561 lines
37 KiB
HTML
561 lines
37 KiB
HTML
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<title>Organism information - BioSample - NCBI</title>
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<div class="header">
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<div class="res_logo"><h1 class="res_name"><a href="/biosample/" title="BioSample home">BioSample</a></h1><h2 class="res_tagline"></h2></div>
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<div class="search"><form method="get" action="/biosample/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="biosample" selected="selected">BioSample</option><option value="snp">SNP</option><option value="gene">Gene</option><option value="assembly" class="last">Assembly</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search BioSample" value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="isEnabled:false,disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'yes'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div></form><ul class=" inline_list searchlinks"><li>
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<a href="/biosample/advanced">Advanced</a>
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</li></ul></div>
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<div class="nav_and_browser">
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</div>
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<!-- was itemctrl -->
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<div class="container">
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<div id="maincontent" class="content col twelve_col last">
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<div class="col1">
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<div id="str" class="lineheight2em">
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<h1>Organism information</h1>
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<ul>
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<li><a href="#validorganism">Valid organism</a></li>
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<li><a href="#organismwarning">Organism warning</a></li>
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<li><a href="#metagenomes">Metagenomes (microbiomes)</a></li>
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<li><a href="#mag">Metagenome-assembled genomes</a></li>
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</ul>
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<h2 id="validorganism">Valid organism</h2>
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<p>
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In general, NCBI BioSample requires each record to have a single organism, with a valid taxonomy name to the species level.
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</p>
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<p>
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In most cases, you should enter the binomial scientific name, with complete genus and species. This includes model organisms and species with well-known common names. Examples:
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</p>
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<ul>
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<li>Homo sapiens instead of "human"</li>
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<li>Mus musculus instead of "mouse"</li>
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<li>Escherichia coli instead of "E. coli"</li>
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</ul>
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<p>
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If the name is published and is in the <a href="/taxonomy/">NCBI Taxonomy database</a>, it will be automatically processed.
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</p>
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<h2 id="organismwarning">Organism warning</h2>
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<P>
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If the name is not found in the <a href="/taxonomy/">NCBI Taxonomy database</a>, you will see a message that says:
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</P>
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<pre>
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Warning: Submission processing may be delayed due to necessary curator review.
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Please check spelling of organism, current information could not be resolved
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automatically and will require a taxonomy consult.
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</pre>
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<p>
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First, check that you spelled the organism name correctly.
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For example, "Homo spaiens" instead of "Homo sapiens".
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Make any needed corrections and click "Continue" again to resubmit the page.
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</p>
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<p>
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If the name is spelled correctly, there are valid reasons for the name triggering the Warning message, including:
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</p>
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<ul>
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<li>A validly published name may not yet be in the NCBI Taxonomy database. The database is authoritative but not comprehensive.
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We only add species names when we receive a sequence submission for the organism, so not every valid species is there.</li>
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<li>You may be submitting a new taxonomy name or new combination that is not yet published.</li>
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<li>You may be submitting an organism that you identified to genus or higher taxa, but not species.</li>
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</ul>
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<p>
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If the name submitted is a valid name but not yet in the NCBI taxonomy database, enter the binomial name and our taxonomists will add it to the database.
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</p>
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<p>
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In the case of unpublished or unidentified species, our taxonomists assign a provisional taxID for the organism based on the genus and the strain or isolate name.
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</p>
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<p>
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If your organism is unpublished or unidentified, be sure to include a unique identifier, such as isolate or strain name or a voucher specimen number.
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The identifier should be unique among your samples and should not include the organism name or an abbreviation of the organism name.
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It should be a series of letters or numbers that serve as an identifier for your specimen, for example:
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</p>
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<ul>
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<li>Staphlococcus sp.</li>
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<li>strain= abc123</li>
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</ul>
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<p>
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For an organism not identified to genus, use the lowest taxon (phylum, class, order, or family) that you know.
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</p>
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<p>
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For bacterial or archaeal taxa, append "bacterium" or "archaeon" to the organism name, for example:
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</p>
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<ul>
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<li>Enterobacteriaceae bacterium</li>
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<li>Nanoarchaeales archaeon</li>
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</ul>
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<p>
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For all other organisms, append "sp." to the name, for example:
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</p>
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<ul>
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<li>A termite identified only to Family "Rhinotermitinae" but not to genus would be entered as "Rhinotermitinae sp."</li>
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</ul>
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<p>
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If you submit multiple "[taxon] sp." samples and these are thought to come from more than one putative
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species containing several isolates or strains, please present these as "[taxon] sp. 1," "[taxon] sp. 2," etc.,
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or with other unique identifiers to group them. The common format in NCBI Taxonomy ensure these are unique involve
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appending submitters’ initials and year, for example:
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</p>
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<ul>
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<li>[taxon] sp. 1 ABC-2021</li>
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<li>[taxon] sp. 2 ABC-2021</li>
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</ul>
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<h2 id="metagenomes">Metagenomes (Microbiomes)</h2>
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<p>
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We consider any environmental or clinical sample that may contain multiple organisms to be a "metagenome".
