ELM API

Welcome to the ELM API. This page gives a brief summary on how to use the ELM API to submit sequences to the ELM prediction pipeline.

Via this API it is possible to submit a protein sequence or Uniprot identifier to the ELM prediction pipeline, and retrieve the results as a "tab-separated values" file.

Submitting a protein identifier

To search for motifs in known proteins (i.e., proteins listed in Uniprot), submit a GET request to this URL using the Uniprot ID followed by ".tsv":

http://elm.eu.org/start_search/<uniprot_id>.tsv

Please limit your searches via Uniprot ID to a maximum of 1 every 3 minutes.. If you exceed this limit, you will recieve a "429 Too many requests" error.

Submitting a single sequence

To search for motifs in any protein sequence, submit a GET request to this URL, providing the amino acid sequence:

http://elm.eu.org/start_search/<sequence>

Please limit your searches via sequence to a maximum of 1 per minute.. If you exceed this limit, you will recieve a "429 Too many requests" error. Also please note that this does not always work for sequences longer than 2000 amino acids: URLs may be truncated beyond this length.

Interpreting the results

The results are returned as a "tab-separated values" file, in which each row is a putative motif: a match to one of the regular expressions annotated in ELM. The following information is provided in each column:

• elm_identifier: The ELM class identified.
• start: Amino acid position where the regular expression match starts.
• stop: Amino acid position where the regular expression match ends.
• is_annotated: Whether or not this motif has been annotated in the ELM database as an (experimentally validated) motif instance.
• is_phiblastmatch: Whether or not this match was found by the ELM Instance mapper, indicating that an experimentally validated instance in a homologous sequence was found.
• is_filtered: Whether or not this motif was rejected by any of the ELM prediction filters (structure, topodom or taxon).
• structure: Whether or not this motif was filtered out based on its secondary structure.
• topodomfilter: Wether or not this motif was filtered for topology. Uses information from UniProt to determine the protein's topology with respect to trans-membrane domains or extracellular regions.
• taxonfilter: Whether or not this motif was filtered out by the "Taxonomic Context" filter.