Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems

The amount of genomic and proteomic data that is entered each day into databases and the experimental literature is outstripping the ability of experimental scientists to keep pace. While generic databases derived from automated curation efforts are useful, most biological scientists tend to focus on a class or family of molecules and their biological impact. Consequently, there is a need for molecular class-specific or other specialized databases. Such databases collect and organize data around a single topic or class of molecules. If curated well, such systems are extremely useful as they allow experimental scientists to obtain a large portion of the available data most relevant to their needs from a single source. We are involved in the development of two such databases with substantial pharmacological relevance. These are the GPCRDB and NucleaRDB information systems, which collect and disseminate data related to G protein-coupled receptors and intra-nuclear hormone receptors, respectively. The GPCRDB was a pilot project aimed at building a generic molecular class-specific database capable of dealing with highly heterogeneous data. A first version of the GPCRDB project has been completed and it is routinely used by thousands of scientists. The NucleaRDB was started recently as an application of the concept for the generalization of this technology. The GPCRDB is available via the WWW at http://www.gpcr.org/7tm/ and the NucleaRDB at http://www.receptors.org/NR/.

ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another

ACTIVITY is a database on DNA/RNA site sequences with known activity magnitudes, measurement systems, sequence-activity relationships under fixed experimental conditions and procedures to adapt these relationships from one measurement system to another. This database deposits information on DNA/RNA affinities to proteins and cell nuclear extracts, cutting efficiencies, gene transcription activity, mRNA translation efficiencies, mutability and other biological activities of natural sites occurring within promoters, mRNA leaders, and other regulatory regions in pro- and eukaryotic genomes, their mutant forms and synthetic analogues. Since activity magnitudes are heavily system-dependent, the current version of ACTIVITY is supplemented by three novel sub-databases: (i) SYSTEM, measurement systems; (ii) KNOWLEDGE, sequence-activity relationships under fixed experimental conditions; and (iii) CROSS_TEST, procedures adapting a relationship from one measurement system to another. These databases are useful in molecular biology, pharmacogenetics, metabolic engineering, drug design and biotechnology. The databases can be queried using SRS and are available through the Web, http://wwwmgs.bionet.nsc.ru/systems/Activity/.

rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations

rSNP_Guide is a novel curated database system for analysis of transcription factor (TF) binding to target sequences in regulatory gene regions altered by mutations. It accumulates experimental data on naturally occurring site variants in regulatory gene regions and site-directed mutations. This database system also contains the web tools for SNP analysis, i.e., active applet applying weight matrices to predict the regulatory site candidates altered by a mutation. The current version of the rSNP_Guide is supplemented by six sub-databases: (i) rSNP_DB, on DNA–protein interaction caused by mutation; (ii) SYSTEM, on experimental systems; (iii) rSNP_BIB, on citations to original publications; (iv) SAMPLES, on experimentally identified sequences of known regulatory sites; (v) MATRIX, on weight matrices of known TF sites; (vi) rSNP_Report, on characteristic examples of successful rSNP_Tools implementation. These databases are useful for the analysis of natural SNPs and site-directed mutations. The databases are available through the Web, http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/.

Enrichment of the Phenotypic and Genotypic Data Warehouse analysis using Question Answering systems to facilitate the decision making process in cereal breeding programs

Currently there are an overwhelming number of scientific publications in Life Sciences, especially in Genetics and Biotechnology. This huge amount of information is structured in corporate Data Warehouses (DW) or in Biological Databases (e.g. UniProt, RCSB Protein Data Bank, CEREALAB or GenBank), whose main drawback is its cost of updating that makes it obsolete easily. However, these Databases are the main tool for enterprises when they want to update their internal information, for example when a plant breeder enterprise needs to enrich its genetic information (internal structured Database) with recently discovered genes related to specific phenotypic traits (external unstructured data) in order to choose the desired parentals for breeding programs. In this paper, we propose to complement the internal information with external data from the Web using Question Answering (QA) techniques. We go a step further by providing a complete framework for integrating unstructured and structured information by combining traditional Databases and DW architectures with QA systems. The great advantage of our framework is that decision makers can compare instantaneously internal data with external data from competitors, thereby allowing taking quick strategic decisions based on richer data.

