Mercurial > repos > iuc > ncbi_eutils_egquery
view generate_macros_xml.pl @ 8:f4318232849e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 41f5eb8e0aee5b779d618b5178098c4be89a9ef1
author | iuc |
---|---|
date | Mon, 23 Jan 2023 10:37:41 +0000 |
parents | 5277d159053d |
children |
line wrap: on
line source
#!/usr/bin/env perl #Usage: perl generate_macros_xml.pl > macros.xml #Note, this script uses einfo.py to get database info. It also uses manually compiled data stored at the bottom of this script that is based on: https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly #The data in the table on that page was manipulated to replace nulls with 'none', remove duplicates, and add missing formats based on correspondence with MLN. ## ## use einfo to retrieve all the valid databases ## print STDERR "Retrieving database list\n"; my $dbxml = `python einfo.py --user_email "planemo@galaxyproject.org" --admin_email "planemo@galaxyproject.org;test@bx.psu.edu"`; my(@dblist); my $dbs = {}; my $dbfroms = {}; my $dbnames = {}; foreach(split(/\n/,$dbxml)) { if(/<DbName>(.+)<\/DbName>/) { my $db = $1; push(@dblist,$db); $dbs->{$db} = 0; $dbfroms->{$db} = 0; $dbnames->{$db} = $_; } } ## ## Use einfo to retrieve all the valid links for each database (Note: some databases are not linked) ## my $h = {}; foreach my $db (sort {$dbnames->{$a} cmp $dbnames->{$b}} @dblist) { sleep(2); print STDERR "Retrieving info for $db\n"; my $response = `python einfo.py --db $db --user_email "planemo\@galaxyproject.org" --admin_email "planemo\@galaxyproject.org;test\@bx.psu.edu"`; my $dolinks = 0; my $link = ""; my $name = ""; foreach(split(/\n/,$response)) { if(/<LinkList>/) { $dolinks = 1; #Save whether there exist links from this database $dbfroms->{$db} = 1; } elsif(!$dolinks) { if(/<MenuName>(.+)<\/MenuName>/) {$dbnames->{$db} = "$1 ($db)"} } elsif($dolinks) { if(/<Name>(.+)<\/Name>/) {$link=$1} elsif(/<Menu>(.*)<\/Menu>/) {$name=$1} elsif(/<DbTo>(.+)<\/DbTo>/) { $dbto=$1; push(@{$h->{$db}->{$dbto}},[$link,$name]); $link=""; $name=""; } } } } my @sorted_dblist = sort {$dbnames->{$a} cmp $dbnames->{$b}} @dblist; ## ## Generate XML to govern the valid databases to use with efetch ## my $efetch_dbhash = {}; #->{efetch-compatible-db}->{rettype-retmode-galaxy_format} = format_name (galaxy_format) while(<DATA>) { chomp; my($db,$galaxy_format,$retmode,$rettype,$format_name) = split(/\t/,$_); $efetch_dbhash->{$db}->{"$rettype-$retmode-$galaxy_format"} = "$format_name ($galaxy_format)"; } #EFetch database select list print << 'EOXML'; <xml name="dbselect_efetch" token_name="db_select" token_label="NCBI Database to Query"> <param name="@NAME@" type="select" label="@LABEL@"> EOXML foreach my $db (grep {exists($dbs->{$_})} sort {$dbnames->{$a} cmp $dbnames->{$b}} keys(%$efetch_dbhash)) { my $selected = ''; if($db eq 'pubmed') {$selected = ' selected="True"'} print << " EOXML"; <option value="$db"$selected>$dbnames->{$db}</option> EOXML } print << 'EOXML'; </param> </xml> EOXML #EFetch output formats print << 'EOXML'; <xml name="efetchdb"> <conditional name="db"> <expand macro="dbselect_efetch" /> EOXML foreach my $db (grep {exists($dbs->{$_})} sort {$dbnames->{$a} cmp $dbnames->{$b}} keys(%$efetch_dbhash)) { print << " EOXML"; <when value="$db"> <param name="output_format" type="select" label="Output Format"> EOXML foreach my $eutils_format (sort {$efetch_dbhash->{$db}->{$a} cmp $efetch_dbhash->{$db}->{$b}} keys(%{$efetch_dbhash->{$db}})) { print << " EOXML"; <option value="$eutils_format">$efetch_dbhash->{$db}->{$eutils_format}</option> EOXML } print << " EOXML"; </param> </when> EOXML } print << 'EOXML'; </conditional> </xml> EOXML ## ## Create a select list for the databases linked *from* ## print << 'EOXML'; <xml name="dbselect" token_name="db_select" token_label="NCBI Database to Query"> <param name="@NAME@" type="select" label="@LABEL@"> EOXML foreach my $from (@sorted_dblist) { print << " EOXML"; <option value="$from">$dbnames->{$from}</option> EOXML } print << 'EOXML'; </param> </xml> EOXML ## ## Create a select list for the databases linked *to* ## print << 'EOXML'; <xml name="dbselect_linked" token_name="db_select_linked" token_label="NCBI Database to Use"> <param