WikiPathways: Community Curation of Biological Pathways

Assembling biological pathways from information in scientific literature and biological databases is a challenging task. Building a pathway requires domain knowledge from specialists in various biological research areas. Furthermore, research is generating new biological knowledge continuously, making pathway curation an ongoing and dynamic process. To facilitate this process we developed "WikiPathways":http://www.wikipathways.org/index.php/WikiPathways ^1^, a wiki where users can curate pathways, using an easy to use pathway drawing tool. WikiPathways currently has over 1200 registered users and contains more than 1300 pathways for various organisms, spanning human, mouse, zebrafish, fruit fly, worm, yeast, plants and bacteria. WikiPathways is entering a phase of rapid growth, incorporating new pathway resources and engaging diverse communities with unique pathway needs.

In this presentation we will provide an overview of the background, current state, and future of WikiPathways. We will highlight several approaches we take to improve community-based curation with WikiPathways. And we will provide context for this project within the larger shifts toward data sharing, data curation and new models for publication.
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RCK Domain Model of Calcium Activation in BK Channels

Potassium ion channels are ubiquitously expressed from bacteria to mammals where they are involved in various processes ranging from the regulation of osmotic pressure in a single cell to the electrical response in muscle fibers to the generation of action potentials in neurons. The B K channel family (BK for Big K+ conductance) is an interesting subfamily of K+ channels responsive to both membrane voltage and intracellular calcium ion. The unique, high-affinity Ca2+ sensitivity of B K channels is critical to their physiological function in various cell types. The mechanism by which Ca2+ activates B K channel gating, however, is not well understood. Here we present a structure-based approach to the study of B K channels with the goal of providing a structural and functional model of the Ca2+-activation mechanism. Sequence analysis of BK channel C-terminal domains and domains from prokaryotic homologs reveals the conservation of unique positions defining a novel regulatory domain associated with K conduction, the R C K domain. Crystal structures of R C K domains from prokaryotic sources relate the conservation of sequence to the structure, assembly and function of these domains. W e propose a hypothetical model for the structure and function of the Cterminal domains of B K as a set of R C K domains that conduct the Ca -activation mechanism. The features and constraints predicted by the R C K domain model are tested by the electrophysiological assay of a variety of human B K constructs. The results support a domain structure and assembly consistent with the proposed model for the B K C-terminus. In addition, the results identify residues and regions involved in Ca + activation: the Ca2+-binding event and the transduction of the binding energy through protein conformational changes to the channel domain. The R C K domain model thus provides a framework for the study of Ca2+ activation in B K channels

WikiPathways: Community Curation of Biological Pathways

Assembling biological pathways from information in scientific literature and biological databases is a challenging task. Building a pathway requires domain knowledge from specialists in various biological research areas. Furthermore, research is generating new biological knowledge continuously, making pathway curation an ongoing and dynamic process. To facilitate this process we developed "WikiPathways":http://www.wikipathways.org ^1^, a wiki where users can curate pathways, using an easy to use pathway drawing tool. WikiPathways currently has over 1200 registered users and contains more than 1300 pathways for various organisms, spanning human, mouse, zebrafish, fruit fly, worm, yeast, plants and bacteria. WikiPathways is entering a phase of rapid growth, incorporating new pathway resources and engaging diverse communities with unique pathway needs.

In this presentation we will provide an overview of the background, current state, and future of WikiPathways. We will highlight several approaches we take to improve community-based curation with WikiPathways. And we will provide context for this project within the larger shifts toward data sharing, data curation and new models for publication.
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Proteomic analysis of heart failure hospitalization among patients with chronic kidney disease: The Heart and Soul Study.

BACKGROUND:Patients with chronic kidney disease (CKD) are at increased risk for heart failure (HF). We aimed to investigate differences in proteins associated with HF hospitalizations among patients with and without CKD in the Heart and Soul Study. METHODS AND RESULTS:We measured 1068 unique plasma proteins from baseline samples of 974 participants in The Heart and Soul Study who were followed for HF hospitalization over a median of 7 years. We sequentially applied forest regression and Cox survival analyses to select prognostic proteins. Among participants with CKD, four proteins were associated with HF at Bonferroni-level significance (p<2.5x10(-4)): Angiopoietin-2 (HR[95%CI] 1.45[1.33, 1.59]), Spondin-1 (HR[95%CI] 1.13 [1.06, 1.20]), tartrate-resistant acid phosphatase type 5 (HR[95%CI] 0.65[0.53, 0.78]) and neurogenis locus notch homolog protein 1 (NOTCH1) (HR[95%CI] 0.67[0.55, 0.80]). These associations persisted at p<0.01 after adjustment for age, estimated glomerular filtration and history of HF. CKD was a significant interaction term in the associations of NOTCH1 and Spondin-1 with HF. Pathway analysis showed a trend for higher representation of the Cardiac Hypertrophy and Complement/Coagulation pathways among proteins prognostic of HF in the CKD sub-group. CONCLUSIONS:These results suggest that markers of heart failure differ between patients with and without CKD. Further research is needed to validate novel markers in cohorts of patients with CKD and adjudicated HF events

