URL for NCBI Efetch + XML with full annotation table

Question

[Pierre Lindenbaum]

Looking at How to dump genes from GenBank in GFF3 format? ? i've tried to download the full record of CM000760.3 as XML using Efetch, but it seems that the annotations are not downloaded (which is a new "feature" to me ):

wget -O - "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=CM000760.3&rettype=gb&retmode=xml"

while https://www.ncbi.nlm.nih.gov/nuccore/CM000760?report=gbwithparts shows the full annotation table.

What would be the correct EFetch URL do get the full table ?

[GenoMax]

@Pierre: how about this?

wget -O - "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=CM000760.3&rettype=gbfull&retmode=xml"

[Pierre Lindenbaum]

@genomax: closer but it's not GBXML ( https://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.mod.dtd ) it's Bioseq-set : ( https://www.ncbi.nlm.nih.gov/dtd/NCBI_Seqset.mod.dtd )

and it matters because I can generate a java parser for genbank:

$ xjc -d tmp -dtd "https://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd"
parsing a schema...
compiling a schema...
generated/GBAltSeqData.java
generated/GBAltSeqDataItems.java
generated/GBAltSeqItem.java
generated/GBAltSeqItemInterval.java
generated/GBAltSeqItemIsgap.java
generated/GBAuthor.java
generated/GBComment.java
generated/GBCommentParagraph.java
generated/GBCommentParagraphs.java
generated/GBFeature.java
generated/GBFeatureIntervals.java
generated/GBFeaturePartial3.java
generated/GBFeaturePartial5.java
generated/GBFeatureQuals.java
generated/GBFeatureSet.java
generated/GBFeatureSetFeatures.java
generated/GBFeatureXrefs.java
generated/GBInterval.java
generated/GBIntervalInterbp.java
generated/GBIntervalIscomp.java
generated/GBKeyword.java
generated/GBQualifier.java
generated/GBReference.java
generated/GBReferenceAuthors.java
generated/GBReferenceXref.java
generated/GBSecondaryAccn.java
generated/GBSeq.java
generated/GBSeqAltSeq.java
generated/GBSeqCommentSet.java
generated/GBSeqFeatureSet.java
generated/GBSeqFeatureTable.java
generated/GBSeqKeywords.java
generated/GBSeqOtherSeqids.java
generated/GBSeqReferences.java
generated/GBSeqSecondaryAccessions.java
generated/GBSeqStrucComments.java
generated/GBSeqXrefs.java
generated/GBSeqid.java
generated/GBSet.java
generated/GBStrucComment.java
generated/GBStrucCommentItem.java
generated/GBStrucCommentItems.java
generated/GBXref.java
generated/ObjectFactory.java

but not for the other one:

$ xjc -d tmp -dtd "http://www.ncbi.nlm.nih.gov/dtd/NCBI_Seqset.dtd"
parsing a schema...
compiling a schema...
[ERROR] A class/interface with the same name "generated.SeqFeatSupport" is already in use. Use a class customization to resolve this conflict.
  line 169 of http://www.ncbi.nlm.nih.gov/dtd/NCBI_Seqfeat.mod.dtd

[ERROR] (Relevant to above error) another "SeqFeatSupport" is generated from here.
  line 331 of http://www.ncbi.nlm.nih.gov/dtd/NCBI_Seqfeat.mod.dtd

Answer 1

[osulliva]

i haven't found efetch retmode, but sviewer.cgi can output gff: curl 'https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=gff3&id=1174565284&extrafeat=976&maxplex=1' id param also takes accession.

[Pierre Lindenbaum]

it doesn't answer my needs but you should post this to : How to dump genes from GenBank in GFF3 format?

[watti3460]

i haven't found efetch retmode, but sviewer.cgi can output gff

If you do this you will undoubtedly be blocked, and receive the following from NCBI:

The site was blocked because of an excessive rate of access to the NCBI sequence servers. The NCBI web pages are a public >service and we need to make it available to a large number of different users.  Single sites with very high rates of access can >impact and cause degradation of our performance. This site made over 50,000 NCBI requests, at a rate at or exceeding one per >second. 

Additionally these request were using the source code for a web page pull down menu. This is an unauthorized, insecure and >inefficient method of obtaining data.

NCBI does not permit scripting against the main web servers. We have servers, APIs and other tools for bulk access of the >data: https://www.ncbi.nlm.nih.gov/home/develop/