EMBOSS: dbxobo

| dbxobo

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Index an obo ontology using b+tree indices

## Description

dbxobo indexes an ontology in OBO format, and builds EMBOSS B+tree format index files.

These indexes allow access of flat files larger than 2Gb.

Related application dbxedam provides additional index fields for EDAM-specific namespaces and relations.

## Usage

Here is a sample session with dbxobo

    % dbxobo
    Index an obo ontology using b+tree indices
    Basename for index files: edam
    Standard database name [edam]:
    Resource name [oboresource]: oboresource
    Database directory [.]:
    Wildcard database filename [*.obo]: EDAM.obo
            id : ID
           acc : Synonym
           nam : Name
           isa : Parent
           des : Description
            ns : Namespace
    Index fields [*]: *
    Compressed index files [Y]:
    General log output file [outfile.dbxobo]:

Go to the output files for this example

## Command line arguments

    Index an obo ontology using b+tree indices
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-dbname]            string     Basename for index files (Any string from 2
                                      to 19 characters, matching regular
                                      expression /[A-z][A-z0-9_]+/)
      [-standardname]      string     [$(dbname)] Standard database name (Any
                                      string from 2 to 19 characters, matching
                                      regular expression /[A-z][A-z0-9_]+/)
      [-dbresource]        string     [oboresource] Resource name (Any string from
                                      2 to 19 characters, matching regular
                                      expression /[A-z][A-z0-9_]+/)
       -directory          directory  [.] Database directory
       -filenames          string     [*.obo] Wildcard database filename (Any
                                      string)
       -fields             menu       [*] Index fields (Values: id (ID); acc
                                      (Synonym); nam (Name); isa (Parent); des
                                      (Description); ns (Namespace))
       -[no]compressed     boolean    [Y] Compressed index files
       -outfile            outfile    [*.dbxobo] General log output file

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -release            string     [0.0] Release number (Any string up to 9
                                      characters)
       -date               string     [00/00/00] Index date (Date string dd/mm/yy)
       -exclude            string     Wildcard filename(s) to exclude (Any string)
       -indexoutdir        outdir     [.] Index file output directory

       Associated qualifiers:

       "-directory" associated qualifiers
       -extension          string     Default file extension

       "-indexoutdir" associated qualifiers
       -extension          string     Default file extension

       "-outfile" associated qualifiers
       -odirectory         string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-dbname] (Parameter 1) | string | Basename for index files | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | Required
[-standardname] (Parameter 2) | string | Standard database name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | $(dbname)
[-dbresource] (Parameter 3) | string | Resource name | Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ | oboresource
-directory | directory | Database directory | Directory | .
-filenames | string | Wildcard database filename | Any string | *.obo
-fields | list | Index fields |
id | (ID)
acc | (Synonym)
nam | (Name)
isa | (Parent)
des | (Description)
ns | (Namespace)
| *
-[no]compressed | boolean | Compressed index files | Boolean value Yes/No | Yes
-outfile | outfile | General log output file | Output file | <*>.dbxobo
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-release | string | Release number | Any string up to 9 characters | 0.0
-date | string | Index date | Date string dd/mm/yy | 00/00/00
-exclude | string | Wildcard filename(s) to exclude | Any string |
-indexoutdir | outdir | Index file output directory | Output directory | .
Associated qualifiers
"-directory" associated directory qualifiers
-extension | string | Default file extension | Any string |
"-indexoutdir" associated outdir qualifiers
-extension | string | Default file extension | Any string |
"-outfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

dbxobo reads and indexes OBO format ontology files

## Output file format

dbxobo creates one summary file for the database and two files for each field indexed.

### Output files for usage example

### File: outfile.dbxobo

    Processing directory: /homes/user/test/data/
    Processing file: EDAM.obo
    entries: 143 (143) time: 0.0s (0.0s)
    Total time: 0.0s
    Entry idlen 15 OK. Maximum ID length was 4 for '0004'.
    Field acc acclen 200 OK. Maximum acc term length was 47 for 'HMMER profile alignment (sequences versus HMMs)'.
    Field nam namlen 70 OK. Maximum nam term length was 15 for 'semanticscience'.
    Field isa isalen 15 OK. Maximum isa term length was 4 for '0003'.
    Field ns nslen 20 OK. Maximum ns term length was 10 for 'identifier'.
    Field des deslen 50 OK. Maximum des term length was 17 for 'conceptualisation'.

