<p>I'm running the following command which uses the NCBI e-utilities:</p>
<p><code>esearch -db bioproject -query &quot;PRJNA198476 [PRJA]&quot; | esummary</code></p>
<p>This returns:</p>
<pre><code>&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; ?&gt;
&lt;!DOCTYPE DocumentSummarySet PUBLIC &quot;-//NLM//DTD esummary bioproject 20140903//EN&quot; &quot;https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20140903/esummary_bioproject.dtd&quot;&gt;

&lt;DocumentSummarySet status=&quot;OK&quot;&gt;
&lt;DbBuild&gt;Build211111-1430.1&lt;/DbBuild&gt;

&lt;DocumentSummary&gt;&lt;Id&gt;198476&lt;/Id&gt;
    &lt;TaxId&gt;6239&lt;/TaxId&gt;
    &lt;Project_Id&gt;198476&lt;/Project_Id&gt;
    &lt;Project_Acc&gt;PRJNA198476&lt;/Project_Acc&gt;
    &lt;Project_Type&gt;Primary submission&lt;/Project_Type&gt;
    &lt;Project_Data_Type&gt;Transcriptome or Gene expression&lt;/Project_Data_Type&gt;
    &lt;Sort_By_ProjectType&gt;476331&lt;/Sort_By_ProjectType&gt;
    &lt;Sort_By_DataType&gt;472932&lt;/Sort_By_DataType&gt;
    &lt;Sort_By_Organism&gt;51608&lt;/Sort_By_Organism&gt;
    &lt;Project_Subtype&gt;&lt;/Project_Subtype&gt;
    &lt;Project_Target_Scope&gt;Multiisolate&lt;/Project_Target_Scope&gt;
    &lt;Project_Target_Material&gt;Transcriptome&lt;/Project_Target_Material&gt;
    &lt;Project_Target_Capture&gt;Whole&lt;/Project_Target_Capture&gt;
    &lt;Project_MethodType&gt;Sequencing&lt;/Project_MethodType&gt;
    &lt;Project_Method&gt;&lt;/Project_Method&gt;
    &lt;Project_Objectives_List&gt;
        &lt;Project_Objectives_Struct&gt;
            &lt;Project_ObjectivesType&gt;Expression&lt;/Project_ObjectivesType&gt;
            &lt;Project_Objectives&gt;&lt;/Project_Objectives&gt;
        &lt;/Project_Objectives_Struct&gt;
    &lt;/Project_Objectives_List&gt;
    &lt;Registration_Date&gt;2013/04/22 00:00&lt;/Registration_Date&gt;
    &lt;Project_Name&gt;Caenorhabditis elegans&lt;/Project_Name&gt;
    &lt;Project_Title&gt;Deep sequencing of endogenous mRNA from Caenorhabditis elegans in the presence and absence of arsenite&lt;/Project_Title&gt;
    &lt;Project_Description&gt;Background: Arsenite is one of the most toxic chemical substances known and is assumed to exert detrimental effects on viability even at lowest concentrations. By contrast and unlike higher concentrations, we here find that exposure to low-dose arsenite promotes growth of cultured mammalian cells. In the nematode C. elegans, low-dose arsenite promotes resistance against thermal and chemical stressors, and extends lifespan of this metazoan, whereas higher concentrations reduce longevity. While arsenite causes a transient increase in reactive oxygen species (ROS) levels in C. elegans, co-exposure to ROS scavengers prevents the lifespan-extending capabilities of arsenite, indicating that transiently increased ROS levels act as transducers of arsenite effects on lifespan, a process known as mitohormesis. The RNA-seq data comprises 2 biological replicates for worms exposed to 100nM Arsenite 48h after L4 and 2 biological replicates of the same age as controls Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de) Overall design: 4 samples: 2 mRNA profiles of C.elegans 48h after L4 exposed to Arsenite; 2 mRNA profiles of C.elegans 48h after L4 as controls (H20). The N2 wild type (var. Bristol) strain was used.&lt;/Project_Description&gt;
    &lt;Keyword&gt;&lt;/Keyword&gt;
    &lt;Relevance_Agricultural&gt;&lt;/Relevance_Agricultural&gt;
    &lt;Relevance_Medical&gt;&lt;/Relevance_Medical&gt;
    &lt;Relevance_Industrial&gt;&lt;/Relevance_Industrial&gt;
    &lt;Relevance_Environmental&gt;&lt;/Relevance_Environmental&gt;
    &lt;Relevance_Evolution&gt;&lt;/Relevance_Evolution&gt;
    &lt;Relevance_Model&gt;Yes&lt;/Relevance_Model&gt;
    &lt;Relevance_Other&gt;&lt;/Relevance_Other&gt;
    &lt;Organism_Name&gt;Caenorhabditis elegans&lt;/Organism_Name&gt;
    &lt;Organism_Strain&gt;&lt;/Organism_Strain&gt;
    &lt;Organism_Label&gt;&lt;/Organism_Label&gt;
    &lt;Sequencing_Status&gt;SRA/Trace&lt;/Sequencing_Status&gt;
    &lt;Submitter_Organization&gt;Leibniz Institute for Age Research - Fritz Lipmann Institute&lt;/Submitter_Organization&gt;
    &lt;Submitter_Organization_List&gt;
        &lt;string&gt;Leibniz Institute for Age Research - Fritz Lipmann Institute&lt;/string&gt;
    &lt;/Submitter_Organization_List&gt;
    &lt;Supergroup&gt;Eukaryotes&lt;/Supergroup&gt;
&lt;/DocumentSummary&gt;

