Advanced Query Research Articles

Towards ontology-driven navigation of the lipid bibliosphere

BackgroundThe indexing of scientific literature and content is a relevant and contemporary requirement within life science information systems. Navigating information available in legacy formats continues to be a challenge both in enterprise and academic domains. The emergence of semantic web technologies and their fusion with artificial intelligence techniques has provided a new toolkit with which to address these data integration challenges. In the emerging field of lipidomics such navigation challenges are barriers to the translation of scientific results into actionable knowledge, critical to the treatment of diseases such as Alzheimer's syndrome, Mycobacterium infections and cancer.ResultsWe present a literature-driven workflow involving document delivery and natural language processing steps generating tagged sentences containing lipid, protein and disease names, which are instantiated to custom designed lipid ontology. We describe the design challenges in capturing lipid nomenclature, the mandate of the ontology and its role as query model in the navigation of the lipid bibliosphere. We illustrate the extent of the description logic-based A-box query capability provided by the instantiated ontology using a graphical query composer to query sentences describing lipid-protein and lipid-disease correlations.ConclusionAs scientists accept the need to readjust the manner in which we search for information and derive knowledge we illustrate a system that can constrain the literature explosion and knowledge navigation problems. Specifically we have focussed on solving this challenge for lipidomics researchers who have to deal with the lack of standardized vocabulary, differing classification schemes, and a wide array of synonyms before being able to derive scientific insights. The use of the OWL-DL variant of the Web Ontology Language (OWL) and description logic reasoning is pivotal in this regard, providing the lipid scientist with advanced query access to the results of text mining algorithms instantiated into the ontology. The visual query paradigm assists in the adoption of this technology.

Simulation Subsumption or Déjà vu on the Web

Simulation unification is a special kind of unification adapted to retrieving semi-structured data on the Web. This article introduces simulation subsumption, or containment, that is, query subsumption under simulation unification. Simulation subsumption is crucial in general for query optimization, in particular for optimizing pattern-based search engines, and for the termination of recursive rule-based web languages such as the XML and RDF query language Xcerpt. This paper first motivates and formalizes simulation subsumption. Then, it establishes decidability of simulation subsumption for advanced query patterns featuring descendant constructs, regular expressions, negative subterms (or subterm exclusions), and multiple variable occurrences. Finally, we show that subsumption between two query terms can be decided in O(n!n) where n is the sum of the sizes of both query terms.

A schema-based P2P network to enable publish-subscribe for multimedia content in open hypermedia systems

Open Hypermedia Systems (OHS) aim to provide efficient dissemination, adaptation and integration of hyperlinked multimedia resources. Content available in Peer-to-Peer (P2P) networks could add significant value to OHS provided that challenges for efficient discovery and prompt delivery of rich and up-to-date content are successfully addressed. This paper proposes an architecture that enables the operation of OHS over a P2P overlay network of OHS servers based on semantic annotation of (a) peer OHS servers and of (b) multimedia resources that can be obtained through the link services of the OHS. The architecture provides efficient resource discovery. Semantic query-based subscriptions over this P2P network can enable access to up-to-date content, while caching at certain peers enables prompt delivery of multimedia content. Advanced query resolution techniques are employed to match different parts of subscription queries (subqueries). These subscriptions can be shared among different interested peers, thus increasing the efficiency of multimedia content dissemination.

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures

The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures. This is a new tool to search and analyse RNA structures, directed at the 3D structure modelling. The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a ‘dot-bracket’ notation. The algorithm searching for the requested 3D RNA fragments is very efficient. As of August 2007, the database contains: (i) RNA sequences and secondary structures, in the ‘dot-bracket’ notation, derived from 1065 protein data bank (PDB)-deposited RNA structures and their complexes, (ii) a collection of atom coordinates of unmodified and modified nucleotide residues occurring in RNA structures, (iii) calculated RNA torsion angles and sugar pucker parameters and (iv) information about base pairs. Advanced query involves filters sensitive to: modified residue contents, experimental method used and limits of conformational parameters. The output list of query-matching RNA fragments gives access to their coordinates in the PDB-format files, ready for direct download and visualization, conformational parameters and information about base pairs. The RNA FRABASE is automatically, monthly updated and is freely accessible at http://rnafrabase.ibch.poznan.pl (mirror at http://cerber.cs.put.poznan.pl/rnadb).

