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Questions marked with an asterix (*) are more important.
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Section 0. Contact and confidentiality
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Contact e-mail: simon.jupp@manchester.ac.uk , robert.stevens@manchester.ac.uk
Do you mind your use case being made public on the working group website and
documents?
No
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Section 1. Application
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In this section we ask you to provide some information about the
application for which the vocabulary(ies) and or vocabulary mappings are
being used.
Please note:
-- If your use case does not involve any specific application, but
consists rather in the description of a specific vocabulary, skip
straight to Section 2.
-- If your application makes use of links between different
vocabularies, do not forget to fill in Section 3!
1.1. What is the title of the application?
Sealife - A Semantic Grid Browser for the Life Sciences Applied to the study of Infectious Diseases
1.2. What is the general purpose of the application?
What services does it provide to the end-user?
Develop a grid browser for the life sciences, which will link the web to the current emerging e-science infrastructure.
The Sealife browser will allow users to automatically link a host of Web servers and Web/Grid services to the Web content he/she is visiting.
The browser will identify terms in web pages and documents as they are being browsed using background knowledge held in ontologies and vocabularies.
Through the use of Semantic Hyperlinks, which link identified concepts and terms in pages to servers and services, the Sealife browser will offer
a new dimension to context-based information integration.
*1.3. Provide some examples of the functionality of the application. Try
to illustrate all of the functionalities in which the vocabulary(ies)
and/or vocabulary mappings are involved.
The vocabularies will be used to identify bio-medical terms and concepts on web pages as the user browses the web. Dynamic hyperlinks are
generated around the concepts and link boxes will offer relevant and related services to the user based on terms held in the vocabularies and ontologies.
1.4. What is the architecture of the application?
What are the main components?
Are the components and/or the data distributed across a network,
or across the Web?
The system is built on the Conceptual Open Hypermedia Service (COHSE) system. COHSE's Architecture is composed of a COHSE Distributed Links Service (DLS)
agent and two supporting services: a Knowledge Service (OS) and a Resource Manager (RM). The DLS agent is responsible for adding hyperlinks and drawing
text boxes on the pages using AJAX technology. The knowledge Service stores ontologies (in OWL) or SKOS vocabularies, that are used for term recognition
on web pages. The resource manager allows mapping between concepts and resources, once resources are discovered hyperlinks to the resource are generated
on the page. Services are pluggable components e.g. google web search service.
The COHSE system can be deployed on the web server side, as an intermediary service (e.g. proxy) or in the browser (e.g Mozilla plugin)
1.5. Briefly describe any special strategy involved in the processing
of user actions, e.g. query expansion using the vocabulary structure.
For any term highlighted on a page, resources are provided for broader, narrower and related terms obtained from the underlying vocabulary.
1.6. Are the functionalities associated with the controlled
vocabulary(ies) integrated in any way with functionalities provided by
other means? (For example, search and browse using a structured
vocabulary might be integrated with free-text searching and/or some sort
of social bookmarking or recommender system.)
1.7. Any additional information, references and/or hyperlinks.
http://www.biotec.tu-dresden.de/sealife/
http://cohse.cs.manchester.ac.uk/
Demo- http://cohse.cs.manchester.ac.uk/demo/NELI-demo.avi.zip
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Section 2. Vocabulary(ies)
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In this section we ask you to provide some information about the
vocabulary or vocabularies you would like to be able to represent using
SKOS.
Please note:
-- If you have multiple vocabularies to describe, you may repeat this
section for each one individually or you may provide a single
description that encompasses all of your vocabularies.
-- If your use case describes a generic application of one or more
vocabularies and/or vocabulary mappings, you may skip this section.
-- If your vocabulary case contains cross-vocabulary links (between the
vocabularies you presented or to external vocabularies), please fill in
section 3!
2.1. What is the title of the vocabulary? If you're describing multiple
vocabularies, please provide as many titles as you can.
Our potential vocabularies are any biomedical ontology-like resource. We are targeting the Open biomedical Ontology (ies) (http://obo.sf.net). Others include SNOMed, MeSH, and many more. The OBO Ontologies use their own representation that has OWL semantics. The others have their own proprietory formats. We have already written converters from OBO format to SkOS and one already exists for MeSH.
2.2. Briefly describe the general characteristics of the vocabulary,
e.g. scope, size...