name="@NAME@" type="select" label="@LABEL@"> EOXML foreach my $from (grep {$dbfroms->{$_}} @sorted_dblist) { print << " EOXML"; <option value="$from">$dbnames->{$from}</option> EOXML } print << 'EOXML'; </param> </xml> EOXML ## ## Create empty entries for commands that take no *to* database or link ## print << 'EOXML'; <xml name="none_link_macro"> <conditional name="db_to"> <param name="db_select_to" type="select" label="To NCBI Database (n/a)"> <option value="n/a">Not applicable</option> </param> <when value="n/a"> <param name="linkname" type="select" label="Link Name (n/a)"> <option value="n/a">Not applicable</option> </param> </when> </conditional> </xml> <xml name="db_link_macro"> <conditional name="db_from_link"> <expand macro="dbselect_linked" name="db_select_from_link" label="From NCBI Database" /> EOXML foreach(grep {$dbfroms->{$_}} @sorted_dblist) { print << " EOXML"; <when value="$_"> <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> </when> EOXML } print << 'EOXML'; </conditional> </xml> EOXML ## ## This is the master macro for the command selection ## print << 'EOXML'; <xml name="linkmacro"> <conditional name="cmd"> <param name="cmd_select" type="select" label="Link Method" help="Fetch UIDs from the 'To' Database that are linked to supplied UIDs in the 'From' database"> <option value="neighbor" selected="true">Neighbor (neighbor)</option> <option value="neighbor_history">Neighbor, save result in history server (neighbor_history)</option> <option value="neighbor_score">Neighbor Score (neighbor_score)</option> <option value="acheck">Show available links to any database (acheck)</option> <option value="ncheck">Show available links within the same database (ncheck)</option> <option value="lcheck">Show available links to external sources (LinkOuts) (lcheck)</option> <option value="llinks">Show available URLs and attributes for non-library LinkOut providers (llinks)</option> <option value="llinkslib">Show available URLs and attributes for all LinkOut Providers (llinkslib)</option> <option value="prlinks">Show available primary LinkOut Provider Links (prlinks)</option> </param> <when value="neighbor"> <expand macro="db_db_link_macro" name="link_select" label="Link name" /> <param name="output_format" type="select" label="Output Format"> <option value="xml">ID File (xml)</option> <option value="json">ID File (json)</option> <option value="text" selected="true">ID File (tabular)</option> </param> </when> <when value="neighbor_history"> <expand macro="db_db_link_macro" name="link_select" label="Link name" /> <param name="output_format" type="select" label="Output Format"> <option value="json">History File (json)</option> <option value="xml" selected="true">History File (xml)</option> </param> </when> <when value="neighbor_score"> <expand macro="db_db_link_macro" name="link_select" label="Link name" /> <param name="output_format" type="select" label="Output Format"> <option value="xml">ID File (xml)</option> <option value="json">ID File (json)</option> <option value="text" selected="true">ID File (tabular)</option> </param> </when> <when value="acheck"> <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> <param name="output_format" type="select" label="Output Format"> <option value="xml" selected="True">Link Description File (xml)</option> <option value="json">Link Description File (json)</option> </param> </when> <when value="ncheck"> <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> <param name="output_format" type="select" label="Output Format"> <option value="xml" selected="True">Link Description File (xml)</option> <option value="json">Link Description File (json)</option> </param> </when> <when value="lcheck"> <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> <param name="output_format" type="select" label="Output Format"> <option value="xml" selected="True">Link Description File (xml)</option> <option value="json">Link Description File (json)</option> </param> </when> <when value="llinks"> <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> <param name="output_format" type="select" label="Output Format"> <option value="xml" selected="True">Link Description File (xml)</option> <option value="json">Link Description