BridgeDb: standardized access to gene, protein and metabolite identifier mapping services

Many interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.

Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. BridgeDb provides such an interface layer, in the form of both a Java and REST API.

Because of the standardized interface layer, BridgeDb is not tied to a specific source of mapping information. You can switch easily between flat files, relational databases and several different web services. Mapping services can be combined to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb isn't just yet another mapping service: it tries to build further on existing work, and integrate multiple partial solutions. The framework is intended for customization and adaptation to any identifier mapping service. 

BridgeDb makes it easy to add an important capability to existing tools. BridgeDb has already been integrated into several popular bioinformatics applications, such as Cytoscape, WikiPathways, PathVisio, Vanted and Taverna. To encourage tool developers to start using BridgeDb, we've created code examples, online documentation, and a mailinglist to ask questions. 

We believe that, to meet the challenges that are encountered in bioinformatics today, the software development process should follow a few essential principles: user friendliness, code reuse, modularity and open source. BridgeDb adheres to these principles, and can serve as a useful model for others to follow. BridgeDb can function to increase user-friendliness of graphical applications. It re-uses work from other projects such as BioMart and MIRIAM. BridgeDb consists of several small modules, integrated through a common interface (API). Components of BridgeDb can be left out or replaced, for maximum flexibility. BridgeDb was open source from the very beginning of the project. The philosophy of open source is closely aligned to academic values, of building on top of the work of giants. 

Many interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.

Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. BridgeDb provides such an interface layer, in the form of both a Java and REST API.

Because of the standardized interface layer, BridgeDb is not tied to a specific source of mapping information. You can switch easily between flat files, relational databases and several different web services. Mapping services can be combined to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb isn't just yet another mapping service: it tries to build further on existing work, and integrate multiple partial solutions. The framework is intended for customization and adaptation to any identifier mapping service. 

BridgeDb makes it easy to add an important capability to existing tools. BridgeDb has already been integrated into several popular bioinformatics applications, such as Cytoscape, WikiPathways, PathVisio, Vanted and Taverna. To encourage tool developers to start using BridgeDb, we've created code examples, online documentation, and a mailinglist to ask questions. 

We believe that, to meet the challenges that are encountered in bioinformatics today, the software development process should follow a few essential principles: user friendliness, code reuse, modularity and open source. BridgeDb adheres to these principles, and can serve as a useful model for others to follow. BridgeDb can function to increase user-friendliness of graphical applications. It re-uses work from other projects such as BioMart and MIRIAM. BridgeDb consists of several small modules, integrated through a common interface (API). Components of BridgeDb can be left out or replaced, for maximum flexibility. BridgeDb was open source from the very beginning of the project. The philosophy of open source is closely aligned to academic values, of building on top of the work of giants. 

The BridgeDb library is available at "http://www.bridgedb.org":http://www.bridgedb.org.
A paper about BridgeDb was published in BMC _Bioinformatics_, 2010 Jan 4;11(1):5.

BridgeDb blog: "http://www.helixsoft.nl/blog/?tag=bridgedb":http://www.helixsoft.nl/blog/?tag=bridged

"Cultural additivity" and how the values and norms of Confucianism, Buddhism, and Taoism co-exist, interact, and influence Vietnamese society: A Bayesian analysis of long-standing folktales, using R and Stan

Every year, the Vietnamese people reportedly burned about 50,000 tons of joss papers, which took the form of not only bank notes, but iPhones, cars, clothes, even housekeepers, in hope of pleasing the dead. The practice was mistakenly attributed to traditional Buddhist teachings but originated in fact from China, which most Vietnamese were not aware of. In other aspects of life, there were many similar examples of Vietnamese so ready and comfortable with adding new norms, values, and beliefs, even contradictory ones, to their culture. This phenomenon, dubbed "cultural additivity", prompted us to study the co-existence, interaction, and influences among core values and norms of the Three Teachings--Confucianism, Buddhism, and Taoism--as shown through Vietnamese folktales. By applying Bayesian logistic regression, we evaluated the possibility of whether the key message of a story was dominated by a religion (dependent variables), as affected by the appearance of values and anti-values pertaining to the Three Teachings in the story (independent variables).Comment: 8 figures, 35 page

Constraints on the high-density nuclear equation of state from the phenomenology of compact stars and heavy-ion collisions

