Apollo

Apollo is a genomic annotation viewer and editor. It was originally developed as a collaboration between the Berkeley Drosophila Genome Project (part of the FlyBase consortium) and The Sanger Institute in Cambridge, UK. It was used by the FlyBase biologists to construct the Release 3 and 4 annotations on the finished Drosophila melanogaster genome, and has also beena primary vehicle for sharing these annotations with the community.

Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment.

AmiGO

AmiGO is the official tool for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms.

Using AmiGO, you can:

• search for a gene or gene product, or a list of gene or gene products, and view the GO term associations
• perform a sequence identity BLAST search and view the GO term associations for the genes or proteins returned
• search for GO terms and view the genes or gene products they are annotated to
• browse the GO ontology and view terms

Chado

Chado is a relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals.

Goose

allows arbitrary SQL to be executed over the BBOP or EBI mirror of the GO Database

The GO Database is a relational database external link housing both the Gene Ontology and the annotations of genes and gene products to terms in the GO. The advantage of housing both ontologies and annotations in a single database is that powerful queries can be performed over annotations using the ontology.

MiSO

miSO provides a graphical means to browse the terms in the Sequence Ontology. The view is organised via a parent/child approach. The terms are all linked to the SO term tables web page which displays more details such as the relationship types, the definition, the synonyms and the cross references.

OBD Phenotype

Content for class "BBOP-software" id "OBD" Goes Here http://spade.lbl.gov/OBDUI

Obol

Obol generates logical definitions for ontology terms. The results are stored as .obo files and can be reasoned over. Example files that were generated with Obol are...

Currently the results can be viewed in oboedit, or by using the static html dumps. This will be replaced by a java/template view.

Obo2Owl

OBO2Owl is a simple tool that allows you to convert between OBO and OWL ontologies in either direction.

Suppose there is an OWL ontology you wish to use in an OBO application - for example http://ccdb.ucsd.edu/SAO/1.2/SAO.owl. You can construct a stable URL that points at the syntactic OBO equivalent using the following scheme

OBO-CONVERTER-BASE-URL '?' 'url=' httpEscape(ONTOLOGY-DOWNLOAD-URL) '&' 'format=' FORMAT

OBO-Edit

OBO-Edit is an open source ontology editor written in Java. This project is supported by the Gene Ontology Consortium.

OBO-Edit is optimized for the OBO biological ontology file format. It features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities.

Phenote

Phenote is both a complete piece of software and a software toolkit designed to facilitate the annotation of biological phenotypes using ontologies. It provides an interface and infrastructure to record genotype-phenotype pairs, together with the provenance for the annotation. Typical users of Phenote include literature curators, laboratory researchers, and clinicians looking for a method to record data in a user-friendly and computable way.

Data annotated with Phenote is based on the EQ model for representing phenotypes, combining entities from any ontology with qualities (such as PATO).

Funding and Support

BBOP projects are largely funded through grants from the National Human Genome Research Institute (NHGRI) of the National Institutes of Health NIH (NIH).

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