File (json)</option> </param> </when> <when value="llinkslib"> <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> <param name="output_format" type="select" label="Output Format"> <option value="xml" selected="true">Link Description File (xml)</option> <option value="json">Link Description File (json)</option> </param> </when> <when value="prlinks"> <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> <param name="output_format" type="select" label="Output Format"> <option value="xml" selected="true">Link Description File (xml)</option> <option value="json">Link Description File (json)</option> </param> </when> </conditional> </xml> EOXML ## ## Create selections for valid links for command types neighbor, neighbor_history, and neighbor_score ## print << 'EOXML'; <xml name="db_db_link_macro"> <conditional name="db_from_link"> <expand macro="dbselect_linked" name="db_select_from_link" label="From NCBI Database" /> EOXML foreach my $from (grep {$dbfroms->{$_}} @sorted_dblist) { print STDERR ("Creating Links From: $from\n"); print << " EOXML"; <when value="$from"> <conditional name="db_to"> <param name="db_select_to" type="select" label="To NCBI Database"> EOXML my @dbtos = (grep {exists($h->{$from}) && exists($h->{$from}->{$_})} @sorted_dblist); foreach(@dbtos) { print << " EOXML"; <option value="$_">$dbnames->{$_}</option> EOXML } if(scalar(@dbtos) == 0) { #Provide an option for a self-link: from->from print << " EOXML"; <option value="$from">$dbnames->{$from}</option> EOXML } print << ' EOXML'; </param> EOXML if(exists($h->{$from})) { #There do exist links to invalid(/outdated/non-existant) databases that #would result in an error if they are selected, so we use the original #@dblist instead of the keys present in the sub hash of $h->{$from}, and #then check for existence in the sub-hash foreach my $to (grep {exists($h->{$from}->{$_})} @sorted_dblist) { print STDERR ("\tTo: $to Links: ", join(',',map {$_->[0]} @{$h->{$from}->{$to}}), "\n"); print << " EOXML"; <when value="$to"> <param name="linkname" type="select" label="Link Name"> <option value="None">All Links</option> EOXML foreach(sort {"$a->[1] ($a->[0])" cmp "$b->[1] ($b->[0])"} @{$h->{$from}->{$to}}) { print << " EOXML"; <option value="$_->[0]">$_->[1] ($_->[0])</option> EOXML } print << " EOXML"; </param> </when> EOXML } } else { ## ## Add-on selections for self-links for command types neighbor, ## neighbor_history, and neighbor_score ## Note, I'm not sure this would yield a valid result from elink ## #This shows $from, but this is the 'when' for db_to conditional print << " EOXML"; <when value="$from"> <param name="linkname" type="select" label="Link Name"> <option value="none">All Links</option> </param> </when> EOXML } print << ' EOXML'; </conditional> </when> EOXML } ## ## Add-on selections for self-links for command types neighbor, ## neighbor_history, and neighbor_score ## Note, I'm not sure this would yield a valid result from elink ## foreach my $from (grep {!exists($h->{$_})} @sorted_dblist) { print << "EOXML"; <when value=\"$from\"> <conditional name=\"db_to\"> <param name=\"db_select_to\" type=\"select\" label=\"To NCBI Database\"> <option value=\"none\">Not applicable</option> </param> <when value=\"none\"> <param name=\"linkname\" type=\"select\" label=\"Link Name\"> <option value=\"none\">Not applicable</option> </param> </when> </conditional> </when> EOXML } ## ## This is the corresponding code for using the selections to add the respective command line options ## print << 'EOXML'; </conditional> </xml> EOXML print << 'EOXML'; <token name="@LINK_TOKEN@"> <![CDATA[ #if $cmd.db_from_link.db_to.db_select_to == 'n/a': none #else: $cmd.db_from_link.db_to.db_select_to #end if $cmd.db_from_link.db_select_from_link $cmd.cmd_select #if $cmd.output_format == 'json': --retmode json #elif $cmd.output_format == 'text': --retmode uilist #else: --retmode xml #end if #if $cmd.db_from_link.db_to.linkname != 'None' and $cmd.cmd_select in ('neighbor', 'neighbor_history', 'neighbor_score'): --linkname $cmd.db_from_link.db_to.linkname #end if ]]> </token> EOXML sub startXML { print << ' EOXML'; <?xml version="1.0"?