BioPortal FAQ

Frequently Asked Questions

This FAQ is currently in alpha - please be patient...

General

NCBO

Advancing biology and medicine with tools and methodologies for the structured organization of knowledge.

What is NCBO?

The National Center for Biomedical Ontology (http://www.biontology.org) is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. The Center’s products and technologies include BioPortal, Phenote+, Open Biomedical Resources (OBR), Biomedical Annotations Repository (BAR), and Open Biomedical Data (OBD). Partner technologies include LexGrid, Protege, and Jambalaya. The products and technologies are used to deliver repositories and tools for accessing and using this biomedical information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects (DBPs) to enable their research and to stimulate technology development in the Center. The Center is undertaking outreach and educational activities to train the future generation of researchers in using biomedical ontologies and the Center’s tools to enhance scientific discovery.

BioPortal

Where are the ontologies?

Currently found in BioPortal 1.0 at http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml. We will be rolling out BioPortal 2.0 in August 2008 which will include all ontologies currently found in BioPortal 1.0.

How do I submit an ontology?

The current protocol is:

Send an email to the obo-discuss mailing list, even if the ontology is in planning stages

If the ontology satisfies basic criteria, we will add it to the OBO metadata and it will appear on the OBO site

Soon we will have an ontology submission service on the NCBO website

Ontology Content

Building Ontologies

What is the OBO Foundry?

A collaborative experiment, involving a group of ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain.

Where is the OBO Foundry?

See http://obofoundry.org/

Current Ontologies

incomplete is-a paths

Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).

This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.

Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.

One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.

Technical

Questions for cores 1 and 2

OBO Format

Questions about the OBO text and xml formats

Is OBO Format different from the old GO format?

Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.

Where can I find the spec?

You can find details on the 1.0 spec on the GO home page http://www.geneontology.org/GO.format.shtml#oboflat

This spec is somewhat underspecified

The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006

You can find a preliminary version of the spec here: HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt

Why not use XML?

There is also an obo-xml format. See

http://www.godatabase.org/dev/xml

Currently only available as DTD. Relax-NG and XSD coming soon.

Is there a UML model?

Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:

http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/

What tools support Obo-Format?

The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list

OBO-Edit

(naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.

COBRA

developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies

go-perl

http://search.cpan.org/~cmungall/go-perl

Using Protege with OBO ontologies

You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.

The OBO plugin was developed at the University of Washington, and is no longer supported.

You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.

Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.

Can I convert Obo-format to OWL?

Yes. At this present time, the best way of foing this is to use the xslts included in go-perl. Download and install: http://search.cpan.org/~cmungall/go-perl/ Then run the script

  go2owl myontology.obo

This functionality will soon be available from oboedit

For more details on the mapping, see:

http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html

OK, but can I just download OBO ontologies as OWL without doing the conversion myself?

You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:

http://www.fruitfly.org/~cjm/obo-download

Can I convert Obo-format files to Protege-classic?

Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.

OBD

What is OBD?

OBD is a database for storing data typed using OBO ontologies

Where is it?

In development!

Is there a demo?

See http://www.fruitfly.org/~cjm/obd

Datasets

See the above URL for now