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[ontolog-forum] Open Standard Ontology library: was BioPortal 2.1 Releas

To: "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "Azamat" <abdoul@xxxxxxxxxxxxxx>
Date: Wed, 6 May 2009 16:07:08 +0300
Message-id: <004e01c9ce4b$90f368b0$a104810a@homepc>
"The National Center for Biomedical Ontology is pleased to announce the release of BioPortal 2.1.:"
 

I guess the OBO Foundry (?) may well serve as a lesson how to build an Open Standard Ontology library, as a virtual depository or registry of upper ontologies (for common use across different knowledge fields and business domains and knowledge applications). 

Among things to be done in the first place there are:  

1. Establishing a common unifying structure for ontologies, for their domain entities and relations, for their special axioms, definitions and meanings;

Otherwise, there will be a large number of field models without any clear integrative structure, like the specific biomedical ontologies needing explicit foundational structure.

 2. Establishing the basal ontological relations.

The formal relations of the logic of classes as <class, class>; <instance, class>; <instance, instance> are NOT "genuinely ontological relations...between entities in reality", http://genomebiology.com/2005/6/5/R46.

The "genuine" ontological relations have always being the things like causality, spatial relations, temporal relations, etc. if only I missed some "ontology revolution" in the nature and order of relationships.

 

The subject of biology is nothing but special ontological entities: living beings and animate things or life, their properties (structures and compositions), states, processes and the relationships among organisms, and their constituent parts.

So, dealing with living things, the physico-chemical properties of life, biology is tending to integrate all its knowledge and research, including its interfaces as biophysics, biochemistry, sociobiology, or paleobiology. Such a converging tendency of biological sciences is explained by the fundamental fact that all these many divisions and subdivisions are interrelated by few basic onto-biological principles of living things: Sameness or unity (of structure and function and origin); diversity, change or evolution (natural selection mechanisms); interactions or interrelationships (of animate beings), and continuity (reproductive, successive generations).

That means that bio-ontology allows a single classification of living beings, which are now done by:

the  levels of biological organization, bio-molecules, cells,..., individuals, populations...;

the kinds of living things, plants, animals;

the structure and function or origin of organisms;

the processes of growth and development of living systems

 

It hardly makes a real scientific progress just duplicating the extant structure of special fields of biology, which subject names now followed with "ontology" designation: like as plant ontology and animal ontology or zoo-ontology, genomics ontology or gene ontology, cell ontology or cyto-ontology, tissue ontology and organ ontology, individual ontology, population ontology, eco-ontology or environment ontology; or physiology ontology and morpho-ontology and anatomy ontology, starting from animal anatomy ontology down to fly, spider and mosquito anatomy ontologies ,and so on, http://en.wikipedia.org/wiki/OBO_Foundry.

Before soon it will be practically impossible to count the number of ontologies and so leave any hope for any semantic interoperability, if only ?neon? will give us some light...

Hardly the conceptual progenitors of ontology could foresee such a wild scenario.

 

Bottom line:

Having an Open Standard Ontology (library, depositary, registry, facility) built is not a luxury but a necessity, even an absolute must and urgency.

 

Azamat Abdoullaev

 

 
 ----- Original Message -----
Sent: Wednesday, May 06, 2009 4:48 AM
Subject: [ontolog-forum] BioPortal 2.1 Release

The National Center for Biomedical Ontology is pleased to announce the release of BioPortal 2.1. Highlights of this release are:

-Annotator: a service that identifies mentions of biomedical ontology concepts in text that users submit. You can use the annotator service to tag automatically any item of interest with terms from UMLS and BioPortal ontologies. The Annotator is accessible via the BioPortal user interface [1] and as a REST service [2]

-Advanced user interface for searching ontologies [3] enables users to select which ontologies or categories of ontologies to search, specify search parameters, and filter and navigate easily through the search results

-Ontology-based projects: You can now describe your ontology-based projects, indicate which BioPortal ontologies you use, and provide reviews of those ontologies in the context of your project [4]

-Version management for OWL ontologies: you can download a diff between successive versions of an OWL ontology in tab-delimited format or as a set of RDF instances of the Protégé Change and Annotations ontology. See, for example, the details for the Biomedical Resource Ontology [5], to see a listing of diffs for its versions.

-Within-ontology search: you can use the search box at the top of each ontology tree to type in preferred name or a synonym and jump directly to one of the concepts that matches your search term (look for the "Jump to" box when you are exploring an ontology)

-Support for different hierarchy relations in OBO ontologies: just like in OBO-Edit, you will now see different icons when you browse the tree for an OBO ontologies, indicating the specific relationship between a child and a parent node (such as is-a or part-of)

Numerous improvements in user interaction:
-The new home page enables direct access to key BioPortal functionality, such as searching ontologies for terms, finding a specific ontology of interest, or searching the NCBO Resource index to find resources mentioning a particular concept of interest.
-New look and feel for BioPortal user interface
-Additional details on the ontology metadata page
-It is now easier to add and view reviews for a particular ontology
-Many other user interface improvements and fixes

Prototypes of upcoming features for accessing the NCBO Resource index:
-access to biomedical resources annotated with a specific ontology term when you are viewing the term in BioPortal (in the "Resources" tab)
-search through all resource annotations available in the NCBO Resource index
-the resources that NCBO currently indexes or provides access to include Conserved Domain Database, ArrayExpress, PharmGKB, UniProt KB, ARRS GoldMiner, Online Mendelian Inheritance in Man (OMIM), Reactome, Gene _expression_ Omnibus and NextBio (to check dynamically the list of resource that we currently have in the index, you can call the corresponding REST service [6]).

[1] http://bioportal.bioontology.org/annotate
[2] http://bioontology.org/wiki/index.php/Annotator_Web_service
[3] http://bioportal.bioontology.org/search
[4] http://bioportal.bioontology.org/projects
[5] http://bioportal.bioontology.org/ontologies/39521
[6] http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources



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