An authoring tool for decision support systems in context questions of ecological knowledge

Decision support systems (DSS) support business or organizational decision-making activities, which require the access to information that is internally stored in databases or data warehouses, and externally in the Web accessed by Information Retrieval (IR) or Question Answering (QA) systems. Graphical interfaces to query these sources of information ease to constrain dynamically query formulation based on user selections, but they present a lack of flexibility in query formulation, since the expressivity power is reduced to the user interface design. Natural language interfaces (NLI) are expected as the optimal solution. However, especially for non-expert users, a real natural communication is the most difficult to realize effectively. In this paper, we propose an NLI that improves the interaction between the user and the DSS by means of referencing previous questions or their answers (i.e. anaphora such as the pronoun reference in “What traits are affected by them?”), or by eliding parts of the question (i.e. ellipsis such as “And to glume colour?” after the question “Tell me the QTLs related to awn colour in wheat”). Moreover, in order to overcome one of the main problems of NLIs about the difficulty to adapt an NLI to a new domain, our proposal is based on ontologies that are obtained semi-automatically from a framework that allows the integration of internal and external, structured and unstructured information. Therefore, our proposal can interface with databases, data warehouses, QA and IR systems. Because of the high NL ambiguity of the resolution process, our proposal is presented as an authoring tool that helps the user to query efficiently in natural language. Finally, our proposal is tested on a DSS case scenario about Biotechnology and Agriculture, whose knowledge base is the CEREALAB database as internal structured data, and the Web (e.g. PubMed) as external unstructured information.

Global database of surface ocean particulate organic carbon export fluxes diagnosed from the 234Th technique

Through the processes of the biological pump, carbon is exported to the deep ocean in the form of dissolved and particulate organic matter. There are several ways by which downward export fluxes can be estimated. The great attraction of the 234Th technique is that its fundamental operation allows a downward flux rate to be determined from a single water column profile of thorium coupled to an estimate of POC/234Th ratio in sinking matter. We present a database of 723 estimates of organic carbon export from the surface ocean derived from the 234Th technique. Data were collected from tables in papers published between 1985 and 2013 only. We also present sampling dates, publication dates and sampling areas. Most of the open ocean Longhurst provinces are represented by several measurements. However, the Western Pacific, the Atlantic Arctic, South Pacific and the South Indian Ocean are not well represented. There is a variety of integration depths ranging from surface to 220m. Globally the fluxes ranged from -22 to 125 mmol of C/m**2/d. We believe that this database is important for providing new global estimate of the magnitude of the biological carbon pump.

ICR water utility database system users' guide /

"EPA 814/B-96-004."

A survey of eleven government-developed data element dictionary/directory systems /

Mode of access: Internet.

The NTIS database on ORBIT : a search guide.

"PR-830"--P. [4] of cover.

The NTIS database on BRS : a search guide.

Mode of access: Internet.

Database and datafile resource guide.

Description based on: May 1990.

Database evaluation, quality of care, and utilization review : Task Force report to the Council.

Cover title.

Enhancement of the HWRIC database : year 2 : with an evaluation of database content /

Prepared for Illinois Hazardous Waste Research and Information Center, HWRIC project number 87-005.

Hearing to review the U.S. Department of Agriculture's release of program beneficiaries' social security numbers and the department's information systems, generally : hearing before the Committee on Agriculture, House of Representatives, One Hundred Tenth Congress, first session, May 2, 2007.

Shipping list no.: 2009-0305-P.

Technical profile of seven data element dictionary/directory systems /

Includes bibliographical references (p. 33-38).