&lt;/DocumentSummarySet&gt;
</code></pre>
<p>I'm trying to extract the <code>Submitter_Organization</code> using:</p>
<p><code>esearch -db bioproject -query &quot;PRJNA198476 [PRJA]&quot; | esummary | xtract -pattern DocummentSummary -element Submitter_Organization</code></p>
<p>However, this returns nothing, and I can't figure out why</p>

CC BY-SA 4.0
2021-11-14T13:22:55.403Z
You have a typo in `DocumentSummary`.
vkkodali
CC BY-SA 4.0
2021-11-14T15:32:39.563Z
@vkkodali thank you that was it
An Ignorant Wanderer
<phylogenetics><e-utilities>
xtract from eutilities not exctracting the information I need
# xtract from eutilities not exctracting the information I need

(Asked by: username_0 on 2021-11-14)

I'm running the following command which uses the NCBI e-utilities:
esearch -db bioproject -query "PRJNA198476 [PRJA]" | esummary
This returns:




Build211111-1430.1

198476
    6239
    198476
    PRJNA198476
    Primary submission
    Transcriptome or Gene expression
    476331
    472932
    51608
    
    Multiisolate
    Transcriptome
    Whole
    Sequencing
    
    
        
            Expression
            
        
    
    2013/04/22 00:00
    Caenorhabditis elegans
    Deep sequencing of endogenous mRNA from Caenorhabditis elegans in the presence and absence of arsenite
    Background: Arsenite is one of the most toxic chemical substances known and is assumed to exert detrimental effects on viability even at lowest concentrations. By contrast and unlike higher concentrations, we here find that exposure to low-dose arsenite promotes growth of cultured mammalian cells. In the nematode C. elegans, low-dose arsenite promotes resistance against thermal and chemical stressors, and extends lifespan of this metazoan, whereas higher concentrations reduce longevity. While arsenite causes a transient increase in reactive oxygen species (ROS) levels in C. elegans, co-exposure to ROS scavengers prevents the lifespan-extending capabilities of arsenite, indicating that transiently increased ROS levels act as transducers of arsenite effects on lifespan, a process known as mitohormesis. The RNA-seq data comprises 2 biological replicates for worms exposed to 100nM Arsenite 48h after L4 and 2 biological replicates of the same age as controls Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de) Overall design: 4 samples: 2 mRNA profiles of C.elegans 48h after L4 exposed to Arsenite; 2 mRNA profiles of C.elegans 48h after L4 as controls (H20). The N2 wild type (var. Bristol) strain was used.
    
    
    
    
    
    
    Yes
    
    Caenorhabditis elegans
    
    
    SRA/Trace
    Leibniz Institute for Age Research - Fritz Lipmann Institute
    
        Leibniz Institute for Age Research - Fritz Lipmann Institute
    
    Eukaryotes




I'm trying to extract the Submitter_Organization using:
esearch -db bioproject -query "PRJNA198476 [PRJA]" | esummary | xtract -pattern DocummentSummary -element Submitter_Organization
However, this returns nothing, and I can't figure out why

**Tags:** phylogenetics, e-utilities
> **Comments:**
> **username_1**: You have a typo in `DocumentSummary`.  
> **username_0**: @vkkodali thank you that was it  

---

## 0 answers