The Gene Ontology, for instance has some 20,000 terms. It is a simple taxonomy combined with part-of relationships. It also has thesaurus features of scope note (definition), synonyms, broader than, narrower than and related terms. It covers molecular function, biological process and cellular location of gene products. Other OBO ontologies cover many features of molecular biology from genotype to phenotype. Other ontologies cover disease, anatomy, healthcare, etc. they range in size from a few hundred terms to 100,000's.
2.3. In which language(s) is the vocabulary provided?
In the case of partial translations, how complete are these?
American English.
*2.4. Please provide below some extracts from the vocabulary. Use the
layout or presentation format that you would normally provide for the
users of the vocabulary. Please ensure that the extracts you provide
illustrate all of the features of the vocabulary.
OBO format used to create the ontologies/vocabularies.
[Term]
id: neli:000015
name: Aspergillus
description: ....
Synonym: .... ! narrower
is_a: neli:000011 ! Bacteria
[Term]
id: neli:000016
name: Bacillus
description: ...
Synonym: ... ! broader
is_a: neli:000011 ! Bacteria
2.5. Describe the structure of the vocabulary.
What are the main building blocks?
What types of relationship are used? If you can, provide examples
by referring to the extracts given in paragraph 2.4.
The vocabularies we plan to use cover various aspects of the bio-medical domain. The domain ranges from vocabularies used in the area of molecular
biology and anatomy to infectious disease, taxonomy and medicine. These vocabularies range in size, scope and representation. Many of the biological
ontologies are represented in the OBO format (e.g. The Gene Ontology [http://www.geneontology.org/]) for which we have mapped to SKOS, others are in OWL and some like MeSH (Medical Subject Headings) are in some native representation (e.g. XML). We are also working with the Nation Library of Infectious Disease (NeLI) to generate a new vocabulary that will be used aid user navigation around the NeLI website. This vocabulary will be represented in SKOS and used as a lexical resource for the COHSE system.
All of the vocabularies and ontologies range in their level of expression but share some common features, such as subsumption hierarchies, preferred labels, synonyms and descriptors.
2.6. Is a machine-readable representation of the vocabulary already
available (e.g. as an XML document)? If so, we would be grateful if you
could provide some example data or point us to a hyperlink.
MeSH is available in MeSH XML format, some XSLT is available to do a conversion.
The OBO ontologies are available as OBO XML or in the OBO file format. OBO-Edit API is available.
2.7. Are any software applications used to create and/or maintain the
vocabulary?
Are there any features which these software applications currently
lack which are required by your use case?
We are using a combination of Protege and OBO-edit to generate and edit vocabularies, we then have a set of application that convert these various
formats into a SKOS representation.
2.8. If a database application is used to store and/or manage the
vocabulary, how is the database structured? Illustration by means of
some table sample is welcome.
N/A
2.9. Were any published standards, textbooks or written guidelines
followed during the design and construction of the vocabulary?
Did you decide to diverge from their recommendations in any way,
and if so, how and why?
In most cases we did not develop the vocabularies, they were developed with a different use case in mind, we have adapted them for use within our application.
2.10. How are changes to the vocabulary managed?
2.11. Any additional information, references and/or hyperlinks.
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Section 3. Vocabulary Mappings
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In this section we ask you to provide some information about the
mappings or links between vocabularies you would like to be able to
represent using SKOS.
Please note:
-- If your use case does not involve vocabulary mappings or links, you
may skip this section!
3.1. Which vocabularies are you linking/mapping from/to?
OBO to SKOS.
MeSH to SKOS.
OWL to SKOS.
*3.2. Please provide below some extracts from the mappings or links
between the vocabularies. Use the layout or presentation format that you
would normally provide for the users of the mappings. Please ensure that
the examples you provide illustrate all of the different types of
mapping or link.
- "Mycobacterium Tuberculosis" -> is_a (skos:broaderThan) -> "Mycobacterium"
- "Mycobacterium Tuberculosis" -> causes (skos:relatedTo) -> "Tuberculosis"
- "Azoles" -> Treatment (skos:relatedTo) -> "Tuberculosis"
3.3. Describe the different types of mapping used, with reference to
the examples given in paragraph 3.2.
3.4. Any additional information, references and/or hyperlinks.