Hello,
We are trying to get data from the geoprofiles db, but we cannot find a resource for the formats that are available. -format docsum does seem to work, but we ideally want access to the expression data available from the https website. It there a way to get the info via xml?

Hi,
I started to use the following to download few genomes but it doesn't work as expected.
Although I provide the accession for a specific genome, it downloads all the genomes from that species instead, ending sometimes with absurdly big files with tens or hundreds of genomes mixed together

for genome in AL009126.3
do
esearch -db genome -query ${genome} | elink -target assembly | elink -target nuccore | efetch -format fasta > ${genome}.fasta
done

Thanks
Xabi

PS: great initiative

On the web version of the NCBI site you are able to search using a keyword citedby to find all the articles/papers that cited a given article (eg https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2141773/citedby/). Is there a way to do this using EDirect? Thank you.

I've been tricked by this several times, and thought it would be a good addition to the Cookbook. When using while loops without adding the </dev/null after the input the input, only the first line will be processed. Here is the (slightly modified) example from the docs:

  while read org
  do
    esearch -db taxonomy -query "$org [LNGE] AND family [RANK]" < /dev/null |
    efetch -format docsum |
    xtract -pattern DocumentSummary -lbl "$org" \
      -element ScientificName Division
  done <  organisms


(The "< /dev/null" input redirection construct prevents esearch from "draining" the remaining lines from stdin.)

I can make a pull request is this is repo is still being supported.

Is there a script that can list/rank articles under a certain keyword by the most cited by to the least cited by?

Any help would be much appreciated!

When retrieving runinfo from edirect as follows:

PRJN=PRJNA784998
~/edirect/esearch -db sra -query $PRJN | ~/edirect/efetch -format runinfo

there are different metadata fields than when accessing from the SRA Run Selector, and downloading metadata

This is the bioproject here:
https://www.ncbi.nlm.nih.gov/Traces/study/?page=2&query_key=3&WebEnv=MCID_633332599c0211437bc6a566&o=acc_s%3Aa

Of note: BIOMATERIAL_PROVIDER is not part of the efetch runinfo format. Is there a way to get all metadata through efetch? I have tried accessing that field specifically, but can't find it.

Are those two methods of accessing metadata considered equivalent? Or is efetch --format runinfo accessing different metadata?

Thanks,
Karina

I would like to download the nucleotide sequence associated with a gene ID e.g for gene id 17363256, the nucleotide sequence if I clicked "fasta" link on this page
https://www.ncbi.nlm.nih.gov/gene/?term=17363256

Installation of edirect requires the module LWP::Protocol::https and this needs to be added to the installer script (I'm not sure if this is a cookbook issue per se, but you can't use the cookbook without it!)

I install EDirect correctly, and add the edirect directory path to $PATH.
When I test it(eg: esearch -db pubmed -query "Babalobi OO[au] AND 2008[pdat]" ), I got error like below:

curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: http://curl.haxx.se/docs/sslcerts.html

curl performs SSL certificate verification by default, using a "bundle"
of Certificate Authority (CA) public keys (CA certs). If the default
bundle file isn't adequate, you can specify an alternate file
using the --cacert option.
If this HTTPS server uses a certificate signed by a CA represented in
the bundle, the certificate verification probably failed due to a
problem with the certificate (it might be expired, or the name might
not match the domain name in the URL).
If you'd like to turn off curl's verification of the certificate, use
the -k (or --insecure) option.

Hi

I would like to write a edirect query to extract number of publications per gene per year. The group I am interested in is Viridiplantae. So for all species under this group, given a date range, I would like to get the publication count for each gene in that species. The final output that I am looking for is something like

YEAR Genus_Species Gene_Symbol Publication_Count
1970 Arabidopsis thaliana PHYA 3
1971 Arabidopsis thaliana PHYA 2

I can get [PDAT] to work for -db pubmed but not [GENE] or [ORGN]. Need Help. Thanks

Hey all,

I have a list of PMIDs for which I want to extract the Bio project ID and SRA IDs. I was unable to find anything in the documentation for the same. Any suggestions?

