web2express.org

Content

Current research publishing/communication model: After doing a series of experiments, researchers usually write up a paper to present the findings, interesting results backed by data. Research papers serve as the main communication vehicle within as well as outside the research community. In addition, researchers present their findings in various conferences. Papers and conference talks are typically published in journals, proceedings, and books in print form and/or in electronic form.

The current scientific publishing model has worked pretty well for centuries. However, it also has obvious problems. This first main problem is lack of free access, i.e. access to the published materials is mostly limited to paid-users. This problem is being addressed by the Open Access movement.

The second main problem with current publishing model is that publishing research paper is not an efficient way to share data. There are several reasons for this:

1. Because a research paper usually is a complex synthesis of many experimental facts and interpretations of the facts, it is not an easy task for human, never mind computer, to sort out the individual facts.
2. Most of experiment data are not included in publication and thus remain inaccessible to the research community. For the experiment data used in research paper, typically little detail is given.
3. Long delay of data availability. Usually, the data already becomes several months to a couple of years old when the research paper comes out.

These inefficiencies really hamper data sharing and information discovery. So, new ways of publishing are needed in order to increase the efficiency of sharing research information. I think direct publishing of experiment data on the web presents a good solution. Imaging for a moment that information about every experiment is available at your finger tips, organized by single experiment unit, would that make your search of prior studies in terms of experiments, data, and results much faster and precise? What if every researcher makes their experiment data available in real time or immediately after the experiments are completed? Would that make your research also go faster? The answers are certainly yes, I believe. This is why publishing experiment data makes absolute sense.

You may as why it was not done before? There could be many reasons that require clear understanding. One main reason could be pure economics. Before Internet age, publishing means printing and traditional distribution, which is very costly business. The volume of the experiment data is so huge that no publisher would consider publishing every piece of experiment data a sound business.

Well, what’s different today? Today is a very different environment from 15 years ago. For one thing, Internet technologies and web economy has made the cost of web publishing and distribution almost disappear. Therefore, publishing all experiment data on the web becomes a viable idea now. The benefits of being able to search through every experiment data on the planet efficiently and the potential to accelerate scientific discovery is so high that, I think, this idea is going to become reality in the near future. In fact, data sharing in life sciences has been a very active research subject in recent years. Some good examples include MGET, GO, FUGO, BIOPAX, etc. These projects are developing ontologies for representing data in their specific scientific domains.

Experiment data can be represented at different levels of granularity. Web2express.org is approaching the data sharing problem from the opposite end of the spectrum comparing to the bioscience projects like MGET. It’s developing shallow ontology to represent data across all scientific fields, such as life sciences, computer, social science, etc. Early version (v0.2) of SPE ontology for self-publishing of experiments is being reviewed within W3C HCLS interest group, and demo publishing tool is available online for testing and download.

Subject

Open data, semantic publishing, ontology, SPE, semantic web

Category

Internet software

Author

AJ Chen

Content

Web2x is a new platform for publishing and search content on web2 – the second generation of web consisting of web documents and semantic data. I released the demo for the Web2x publishing software last month. And now, the Web2x search engine is online as a demo. You can check how it searches web documents as well as semantic data on the same site.

Go to Web2x search engine demo, and try search term “semantic web”. Since it is demo only, its current content has web pages and semantic data only from web2express.org.

Web2x platform can potentially bring a new leveled playing field to everyone in the R&D community, including researchers as well as companies providing R&D tools. Researchers can use the free web2x publishing software to self-publish research data to the web in HTML and RDF format at the same time. Current software implements the SPE ontology for self-publishing of experiments. Web2x search engine will crawl web sites that are powered by the web2x publishing software and make the web documents as well as semantic data available for search.

Subject

search engine, semantic search, semantic publishing, semantic web, open data

Category

internet service

Author

AJ Chen

Contact Person

AJ Chen (ajchen AT web2express.org)

Subject

open data, web publishing, semantic publishing, semantic web, BOON, SPE

Product Category

Internet Software

Catalog Number

web2×0001

Model

open source

Version

0.2

Short Description

Web2x Publishing software is an easy-to-use self-publishing platform for publishing information to the current HTML web layer as well as the emerging semantic web layer. It is built on top of the popular open source blogger software called WordPress. Using Web2x Publishing, users can publish specific types of information such as product and experiment in HTML and in RDF at the same time. Information published this way will be searchable by both regular and semantic search engines, and thus will become more widely accessible. Web2x implements ontologies for semantic publishing that are being developed by open communities such as W3C.

Specifications

Current Features
1. Add a semantic dimension to existing company web site. One can publish all the usual web pages in semantic data format, including products, services, licensing opportunity, technology, news, events, and company information.
2. Semantically publish any experiment and related information by writing specific types of posts and pages, including Experiment, Project, Protocol, Publication.
3. Automatically pre-fill the editor with template corresponding to the semantic post or page.
4. Automatically save semantic post and page to RDF file. As a result, each specific post or page is presented in two forms: HTML and RDF.
5. Provide RDF link on each HTML page for the published semantic data.
6. Create a site map, which is dynamically generated each time when the page is viewed and thus always up-to-date.
7. Create product catalog page listing all products.