AlzPharm: integration of neurodegeneration data using RDF

BackgroundNeuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data.ResultsWe have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion.ConclusionAccessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields.

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions

SNAPPI-DB, a high performance database of Structures, iNterfaces and Alignments of Protein–Protein Interactions, and its associated Java Application Programming Interface (API) is described. SNAPPI-DB contains structural data, down to the level of atom co-ordinates, for each structure in the Protein Data Bank (PDB) together with associated data including SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, Protein Quaternary Structures (PQS) and secondary structure information. Domain–domain interactions are stored for multiple domain definitions and are classified by their Superfamily/Family pair and interaction interface. Each set of classified domain–domain interactions has an associated multiple structure alignment for each partner. The API facilitates data access via PDB entries, domains and domain–domain interactions. Rapid development, fast database access and the ability to perform advanced queries without the requirement for complex SQL statements are provided via an object oriented database and the Java Data Objects (JDO) API. SNAPPI-DB contains many features which are not available in other databases of structural protein–protein interactions. It has been applied in three studies on the properties of protein–protein interactions and is currently being employed to train a protein–protein interaction predictor and a functional residue predictor. The database, API and manual are available for download at: .

Mouse Tumor Biology Database (MTB): status update and future directions

The Mouse Tumor Biology (MTB) database provides access to data about endogenously arising tumors (both spontaneous and induced) in genetically defined mice (inbred, hybrid, mutant and genetically engineered mice). Data include information on the frequency and latency of mouse tumors, pathology reports and images, genomic changes occurring in the tumors, genetic (strain) background and literature or contributor citations. Data are curated from the primary literature or submitted directly from researchers. MTB is accessed via the Mouse Genome Informatics web site (). Integrated searches of MTB are enabled through use of multiple controlled vocabularies and by adherence to standardized nomenclature, when available. Recently MTB has been redesigned and its database infrastructure replaced with a robust relational database management system (RDMS). Web interface improvements include a new advanced query form and enhancements to already existing search capabilities. The Tumor Frequency Grid has been revised to enhance interactivity, providing an overview of reported tumor incidence across mouse strains and an entrée into the database. A new pathology data submission tool allows users to submit, edit and release data to the MTB system.

Sub-part correspondence by structural descriptors of 3D shapes

To fully exploit the valuable knowledge embedded in repositories of digital models, it is crucial to devise search engines capable of expressing high-level and advanced queries, which can effectively support the re-use of CAD models. The retrieval mechanism should be able to return not only global similarity measures among objects, but it should also be coupled with methods for the automatic identification of similar sub-parts in the query and retrieved models, possibly highlighting automatically the object differences. This paper describes a method for partial shape-matching able to recognize similar sub-parts of objects represented as 3D polygonal meshes. The geometry and the structure of the shapes are coupled in a descriptor that provides a flexible coding, grounded on solid mathematical theories, and that can be adapted to the user’s needs and to the context of applications. The matching framework for sub-part correspondence is achieved through a graph-matching technique, which builds the common sub-graphs between the two shapes and highlights the maximal sub-parts having similar structure and similar space distribution.

