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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: drfindid
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
drfindid
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Find public databases by identifier
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>
    Description
</H2>



<b>drfindid</b> searches the Data Resource Catalogue to find entries
with EDAM data identifier terms matching a query string.





<H2>
    Algorithm
</H2>


The first search is of the EDAM ontology data namespace, using the
term names and their synonynms. All child terms are automatically
included in the set of matches inless the <tt>-nosubclasses</tt>
qualifier is used.

<p>
The <tt>-sensitive</tt> qualifier also searches the definition strings.

<p>
The set of EDAM terms are then compared to entries in the Data
Resource Catalogue, searching the 'eid' EDAM identifier index.










<H2>
    Usage
</H2>

<!--  
	Example usage, as run from the command-line.
        Many examples illustrating different behaviours is good.
 -->

Here is a sample session with <b>drfindid</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>drfindid "uniprot accession" </b>
Find public databases by identifier
Data resource output file [drfindid.drcat]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.1">Go to the output files for this example</a><p><p>



<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Find public databases by identifier
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-query]             string     List of EDAM data keywords (Any string)
  [-outfile]           outresource [*.drfindid] Output data resource file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -sensitive          boolean    [N] By default, the query keywords are
                                  matched against the EDAM term names (and
                                  synonyms) only. This option also matches the
                                  keywords against the EDAM term definitions
                                  and will therefore (typically) report more
                                  matches.
   -[no]subclasses     boolean    [Y] Extend the query matches to include all
                                  terms which are specialisations (EDAM
                                  sub-classes) of the matched type.

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   -oformat2           string     Data resource output format

   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

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-query]<br>(Parameter 1)</td>
<td>string</td>
<td>List of EDAM data keywords</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>outresource</td>
<td>Output data resource file name</td>
<td>Data resource entry</td>
<td><i>&lt;*&gt;</i>.drfindid</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-sensitive</td>
<td>boolean</td>
<td>By default, the query keywords are matched against the EDAM term names (and synonyms) only. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]subclasses</td>
<td>boolean</td>
<td>Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outresource qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory2<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -oformat2<br>-oformat_outfile</td>
<td>string</td>
<td>Data resource output format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->








<H2>
    Input file format
</H2>

None.

<p>






<H2>
    Output file format
</H2>

<p>

The output is a standard EMBOSS resource file. 

<p>

The results can be output in one of several styles by using the
command-line qualifier <tt>-oformat xxx</tt>, where 'xxx' is replaced by
the name of the required format.  The available format names are: 
drcat, basic, wsbasic, list.
<p>

See:
<A href="http://emboss.sf.net/docs/themes/ResourceFormats.html">
http://emboss.sf.net/docs/themes/ResourceFormats.html</A>
for further information on resource formats.

<p>

<p>

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: drfindid.drcat</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
ID      PRIDE
Acc     DB-0130
Name    PRIDE proteomics identifications database
Desc    Standards compliant, public data repository for proteomics data, protein and peptide identifications together with the evidence supporting these identifications.
URL     http://www.ebi.ac.uk/pride
URLrest http://www.ebi.ac.uk/pride/prideMartWebService.do
Cat     Proteomic databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMtpc 0121 | Proteomics
EDAMdat 2536 | Mass spectrometry data
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query    Mass spectrometry data {PRIDE entry} | HTML | UniProt accession | http://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&amp;identificationAccessionNumber=%s
Example UniProt accession | P29375

ID      PhosSite
Acc     DB-0076
Name    Phosphorylation site database for Archaea and Bacteria
Desc    Phosphorylation site database for Archaea and Bacteria
URL     http://www.phosphorylation.biochem.vt.edu/
Cat     PTM databases
Taxon   2 | Bacteria
Taxon   2157 | Archaea
EDAMtpc 0751 | Phosphorylation sites
EDAMdat 2071 | Sequence motif (protein)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query    Sequence motif (protein) {PhosSite entry} | HTML | UniProt accession | http://www.phosphorylation.biochem.vt.edu/xpd2.cfm?extf=uniprot&amp;extref=%s
Example UniProt accession | P36683

