Web services

The EMBL-EBI provides RESTful web services for the LRG project. It also provides client tools in several programming languages to query their RESTful web services and parse their outputs. This replaces the now deprecated LRG web services previously available from the old website.

The EMBL-EBI RESTful web services provide several output formats such as XML, JSON, CSV or TSV.

Two main types of queries are available:

The list of fields retrievables are listed here

Search LRG(s)

Retrieve a LRG using a HGNC symbol
Query:
https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=name:<HGNC_symbol>
Example:
Output format Example URL Example output
XML (default) https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=name:COL1A1
JSON https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=name:COL1A1&format=json
Retrieve a LRG using external references
Query:
https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=<xref_id>
Example:
Output format Example URL Example output
XML (default) https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=ENSG00000108821
JSON https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=ENSG00000108821&format=json
Get the list of public LRG
Query:
https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=status:public
Example:
Output format Example URL Example output
XML (default) https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=status:public&size=100
JSON https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=status:public&size=100&format=json

The particularity of the EMBL-EBI REST web service is it only returns a maximum of 100 results at a time.

To retrieve all the data, if the total of entries is greater than 100, you need to use the pagination, e.g.:
Looking at the tag "hitCount" you can see how many entries have been found, and then you can loop over this number to retrieve all the results. Let's say the total number of result is <hitCount>665</hitCount>, we have to loop like this:

https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=status:public&size=100&start=0

https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=status:public&size=100&start=100

...

https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=status:public&size=100&start=600

Get the list of pending LRG
Query:
https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=status:pending

Same as the section above "Get list of public LRGs", replacing the status "public" by "pending".</span>


Get LRG data annotation from one or several entries

Get the genomic coordinates of a list of LRGs
Example URL syntax:
https://www.ebi.ac.uk/ebisearch/ws/rest/lrg/entry/<lrg_ids_list>?fields=<list_of_fields>
Example for GRCh37 coordinates:
Output format Example URL Example output
XML (default) /entry/LRG_1?fields=chr_name_grch37,chr_start_grch37,chr_end_grch37,chr_strand_grch37
JSON /entry/LRG_1?fields=chr_name_grch37,chr_start_grch37,chr_end_grch37,chr_strand_grch37&format=json
Example for GRCh38 coordinates:
Output format Example URL Example output
XML (default) /entry/LRG_1?fields=chr_name_grch38,chr_start_grch38,chr_end_grch38,chr_strand_grch38
JSON /entry/LRG_1?fields=chr_name_grch38,chr_start_grch38,chr_end_grch38,chr_strand_grch38&format=json
Example with several LRGs in 1 query (GRCh38 coordinates):
Output format Example URL Example output
XML (default) /entry/LRG_1,LRG_2?fields=chr_name_grch38,chr_start_grch38,chr_end_grch38,chr_strand_grch38
JSON /entry/LRG_1,LRG_2?fields=chr_name_grch38,chr_start_grch38,chr_end_grch38,chr_strand_grch38&format=json
Get the HGNC symbols of a list of LRGs
Example URL syntax:
https://www.ebi.ac.uk/ebisearch/ws/rest/lrg/entry/<lrg_ids_list>?fields=name
Example for one LRG:
Output format Example URL Example output
XML (default) https://www.ebi.ac.uk/ebisearch/ws/rest/lrg/entry/LRG_1?fields=name
JSON https://www.ebi.ac.uk/ebisearch/ws/rest/lrg/entry/LRG_1?fields=name&format=json
Example for several LRGs:
Output format Example URL Example output
XML (default) https://www.ebi.ac.uk/ebisearch/ws/rest/lrg/entry/LRG_1,LRG_2?fields=name
JSON https://www.ebi.ac.uk/ebisearch/ws/rest/lrg/entry/LRG_1,LRG_2?fields=name&format=json
Get the status of a list of LRGs
Example URL syntax:
https://www.ebi.ac.uk/ebisearch/ws/rest/lrg/entry/<lrg_ids_list>?fields=status
Example for one LRG:
Output format Example URL Example output
XML (default) https://www.ebi.ac.uk/ebisearch/ws/rest/lrg/entry/LRG_1?fields=status
JSON https://www.ebi.ac.uk/ebisearch/ws/rest/lrg/entry/LRG_1?fields=status&format=json
Example for several LRGs:
Output format Example URL Example output
XML (default) https://www.ebi.ac.uk/ebisearch/ws/rest/lrg/entry/LRG_1,LRG_9?fields=name
JSON https://www.ebi.ac.uk/ebisearch/ws/rest/lrg/entry/LRG_1,LRG_9?fields=name&format=json
The results can be "public" (finalised LRG and thus made public) or "pending" (in working progress to agree on the LRG sequences and the choice of transcript(s)).


List of fields available

Type Field Description Example (using LRG_1)
GRCh37 coordinates assembly_grch37 Version of the GRCh37 assembly GRCh37.p13
chr_name_grch37 Chromosome name where the LRG is mapped on the GRCh37 assembly 17
chr_start_grch37 Location start of the LRG when it is mapped on the GRCh37 assembly 48259457
chr_end_grch37 Location end of the LRG when it is mapped on the GRCh37 assembly 48284000
chr_strand_grch37 Location strand of the LRG when it is mapped on the GRCh37 assembly.
  • "1": corresponds to the forward strand
  • "-1": corresponds to the reverse strand
-1
GRCh38 coordinates assembly_grch38 Version of the GRCh38 assembly GRCh38.p7
chr_name_grch38 Chromosome name where the LRG is mapped on the GRCh38 assembly 17
chr_start_grch38 Location start of the LRG when it is mapped on the GRCh38 assembly 50182096
chr_end_grch38 Location end of the LRG when it is mapped on the GRCh38 assembly 50206639
chr_strand_grch38 Location strand of the LRG when it is mapped on the GRCh37 assembly.
  • "1": corresponds to the forward strand
  • "-1": corresponds to the reverse strand
-1
Other information description Corresponding gene short description collagen type I alpha 1 chain
id LRG identifier LRG_1
in_ensembl Flag informing whether the LRG is available in Ensembl or not.
  • "1": The LRG is available in Ensembl
  • "0": The LRG is not available in Ensembl
1
last_modification_date Date of the last modification of the updatable section in the format YYYYMMDD 20161107
name Corresponding HGNC gene symbol COL1A1
organism Organism associated with the LRG Homo sapiens
status Curation status of the LRG.
  • "public": The LRG has been publicly released and its genomic, transcript and protein sequences won't change.
  • "pending": The LRG curation is still in working progress, which means that the genomic, transcript and protein sequences can change
public