### File: edam.ent

    # Number of files: 1
    # Release: 0.0
    # Date:    00/00/00
    Single filename database
    EDAM.obo

### File: edam.pxac

    Type         Identifier
    Compress     Yes
    Pages        3
    Secpages     0
    Order        76
    Fill         74
    Level        0
    Pagesize     16384
    Cachesize    2000
    Order2       816
    Fill2        1364
    Secpagesize  16384
    Seccachesize 2000
    Count        143
    Fullcount    143
    Kwlimit      200
    Reffiles     0

### File: edam.pxde

    Type         Secondary
    Compress     Yes
    Pages        21
    Secpages     562
    Order        64
    Fill         57
    Level        0
    Pagesize     4096
    Cachesize    2000
    Order2       144
    Fill2        204
    Secpagesize  4096
    Seccachesize 2000
    Count        562
    Fullcount    2167
    Kwlimit      50
    Idlimit      15

### File: edam.pxid

    Type         Identifier
    Compress     Yes
    Pages        5
    Secpages     0
    Order        71
    Fill         56
    Level        0
    Pagesize     2048
    Cachesize    2000
    Order2       22
    Fill2        41
    Secpagesize  512
    Seccachesize 2000
    Count        143
    Fullcount    143
    Kwlimit      15
    Reffiles     0

### File: edam.pxis

    Type         Secondary
    Compress     Yes
    Pages        4
    Secpages     96
    Order        71
    Fill         56
    Level        0
    Pagesize     2048
    Cachesize    2000
    Order2       16
    Fill2        24
    Secpagesize  512
    Seccachesize 2000
    Count        90
    Fullcount    225
    Kwlimit      15
    Idlimit      15

### File: edam.pxnm

    Type         Secondary
    Compress     Yes
    Pages        5
    Secpages     323
    Order        196
    Fill         179
    Level        0
    Pagesize     16384
    Cachesize    2000
    Order2       583
    Fill2        818
    Secpagesize  16384
    Seccachesize 2000
    Count        323
    Fullcount    725
    Kwlimit      70
    Idlimit      15

### File: edam.pxns

    Type         Secondary
    Compress     Yes
    Pages        3
    Secpages     12
    Order        60
    Fill         49
    Level        0
    Pagesize     2048
    Cachesize    2000
    Order2       16
    Fill2        24
    Secpagesize  512
    Seccachesize 2000
    Count        5
    Fullcount    143
    Kwlimit      20
    Idlimit      15

### File: edam.xac

This file contains non-printing characters and so cannot be displayed here.

### File: edam.xde

This file contains non-printing characters and so cannot be displayed here.

### File: edam.xid

This file contains non-printing characters and so cannot be displayed here.

### File: edam.xis

This file contains non-printing characters and so cannot be displayed here.

### File: edam.xnm

This file contains non-printing characters and so cannot be displayed here.

### File: edam.xns

This file contains non-printing characters and so cannot be displayed here.

## Data files

## Notes

## References

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
dbiblast | Index a BLAST database
dbifasta | Index a fasta file database
dbiflat | Index a flat file database
dbigcg | Index a GCG formatted database
dbxcompress | Compress an uncompressed dbx index
dbxedam | Index the EDAM ontology using b+tree indices
dbxfasta | Index a fasta file database using b+tree indices
dbxflat | Index a flat file database using b+tree indices
dbxgcg | Index a GCG formatted database using b+tree indices
dbxreport | Validate index and report internals for dbx databases
dbxresource | Index a data resource catalogue using b+tree indices
dbxstat | Dump statistics for dbx databases
dbxtax | Index NCBI taxonomy using b+tree indices
dbxuncompress | Uncompress a compressed dbx index

## Author(s)

Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## History

## Target users

This program is intended to be used by administrators responsible for software and database installation and maintenance.

## Comments

None