Web2x is built on top of WordPress, which has many useful features, including:

1. Organize published information in categories, and archive information by month and day.
2. Allow readers to provide comments to the published information, an effective way to interact with everyone in the community.
3. User account and privilege control.
4. Hundreds of themes to choose from.
5. Optimized for search engines.
6. RSS feed available.

Key Technology

Implements BOON ontology and SPE ontology. Represents web information in both HTML and RDF.

Applications

Intended Users:

Researchers: Any researcher or laboratory doing research and development can use this self-publishing tool to publish individual experiments, projects, protocols, and researcher information as web pages and semantic data objects (RDF file).

Product providers: Any product providers, either manufacturers or distributors, can use this self-publishing tool to publish their web site information, particularly product catalog, as web pages and semantic objects.

User Benefits:

For researchers:
• Unlock your most precious assets – experiment data. Traditionally, you publish your research results and selected data as papers in research journals. This process leaves out most of your experiment data. Even for the data published in papers, they most likely are not available for search through popular free search engines because papers’ full-texts are kept behind wall by publishers. Such traditional publishing model provides public exposure to only a tiny portion of your research information. Now, web2x self-publishing platform empowers you to share your research information with the world quick and easy, fully unlocking the values of your most precious assets.
• Maximize your visibility. The experiment information published by this tool becomes immediately available on the web in both HTML and RDF forms. This means your work will be accessible to not only regular search engines like Google and Yahoo but also semantic web search engines, which will increase your visibility.
• Better data sharing and searching. Experiment information published in RDF enables much more effective search based on semantics. Web2x implements ontologies developed by open communities like W3C and thus ensure your data can be shared and discovered by the largest number of people as well as applications.
• Open new doors for collaboration. Since your published data will be in semantic format, they can be accurately cross-referenced and integrated. Other people may discover one or more of your experiments can be re-used in their studies, which will bring to you unexpected opportunities for collaboration.
• Publish and share your data at your own pace. Web2x is built on popular blogger software WordPress, which is designed to be installed on your web server in a few simple steps. With the publishing tool under your control, you can publish whenever you want and own whatever you publish.

For product providers:
• Optimize search engine marketing by leveraging the semantic web. Web2x publishes your product information on the web in both html and RDF formats. Not only regular search engines but also semantic web search engines will be able to find your products.
• Maximally expose your products. By publishing all your products with Web2x, your products are no longer locked in the database.
• Bring your products much closer to your customers. Your products published by Web2x will be given unique identifiers called URI. With these URIs available, your customers will be able to precisely identify the reagents and tools used in their experiments when they publish the experiments using Web2x.

User Manual

User Manual Link

http://web2express.org/openlab/docs/web2x-publishing.html

Image Link

References

Manufacturer

web2express.org

Distributor

Price (amount)

free

Price (currency)

Promotion

Launch Date

10 /19/2006

Alternative Web Page

Content

The semantic web publishing tool – Wex2x uses ontologies for business objects (BOON) and experiment data (SPE). BOON’s specification is now available here for community comment. Everyone is welcome to make comments or participate in refining the ontology. The SPE ontology is reviewed under the W3C HCLS Scientific Publishing Task. These ontologies re-use many terms from Dublin Core vocabulary. One may use BOON and SPE ontologies to implement complete semantic web site for better data sharing and search engine optimization. Alternatively, download the open source web2x software here and start to benefit from the semantic web right away. See Demo.

Subject

semantic web, ontology, Boon, web publishing, open data

Category

Internet

Author

AJ Chen

Contact Person

AJ CHen

Content

A new set of semantic objects are added to the Web2x Semantic Publishing tool for organizations to create a semantic dimension to their web site and online catalogs. Now, any organization can easily use this tool to publish product information and business related information as web page and RDF file at the same time. This new version (v0.2) supports the information types that normally are the core of any organization web site, including product, service, licensing, technology, job, news and events.

The emerging semantic web search engines offer more precise search of information that are represented in semantic format. To businesses, this newly available semantic layer within the current web can become new sources of traffics to their web sites. And it only requires a small effort to wrap a company’s existing web site in semantic format. A very large site may take a little bit more time, but the process should be easy to manage using the web2x semantic publishing tool.

Demo is available. Try it to see how easy to create a semantic web page for product and product catalog.

For administration features, you would need to download and install the software on your own server.

The software is developed as open source software and free to everyone. Developers are welcome to participate in the open source development.

Enjoy the ride of the rising semantic web wave.

Subject

semantic publishing, web site, semantic web

Category

Software, Internet

Author

AJ Chen

Contact Person

AJ Chen (ajchen AT web2express.org)