OntoShell

OntoShell provides a uniform command line interface (mimicking a traditional UNIX shell) to multiple functional catalogs such as GO, KEGG, and MIPS. Ontology terms are laid out like directories in a file system, with gene annotations serving as files. The structure of the catalogs can be listed and explored, individual genes' annotations can be catted, and TermFinder queries can be processed either interactively or from the command line.

Usage

Basic Usage

 OntoShell -o gene_ontology.obo -g <gene_association.sgd> -k ko -K <org>
        -m funcat-2.0_scheme -a <funcat-2.0_data_18052006>

Initiate an interactive command prompt exploring functional catalogs and annotations from the Gene Ontology (gene_ontology.obo and gene_association.sgd), KEGG (ko and the three-letter organism code org, e.g. SCE, HSA, etc.), and MIPS (funcat_scheme and funcat_data).

 OntoShell -o gene_ontology.obo -g <gene_association.sgd> -k ko -K <org>
        -m funcat-2.0_scheme -a <funcat-2.0_data_18052006> -x "<command>"

Initiate a non-interactive session using the requested functional catalogs; executes the command string command (which may contain multiple commands separated by semicolons) and outputs the results to standard output.

 OntoShell -c <configuration.ini>

Executes OntoShell using the gengetopt command line arguments stored in the configuration file configuration.ini. This can be extremely useful for storing complex command lines, e.g. the paths to all of the functional catalog files.

Detailed Usage

package "OntoShell"
version "1.0"
purpose "Ontology exploration utility"

section "Main"
option  "exec"          x   "Command to execute"
                            string
option  "altids"        l   "Force alternate (human) IDs"
                            flag    off
option  "dbids"         b   "Include GO database IDs"
                            flag    off

section "Function Catalogs"
option  "go_onto"       o   "GO ontology"
                            string  typestr="filename"
option  "go_anno"       g   "GO annotations"
                            string  typestr="filename"
option  "kegg"          k   "KEGG ontology"
                            string  typestr="filename"
option  "kegg_org"      K   "KEGG organism"
                            string  default="SCE"
option  "mips_onto"     m   "MIPS ontology"
                            string  typestr="filename"
option  "mips_anno"     a   "MIPS annotations"
                            string  typestr="filename"
option  "mipsp_onto"    M   "MIPS phenotypes ontology"
                            string  typestr="filename"
option  "mipsp_anno"    A   "MIPS phenotypes annotations"
                            string  typestr="filename"
option  "features"      f   "SGD gene features"
                            string  typestr="filename"

section "Optional"
option  "zeroes"        z   "Tab-complete zero entries"
                            flag    off
option  "config"        c   "Command line config file"
                            string  typestr="filename"  default="OntoShell.ini"
option  "verbosity"     v   "Message verbosity"
                            int default="5"

Flag	Default	Type	Description
-x	None	String	If given, rather than providing the user with an interactive command prompt, execute the given command (with results going to standard output) and exit. This is useful for tasks such as saving the results of a TermFinder query to a file.
-l	off	Flag	If on, open GO and KEGG using alternate gene IDs (the first synonym rather than the systematic ID) suitable for processing human (rather than yeast etc.) annotations.
-b	off	Flag	If on, include annotation database IDs in the gene synonym lists (suitable for WormBase and FlyBase IDs).
-o	None	OBO text file	OBO file containing the structure of the Gene Ontology.
-g	None	Annotation text file	Gene Ontology annotation file for the desired organism.
-k	None	KEGG orthology text file	ko file containing the structure and annotations of the KEGG orthology.
-K	SCE	KEGG organism code	Three letter organism code of annotations to be read from the ko file. Options include SCE for yeast, HSA for human, DME for fly, CEL for worm, and MMU for mouse.
-m	None	MIPS schema text file	File containing the schema (structure) of the MIPS functional catalog.
-a	None	MIPS annotation text file	File containing the annotations to be used with the MIPS functional catalog.
-M	None	MIPS phenotypes schema text file	File containing the schema (structure) of the MIPS phenotype catalog.
-A	None	MIPS phenotype annotation text file	File containing the annotations to be used with the MIPS phenotype catalog.
-f	None	SGD features text file	If given, use gene names and information from the given SGD_features.tab file to annotate genes.
-z	off	Flag	If on, perform tab-completion on terms containing zero annotations; otherwise, exclude terms with no genes from the tab-completion list.