> <macros> <token name="@PROFILE@">18.01</token> <token name="@WRAPPER_VERSION@">1.70</token> <token name="@EMAIL_ARGUMENTS@"> --user_email "$__user_email__" #set admin_emails = ';'.join(str($__admin_users__).split(',')) --admin_email "$admin_emails" </token> <!-- TODO: citation --> <token name="@REFERENCES@"><![CDATA[ ]]></token> <token name="@DISCLAIMER@"><![CDATA[ Usage Guidelines and Requirements ================================= Frequency, Timing, and Registration of E-utility URL Requests ------------------------------------------------------------- In order not to overload the E-utility servers, NCBI recommends that users limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time during weekdays. Failure to comply with this policy may result in an IP address being blocked from accessing NCBI. Minimizing the Number of Requests --------------------------------- If a task requires searching for and/or downloading a large number of records, it is much more efficient to use the Entrez History to upload and/or retrieve these records in batches rather than using separate requests for each record. Please refer to Application 3 in Chapter 3 for an example. Many thousands of IDs can be uploaded using a single EPost request, and several hundred records can be downloaded using one EFetch request. Disclaimer and Copyright Issues ------------------------------- In accordance with requirements of NCBI's E-Utilities, we must provide the following disclaimer: Please note that abstracts in PubMed may incorporate material that may be protected by U.S. and foreign copyright laws. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. Transmission or reproduction of protected items beyond that allowed by fair use (PDF) as defined in the copyright laws requires the written permission of the copyright owners. NLM provides no legal advice concerning distribution of copyrighted materials. Please consult your legal counsel. If you wish to do a large data mining project on PubMed data, you can enter into a licensing agreement and lease the data for free from NLM. For more information on this please see `https://www.nlm.nih.gov/databases/download/data_distrib_main.html <https://www.nlm.nih.gov/databases/download/data_distrib_main.html>`__ The `full disclaimer <https://www.ncbi.nlm.nih.gov/home/about/policies/>`__ is available on their website Liability ~~~~~~~~~ For documents and software available from this server, the U.S. Government does not warrant or assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed. Endorsement ~~~~~~~~~~~ NCBI does not endorse or recommend any commercial products, processes, or services. The views and opinions of authors expressed on NCBI's Web sites do not necessarily state or reflect those of the U.S. Government, and they may not be used for advertising or product endorsement purposes. External Links ~~~~~~~~~~~~~~ Some NCBI Web pages may provide links to other Internet sites for the convenience of users. NCBI is not responsible for the availability or content of these external sites, nor does NCBI endorse, warrant, or guarantee the products, services, or information described or offered at these other Internet sites. Users cannot assume that the external sites will abide by the same Privacy Policy to which NCBI adheres. It is the responsibility of the user to examine the copyright and licensing restrictions of linked pages and to secure all necessary permissions. ]]></token> <token name="@LIST_OR_HIST@"> #if $query_source.qss == "history_json": --history_file $query_source.history_file #else if $query_source.qss == "history_xml": --history_xml $query_source.history_xml #else if $query_source.qss == "id_file": --id_list $query_source.id_file #else if $query_source.qss == "id_list": --id $query_source.id_list #else if $query_source.qss == "id_xml": --id_xml $query_source.id_xml #else if $query_source.qss == "id_json": --id_json $query_source.id_json #end if </token> <xml name="list_or_hist"> <conditional name="query_source"> <param name="qss" type="select" label="Enter Query IDs by..." help="Files output by ELink or ESearch are acceptable. Query IDs in an ELink result are ignored."