Applications

This page lists some applications using blip

blip kit

This is a command-line interface to much of the blip module functionality, accessed via the unix command

blip

Here is the blip help output. You can also get help on a specific command by typing

blip -h COMMAND

unix$ blip -h
Usage: blip <OPTIONS> COMMAND <COMMAND-OPTIONS> <COMMAND-ARGS>
General Options:
-trace
    If set, enters prolog trace mode
-pregoal ATOM, -pre ATOM [*]
    A prolog goal to be satisfied
-debug ATOM [*]
    A debug category, eg "load"
-goal ATOM
    A prolog goal to be satisfied
-format ATOM, -from ATOM, -f ATOM
    Input format, see io module for full list
-i ATOM, -input ATOM [*]
    Input file, format specified by filename suffix or -from
-r ATOM, -resource ATOM [*]
    Input resource, must be defined in bioconf.pro
-v, -verbose
    If set, prints informational messages
-h, -help
    General help, or help on a specific command if specified
-c ATOM, -conf ATOM [*]
    Prolog conf files to be loaded
-u ATOM, -use ATOM [*]
    Name of blip module to be used; eg a bridge module

Options marked [*] can be specified multiple times

Commands:
ontol-validate 
    basic ontology validation
ontol-stats 
    various statistics on one ontology
ontol-coverset 
    given ids, find minimal id(s) that cover this
ontol-subset 
    exports a subset of an ontology
sb-query 
    Basic queries on sb entities: by species, component, reaction ID
sb-query-by-annot 
    As sb-query; id or name is for a class in some ontology used to annotate s/c/r
sb-summarize 
    Summarise a sb_db file or dataset (try running on a SBML file)
go-show-minset 
    Summarise gene products in go_assoc file by minimal cover set
go-list-assocs 
    Show gene associations by a GO class or similar
prolog 
    query blip resources via prolog shell
config 
    Setup a user's bioconf.pro file in ~/.blip/
io-convert 
    converts from one format to another: see io module
io-diff 
    compares two files at the prolog fact level


Examples:
 blip -r go ontol-coverset [list of GO IDs]

The blip script is extendable - just add your own blipkit module. See exististing blipkit_* modules in the source download for details.

AmiGO-NG

This is a prototype and reference implementation for the next generation of the AmiGO Gene Ontology browser. The current AmiGO is written in object oriented perl and template toolkit, querying a MySQL database. The data model is fairly rigid, making it hard to explore new implementation ideas such as OWL-style ontologies, combinatorial annotations and other kinds of instance data beside GO association files. AmiGO-NG may not ever be the public interface for GO or OBO, but it is currently proving very useful as a rapid prototying tool for demoing new ideas, and will serve as a reference implementation for the final production version.

AmiGO-NG is written using serval. The core model provides generic queries over classes and instances. Different plugins allow different data models (which may be views over the instance data) and different user interfaces.

Demo Apps

These are running on a desktop machine and may not be stable

• OBD - browse genetic and phenotypic data (test dataset). This uses specific plugins for showing a less generic view to the user than the generic instance browser
• Semantic Bible - this is a random OWL ontology which is sort of interesting. This shows AmiGO with the generic instance browser

Obol

Obol is written in XSB Prolog, so it cannot use blip directly. However, Obol uses the same predicates as defined in ontol_db - Obol may at some point be converted to SWI-Prolog and blip.

See the Obol page for details

Obol is currently being ported to SWI-Prolog, see the directory blip/apps/obol for details. Also see blip/apps/nlp for some preliminary Bio-NLP apps.