overlap of concepts, APM is a fully polynomial time approximation scheme. We also prove that if the relevant concepts are mutually exclusive, APM has a constant approximation ratio and AAM is a fully polynomial time approximation scheme. Our empirical results using Wikipedia collection and a search engine query log validate the proposed formalization of the problem and show that APM and AAM efficiently compute conceptual designs. They also indicate that in general APM delivers the optimal conceptual designs if the relevant concepts are not mutually exclusive. Also, if the relevant concepts are mutually exclusive, the conceptual designs delivered by AAM improve the effectiveness of answering queries over the collection more than the solutions provided by APM.

Background Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeutic targets and modalities. The NCATS Biomedical Data Translator project is working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and the broader field, there is a need for a framework that can efficiently and reproducibly build an integrated, standards-compliant, and comprehensive biomedical knowledge graph that can be downloaded in standard serialized form or queried via a public application programming interface (API). Results To create a knowledge provider system within the Translator project, we have developed RTX-KG2, an open-source software system for building—and hosting a web API for querying—a biomedical knowledge graph that uses an Extract-Transform-Load approach to integrate 70 knowledge sources (including the aforementioned core six sources) into a knowledge graph with provenance information including (where available) citations. The semantic layer and schema for RTX-KG2 follow the standard Biolink model to maximize interoperability. RTX-KG2 is currently being used by multiple Translator reasoning agents, both in its downloadable form and via its SmartAPI-registered interface. Serializations of RTX-KG2 are available for download in both the pre-canonicalized form and in canonicalized form (in which synonyms are merged). The current canonicalized version (KG2.7.3) of RTX-KG2 contains 6.4M nodes and 39.3M edges with a hierarchy of 77 relationship types from Biolink. Conclusion RTX-KG2 is the first knowledge graph that integrates UMLS, SemMedDB, ChEMBL, DrugBank, Reactome, SMPDB, and 64 additional knowledge sources within a knowledge graph that conforms to the Biolink standard for its semantic layer and schema. RTX-KG2 is publicly available for querying via its API at arax.rtx.ai/api/rtxkg2/v1.2/openapi.json. The code to build RTX-KG2 is publicly available at github:RTXteam/RTX-KG2.

No abstract

Learning novel concepts and relations from relational databases is an important problem with many applications in database systems and machine learning. Relational learning algorithms learn the definition of a new relation in terms of existing relations in the database. Nevertheless, the same data set may be represented under different schemas for various reasons, such as efficiency, data quality, and usability. Unfortunately, the output of current relational learning algorithms tends to vary quite substantially over the choice of schema, both in terms of learning accuracy and efficiency. This variation complicates their off-the-shelf application. In this paper, we introduce and formalize the property of schema independence of relational learning algorithms, and study both the theoretical and empirical dependence of existing algorithms on the common class of (de) composition schema transformations. We study both sample-based learning algorithms, which learn from sets of labeled examples, and query-based algorithms, which learn by asking queries to an oracle. We prove that current relational learning algorithms are generally not schema independent. For query-based learning algorithms we show that the (de) composition transformations influence their query complexity. We propose Castor, a sample-based relational learning algorithm that achieves schema independence by leveraging data dependencies. We support the theoretical results with an empirical study that demonstrates the schema dependence/independence of several algorithms on existing benchmark and real-world datasets under (de) compositions.