> <option value="history_json">History File (JSON)</option> <option value="history_xml">History File (XML)</option> <option value="id_file" selected="True">ID file (Tabular)</option> <option value="id_xml">ID File (XML)</option> <option value="id_json">ID File (JSON)</option> <option value="id_list">Paste IDs</option> </param> <when value="history_json"> <param label="History File (JSON)" name="history_file" type="data" format="json" help="A JSON file containing the WebEnv ID and Query Key referencing the search on the NCBI history server"/> </when> <when value="history_xml"> <param label="History File (XML)" name="history_xml" type="data" format="xml" help="An XML file containing the WebEnv ID and Query Key referencing the search on the NCBI history server"/> </when> <when value="id_file"> <param label="ID File (Text)" name="id_file" type="data" format="txt,tabular" help="A Text file containing one ID per line"/> </when> <when value="id_xml"> <param label="ID File (XML)" name="id_xml" type="data" format="xml" help="ESearch or ELink Result XML file"/> </when> <when value="id_json"> <param label="ID File (JSON)" name="id_json" type="data" format="json" help="ESearch or ELink Result JSON file"/> </when> <when value="id_list"> <param label="Paste ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/> </when> </conditional> </xml> <xml name="citations"> <citations> <citation type="bibtex">@Book{ncbiEutils, author = {Eric Sayers}, title = {Entrez Programming Utilities Help}, year = {2010}, publisher = {National Center for Biotechnology Information, Bethesda, Maryland}, note = {https://www.ncbi.nlm.nih.gov/books/NBK25500/} }</citation> </citations> </xml> <xml name="requirements"> <requirements> <requirement type="package" version="1.70">biopython</requirement> </requirements> </xml> <token name="@EFETCH_FORMAT_TOKEN@"> <![CDATA[ ## This token must go at the end of the efetch command #set rettype, retmode, format = str($db.output_format).split('-') #if retmode != "none": --retmode $retmode #end if ## Otherwise, defaults to a None/empty which implies 'default' to NCBI #if rettype != "none": --rettype $rettype #end if --galaxy_format $format ]]> </token> EOXML } sub endXML { print << ' EOXML'; </macros> EOXML } BEGIN {startXML()} END {endXML()} ## ## Output formats for efetch mapped to galaxy formats ## #Based on: #https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly #Note: While json works for esearch and elink, the only database that supports #json (according to an NLM support ticket I have about this) is snp #The output_format param value for these will be "rettype-retmode-format" #db galaxy retmode rettype format_name __DATA__ bioproject tabular text uilist List of UIDs bioproject xml xml docsum Document summary bioproject xml xml uilist List of UIDs bioproject xml xml xml Full record biosample tabular text uilist List of UIDs biosample txt text full Full record biosample xml xml docsum Document summary biosample xml xml full Full record biosample xml xml uilist List of UIDs biosystems tabular text uilist List of UIDs biosystems xml xml docsum Document summary biosystems xml xml uilist List of UIDs biosystems xml xml xml Full record clinvar tabular text uilist List of UIDs clinvar xml xml clinvarset ClinVar Set clinvar xml xml docsum Document summary clinvar xml xml uilist List of UIDs clinvar xml none none Full gds tabular text uilist List of UIDs gds txt text summary Summary gds xml xml docsum Document summary gds xml xml uilist List of UIDs gds xml none none Full gene txt text gene_table Gene table gene tabular text uilist List of UIDs gene txt asn.1 none text ASN.1 gene xml xml docsum Document summary gene xml xml none Full gene xml xml uilist List of UIDs gtr tabular text uilist List of UIDs gtr xml xml docsum Document summary gtr xml xml gtracc GTR Test Report gtr xml xml uilist List of UIDs gtr xml none none Full homologene fasta text fasta FASTA homologene tabular text alignmentscores Alignment scores homologene tabular text uilist List of UIDs homologene txt asn.1 none text ASN.1 homologene txt text homologene HomoloGene homologene xml xml docsum Document summary homologene xml xml none Full homologene xml xml uilist List of UIDs mesh tabular text uilist List of UIDs mesh txt text full Full record mesh xml xml docsum Document summary mesh xml