Looking forward to your replies!

Almost there, just need to phrase element:

esearch -db sra -query SRR5381359 | elink -target biosample | efetch -format xml | xtract -pattern DocumentSummary -element

I have a sample xml file (shown below) from BioSample and my objective is to extract the SRA and BioProject ids.

</BioSample><BioSample submission_date="2009-11-25T14:28:04.407" access="public" last_update="2015-01-29T02:30:16.280" publication_date="2009-11-25T14:28:09.680" id="5124" accession="SAMN00005124">
  <Ids>
    <Id is_primary="1" db="BioSample">SAMN00005124</Id>
    <Id db="SRA">SRS007221</Id>
    <Id db="GEO">GSM451804</Id>
  </Ids>
  <Description>
    <Title>AdultMale_combined_RNAseq_1, 2</Title>
    <Organism taxonomy_id="7227" taxonomy_name="Drosophila melanogaster">
      <OrganismName>Drosophila melanogaster</OrganismName>
    </Organism>
  </Description>
  <Owner>
    <Name>Institute for Genomics and Systems Biology, University of Chicago</Name>
    <Contacts>
      <Contact email="[email protected]">
        <Name>
          <First>Kevin</First>
          <Last>White</Last>
        </Name>
      </Contact>
    </Contacts>
  </Owner>
  <Models>
    <Model>Generic</Model>
  </Models>
  <Package display_name="Generic">Generic.1.0</Package>
  <Attributes>
    <Attribute attribute_name="source_name" display_name="source name" harmonized_name="source_name">AdultMale</Attribute>
    <Attribute attribute_name="development stage" display_name="development stage" harmonized_name="dev_stage">AdultMale</Attribute>
  </Attributes>
  <Links>
    <Link label="GEO Sample GSM451804" type="url">http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM451804</Link>
    <Link label="PRJNA116485" type="entrez" target="bioproject">116485</Link>
    <Link label="PRJNA168994" type="entrez" target="bioproject">168994</Link>
    <Link label="PRJNA63467" type="entrez" target="bioproject">63467</Link>
  </Links>

Initially the command i used generated this output:

SAMN00014503    SRS074435   128909,129179
SAMN00014655    SRS074533   127185
SAMN00014812    129305,127109

The issue is that the columns shifted to the left when the SRA id isn't present on the xml file.

So after i got in touch with the NCBI staff and together we came up with this answer:

xtract -input out001.xml -pattern BioSample -SRA "(-)" \
-block Id -if Id@db -equals "SRA" -SRA Id \
-block Ids -first Id -element "&SRA" \
-block Link -if Link@target -equals "bioproject" -tab "," -element Link

Then it generated the desired output:

SAMN00014503    SRS074435   128909,129179
SAMN00014655    SRS074533   127185
SAMN00014812    -   129305,127109
SAMN00031920    -
SAMN00032070    -
SAMN00032222    -
SAMN00032375    -

zgrep -v "^#" interim_GRCh38.p10_top_level_2017-05-03.gff3.gz | awk 'BEGIN{FS="\t";OFS="\t"}$3 == "biological_region"{print $0}'

I am interested in getting all the Transcription Factor Chip-seq experiments from GEO and SRA using esearch. Kindly assist me on this I am new to this tool

Hi
I have a list ~500 refseq accession numbers (all bacterial genomes), ~100 of them are completed genomes (CP009681 etc.) while others are assemblies (LALG00000000.1 etc). Most of them are not published and therefore do not have PMID number associate with it. My goal is identify the accession numbers which are published and extract the PMID associated with them. In other words, I want to extract PMID for each accession number if available.
accessions.txt. Accession numbers are in a file, one accession per line. Here is what I have done so far-

cat accessions.txt | epost -db nuccore -format acc | elink -target pubmed | efetch -format xml | xtract -pattern PubmedArticleSet -element PMID

27152133 26048971 25767217 25250641 24970829 24962815 24723721 24051324 23770143

The above output is not in correct format. I need the output in this format-

CP009681 27152133
CP010295 25767217
CP010296 25767217
CP007176 25250641
LALG01000000 26048971
LALH01000000 26048971
LALI01000000 26048971

Any help will be highly appreciated

Tauqeer

16S would be ideal but all mitochondria would be ok

Using the following pubmed id: 28634180

You can see here that the title contains an italic word (MUTYH).