Webwatch

BioTechniquesVol. 41, No. 3 WebWatchOpen AccessWebWatchKevin AhernKevin AhernSearch for more papers by this authorPublished Online:21 May 2018https://doi.org/10.2144/000112249AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInRedditEmail Much Mus musculusIn the beginning of the genomic era, there were sequences, and they were good. And they were annotated and put into databases, and that was good. And then there were expression and anatomical data and needs to cross-reference and retrieve the new information, and thus were born broader organism-specific databases, and this is how GenePaint came to be. And (fortunately), it too is good. Hosted by the Max Planck Institute of Experimental Endocrinology, GenePaint is to mouse research what Google Maps is to geography. Visitors can scan the organismal terrain from above with a virtual microscope and retrieve “population data” of expressed genes sorted by tissue or gene name. Advanced and simple query options provide easy access to complicated data.@ www.genepaint.org/Frameset.htmlsGrowing to Great LengthsLiving life as one of the most elongated organisms on earth is easy, if you're gelatinous and have a home in the sea, that is. Hail to the siphonophores, a collection of over 175 diverse species that includes corals, hydroids, and true jellyfish. Some members can, depending on the species, grow and grow and grow some more, with specimens over 40 meters long. Popular multicellular study subjects for their simple design, some siphonophores make it even easier for researchers, with see-through bodies that are almost completely transparent, save for their digestive and circulatory systems. At the siphonophores site, organized by Casey Dunn, you'll learn about and view these remarkable colonial organisms that challenge our notions of what constitutes an individual—the colony or the individual zooids comprising it.@ www.siphonophores.orgPublic AnemonesTiny wormlike creatures about half an inch long with tentacles surrounding an opening that serves both for the entry of food and exit of waste, starlet anemones are creatures only a biologist could love. And, love them they do, if the significance of having their complete genome sequenced is any measure. There is a lot to appreciate at the Nematostella and StellaBase sites, organized by John Finnerty at Boston University. With complementary aims, the sites provide public access to genomic/expression data (StellaBase) and broader perspectives of genomics, ecological, ontogenic, morphological, and evolutionary information of these mud-burrowing (and possibly endangered) worms at Nematostella. Notable for a sexual/asexual life cycle and being one of the simplest organisms with bilateral symmetry, the starlet anemone deserves all the attention it is getting. Clearly, a fascinatingly simple model organism for developmental biology.@ www.nematostella.org & www.stellabase.orgLooking at LookingIn Webvision, Drs. Kolb, Fernandez, and Nelson, at the University of Utah's John Moran Eye Center, have assembled what surely is an educational masterpiece for anyone interested in the mammalian retina. Organized as a hyperlinked repository of text, informative figures, and even QuickTime movies, Webvision puts a mountain of content into the molehill of a single web page. Topics are broadly organized into 11 subjects—Introduction, Anatomy/Physiology, Retinal Circuits, Neuroactive Substances, Receptors, Bipolar Cell Pathways, Cell Development/Connections, Color Vision, GABAc Receptors, Psychophysics, and Primary Visual Cortex. Under each heading are hyperlinked subheadings that make access to educational material a snap or, better yet, a click.@ webvision.med.utah.eduMolecular SupermodelsLet's face it. With over 37,000 structures under the hood, the Protein Data Bank probably isn't a place where you'll wander through looking at images, and that's too bad. Recognizing this, Dr. David Goodsell at The Scripps Research Institute began, in 2000, a popular educational feature of the site called Molecule of the Month that has pulled in nonstructural biologists galore to check out the excitement. With interpretive drawings and in formative descriptions low on the ‘techie’ side, Molecule of the Month achieves its purpose—introducing nonpractitioners to an environment where relationships between structure and function become apparent.@ www.rcsb.org/pdb/Welcome.doFiguresReferencesRelatedDetails Vol. 41, No. 3 Follow us on social media for the latest updates Metrics History Published online 21 May 2018 Published in print September 2006 Information© 2006 Author(s)PDF download

Note segmentation and quantization for music information retrieval

Much research in music information retrieval has focused on query-by-humming systems, which search melodic databases using sung queries. The database retrieval aspect of such systems has received considerable attention, but query processing and the melodic representation have not been examined as carefully. Common methods for query processing are based on musical intuition and historical momentum rather than specific performance criteria; existing systems often employ rudimentary note segmentation or coarse quantization of note estimates. In this work, we examine several alternative query processing methods as well as quantized melodic representations. One common difficulty with designing query-by-humming systems is the coupling between system components. We address this issue by measuring the performance of the query processing system both in isolation and coupled with a retrieval system. We first measure the segmentation performance of several note estimators. We then compute the retrieval accuracy of an experimental query-by-humming system that uses the various note estimators along with varying degrees of pitch and duration quantization. The results show that more advanced query processing can improve both segmentation performance and retrieval performance, although the best segmentation performance does not necessarily yield the best retrieval performance. Further, coarsely quantizing the melodic representation generally degrades retrieval accuracy.

