Web services

https://www.ebi.ac.uk/ebisearch/ws/rest/lrg

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:

Search LRG(s) using differents terms/IDs, e.g. LRG ID, HGNC symbol, Ensembl accession, NCBI accession, …
Get LRG data annotation from one or several entries

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

Example XML output

<result>
    <hitCount>1</hitCount>
    <entries>
        <entry id="LRG_1" source="lrg"/>
    </entries>
    <facets/>
</result>

Example JSON output

{
  "hitCount": 1,
  "entries": [
               {
                 "id": "LRG_1",
                 "source": "lrg"
               }
             ],
  "facets": []
}

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

Example XML output

<result>
    <hitCount>1</hitCount>
    <entries>
        <entry id="LRG_1" source="lrg"/>
    </entries>
    <facets/>
</result>

Example JSON output

{
  "hitCount": 1,
  "entries": [
               {
                 "id": "LRG_1",
                 "source": "lrg"
               }
             ],
  "facets": []
}

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

Example XML output

<result>
  <hitCount>665</hitCount>
  <entries>
    <entry id="LRG_100" source="lrg"/>
    <entry id="LRG_886" source="lrg"/>
    <entry id="LRG_96" source="lrg"/>
    ... up to 100 entries
  </entries>
  <facets/>
</result>

Example JSON output

{
  "hitCount": 665,
  "entries":
            [
              {"id": "LRG_100", "source": "lrg"},
              {"id": "LRG_886", "source": "lrg"},
              {"id": "LRG_96", "source": "lrg"},
              ... up to 100 entries
            ],
  "facets": []
}

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

Example:

Output format	Example URL
XML (default)	https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=status:pending&size=100
JSON	https://www.ebi.ac.uk/ebisearch/ws/rest/lrg?query=status:pending&size=100&format=json

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 XML output

<result>
  <entries>
    <entry id="LRG_1" source="lrg">
      <fields>
        <field id="chr_name_grch37">
          <values>
            <value>17</value>
          </values>
        </field>
        <field id="chr_start_grch37">
          <values>
            <value>48259457</value>
          </values>
        </field>
        <field id="chr_end_grch37">
          <values>
            <value>48284000</value>
          </values>
        </field>
        <field id="chr_strand_grch37">
          <values>
            <value>-1</value>
          </values>
        </field>
      </fields>
    </entry>
  </entries>
</result>

Example JSON output

{
  "entries": 
    [
      {
        "id": "LRG_1",
        "source": "lrg",
        "fields": 
          {
            "chr_name_grch37": ["17"],
            "chr_start_grch37": ["48259457"],
            "chr_end_grch37": ["48284000"],
            "chr_strand_grch37": ["-1"]
          }
      }
    ]
}

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 XML output

<result>
  <entries>
    <entry id="LRG_1" source="lrg">
      <fields>
        <field id="chr_name_grch38">
          <values>
            <value>17</value>
          </values>
        </field>
        <field id="chr_start_grch38">
          <values>
            <value>50182096</value>
          </values>
        </field>
        <field id="chr_end_grch38">
          <values>
            <value>50206639</value>
          </values>
        </field>
        <field id="chr_strand_grch38">
          <values>
            <value>-1</value>
          </values>
        </field>
      </fields>
    </entry>
  </entries>
</result>

Example JSON output

{
  "entries": 
    [
      {
        "id": "LRG_1",
        "source": "lrg",
        "fields": 
          {
            "chr_name_grch38": ["17"],
            "chr_start_grch38": ["50182096"],
            "chr_end_grch38": ["50206639"],
            "chr_strand_grch38": ["-1"]
          }
      }
    ]
}