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Typically, metagenome samples are composed of microbial organisms, including archaea, bacteria and fungi, but are not restricted to those.
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The terminology is partially historical, since the first instances of this sample type were for genomic sequencing,
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but it now includes any sample of this type, regardless of the type of data that will be generated.
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You can think of NCBI "metagenome" taxonomy nodes as meaning "microbiomes".
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</p>
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<p>
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If you are submitting sequences from such a sample, you need to use one of a special set of taxonomy nodes.
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The <a href="/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169">metagenome taxonomy nodes</a> are under "unclassified sequences",
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since there is not a specific lineage. These are mostly divided into
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<a href="/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=410657&lvl=3&lin=f&keep=1&srchmode=1&unlock">ecological metagenomes</a> and
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<a href="/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=410656&lvl=3&lin=f&keep=1&srchmode=1&unlock">organismal metagenomes</a>.
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These are created on an as-needed basis, so not every imaginable type is present.
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Current practice is to use an existing node wherever possible and to provide more detailed information in the
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isolation_source and/or host attribute. The metagenome names are reflective of the source, not the organisms that will be identified.
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You should use the same name regardless of the type of sequencing you will be using. For example, if you are using 16S RNA primers to
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target bacterial species or ITS primers to target eukaryotic species, the metagenome name to use remains the same.
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</p>
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<p>
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Browse the list and use the taxonomy name that best describes your sample. Some judgement is involved in choosing names
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and you should consider the intention of the study. There are minimal checks on the name you choose,
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to allow for maximum flexibility, but it must be in the NCBI Taxonomy database. Examples include:
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</p>
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<ul>
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<li>A soil sample could use "soil metagenome" or perhaps "rhizome metagenome".</li>
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<li>A plant sample would use "plant metagenome" or might use more specific names like "root metagenome" or "leaf metagenome" if only those tissues were sampled.</li>
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<li>If the sample is from a specific organ of an animal, use a tissue-specific name where available,
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such as "skin metagenome" or "liver metagenome", or you can use one of the organism-specific names, such as "mouse metagenome" or "human metagenome",
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or the generic "insect metagenome" or "mollusk metagenome".</li>
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<li>A sample from a goat rumen or from mouse cecum would use "gut metagenome". In such cases, be sure to include the host organism in the "host" field.</li>
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<li>Stool or feces samples would also use "gut metagenome" if the target of the study is the intestinal microbiota of the organism.
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Alternately, if the bacterial community that develops on weathering feces outside the animal is the target of the study, use "feces metagenome".
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In either case provide the source organism name in the host field.</li>
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<li>Note that there are a few specific gut metagenomes for commonly studied organisms, including "human gut metagenome", "mouse gut metagenome", and others.</li>
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<li>A cyanobacterial enrichment culture would usually use "freshwater metagenome".</li>
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<li>An artificial community put together from a set of known organisms as a test sample should use "synthetic metagenome"</li>
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</ul>
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<h2 id="mag">Metagenome-assembled genomes</h2>
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<p>
|
||
Metagenome-assembled genomes (MAGs) represent individual organisms computationally binned from samples containing a mixture of one or more organisms.
|
||
The organism names for MAGs are often assigned using clustering tools such as SILVA or <a href="https://gtdb.ecogenomic.org/">GTDB</a> which may use unpublished taxonomic names.
|
||
Please convert unpublished names to the equivalent NCBI taxonomic names. We want names that are taxonomically meaningful,
|
||
at the lowest rank that's reliable (division, phylum, class, order, family, genus). Use "bacterium" or "archaeon" or "Eukaryota sp."
|
||
if you don’t have more information. See this <a href="/genbank/wgsfaq/#metagen">FAQ</a> about submitting prokaryotic or eukaryotic MAGs to GenBank.
|
||
</p>
|
||
<p>
|
||
MAGs also require a unique alpha-numeric code to distinguish each organism. The identifier should be added as an isolate name,
|
||
but we realize each organism was computationally binned and not isolated. The identifier should be unique and is often the same as the sample_name.
|
||
It should not include the organism name or an abbreviation of the organism name. It should be a series of letters or numbers that serve
|
||
as an identifier for your organism assembly.
|
||
</p>
|
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<p>
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For any of the above cases where a Warning message is received, you can click the "Continue" button again and the submission will proceed to the next step.
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At the final step of your submission, you will again be notified that the submission will be delayed for manual review.
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In most cases, this review takes about two business days.
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