Related papers: SBtab - Conventions for structured data tables in …
Large systems biology projects can encompass several workgroups often located in different countries. An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data…
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we…
Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current…
A central challenge in science is to understand how systems behaviors emerge from complex networks. This often requires aggregating, reusing, and integrating heterogeneous information. Supplementary spreadsheets to articles are a key data…
Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, non-standardized spreadsheets, or data repositories. This lack of structure challenges…
In this paper we introduce the SchemaDB data-set; a collection of relational database schemata in both sql and graph formats. Databases are not commonly shared publicly for reasons of privacy and security, so schemata are not available for…
Biological science produces large amounts of data in a variety of formats, which necessitates the use of computational tools to process, integrate, analyse, and glean insights from the data. Researchers who use computational biology tools…
Documents are a common way to store and share information, with tables being an important part of many documents. However, there is no real common understanding of how to model documents and tables in particular. Because of this lack of…
Molecular biology data are subject to terms of use that vary widely between databases and curating institutions. This research presents a taxonomy of contractual and technical restrictions applicable to databases in life science. It builds…
Context: Tables are ubiquitous formats for data. Therefore, techniques for writing correct programs over tables, and debugging incorrect ones, are vital. Our specific focus in this paper is on rich types that articulate the properties of…
The complexity of molecular and cellular processes forces experimental studies to focus on subsystems. To study the functioning of biological systems across levels of structural and functional organisation, we require tools to compose and…
In the past few decades, the life sciences have experienced an unprecedented accumulation of data, ranging from genomic sequences and proteomic profiles to heavy-content imaging, clinical assays, and commercial biological products for…
In this paper, we introduce a scientific format for text-based data files, which facilitates storing and communicating tabular data sets. The so-called Full-Metadata Format builds on the widely used INI-standard and is based on four…
In this paper, we observe that semi-structured tabulated text is ubiquitous; understanding them requires not only comprehending the meaning of text fragments, but also implicit relationships between them. We argue that such data can prove…
Despite the prevalence of images and texts in machine learning, tabular data remains widely used across various domains. Existing deep learning models, such as convolutional neural networks and transformers, perform well however demand…
Spreadsheet tables are often labeled, and these labels effectively constitute types for the data in the table. In such cases tables can be considered to be built from typed data where the placement of values within the table is controlled…
Tables in scientific papers contain a wealth of valuable knowledge for the scientific enterprise. To help the many of us who frequently consult this type of knowledge, we present Tab2Know, a new end-to-end system to build a Knowledge Base…
There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types -- such as disease names, cell types or chemicals -- that are used in metadata associated with…
In this paper, we present BIMS (Biomedical Information Management System). BIMS is a software architecture designed to provide a flexible computational framework to manage the information needs of a wide range of biomedical research…
The abundance of the data in the Internet facilitates the improvement of extraction and processing tools. The trend in the open data publishing encourages the adoption of structured formats like CSV and RDF. However, there is still a…