Now let's extract the XML of this paper via the API:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi?db=pubmed&id=28634180
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&query_key=1&WebEnv=<INSERT_WEBENV_HERE>&retype=xml

Here is the "title" entry:
<Item Name="Title" Type="String">A &lt;i&gt;MUTYH&lt;/i&gt; germline mutation is associated with small intestinal neuroendocrine tumors.</Item>

We can see that the italic tag is present in the title in it's escaped form.

I'm a little concerned of a possible security hole if it's possible to submit a title with html code embedded in it. I know nothing about the process of uploading a paper in pubmed (like whether the user input is sanitized or not, who sends papers to pubmed and how). I've just noticed the tags when displaying a summary of the paper above on my website. Since, the NCBI website displays the title with the italic code actually interpreted, I'm wondering what else can be passed to the title (or other) field.

There is a suggestion to "PLEASE UPDATE TO THE LATEST VERSION of E-Direct when possible to avoid a bug in older versions associated with the new NCBI API rate limit policy and API keys".

How does one find the current version of the edirect tools that is installed, and the newest version of the tools available online?

Hi,

I would like to retrieve all NCBI bioproject IDs and the related SRAs for bioprojects that were created within a certain timeframe.
I saw the code that retrieves the SRAs for a given bioproject which works, however, I don't manage to limit my search to a specific timeframe.

What I tried to only retrieve bioproject IDs within a given timeframe:

1. esearch -db bioprojects -query "Mycobacterium tuberculosis" retmax = 10000 | efilter -mindate 2020/02/21 -maxdate 2020/05/01 -datetype crdt
   --> no error message, but the efilter is ignored
2. esearch -db bioproject -query "Mycobacterium tuberculosis" -mindate "2020/02/21" -maxdate "2020/05/01" -datetype "CRDT"

Does someone know what I am doing wrong/how I am able to retrieve only results from a specific time range?

Is it possible to parse out the "Overall design" field? For example: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148355

I am trying to extract all the attributes in each BioSample record. Since each BioSample record has a different set of attributes (for example, some has "source_name" and "development stage"; some has “cell line”, “cell type”, “tissue”, etc.), I want to get the <name value> pairs of all the attributes each BioSample record contains.

When I use the following command:
efetch -db biosample -id SAMN04383980 -format xml | xtract -pattern BioSampleSet -division BioSample -group Attributes -element Attribute
It only outputs the values of all the attributes in BioSample SAMN04383980 as the following:

H7 hESCs       H7 derived

In this output, I do not know which attribute name each of these values belongs to.

I also tried the following command:
efetch -db biosample -id SAMN04383980 -format xml | xtract -pattern BioSampleSet -division BioSample -group Attributes -element Attribute@attribute_name -element Attribute
I got the following output (without <name value> correspondence):

source_name     cell line       H7 hESCs        H7 derived

So I was wondering if there is a way by which I can get <name value> pairs of all the attributes in a BioSample record, like the following:

source_name    cell line
H7 hESCs       H7 derived

I would appreciate your advice.

Thank you very much!

I am trying to extract metadata from a list of Bioprojects Ids.
The script I have works fine, but it cannot deal well with missing data. I read that in the xtract help that I could use the flag -def as Default placeholder for missing fields.
So I tried to add the -def "NA" flag, but it does not change anything in the output.