Diagnóstico y optimización de la planta de tratamiento de agua potable del municipio de Apulo en el departamento de Cundinamarca

Trabajo de InvestigaciónEl presente proyecto está basado en la evaluación y optimización de la planta de tratamiento de agua potable del municipio de Apulo, con el fin de mejorar la calidad de agua y calidad de vida de los habitantes del municipio, con base al diagnóstico se establecen algunas recomendaciones de optimización, con el objetivo de que sean utilizadas por la empresa Empoapulo .INTRODUCCIÓN 1. INFORMACION GENERAL DEL MUNICIPIO, FUENTE HIDRICA Y PTAP DE APULO 2. DIAGNOSTICO ESTRUCTURAS EXISTENTES 3. OPTIMIZACION DE TRATAMIENTO DE AGUA POTABLE DEL MUNICIPIO DE APULO 3. CONCLUSIONES 4. RECOMENDACIONES BIBLIOGRAFÍA ANEXOSPregradoIngeniero Civi

Perturbaciones generadas en el sistema por generación Eólica

In the present work, the wind generation system and its difficulty to stabilize the electrical system were analyzed, due to the uncertainty of the primary resource (wind), its acquisition occurs in places of difficult access, due to priority conditions for its correct performance as : speed and stability of the fluid, for which a robust infrastructure, both external and internal, is essential to be able to capture and transport electrical energy, knowing that the wind is a variable resource which can destabilize the parameters of the Electrical Power System (SEP), the aforementioned system uses power electronics, which injects harmonics, which can cause distortion in the frequency wave and voltage fluctuations, methods are determined to reduce these disturbances so that they do not affect the quality of the product using simulation programs, thus maintaining energy quality standards in the Electric Power System (SEP).En el presente trabajo se analizó el sistema de generación eólica y su dificultad para estabilización del sistema eléctrico, debido a la incertidumbre del recurso primario (viento), su adquisición se dan en sitios de difícil acceso, debido a condiciones prioritarias para su correcto desempeño como: velocidad y estabilidad de fluido, por lo cual es indispensable una infraestructura robusta tanto externa como interna para poder captar y transportar la energía eléctrica, a sabiendas que el viento es un recurso variable el cual puede llegar a desestabilizar los parámetros del Sistema Eléctrico de Potencia (SEP), el mencionado sistema utiliza electrónica de potencia, la cual inyecta armónicos, que puede provocar distorsión en la onda de frecuencia y fluctuaciones en el voltaje, se determina métodos que permitan reducir estas perturbaciones para que no afecten a la calidad del producto utilizando programas de simulación, manteniendo de esta forma estándares de calidad de energía en el sistema Eléctrico de Potencia (SEP)

Factores limitantes al sistema de referencia y contrarreferencia en el área de estomatología de una institución pública de Ecuador, 2022

Este estudio tuvo como objetivo determinar la asociación de los factores limitantes y el sistema de referencia-contrarreferencia en el área de estomatología de una institución pública. Fue una investigación con enfoque cuantitativo, con finalidad básica y alcance comparativo, con diseño no experimental y tipo transversal, se encuestó 146 odontólogos y analizó 146 referencias. Se encontró que si existe relación entre el sistema de referencia-contrarreferencia y los factores transferencia de exámenes, responsable de referencia y contrarreferencia; los factores limitantes como la comunicación es importante al momento de la transferencia de información y el conocimiento para poder utilizar de manera ordena y correcta el sistema de referencia-contrarreferencia; las referencias que se analizaron demostraron que su nivel es regular en el sistema y que la mayor cantidad de referencias está siendo mal direccionada a los especialistas; Al comparar el sistema con los factores se puede observar la baja calidad de referencias debido a poco conocimiento y comunicación regular. Se concluyó asociación entre los factores limitantes y el sistema de referencia y contrarreferencia esto puede haría que el sistema tenga un mal funcionamiento

WikiPathways: building research communities on biological pathways.

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further

From Scientific Discovery to Cures: Bright Stars within a Galaxy

We propose that data mining and network analysis utilizing public databases can identify and quantify relationships between scientific discoveries and major advances in medicine (cures). Further development of such approaches could help to increase public understanding and governmental support for life science research and could enhance decision making in the quest for cures

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