xml uilist List of UIDs nlmcatalog tabular text uilist List of UIDs nlmcatalog txt text none Full record nlmcatalog xml xml docsum Document summary nlmcatalog xml xml none Full nlmcatalog xml xml uilist List of UIDs nuccore binary asn.1 none binary ASN.1 nuccore fasta text fasta FASTA nuccore fasta text fasta_cds_aa CDS protein FASTA nuccore fasta text fasta_cds_na CDS nucleotide FASTA nuccore genbank text gb GenBank flat file nuccore genbank text gbwithparts GenBank flat file with full sequence (contigs) nuccore tabular text acc Accession number(s) nuccore txt text ft Feature table nuccore tabular text seqid SeqID string nuccore tabular text uilist List of UIDs nuccore txt text none text ASN.1 nuccore xml xml docsum Document summary nuccore xml xml fasta TinySeq nuccore xml xml gb GBSeq nuccore xml xml gbc INSDSeq nuccore xml xml native Full record nuccore xml xml uilist List of UIDs nucest binary asn.1 none binary ASN.1 nucest fasta text fasta FASTA nucest genbank text gb GenBank flat file nucest tabular text acc Accession number(s) nucest tabular text seqid SeqID string nucest tabular text uilist List of UIDs nucest txt text est EST report nucest txt text none text ASN.1 nucest xml xml docsum Document summary nucest xml xml fasta TinySeq nucest xml xml gb GBSeq nucest xml xml gbc INSDSeq nucest xml xml native Full record nucest xml xml uilist List of UIDs nucgss binary asn.1 none binary ASN.1 nucgss fasta text fasta FASTA nucgss genbank text gb GenBank flat file nucgss tabular text acc Accession number(s) nucgss tabular text seqid SeqID string nucgss tabular text uilist List of UIDs nucgss txt text gss GSS report nucgss txt text none text ASN.1 nucgss xml xml docsum Document summary nucgss xml xml fasta TinySeq nucgss xml xml gb GBSeq nucgss xml xml gbc INSDSeq nucgss xml xml native Full record nucgss xml xml uilist List of UIDs pmc tabular text uilist List of UIDs pmc txt text medline MEDLINE pmc xml xml docsum Document summary pmc xml xml none FULL pmc xml xml uilist List of UIDs popset binary asn.1 none binary ASN.1 popset fasta text fasta FASTA popset genbank text gb GenBank flat file popset tabular text acc Accession number(s) popset tabular text seqid SeqID string popset tabular text uilist List of UIDs popset txt text none text ASN.1 popset xml xml docsum Document summary popset xml xml fasta TinySeq popset xml xml gb GBSeq popset xml xml gbc INSDSeq popset xml xml native Full record popset xml xml uilist List of UIDs protein binary asn.1 none binary ASN.1 protein fasta text fasta FASTA protein tabular text acc Accession number(s) protein txt text ft Feature table protein tabular text seqid SeqID string protein tabular text uilist List of UIDs protein txt text gp GenPept flat file protein txt text none text ASN.1 protein xml xml docsum Document summary protein xml xml fasta TinySeq protein xml xml gp GBSeq protein xml xml gpc INSDSeq protein xml xml ipg Identical Protein protein xml xml native Full record protein xml xml uilist List of UIDs pubmed tabular text uilist List of UIDs pubmed txt asn.1 none text ASN.1 pubmed txt text abstract Abstract pubmed txt text medline MEDLINE pubmed xml xml docsum Document summary pubmed xml xml none Full pubmed xml xml uilist List of UIDs sequences fasta text fasta FASTA sequences tabular text acc Accession number(s) sequences tabular text seqid SeqID string sequences tabular text uilist List of UIDs sequences txt text none text ASN.1 sequences xml xml docsum Document summary sequences xml xml uilist List of UIDs sequences xml none none Full snp fasta text fasta FASTA snp json json docsum Document summary snp json json uilist List of UIDs snp tabular text ssexemplar SS Exemplar list snp tabular text uilist List of UIDs snp txt asn.1 none text ASN.1 snp txt text chr Chromosome report snp txt text docset Summary snp txt text flt Flat file snp txt text rsr RS Cluster report snp xml xml docsum Document summary snp xml xml none XML snp xml xml uilist List of UIDs sra tabular text uilist List of UIDs sra xml xml docsum Document summary sra xml xml full Full taxonomy tabular text uilist List of UIDs taxonomy xml xml none Full taxonomy xml xml docsum Document summary taxonomy xml xml uilist List of UIDs