This is my code:

for i in $(cat $A); 
	do ll=$(esearch -db bioproject -query $i | 
	efetch -format xml |
	xtract -pattern DocumentSummary -element \
	$G,$S,$M,$O,$OT,$TR,$H,$Sa,$BR,$Tro,$Sco,$Org,$E,$Otr,\
	$Phen,$Dis -def "Na" )
	echo -e "$i\t$ll" >> $B;
	done

This s my output:

PRJNA310173
PRJNA253675 eNegative eBacilli eNo eAerobic eMesophilic eHostAssociated Tularemia

This is what I would like to have:

PRJNA310173 Na Na Na Na Na Na Na
PRJNA253675 eNegative eBacilli eNo eAerobic eMesophilic eHostAssociated Tularemia

I was trying to use the “-if “statement in xtract to print out the values of only the Attributes that have harmonized_name in a BioSample record, but all the Attributes values are printed out even though some of them have no harmonized_name.

I have the following xml of a BioSample record by using efetch:

<?xml version="1.0" ?>
<BioSampleSet><BioSample access="public" publication_date="2019-05-30T00:00:00.000" last_update="2019-05-30T15:01:23.120" submission_date="2019-05-30T14:12:04.357" id="11893672" accession="SAMN11893672">   
<Ids>     
    <Id db="BioSample" is_primary="1">SAMN11893672</Id>     
    <Id db_label="Sample name">RS0002</Id>     
    <Id db="SRA">SRS4847476</Id>   
</Ids>   
<Description>     
    <Title>SK-MEL-28_1</Title>     
    <Organism taxonomy_id="9606" taxonomy_name="Homo sapiens">       
        <OrganismName>Homo sapiens</OrganismName>     
    </Organism>   
</Description>   
<Owner>     
    <Name>Research Center for Molecular Medicine of the Austrian Academy of Sciences</Name>     
    <Contacts>       
        <Contact email="[email protected]">         
            <Name>           
                <First>Vitaly</First>           
                <Last>Sedlyarov</Last>         
            </Name>       
        </Contact>     
    </Contacts>   
</Owner>   
<Models>     
    <Model>Human</Model>   
</Models>   
<Package display_name="Human; version 1.0">Human.1.0</Package>   
<Attributes>     
    <Attribute attribute_name="isolate" harmonized_name="isolate" display_name="isolate">cell line</Attribute>     
    <Attribute attribute_name="age" harmonized_name="age" display_name="age">51</Attribute>     
    <Attribute attribute_name="biomaterial_provider" harmonized_name="biomaterial_provider" display_name="biomaterial provider">ATCC</Attribute>     
    <Attribute attribute_name="sex" harmonized_name="sex" display_name="sex">male</Attribute>     
    <Attribute attribute_name="tissue" harmonized_name="tissue" display_name="tissue">skin</Attribute>     
    <Attribute attribute_name="cell_line" harmonized_name="cell_line" display_name="cell line">SK-MEL-28</Attribute>     
    <Attribute attribute_name="replicate">1</Attribute>   
</Attributes>   
<Links>     
    <Link type="entrez" target="bioproject" label="PRJNA545487">545487</Link>   
</Links>   
<Status status="live" when="2019-05-30T14:12:04.358"/> </BioSample> </BioSampleSet>

I use the following command in order to extract only the Attributes that have harmonized_name:

efetch -db biosample -id SAMN11893672 -format xml | xtract -pattern BioSampleSet -division BioSample -group Attributes -if Attribute@harmonized_name -sep ",\t" -element Attribute

However, I got the following output which includes the values of all the Attributes:

cell line,      51,     ATCC,   male,   skin,   SK-MEL-28,      1

The last Attribute (attribute_name=“replicate”, value=1) has no harmonized_name, but its value “1” was also printed out for some reason.
So it looks like my statement -if Attribute@harmonized_name did not work as expected.
Could you please point out any issue in my usage which may have caused this problem?

I was also trying to use the “-unless” statement in xtract to filter out certain Attribute (e.g. filter out the Attribute with harmonized_name="isolate"), but all the Attributes are filtered out for some reason.