Patika web: a Web interface for analyzing biological pathways through advanced querying and visualization

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

The Integration of Grid-enabled Internet GIServices and Geographic Semantic Web Technologies

This paper presents a new framework for Grid-enabled GIService web portals to facilitate the building of high-level intelligent Internet GIServices. The five-tier architecture suggested here can support advanced semantic search and query functions for distributed GIServices by combining Grid computing, Semantic Web, and software agent technologies. The design of the web portal user interface with software agents can help end users combine and integrate computing power with geospatial data and services. Geospatial ontologies are incorporated into the framework by using geographic web ontology language (G-OWL). Intelligent software agent (GeoAgent) techniques are used to automate the procedures for searching, retrieving and processing geospatial data. The proposed Internet GIService architecture will provide a blue print for the establishment of Grid-enabled Internet GIServices and will help the GIS community to identify potential technical challenges to implement intelligent Internet GIServices.

Single nucleotide polymorphisms associated with rat expressed sequences.

Single nucleotide polymorphisms (SNPs) are the most common source of genetic variation in populations and are thus most likely to account for the majority of phenotypic and behavioral differences between individuals or strains. Although the rat is extensively studied for the latter, data on naturally occurring polymorphisms are mostly lacking. We have used publicly available sequences consisting of whole-genome shotgun (WGS), expressed sequence tag (EST), and mRNA data as a source for the in silico identification of SNPs in gene-coding regions and have identified a large collection of 33,305 high-quality candidate SNPs. Experimental verification of 471 candidate SNPs using a limited set of rat isolates revealed a confirmation rate of approximately 50%. Although the majority of SNPs were identified between Sprague-Dawley (EST data) and Brown Norway (WGS data) strains, we found that 66% of the verified variations are common among different rat strains. All SNPs were extensively annotated, including chromosomal and genetic map information, and nonsynonymous SNPs were analyzed by SIFT and PolyPhen prediction programs for their potential deleterious effect on protein function. Interestingly, we retrieved three SNPs from the database that result in the introduction of a premature stop codon and that could be confirmed experimentally. Two of these "in silico-identified knockouts" reside in interesting QTL regions. Data are publicly available via a Web interface (http://cascad.niob.knaw.nl), allowing simple and advanced search queries.

A score‐driven approach to music information retrieval

AbstractAs the dimension and number of digital music archives grow, the problem of storing and accessing multimedia data is no longer confined to the database area. Specific approaches for music information retrieval are necessary to establish a connection between textual and content‐based metadata. This article addresses such issues with the intent of surveying our perspective on music information retrieval. In particular, we stress the use of symbolic information as a central element in a complex musical environment. Musical themes, harmonies, and styles are automatically extracted from electronic music scores and employed as access keys to data. The database schema is extended to handle audio recordings. A score/audio matching module provides a temporal relationship between a music performance and the score played. Besides standard free‐text search capabilities, three levels of retrieval strategies are employed. Moreover, the introduction of a hierarchy of input modalities assures meeting the needs and matching the expertise of a wide group of users. Singing, playing, and notating melodic excerpts is combined with more advanced musicological queries, such as querying by a sequence of chords. Finally, we present some experimental results and our future research directions.

A database for G proteins and their interaction with GPCRs

BackgroundG protein-coupled receptors (GPCRs) transduce signals from extracellular space into the cell, through their interaction with G proteins, which act as switches forming hetero-trimers composed of different subunits (α,β,γ). The α subunit of the G protein is responsible for the recognition of a given GPCR. Whereas specialised resources for GPCRs, and other groups of receptors, are already available, currently, there is no publicly available database focusing on G Proteins and containing information about their coupling specificity with their respective receptors.DescriptiongpDB is a publicly accessible G proteins/GPCRs relational database. Including species homologs, the database contains detailed information for 418 G protein monomers (272 Gα, 87 Gβ and 59 Gγ) and 2782 GPCRs sequences belonging to families with known coupling to G proteins. The GPCRs and the G proteins are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature searchs. The main innovation besides the classification of both G proteins and GPCRs is the relational model of the database, describing the known coupling specificity of the GPCRs to their respective α subunit of G proteins, a unique feature not available in any other database. There is full sequence information with cross-references to publicly available databases, references to the literature concerning the coupling specificity and the dimerization of GPCRs and the user may submit advanced queries for text search. Furthermore, we provide a pattern search tool, an interface for running BLAST against the database and interconnectivity with PRED-TMR, PRED-GPCR and TMRPres2D.ConclusionsThe database will be very useful, for both experimentalists and bioinformaticians, for the study of G protein/GPCR interactions and for future development of predictive algorithms. It is available for academics, via a web browser at the URL:

MyMED: A database system for biomedical research on MEDLINE data

MyMED is a database system that mirrors MEDLINE™ data and that provides access to the data locally, without the restrictions involved in accessing the National Library of Medicine Web site. The implementation of MyMED is based on the IBM DB2 Universal Database™, the DB2® XML Extender and the DB2 Text Information Extender. The resulting system supports advanced queries, including wildcard searching abilities, proximity searching, scoring functions, and capabilities to build a thesaurus, and constitutes an important research tool for text mining of biomedical-citation data. The paper describes the challenges encountered in the use of DB2 Extenders™ products, the methods used to overcome these challenges, and the implementation of MyMED. The benefits of MyMED are illustrated through some use cases, and directions for future work are outlined.

Coverage, relevance, and ranking

Research has reported that about 10% of Web searchers utilize advanced query operators, with the other 90% using extremely simple queries. It is often assumed that the use of query operators, such as Boolean operators and phrase searching, improves the effectiveness of Web searching. We test this assumption by examining the effects of query operators on the performance of three major Web search engines. We selected one hundred queries from the transaction log of a Web search service. Each of these original queries contained query operators such as AND, OR, MUST APPEAR (+), or PHRASE (" "). We then removed the operators from these one hundred advanced queries. We submitted both the original and modified queries to three major Web search engines; a total of 600 queries were submitted and 5,748 documents evaluated. We compared the results from the original queries with the operators to the results from the modified queries without the operators. We examined the results for changes in coverage, relative precision, and ranking of relevant documents. The use of most query operators had no significant effect on coverage, relative precision, or ranking, although the effect varied depending on the search engine. We discuss implications for the effectiveness of searching techniques as currently taught, for future information retrieval system design, and for future research.

Advanced query language for manipulating complex entities

Complex entities are one of the most popular ways to model relationships among data. Especially complex entities, known as physical assemblies, are popular in several applications. Typically, complex entities consist of several parts organized at many nested levels. Contemporary query languages intended for manipulating complex entities support only extensional queries. Likewise, the user has to master the structures of complex entities completely, which is impossible if a physical assembly consists of a huge number of parts. Further, query languages do not support the manipulation of documents related to parts of physical assemblies. In this paper we introduce a novel, declarative and powerful query language, in which the above deficiencies have been eliminated. Our query language supports text information retrieval related to parts and it contains intensional and combined extensional–intensional query features. These features support making queries of new types. In the paper we give several sample queries, which demonstrate the usefulness of these query types. In addition, we show that conventional extensional queries can be formulated intuitively and compactly in our query language. Among other things this is due to our query primitives allowing removal of the explicit specification of navigation from the user.

PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.

Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named Patika (Pathway Analysis Tool for Integration and Knowledge Acquisition). Patika is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that Patika will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development. A prototype of Patika is available upon request from the authors.

The Celera Discovery System.

The Celera Discovery System (CDS) is a web-accessible research workbench for mining genomic and related biological information. Users have access to the human and mouse genome sequences with annotation presented in summary form in BioMolecule Reports for genes, transcripts and proteins. Over 40 additional databases are available, including sequence, mapping, mutation, genetic variation, mRNA expression, protein structure, motif and classification data. Data are accessible by browsing reports, through a variety of interactive graphical viewers, and by advanced query capability provided by the LION SRS search engine. A growing number of sequence analysis tools are available, including sequence similarity, pattern searching, multiple sequence alignment and Hidden Markov Model search. A user workspace keeps track of queries and analyses. CDS is widely used by the academic research community and requires a subscription for access. The system and academic pricing information are available at http://cds.celera.com.