ens (human)" refers to the name of the pathway.
+ GetPathwayInteractions: Returns all interactions within a pathway of a database. Passing in the ID of the pathway, the API will return all the interactions within the pathway. http://www.pathwayapi.com/api/API_GetPathwayInteractions.php?Pathway = 7 will result in [["231","AKR1B1","2584","GALK1","Activate"],["231","AKR1B1","2585","GALK2","Activate"]] In the example above: "231" and "2584" refers to the IDs of the gene pair "AKR1B1" and "GALK1" refers to the corresponding genes of the ID.
This gives the following results where: [["AKR1B1","G6PC","GAA","GALE","GALK1"], ["ALDH2","ALDH3A1"], ["AKR1B1_GALK1","AKR1B1_GALK2","AKR1B1_GLA"],[]] Where ["AKR1B1","G6PC","GAA","GALE","GALK1"] refers to the genes within pathway 7 not in pathway 8.
["ALDH2","ALDH3A1"] refers to the genes within pathway 8 not in pathway 7.
["AKR1B1_GALK1","AKR1B1_GALK2","AKR1B1_GLA"] refers to the gene interactions within pathway 7 not in pathway 8.
[] refers to the gene interactions within pathway 8 not in pathway 7. This set is empty because all interactions in pathway 8 are in pathway 7.
It is widely accepted that analyzing microarray experiments with biological information provides biological inferences of a greater detail. Examples of such analysis are [22–24].
However, such techniques run into issues if the data source used is not consistent or comprehensive. For example, using the same technique on a different database yields a differing analysis result.
Faced with such an issue, the solution is to integrate biological information across different data sources to obtain a more wholesome analysis. Yet the incompatibility of the different data sources renders this option extremely challenging.
Furthermore, we investigated and discovered low levels of consistency, comprehensiveness and compatibility among three popular pathway databases (KEGG, Ingenuity and Wikipathways).
However we understand the limitations faced by such systems. For instance, in the event that two databases provide conflicting definitions of the same pathway, both pieces of conflicting definitions will be included within the pathway information itself. The integrated database is also more comprehensive because it is the union of the data sources. Every gene/edge in any of the three data sources is also in the integrated database. Furthermore, the integrated database is equipped with a API to allow the user to conveniently identify inconsistencies and to resolve them in accordance to his specific application needs. To ensure fast responsiveness, API connections are made towards a central unified database which keeps a cached copy of the records of the other databases. To make certain that the cached entries are always kept up to date, entries from the cache are flushed periodically and automatically updated again for the reference databases wikipathways and KEGG. As data from Ingenuity is obtained in a manual fashion, updates from Ingenuity can only be achieved laboriously by curators importing new data physically from Ingenuity. Note that data from Ingenuity will not be released.
There are many efforts on the aggregation of pathways data (like Reactome [25], PathCase [26, 27] and MappFinder [28]). There are also many tools to explore, edit and export biological pathways (such as GenMapp [29], BioCyc [30], PathVisio [31], Cytoscape [32]).
However manipulation of pathways in these earlier works still relies heavily on human intervention with little provision for programming interfaces. Indeed projects like Cytoscape and Pathcase have very sophisticated GUI visualization tools to help researchers manipulate pathways. Such visualization tools are impractical when you are required to analyze thousands of genes across hundreds of pathways for each microarray experiment. The nearest to a programming interface was the provision of a AQI (Application Query Interface) [26] where users can recall predefined queries using a web interface. Yet the scope of such queries remains limited and insufficient.
Two of the projects that are similar to this work are Pathway Commons [33] and BioWarehouse [34]. BioWarehouse is an open-source software environment and is often used for integrating a set of biological databases into a single physical database management system for data management, mining, and exploration. They are able to do so by first deciding on a standard database schema and having database loaders to import certain pathway database formats (eg BioPax) into their environment. Being more of a software environment, they act more as a tool to give researchers a easy way to merge data whereas we focus on allowing researchers easy access to the data and on analysing the completeness and consistency of the data. PathwayCommons is an aggregated pathway database as well. Most of the databases they host support the BioPax data format. However they do not host any of the three databases that we aggregate. Thus our unified database and API are very much complementary to the contributions Pathway Commons has done.
One issue we have with most data aggregators is their lack of explanation on how their data is kept updated. For instance, little mention is made on how the aggregated data is updated from the various repositories. In fact this issue is acknowledged in [26]. Here we set an expiry date for every data entry and once it expires, automated scripts are fired off to extract data from the data sources and populate them within our database cache.
Our final point deals with the aggregator's inaction to develop integrated pathway data from their diverse data sources. By standardizing gene references and key features within pathways, we have the ability to integrate similar pathways together. As a result our integrated pathways are more comprehensive. Contrasting to prior available methods, researchers can easily use our API to obtain data for each pathway either from the integrated database or from a specific database of their choice. This gives researchers a straightforward mechanism for incorporating pathway information into their microarray analysis.
The database is available at http://www.pathwayapi.com. Data from the sources can be accessed via the API as described. In addition, the data will be available for download as a CSV or SQL file. The database schema and instructions on their usage are stated in the downloaded file. All information will be provided free of charge. Information from Ingenuity will however not be released as it is proprietary (unless the requester has a valid subscription to Ingenuity). The latest number of pathways in each database are shown in Figure 9 while Figure 10 shows the distribution of pathway sizes in terms of genes and gene pairs. The recommended requirements are: 1 Mbps internet connection, 1GHz Processor, 512MB Memory.
Number of pathways in each database. The number of pathways in each database.
Nurseitov N, Paulson M, Reynolds R, Izurieta C: Comparison of JSON and XML Data Interchange Formats: A Case Study. CAINE 2009, 157–162.
Karp PD, Lee TJ, Wagner V: BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats. DILS 2008, 5–7.
Correspondence to Donny Soh.
DS developed the software and database. DD provided the data from Ingenuity and pathway analysis. DS and LW wrote the manuscript. All authors contributed to design of analytical algorithms. All authors read and approved the final manuscript. This research is supported in part by an A*STAR AIP scholarship (DS), a A*STAR grant SERC |||PHONE_NUMBER|||  (LW, DD).
IN: French:

One country replied that a home page designed for public dissemination were likely to be considered as available to the public even if it was not locatable by any search engine.
OUT: Un pays a répondu qu’une page d’accueil conçue pour la diffusion publique sera normalement considérée comme étant à la disposition du public même si elle n’est localisable par aucun moteur de recherche.
IN: French:

Figure 2 - Greenhouse Ornamental Flower and Plant Sales in Canada, 2004 In 2004, the main varieties of cut flowers produced in Canada were tulips, followed by roses and gerbera.
OUT: Figure 2 - Ventes de fleurs et de plantes ornementales de serre au Canada, 2004 En 2004, les principales variétés de fleurs coupées au Canada étaient les tulipes, suivi des roses et des gerberas.
IN: French:

Overview of the ITC's subsidiary bodies
OUT: V. EXAMEN DES TRAVAUX DES ORGANES SUBSIDIAIRES DU COMITÉ
IN: French:

Valentino's driving style has changed a lot since he switched to Yamaha, he is focusing more on precision.
OUT:
Le style de pilotage de Valentino a beaucoup changé depuis qu'il a rejoint Yamaha, il se concentre davantage sur la précision.IMO (not that it matters), the problem with "Thor: The Dark World" is that Marvel hadn't quite figured out the formula just yet.

It was trying to be all things to all people, with a universe-ending villain, and yet also endless quips and comedy (Darcy saying'meow meow') that threw it off the rails.

Then - through endless market research and audience tests - Marvel figured out that the