For the same BioSample record as described above, when I use the following command:

efetch -db biosample -id SAMN11893672 -format xml | xtract -pattern BioSampleSet -division BioSample -group Attributes -sep ",\t" -element Attribute@harmonized_name

I am able to print out the harmonized_name of all the Attributes as below:

isolate,        age,    biomaterial_provider,   sex,    tissue, cell_line

However, when I try to filter out the Attribute with harmonized_name="isolate" by using the following command:

efetch -db biosample -id SAMN11893672 -format xml | xtract -pattern BioSampleSet -division BioSample -group Attributes -unless Attribute@harmonized_name -equals "isolate" -sep ",\t" -element Attribute@harmonized_name

Nothing is printed out--- all the Attributes are filtered out for some reason.
So it looks like my statement -unless Attribute@harmonized_name -equals "isolate" did not work as expected.
Could you please point out any issue in my usage which may have caused this problem?

I would really appreciate your help!

Thank you very much!

I have a pretty long list of SRA entries that I want to download but before I download everything I would like to know how big I can expect each of the files to be and how big all files will be in sum.
My list contains IDs that start with ERR or PRJNA if that is important.

that correspond to something like

NT5C2 D407Y

Hey All,

I am interested in extracting out the fastq reads of accession ids. But I cant find the element FtpPath in the document summary information.
I am trying something like this-
esearch -db sra -query "ERX4643323" | elink -target biosample | efetch -format docsum | xtract -pattern DocumentSummary -element FtpPath_RefSeq

Is It possible?

Regards
Jigyasa

Stuck here so far: esearch -db bioproject -query "PRJNA356464" | elink -target sra | efetch -format docsum

Perhaps the installation could be easier... i.e. a container and/or homebrew recipe for linux/mac...

Is there a way to tell efetch to download FASTA records such that record headers include the GI number? For example, a given header would look like this
>gi|2248537881|ref|NM_001407571.1| Homo sapiens BRCA1 DNA repair associated (BRCA1), transcript variant 6, mRNA
instead of like this
>NM_001407571.1 Homo sapiens BRCA1 DNA repair associated (BRCA1), transcript variant 6, mRNA

The command I'm using is efetch -db nuccore -input accNosRandom.txt -format fasta > seq.fna where accNosRandom.txt contains a list of accession numbers. It results in the non-GI number format.

I was trying to use efetch to obtain the Attributes of a BioSample record, but I found that for some BioSample records, the Attributes reported in the xml are completely different from those displayed at the NCBI website. And the BioSample Id reported in the xml is different from the BioSample Id specified in the efetch command.
I use the following command to get the xml of a BioSample record:
efetch -db biosample -id SAMEA5244969 -format xml

Example 1: for BioSample SAMEA5244969, the NCBI website displays the Attributes as shown at https://www.ncbi.nlm.nih.gov/biosample/10858554
However, the efetch command reported the following xml:

<?xml version="1.0" ?>
<BioSampleSet>
   <BioSample access="public" publication_date="2016-06-04T00:00:00.000" last_update="2017-01-23T16:11:22.000" submission_date="2016-06-14T11:27:28.390" id="5244969" accession="SAMEA4457316">   
      <Ids>     
         <Id db="BioSample" is_primary="1">SAMEA4457316</Id>   
      </Ids>   
      <Description>     
         <Title>Sample from Homo sapiens</Title>     
         <Organism taxonomy_id="9606" taxonomy_name="Homo sapiens">       
            <OrganismName>Homo sapiens</OrganismName>     
         </Organism>   
      </Description>   
      <Owner>     
         <Name>EBI</Name>   
      </Owner>   
      <Models>     
         <Model>Generic</Model>   
      </Models>   
      <Package display_name="Generic">Generic.1.0</Package>   
      <Attributes>     
         <Attribute attribute_name="Sample Name" harmonized_name="sample_name" display_name="sample name">source 4</Attribute>     
         <Attribute attribute_name="Sex" harmonized_name="sex" display_name="sex">male</Attribute>     
         <Attribute attribute_name="disease state" harmonized_name="disease" display_name="disease">normal</Attribute>     
         <Attribute attribute_name="organism part" harmonized_name="tissue" display_name="tissue">colon</Attribute>     
         <Attribute attribute_name="specimen with known storage state">frozen specimen</Attribute>  
      </Attributes>   
      <Status status="live" when="2016-06-14T11:27:28.393"/> 
   </BioSample> 
</BioSampleSet>

The Attributes in this xml are completely different from those displayed at the NCBI website. And the reported BioSample Id (SAMEA4457316) in this xml is different from the BioSample Id (SAMEA5244969) specified in the efetch command.

