FAQ

1. What is BiologicalNetworks?
2. What is PathSys?
3. Why do we need BiologicalNetworks?
4. What is GeneOntology?
5. Where can I view or download the complete sets of GO annotations?
6. How can I update my GeneOntology annotations?

1. BiologicalNetworks is a general-purpose software environment for retrieval, construction, and visualization of complex biological networks. BiologicalNetworks provides querying services (querying languages and a querying engine) and an information management framework over PathSys system.
2. PathSys is a data integration platform that provides dynamic integration over diverse set of databases.
3. Due to difficulties in integrating heterogeneous data types coping with continuous updating of existing databases or with disparate confidence levels associated with different data sets, most biological databases are focused on a specific subset of biological knowledge. To facilitate this process, we constructed PathSys system and BiologicalNetworks framework over it.
4. Ontologies are 'specifications of a relational vocabulary'. In other words they are sets of defined terms like the sort that you would find in a dictionary, but the terms are networked. The terms in a given vocabulary are likely to be restricted to those used in a particular field, and in the case of GO, the terms are all biological.
5. You do not need update your GO annotations. Every time you run BiologicalNetworks Java Web Start version, programs checks the last version of GO you have, and automatically updates it if needed.
6. As with the vocabularies, the gene product/GO association sets from contributing groups are available at the GO web site. Tab-delimited files of the associations between gene products and GO terms that are made by the member organizations are available from their individual FTP sites or from a link on the Current Annotations table.