A new scheme for testing nuclear matter equations of state (EsoS) at high densities using constraints from neutron star phenomenology and a flow data analysis of heavy-ion collisions is suggested. An acceptable EoS shall not allow the direct Urca process to occur in neutron stars with masses below $1.5~M_{\odot}$, and also shall not contradict flow and kaon production data of heavy-ion collisions. Compact star constraints include the mass measurements of 2.1 +/- 0.2 M_sun (1 sigma level) for PSR J0751+1807, of 2.0 +/- 0.1 M_sun from the innermost stable circular orbit for 4U 1636-536, the baryon mass - gravitational mass relationships from Pulsar B in J0737-3039 and the mass-radius relationships from quasiperiodic brightness oscillations in 4U 0614+09 and from the thermal emission of RX J1856-3754. This scheme is applied to a set of relativistic EsoS constrained otherwise from nuclear matter saturation properties with the result that no EoS can satisfy all constraints simultaneously, but those with density-dependent masses and coupling constants appear most promising.Comment: 15 pages, 8 figures, 5 table

Branes from a non-Abelian (2,0) tensor multiplet with 3-algebra

In this paper, we study the equations of motion for non-Abelian N=(2,0) tensor multiplets in six dimensions, which were recently proposed by Lambert and Papageorgakis. Some equations are regarded as constraint equations. We employ a loop extension of the Lorentzian three-algebra (3-algebra) and examine the equations of motion around various solutions of the constraint equations. The resultant equations take forms that allow Lagrangian descriptions. We find various (5+d)-dimensional Lagrangians and investigate the relation between them from the viewpoint of M-theory duality.Comment: 44+1 pages, reference added, typos corrected, and several discussions added; v3, reference added, many typos corrected, the language improved; v4, some typos and references corrected, final version to appear in J. Phys.

Supermassive black holes do not correlate with dark matter halos of galaxies

Supermassive black holes have been detected in all galaxies that contain bulge components when the galaxies observed were close enough so that the searches were feasible. Together with the observation that bigger black holes live in bigger bulges, this has led to the belief that black hole growth and bulge formation regulate each other. That is, black holes and bulges "coevolve". Therefore, reports of a similar correlation between black holes and the dark matter halos in which visible galaxies are embedded have profound implications. Dark matter is likely to be nonbaryonic, so these reports suggest that unknown, exotic physics controls black hole growth. Here we show - based in part on recent measurements of bulgeless galaxies - that there is almost no correlation between dark matter and parameters that measure black holes unless the galaxy also contains a bulge. We conclude that black holes do not correlate directly with dark matter. They do not correlate with galaxy disks, either. Therefore black holes coevolve only with bulges. This simplifies the puzzle of their coevolution by focusing attention on purely baryonic processes in the galaxy mergers that make bulges.Comment: 12 pages, 9 Postscript figures, 1 table; published in Nature (20 January 2011

Energetic radiation and the sulfur chemistry of protostellar envelopes: Submillimeter interferometry of AFGL 2591

CONTEXT: The chemistry in the inner few thousand AU of accreting envelopes around young stellar objects is predicted to vary greatly with far-UV and X-ray irradiation by the central star. Aim We search for molecular tracers of high-energy irradiation by the protostar in the hot inner envelope. METHODS: The Submillimeter Array (SMA) has observed the high-mass star forming region AFGL 2591 in lines of CS, SO, HCN, HCN(v2=1), and HC15N with 0.6" resolution at 350 GHz probing radial scales of 600-3500 AU for an assumed distance of 1 kpc. The SMA observations are compared with the predictions of a chemical model fitted to previous single-dish observations. RESULTS: The CS and SO main peaks are extended in space at the FWHM level, as predicted in the model assuming protostellar X-rays. However, the main peak sizes are found smaller than modeled by nearly a factor of 2. On the other hand, the lines of CS, HCN, and HC15N, but not SO and HCN(v2=1), show pedestal emissions at radii of about 3500 AU that are not predicted. All lines except SO show a secondary peak within the approaching outflow cone. A dip or null in the visibilities caused by a sharp decrease in abundance with increasing radius is not observed in CS and only tentatively in SO. CONCLUSIONS: The emission of protostellar X-rays is supported by the good fit of the modeled SO and CS amplitude visibilities including an extended main peak in CS. The broad pedestals can be interpreted by far-UV irradiation in a spherically non-symmetric geometry, possibly comprising outflow walls on scales of 3500 -- 7000 AU. The extended CS and SO main peaks suggest sulfur evaporation near the 100 K temperature radius.Comment: Astronomy and Astrophysics, in pres