Example 2: for BioSample SAMEA104565009, the NCBI website displays the Attributes as shown at https://www.ncbi.nlm.nih.gov/biosample/11349430
However, the efetch command reported the following xml:

<?xml version="1.0" ?>

This xml does not contain any elements even though a list of Attributes are displayed at the NCBI website.

Example 3: for BioSample SAMEA5099860, the NCBI website displays the Attributes as shown at https://www.ncbi.nlm.nih.gov/biosample/10655621
However, the efetch command reported the following xml:

<?xml version="1.0" ?>
<BioSampleSet>
   <BioSample access="public" publication_date="2014-10-22T00:00:00.000" last_update="2016-10-25T08:32:28.000" submission_date="2016-05-19T19:48:00.303" id="5099860" accession="SAMEA3067264">   
      <Ids>     
         <Id db="BioSample" is_primary="1">SAMEA3067264</Id>   
      </Ids>   
      <Description>     
         <Title>Sample from Homo sapiens</Title>     
         <Organism taxonomy_id="9606" taxonomy_name="Homo sapiens">  
            <OrganismName>Homo sapiens</OrganismName>     
         </Organism>     
         <Comment>       
            <Paragraph>ExAC_v0.1_Sample_52281</Paragraph>     
         </Comment>   
      </Description>   
      <Owner>     
         <Name>EBI</Name>   
      </Owner>   
      <Models>     
         <Model>Generic</Model>   
      </Models>   
      <Package display_name="Generic">Generic.1.0</Package>   
      <Attributes>     
         <Attribute attribute_name="Sample Name" harmonized_name="sample_name" display_name="sample name">52281</Attribute>   
      </Attributes>   
      <Status status="live" when="2016-05-19T19:48:00.305"/> 
   </BioSample> 
</BioSampleSet>

The Attributes in this xml are completely different from those displayed at the NCBI website. And the reported BioSample Id (SAMEA3067264) in this xml is different from the BioSample Id (SAMEA5099860) specified in the efetch command.

I was wondering if you have some ideas about why the efetch command did not work correctly for the above BioSamples?

I’d greatly appreciate your help!

Thank you very much!

Hi everyone,

I would like to use a list of gene ids to get FASTA formats of the proteins coded in those genes and the mRNA sequence without introns.

So far with this command I can get the protein sequence:
os.system('esearch -db gene -query "'+ "102888688" + ' [ID]" | elink -target protein -name gene_protein_refseq -cmd neighbor | xtract -pattern LinkSet -block IdList -element Id -block LinkSetDb -element Id | efetch -db protein -format fasta')

With this command I can get the mRNA with introns, which I don't want:
os.system('elink -db gene -id ' + "102888688" + ' -target nuccore -name gene_nuccore_refseqrna | efetch -format fasta')

Dear all,

I am trying to retrieve all bacterial genomic sequences in the refseq database that were collected from oceanic environment. I am trying to do this by limiting the search results to the ones that have the word "marine" or "oceanic" in the field "Isolation source" under Features in the description, but I cannnot figure out how and I am struggling with it.
Could anybody give me suggestions on how?

Thanks in advance.

I think I've seen this somewhere, but can't find it...

So I'm running something like

esearch -db sra -query "XXXXXX YYYYY[orgn] AND \"biomol rna\"[Properties]" | efetch -format docsum | xtract.Linux -pattern DocumentSummary -ACC @acc -LIB Library_descriptor/LIBRARY_NAME -element "&ORGN" Biosample "&ACC" "&LIB"

but the LIBRARY_NAME doesn't always exist (or doesn't have data). So how can I print an empty field (instead of nothing) if no data is found?