ID      UniProtKB_Swiss-Prot
IDalt   SwissProt
Name    Universal protein resource knowledge base / Swiss-Prot
Desc    Section of the UniProt knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature
URL     http://www.uniprot.org
Taxon   1 | all
EDAMtpc 0639 | Protein sequence analysis
EDAMdat 2201 | Sequence record full
EDAMid  3021 | UniProt accession
EDAMfmt 1929 | FASTA format
EDAMfmt 2376 | RDF
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    EMBL_explicit | UniProt accession
Query    Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s
Query    Sequence record full | Text | UniProt accession | http://www.uniprot.org/uniprot/%s.txt
Query    Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml


<font color=red>  [Part of this file has been deleted for brevity]</font>

EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query    2D PAGE spot annotation | HTML | UniProt accession | http://www.mpiib-berlin.mpg.de/mpiib-cgi/RAT-HEART/get-2d-entry?%s
Example UniProt accession | P62738

ID      PHCI-2DPAGE
Acc     DB-0075
Name    Parasite host cell interaction 2D-PAGE database (PHCI-2DPAGE)
Desc    Two-dimensional polyacrylamide gel electrophoresis database.
URL     http://www.gram.au.dk/2d/2d.html
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query    Experiment annotation (2D PAGE) | HTML | UniProt accession | http://www.gram.au.dk/cgi-bin/get-2d-entry?%s
Example UniProt accession | P17821

ID      Bgee
Acc     DB-0133
Name    Bgee database for gene expression evolution
Desc    Bgee is a database to retrieve and compare gene expression patterns between animal species.  Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on anatomical and developmental ontologies.  Then, in order to perform automated cross species comparisons, homology relationships across anatomical ontologies, and comparison criteria between developmental ontologies, are designed.
URL     http://bgee.unil.ch
Cat     Gene expression databases
Taxon   1 | all
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0203 | Transcriptomics
EDAMdat 0929 | Gene annotation (expression)
EDAMdat 0928 | Gene expression profile
EDAMdat 0916 | Gene annotation
EDAMdat 2579 | Gene annotation (expressed gene list)
EDAMid  3021 | UniProt accession
EDAMid  1033 | Gene ID (Ensembl)
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query    Gene annotation | HTML | UniProt accession | http://bgee.unil.ch/bgee/bgee?uniprot_id=%s
Query    Gene annotation | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=gene&amp;action=expression&amp;gene_id=%s
Query    Gene expression profile | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=gene&amp;action=expression&amp;gene_id=%s
Query    Gene annotation (expression) | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&amp;action=data&amp;gene_id=%s
Query    Gene annotation (expressed gene list) {Bgee ID file} | Text | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&amp;action=genes&amp;search_by=1&amp;organ_children=on&amp;gene_organ_stage_information=on&amp;attribut_list=species_name&amp;attribut_list=gene_name&amp;attribut_list=gene_id&amp;gene_id=%s&amp;display_type=tsv
Query    Gene annotation (expressed gene list) {Bgee ID file with expression data} | Text | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&amp;action=genes&amp;search_by=1&amp;organ_children=on&amp;gene_organ_stage_information=on&amp;attribut_list=species_name&amp;attribut_list=gene_name&amp;attribut_list=gene_id&amp;gene_id=%s&amp;display_type=tsv&amp;gene_information=2
Query    Gene annotation (expressed gene list) {Bgee ID file with expression data count} | Text | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&amp;action=genes&amp;search_by=1&amp;organ_children=on&amp;gene_organ_stage_information=on&amp;attribut_list=species_name&amp;attribut_list=gene_name&amp;attribut_list=gene_id&amp;gene_id=%s&amp;display_type=tsv&amp;gene_information=1
Query    Gene annotation (expressed gene list) {Bgee ID file} | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&amp;action=genes&amp;search_by=1&amp;organ_children=on&amp;gene_organ_stage_information=on&amp;attribut_list=species_name&amp;attribut_list=gene_name&amp;attribut_list=gene_id&amp;gene_id=%s
Query    Gene annotation (expressed gene list) {Bgee ID file with expression data} | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&amp;action=genes&amp;search_by=1&amp;organ_children=on&amp;gene_organ_stage_information=on&amp;attribut_list=species_name&amp;attribut_list=gene_name&amp;attribut_list=gene_id&amp;gene_id=%s&amp;gene_information=2
Query    Gene annotation (expressed gene list) {Bgee ID file with expression data count} | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&amp;action=genes&amp;search_by=1&amp;organ_children=on&amp;gene_organ_stage_information=on&amp;attribut_list=species_name&amp;attribut_list=gene_name&amp;attribut_list=gene_id&amp;gene_id=%s&amp;gene_information=1
Example Gene ID (Ensembl) | ENSG00000091831
Example UniProt accession | P32234

</pre>
</td></tr></table><p>





<H2>
    Data files
</H2>

<!-- 
        Any data files used (e.g. translation table file)
        This includes example data file formats if they are
        not obvious.

