This is an experimental browser for OBO ontologies
Each ontology class has its own page, with a URL of the form
http://berkeleybop.org/obo/
[OBO-ID]For example:
You can also use the primary label as the ID, for example: CL:neuron -- neuron, in CL
A graph view is shown for each class. The default
behavior is to show the closure of the subclass
relation. For some ontologies the defauly behavior is
different. For example, many anatomy ontologies will by
default show the partonomy and the ontogeny (develops
from relations). Ontologies that follow strict single
isa inheritance (such as the FMA), the default behavior
may be to show subclass relationships via
containment -- this can be seen for example with
the FMA class "Heart" (shown)
In all cases the default behavior can be overridden by clicking on the graph config panel which allows the display of additional relations, and the selection of a containment relation. Note that behavior is undefined when a multiple parentage relation is selected for containment
If an ontology has wikipedia cross-references (e.g. GO, UBERON), then the wikipedia page will be embedded in the OBO page. See for example UBERON:0001474
A number of download options are available, including obo, owl and owl2 (the latter uses the new purl.obolibrary.org URI scheme, and IAO for ontology metadata). The default approach is to perform the subclass closure, but this can be overridden by appending "?rel=<REL>" to the URL, or "?rel=all" for all relations. In future there will be a more intuitive interface for this. Some examples follow:
It is possible to view multiple classes together using URLs such as CL:0000084+CL:0000236
This is also possible for classes in different ontologies. For example: UBERON:0000019+ZFA:0000107+MA:0000261
URLs such as this are constructed automatically as links from xrefs. See for example any Uberon page (e.g. UBERON:eye).
Eye in Uberon, ZFA and MA:
Allows search of google, pubmed and in future other resources using ontology-based term expansion. Currently only subclass relationships are used
One of the goals of the OBO Foundry is to have all ontologies integrated, interoperable and interconnected. Clicking this button will show classes in external ontologies that reference this one. Logical definition bridge files are also searched here.
See for example MP:0000100?import=MP_XP -- abnormal ethmoidal bone morphology, with logical definitions from PATO and MA loaded
See for example: metadata/CARO
See for example: CARO and type in a search term to the text box. Search is currently quite primitive. You can also use the OBO firefox plugin or search via URLs such as this one
This web interface also serves as a data source for the Berkeley Galaxy Service
Advanced prolog queries can be executed from the query page for each ontology. E.g. query/FBbt -- see blipkit ontol_db module for details.
In future DL queries and Thea POPL transformations will be possible