To determine which bacterial species/substrains (E. coli, to test) have specific plasmids, a plasmid Blast database was created and Magicblasted with E. coli SRA reads. Most of the hits are to 16S rRNA and tRNA sequences in the plasmids. This issue is how to use the rRNA/tRNA Feature sequences in the Nucleotide db for masking these reads.

For example, how to extract the sequence by using the Feature tag:

rRNA complement(276650..278200)
/locus_tag="BTV67_11800"
/product="16S ribosomal RNA"
(from: https://www.ncbi.nlm.nih.gov/nuccore/CP020346.1)

And then using the sequence it links to for masking the reads that hit it.

What I want to do is

1. search SRA, find all deposited RNAseq for an organism of interest and extract SRA experiment, study, run etc
2. link to BioSample and extract the sample attributes (tissue, developmental stage etc) for the same SRA records.

So far, I've been able to complete the first part like so

esearch -db sra -query "Adoxophyes honmai[orgn] AND \"biomol rna\"[Properties]" | efetch -format docsum | xtract.Linux -pattern DocumentSummary -ACC @acc -element Biosample "&ACC"

And I also know how to "jump" from one database to another with elink

esearch -db sra -query "Adoxophyes honmai[orgn] AND \"biomol rna\"[Properties]" | elink -target biosample | efetch -format docsum | xtract.Linux -pattern SampleData -element OrganismName Id Attribute

However, as soon as I "jump" from SRA to BioSample I can't access information that is only found in SRA (e.g. the SRA Run, Experiment, Study IDs). I guess I'm looking for the equivalent of join in SQL...

Hi all,

I want to download a specific number (e.g., 1,000) of random--it's essential that they be random, although "representative" is perhaps a better word--RNA reference sequence transcripts, preferably from a specific reference build (e.g., GRCh38), although this isn't super important. Any thoughts on how to do this?

By random I mean that there would be nothing to distinguish one batch of 1,000 sequences from another, e.g., in the number of curated (NM_, NR_) versus model (XM_, XR_) sequences. As alluded to above, my goal is to have a completely representative subset of transcript sequences.

Mark

How do you insert the api_key into edirect?

If you are piping between commands (e.g. an epost and then an esummary) does the key need to be supplied to both commands?

Use case is fairly simple:

Given a group (e.g. vertebrates) return all child taxids.

There are a couple biostars posts.

One suggests making a sqlite db sim to @jpb initial suggestion

Second points to this set of tools:

http://etetoolkit.org/docs/2.3/tutorial/tutorial_ncbitaxonomy.html

esearch -db gds -query PRJNA313294[ACCN]

will not work because of the brackets

it needs to be

esearch -db gds -query "PRJNA313294[ACCN]"

I was hoping to do something like this to get recently assembled genomes

esearch -db assembly -query "eucaryotes" -retmax 100 -sort "recently added"

But retmax does not work

Using -days to seek into the past e.g. days 10 always returns none

I use [crdt] in all my PubMed searches and there seems to be no way to pull this date from xml. So I either need a way to pull that data, or even better I want to know the gap where the crdt date is different than the entrez date for the year 2017. If the gap is very small I can use entrez in my EDirect as a direct replacement of [crdt], but if 10-20 percent or more don't match then I can't and need another method to pull [crdt]. So I need a list when they are diff with PMID, crdt date and entrez date for 2017. I can then see how many records are different and the average gap in days between the two when they are different.

Any help or suggestions are greatly appreciated!
Tom

In the example for esearch:

esearch -db assembly -query "Leptospira alstonii[ORGN] AND latest[SB]"

What is [SB]?

If I look for the fields in assembly, e.g. einfo -db assembly -fields

There is no SB listed.

Given a list of accession.version numbers, is there a way to download the official gene symbol (only) of the corresponding gene using one of the EDirect utilities? If not, any thoughts on how this might be best accomplished?