Define requirements for SPE ontology
Associated Project
Ontology
Subject
Ontology, web publishing, semantic web, self-publishing experiment, open data
Introduction
Publishing information of single experiment as a unit is a simple concept. But, it’s also a complicated matter when considering the breath and depth that an experiment may have. For practical reason, it would be helpful to recognize that one ontology may not be appropriate to describe every aspect of a single experiment. Thus, we should expect multiple ontologies will be developed for this purpose of scientific publishing in the future. For now, we will tackle one problem at a time while making sure there is a consistency among the present effort and other future efforts.
An experiment can be described in general terms and/or domain-specific terms. Whether to focus on general description or domain-specific description depends on the applications that the resulted ontology is intended to augment. Ontology for self-publishing of experiment (SPE) will be focused in general description of experiment for the purpose of better data sharing and discovery on the web.
Use Cases:
- 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.
- Any tool providers (manufacturers and distributors) can publish product information using this ontology. The products include reagents, materials, instruments, and software that are used by researchers to do their experiments.
- New self-publishing tools can be developed to use the ontology for supporting researchers to self-publish experiment information on the web. Particularly, easy-to-use tools are critical to make the promise of semantic web a reality. Hopefully, an ontology with potentially large user base (all research areas instead of one specific area such as microarray) will be attractive enough to tool developers.
- New search engines can aggregate the experiment information published with the ontology and make the experiment information searchable to everyone on the web.
- Anyone can use the new search engines to find all experiments available on the web. Compared to traditional literature search like Medline, this semantic web search will find much more relevant information with much higher specificity in a much bigger scale. For examples, users can get answers to the following questions: (please add your questions here)
- What experiments have been done on this protein or gene?
- What projects are related to this protein or gene?
- Who are studying this protein or gene? Rank them by the amount of experiments done or by the number of references (i.e. hyperlinks) to their published experiments.
- What hypothesis have people proposed for this protein or gene?
- What are the conclusions people have drawn for this protein or gene?
- What tools/reagents/instrument/protocols have been used in characterize the toxicity of this compound?
Hypothesis
Procedure
I engaged in the W3C HCLS group and coordinated the scientific publishing task force to develop a community-supported ontology requirements.
- Reviewed all relevant ontologies available, and tried to reuse existing terms and objects.
- Proposed a draft requirements document and upload it to the W3C HCLS group’s wiki for group review.
- Integrated comments and feedback from the group into the requirements document.
Protocols Used
Tools Used
Data
Data Links
Result
Requirements
The ontology should not be too complicated to use. If a user feels overwhelmed by the large number of parameters required to describe an experiment, this user may hesitate to do it. So, we need to find a good balance: The ontology shoud be as simple as possible as long as it supports the intended applications.
An experiment can be described by the following objects and properties in order to support the above use cases. Note that it’s allowed to use only a subset of these objects and properties to publish any specific experiment.
Properties of Experiment object:
- URI identifier
- Associated project (A Project object)
- Name
- Description
- Hypothesis (Literal or object?)
- Experiment Procedures (A Procedure object)
- Data (Literal or object?)
- Result
- Discussion (Literal or object?)
- Experiment type or category
- Special technologies used in the experiment
- Start time
- Finish time
- Persons who did the experiment
- Related resources
- Related publications
- Homepage
Properties of Project object:
- URI identifier
- Name
- Description
- Category
- Status
- Owner
- Members (researchers)
- Funding sources
- Homepage
- Related resource
- Related publications
- Start date
- Finish date
Properties of Procedure object:
- URI identifier
- Procedure steps
- Any protocol used in the procedure (A Protocol object)
- Material used
- Equipment used
- Software used
Protocol:
- URI identifier
- Title
- Subject or category
- Procedure steps (A Procedure object)
- References
- Creation time
- Who created it
- Modification time
- Who modified it
- Owner
- Homepage
Properties of Product object:
- URI identifier
- Name
- Model
- Type
- Specifications
- Manufacturer
- Homepage
Properties of Person object:
- URI identifier
- Full name
- Job Title
- Salutation
- Working group
- Interests
- Expertise
- Publications
- Weblog
- Homepage
- Contact info
Properties of Group object:
- URI identifier
- Name
- Members
- Organization
- Homepage
- contact info
There were many comments from W3C HCLS group. These comments were incorporated into the requirements wiki page at http://esw.w3.org/topic/HCLS/SciPubSPERequirements
Conclusion
Discussion
Main Concepts
Published In
References
Researcher
AJ Chen
PI
Start Time
6/1/2006
End Time
6/18/2006
Status
finished
Alternative Web Page
http://esw.w3.org/topic/HCLS/SciPubSPERequirements