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

Example XML output

<result>
  <entries>
    <entry id="LRG_1" source="lrg">
      <fields>
        <field id="chr_name_grch38">
          <values>
            <value>17</value>
          </values>
        </field>
        <field id="chr_start_grch38">
          <values>
            <value>50182096</value>
          </values>
        </field>
        <field id="chr_end_grch38">
          <values>
            <value>50206639</value>
          </values>
        </field>
        <field id="chr_strand_grch38">
          <values>
            <value>-1</value>
          </values>
        </field>
      </fields>
    </entry>
    <entry id="LRG_2" source="lrg">
      <fields>
        <field id="chr_name_grch38">
          <values>
            <value>7</value>
          </values>
        </field>
        <field id="chr_start_grch38">
          <values>
            <value>94389561</value>
          </values>
        </field>
        <field id="chr_end_grch38">
          <values>
            <value>94433232</value>
          </values>
        </field>
        <field id="chr_strand_grch38">
          <values>
            <value>1</value>
          </values>
        </field>
      </fields>
    </entry>
  </entries>
</result>

Example JSON output

{
  "entries": 
    [
      {
        "id": "LRG_1",
        "source": "lrg",
        "fields": 
          {
            "chr_name_grch38": ["17"],
            "chr_start_grch38": ["50182096"],
            "chr_end_grch38": ["50206639"],
            "chr_strand_grch38": ["-1"]
          }
      },
      {
        "id": "LRG_2",
        "source": "lrg",
        "fields": 
          {
            "chr_name_grch38": ["7"],
            "chr_start_grch38": ["94389561"],
            "chr_end_grch38": ["94433232"],
            "chr_strand_grch38": ["1"]
          }
      }
    ]
}

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 XML output

<result>
  <entries>
    <entry id="LRG_1" source="lrg">
      <fields>
        <field id="name">
          <values>
            <value>COL1A1</value>
          </values>
        </field>
      </fields>
    </entry>
  </entries>
</result>

Example JSON output

{
  "entries": 
    [
      {
        "id": "LRG_1",
        "source": "lrg",
        "fields": 
          {
            "name": ["COL1A1"],
          }
      }
    ]
}

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

Example XML output

<result>
  <entries>
    <entry id="LRG_1" source="lrg">
      <fields>
        <field id="name">
          <values>
            <value>COL1A1</value>
          </values>
        </field>
      </fields>
    </entry>
    <entry id="LRG_2" source="lrg">
      <fields>
        <field id="name">
          <values>
            <value>COL1A2</value>
          </values>
        </field>
      </fields>
    </entry>
  </entries>
</result>

Example JSON output

{
  "entries": 
    [
      {
        "id": "LRG_1",
        "source": "lrg",
        "fields": 
          {
            "name": ["COL1A1"],
          }
      },
      {
        "id": "LRG_1",
        "source": "lrg",
        "fields": 
          {
            "name": ["COL1A2"],
          }
      }
    ]
}

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 XML output

<result>
  <entries>
    <entry id="LRG_1" source="lrg">
      <fields>
        <field id="status">
          <values>
            <value>public</value>
          </values>
        </field>
      </fields>
    </entry>
  </entries>
</result>

Example JSON output

{
  "entries": 
    [
      {
        "id": "LRG_1",
        "source": "lrg",
        "fields": 
          {
            "status": ["public"],
          }
      }
    ]
}

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

Example XML output

<result>
  <entries>
    <entry id="LRG_1" source="lrg">
      <fields>
        <field id="status">
          <values>
            <value>public</value>
          </values>
        </field>
      </fields>
    </entry>
    <entry id="LRG_9" source="lrg">
      <fields>
        <field id="status">
          <values>
            <value>pending</value>
          </values>
        </field>
      </fields>
    </entry>
  </entries>
</result>

Example JSON output

{
  "entries": 
    [
      {
        "id": "LRG_1",
        "source": "lrg",
        "fields": 
          {
            "status": ["public"],
          }
      },
      {
        "id": "LRG_9",
        "source": "lrg",
        "fields": 
          {
            "status": ["pending"],
          }
      }
    ]
}

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