A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

Experimental evaluation of big data querying tools

Nos últimos anos, o termo Big Data tornou-se um tópico bastanta debatido em várias áreas de negócio. Um dos principais desafios relacionados com este conceito é como lidar com o enorme volume e variedade de dados de forma eficiente. Devido à notória complexidade e volume de dados associados ao conceito de Big Data, são necessários mecanismos de consulta eficientes para fins de análise de dados. Motivado pelo rápido desenvolvimento de ferramentas e frameworks para Big Data, há muita discussão sobre ferramentas de consulta e, mais especificamente, quais são as mais apropriadas para necessidades analíticas específica. Esta dissertação descreve e compara as principais características e arquiteturas das seguintes conhecidas ferramentas analíticas para Big Data: Drill, HAWQ, Hive, Impala, Presto e Spark. Para testar o desempenho dessas ferramentas analíticas para Big Data, descrevemos também o processo de preparação, configuração e administração de um Cluster Hadoop para que possamos instalar e utilizar essas ferramentas, tendo um ambiente capaz de avaliar seu desempenho e identificar quais cenários mais adequados à sua utilização. Para realizar esta avaliação, utilizamos os benchmarks TPC-H e TPC-DS, onde os resultados mostraram que as ferramentas de processamento em memória como HAWQ, Impala e Presto apresentam melhores resultados e desempenho em datasets de dimensão baixa e média. No entanto, as ferramentas que apresentaram tempos de execuções mais lentas, especialmente o Hive, parecem apanhar as ferramentas de melhor desempenho quando aumentamos os datasets de referência

RegenBase: a knowledge base of spinal cord injury biology for translational research.

Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org

DataHub: Collaborative Data Science & Dataset Version Management at Scale

Relational databases have limited support for data collaboration, where teams collaboratively curate and analyze large datasets. Inspired by software version control systems like git, we propose (a) a dataset version control system, giving users the ability to create, branch, merge, difference and search large, divergent collections of datasets, and (b) a platform, DataHub, that gives users the ability to perform collaborative data analysis building on this version control system. We outline the challenges in providing dataset version control at scale.Comment: 7 page

The Semantic Web MIDI Tape: An Interface for Interlinking MIDI and Context Metadata

The Linked Data paradigm has been used to publish a large number of musical datasets and ontologies on the Semantic Web, such as MusicBrainz, AcousticBrainz, and the Music Ontology. Recently, the MIDI Linked Data Cloud has been added to these datasets, representing more than 300,000 pieces in MIDI format as Linked Data, opening up the possibility for linking fine-grained symbolic music representations to existing music metadata databases. Despite the dataset making MIDI resources available in Web data standard formats such as RDF and SPARQL, the important issue of finding meaningful links between these MIDI resources and relevant contextual metadata in other datasets remains. A fundamental barrier for the provision and generation of such links is the difficulty that users have at adding new MIDI performance data and metadata to the platform. In this paper, we propose the Semantic Web MIDI Tape, a set of tools and associated interface for interacting with the MIDI Linked Data Cloud by enabling users to record, enrich, and retrieve MIDI performance data and related metadata in native Web data standards. The goal of such interactions is to find meaningful links between published MIDI resources and their relevant contextual metadata. We evaluate the Semantic Web MIDI Tape in various use cases involving user-contributed content, MIDI similarity querying, and entity recognition methods, and discuss their potential for finding links between MIDI resources and metadata

Towards Conceptual and Logical Modelling of NoSQL Databases

NoSQL databases support the ability to handle large volumes of data in the absence of an explicit data schema. On the other hand, schema information is sometimes essential for applications during data retrieval. Consequently, there are approaches to schema construction in, e.g., the JSON DB and graph DB communities. The difference between a conceptual and database schema is often vague in this case. We use functional constructs – typed attributes for a conceptual view of DB that provide a sufficiently structured approach for expressing semantics of document and graph data. Attribute names are natural language expressions. Such typed functional data objects can be manipulated by terms of a typed λ-calculus, providing powerful nonprocedural query features for considered data structures. The calculus is extendible. Logical, arithmetic, and aggregation functions can be included there. Conceptual and database modelling merge in this case