web2express.org

[::Subject::]

Scientific publishing, semantic web, ontology, experiment publishing, web publishing

[::Objectives::]

To develop a general purpose ontology for self-publishing single experiment in RDF format that will facilitate data sharing, discovery and integration. Applications such as web-publishing tool and semantic search engine that are built on top of this ontology will demonstrate the emerging semantic standards and technologies can help developing more interactive scientific communities centered around user-generated scientific contents on the web.

[::Design::]

Today, scientific research data and results are shared primarily through publishing paper. A paper is usually composed of many experiments. While it’s an important form of knowledge representation and sharing, scientific paper is far from an ideal form for finding and sharing experiment data. One can easily imagine how many new possibilities will open up if most of research data are available on the web as units of single experiment, which can be searched by everyone and consumed by computers. Of course, the challenge is how to get the scientific community to publish experiment data on the web in an appropriate format.

 

We should realize that scale is critical in establishing a new paradigm. In order to encourage large scale participation from everyone in the scientific community, two requirements are placed on the ontology to be developed here: (1) the terms should be as general as possible so that researchers across all disciplines can use the ontology; and (2) the ontology should facilitate development of easy-to-use self-publishing tools that everyone will like to use.

Note that there are some domain-specific ontologies, such as microarray experiment ontology, already existed today. However, the scope of the current task is broader than any of these. In fact, the ontology to be developed here will not be specific to any research domain.

Use Cases:

1. Any researcher can publish his or her experiment data as single unit of experiment in RDF format using this ontology. Ideally, a new easy-to-use self-publishing tool specifically designed for such purpose will encourage the use of the ontology. However, any ontology editor can be used to create RDF content. Because data in such format can be searched by semantic web search engine, it offers a new channel for data sharing and retrieval that will accelerate scientific discovery as well as increase the researcher’s visibility.
2. Anyone can search for all experiments available on the web at various property levels. This use case requires a search engine that aggregates published experiment data in RDF format. Compared to traditional literature search, this semantic web search engine will provide much more relevant information.

Development process:

1. Define requirements for representing experiment and related information.
2. Define specifications for ontology that will be used for self-publishing experiment (SPE).
3. Create SPE ontology file in owl or rdf.

[::Resources::]

RDF/XML
http://www.w3.org/TR/rdf-syntax-grammar/

RDFS
http://www.w3.org/TR/rdf-schema/

OWL
http://www.w3.org/TR/owl-ref/

XML
http://www.w3.org/TR/xmlschema-1/
http://www.w3.org/TR/2001/REC-xmlschema-2-20010502/

DC
http://dublincore.org/documents/dcmi-terms/
http://purl.org/dc/elements/1.1/
http://purl.org/dc/terms/

FOAF ontology:
http://xmlns.com/foaf/0.1/

vCard:
http://www.w3.org/TR/vcard-rdf

SUMO
http://ontology.teknowledge.com/

SKOS Core Vocabulary
http://www.w3.org/TR/swbp-skos-core-spec/

Ebiquity ontologies including project, publication, person, and contact
http://ebiquity.umbc.edu/ontology/

DOAP
http://usefulinc.com/doap

FuGO
http://fugo.sourceforge.net/ontologyInfo/ontology.php

BOSS
http://www.charlestoncore.org/ont/boss.html

EXPO
http://sourceforge.net/projects/expo

[::Start Time::]

5/8/2006

[::End Time::]

[::Status::]

In progress

[::Owner::]

AJ Chen

[::Project Lead::]

[::Current Members::]

[::Past Members::]

[::References::]

[::Publications::]

[::Funding Sources::]

[::Alternative Web Page::]

http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce

[::Rights::]

[::Subject::]

web publishing, semantic web, RDF, self-publishing experiment, semantic publishing

[::Objectives::]

To develop a easy-to-use web publishing tool for self-publishing experiment and related information as semantic data model.

[::Design::]

Requirements:

1. web application for one-click publishing to the web
2. for user to self-publish information on experiment and research tools as HTML web page and RDF file, implementing the SPE ontology.
3. allows interaction with readers of the published content, such as commenting by user
4. has basic content management features for organizing, archiving and searching published content.
5. easy to install and maintain by user

Open source development:

The developed software product is intended to be used by anyone for free. I expect that I can create the initial version with basic features. But, it will require more resources, possibly 2-3 developers to implement other necessary features for the first major release. I think this is a perfect project for open source development. So, I’ll create a open source project at sourceforge.org, deposite the initial code, and call for developers to contribute to the project.

Deliverbles:

Software release for free download, source code for check out, user documentation, developer documentation.

[::Resources::]

[::Start Time::]

5/1/2006

[::End Time::]

[::Status::]

In progress

[::Owner::]

AJ Chen

[::Project Lead::]

[::Current Members::]

[::Past Members::]

[::References::]

[::Publications::]

[::Funding Sources::]

None

[::Alternative Web Page::]

[::Rights::]