EMBOSS: dbxedam

| dbxedam

## 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 the EDAM ontology using b+tree indices

## Description

dbxedam indexes the EDAM ontology in OBO format, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb.

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

Related application dbxobo can also index the EDAM input file. dbxedam provides additional index fields for EDAM-specific namespaces and relations.

## Usage

Here is a sample session with dbxedam

    % dbxedam
    Index the EDAM ontology using b+tree indices
    Basename for index files [edam]:
    Standard database name [edam]:
    Resource name [edamresource]:
    Database directory [.]:
    Wildcard database filename [EDAM*.obo]:
            id : ID
           acc : Synonym
           nam : Name
           isa : Parent
           des : Description
            ns : Namespace
         hasin : has_input
        hasout : has_output
          isid : is_identifier_of
         isfmt : is_format_of
    Index fields [*]:
    Compressed index files [Y]:
    General log output file [outfile.dbxedam]:

Go to the output files for this example

## Command line arguments

    Index the EDAM ontology using b+tree indices
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-dbname]            string     [edam] 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     [edamresource] Resource name (Any string
                                      from 2 to 19 characters, matching regular
                                      expression /[A-z][A-z0-9_]+/)
       -directory          directory  [.] Database directory
       -filenames          string     [EDAM*.obo] Wildcard database filename (Any
                                      string)
       -fields             menu       [*] Index fields (Values: id (ID); acc
                                      (Synonym); nam (Name); isa (Parent); des
                                      (Description); ns (Namespace); hasin
                                      (has_input); hasout (has_output); isid
                                      (is_identifier_of); isfmt (is_format_of))
       -[no]compressed     boolean    [Y] Compressed index files
       -outfile            outfile    [*.dbxedam] 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_]+/ | edam
[-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_]+/ | edamresource
-directory | directory | Database directory | Directory | .
-filenames | string | Wildcard database filename | Any string | EDAM*.obo
-fields | list | Index fields |
id | (ID)
acc | (Synonym)
nam | (Name)
isa | (Parent)
des | (Description)
ns | (Namespace)
hasin | (has_input)
hasout | (has_output)
isid | (is_identifier_of)
isfmt | (is_format_of)
| *
-[no]compressed | boolean | Compressed index files | Boolean value Yes/No | Yes
-outfile | outfile | General log output file | Output file | <*>.dbxedam
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

dbxedam reads and indexes the EDAM ontology file in OBO format.

## Output file format

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

- dbalias.ent is the master file containing the names of the files that have been indexed. It is an ASCII file. This file also contains the database release and date information.
- dbalias.xid is the B+tree index file for the ID names. It is a binary file.
- dbalias.pxid is an ASCII file containing information regarding the structure of the ID name index.

### Output files for usage example

### File: outfile.dbxedam

    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 80 OK. Maximum acc term length was 47 for 'HMMER profile alignment (sequences versus HMMs)'.
    Field nam namlen 32 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 15 OK. Maximum ns term length was 10 for 'identifier'.
    Field des deslen 30 OK. Maximum des term length was 17 for 'conceptualisation'.
    Field hasin hasinlen 15 OK. Maximum hasin term length was 4 for '0006'.
    Field hasout hasoutlen 15 OK. Maximum hasout term length was 4 for '0006'.
    Field isid isidlen 15 OK. Maximum isid term length was 4 for '0006'.
    Field isfmt isfmtlen 15 OK. Maximum isfmt term length was 4 for '0006'.

### 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        87
    Fill         80
    Level        0
    Pagesize     8192
    Cachesize    2000
    Order2       406
    Fill2        681
    Secpagesize  8192
    Seccachesize 2000
    Count        143
    Fullcount    143
    Kwlimit      80
    Reffiles     0

### File: edam.pxde

    Type         Secondary
    Compress     Yes
    Pages        14
    Secpages     562
    Order        93
    Fill         80
    Level        0
    Pagesize     4096
    Cachesize    2000
    Order2       144
    Fill2        204
    Secpagesize  4096
    Seccachesize 2000
    Count        562
    Fullcount    2167
    Kwlimit      30
    Idlimit      15

### File: edam.pxhasin

    Type         Secondary
    Compress     Yes
    Pages        3
    Secpages     2
    Order        71
    Fill         56
    Level        0
    Pagesize     2048
    Cachesize    2000
    Order2       16
    Fill2        24
    Secpagesize  512
    Seccachesize 2000
    Count        2
    Fullcount    2
    Kwlimit      15
    Idlimit      15

### File: edam.pxhasout

    Type         Secondary
    Compress     Yes
    Pages        3
    Secpages     2
    Order        71
    Fill         56
    Level        0
    Pagesize     2048
    Cachesize    2000
    Order2       16
    Fill2        24
    Secpagesize  512
    Seccachesize 2000
    Count        2
    Fullcount    2
    Kwlimit      15
    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.pxisfmt

    Type         Secondary
    Compress     Yes
    Pages        3
    Secpages     5
    Order        71
    Fill         56
    Level        0
    Pagesize     2048
    Cachesize    2000
    Order2       16
    Fill2        24
    Secpagesize  512
    Seccachesize 2000
    Count        5
    Fullcount    5
    Kwlimit      15
    Idlimit      15

### File: edam.pxisid

    Type         Secondary
    Compress     Yes
    Pages        3
    Secpages     1
    Order        71
    Fill         56
    Level        0
    Pagesize     2048
    Cachesize    2000
    Order2       16
    Fill2        24
    Secpagesize  512
    Seccachesize 2000
    Count        1
    Fullcount    1
    Kwlimit      15
    Idlimit      15

### File: edam.pxnm

    Type         Secondary
    Compress     Yes
    Pages        11
    Secpages     331
    Order        44
    Fill         38
    Level        0
    Pagesize     2048
    Cachesize    2000
    Order2       16
    Fill2        24
    Secpagesize  512
    Seccachesize 2000
    Count        323
    Fullcount    725
    Kwlimit      32
    Idlimit      15

### File: edam.pxns

    Type         Secondary
    Compress     Yes
    Pages        3
    Secpages     12
    Order        71
    Fill         56
    Level        0
    Pagesize     2048
    Cachesize    2000
    Order2       16
    Fill2        24
    Secpagesize  512
    Seccachesize 2000
    Count        5
    Fullcount    143
    Kwlimit      15
    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.xhasin

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

### File: edam.xhasout

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.xisfmt

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

### File: edam.xisid

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

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 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
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
dbxobo | Index an obo ontology 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