	If you wish to include the standard description of what data
	files are and how to use embossdata to inspect and retrieve
	them, use:

        #include file="inc/localfiles.ihtml"
   -->


The Data Resource Catalogue is included in EMBOSS as local
database <b>drcat</b>.


The EDAM Ontology is included in EMBOSS as local
database <b>edam</b>.





<H2>
    Notes
</H2>

<!-- 
        Restrictions.
        Interesting behaviour.
        Useful things you can do with this program.
   -->

None.







<H2>
    References
</H2>

<!-- 
        Bibliography for methods used.
<ol>

<li>

</ol>

   -->

None.








<H2>
    Warnings
</H2>

<!-- 
        Potentially stupid things the program will let you do.
   -->

None.







<H2>
    Diagnostic Error Messages
</H2>

<!-- 
        Error messages specific to this program, eg:
        "FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
   -->

None.







<H2>
    Exit status
</H2>

<!-- 
        Description of the exit status for various error conditions
   -->

It always exits with status 0.








<H2>
    Known bugs
</H2>


<!-- 
        Bugs noted but not yet fixed.
   -->

None.








<!--
<H2>
    See also
</H2>
-->
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="drfinddata.html">drfinddata</a></td>
<td>Find public databases by data type</td>
</tr>

<tr>
<td><a href="drfindformat.html">drfindformat</a></td>
<td>Find public databases by format</td>
</tr>

<tr>
<td><a href="drfindresource.html">drfindresource</a></td>
<td>Find public databases by resource</td>
</tr>

<tr>
<td><a href="drget.html">drget</a></td>
<td>Get data resource entries</td>
</tr>

<tr>
<td><a href="drtext.html">drtext</a></td>
<td>Get data resource entries complete text</td>
</tr>

<tr>
<td><a href="edamdef.html">edamdef</a></td>
<td>Find EDAM ontology terms by definition</td>
</tr>

<tr>
<td><a href="edamhasinput.html">edamhasinput</a></td>
<td>Find EDAM ontology terms by has_input relation</td>
</tr>

<tr>
<td><a href="edamhasoutput.html">edamhasoutput</a></td>
<td>Find EDAM ontology terms by has_output relation</td>
</tr>

<tr>
<td><a href="edamisformat.html">edamisformat</a></td>
<td>Find EDAM ontology terms by is_format_of relation</td>
</tr>

<tr>
<td><a href="edamisid.html">edamisid</a></td>
<td>Find EDAM ontology terms by is_identifier_of relation</td>
</tr>

<tr>
<td><a href="edamname.html">edamname</a></td>
<td>Find EDAM ontology terms by name</td>
</tr>

<tr>
<td><a href="wossdata.html">wossdata</a></td>
<td>Find programs by EDAM data</td>
</tr>

<tr>
<td><a href="wossinput.html">wossinput</a></td>
<td>Find programs by EDAM input data</td>
</tr>

<tr>
<td><a href="wossoperation.html">wossoperation</a></td>
<td>Find programs by EDAM operation</td>
</tr>

<tr>
<td><a href="wossoutput.html">wossoutput</a></td>
<td>Find programs by EDAM output data</td>
</tr>

<tr>
<td><a href="wossparam.html">wossparam</a></td>
<td>Find programs by EDAM parameter</td>
</tr>

<tr>
<td><a href="wosstopic.html">wosstopic</a></td>
<td>Find programs by EDAM topic</td>
</tr>

</table>
<!-- 
        Add any comments about other associated programs (to prepare
        data files?) that seealso doesn't find. 
   -->










<H2>
    Author(s)
</H2>

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

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.

<H2>
    History
</H2>
<!--
        Date written and what changes have been made go in this file.
   -->




<H2>
    Target users
</H2>
<!--
        For general users, use this text
   -->
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
<!--
        User/developer/other comments go in this file.
   -->
None


</BODY>
</HTML>