ELM Downloads
Below you'll find examples of the different ways that can be used to query ELM programmatically. No special client is needed for this just a browser or maybe "curl"/"wget" for scripted access. By using these access methods you implicitly agree to using/distributing this data according to the ELM Software License Agreement.
ClassesLast modified on: Oct. 7, 2024, 3:27 a.m.
Here you can download a list of ELM classes, either all at once or limit the list by providing a query term "q".
| Name | Example | URL |
|---|---|---|
| all | /elms/elm_index.html | |
| all | /elms/elms_index.tsv | |
| by query term | /elms/elms_index.tsv?q=PCSK | |
| by ELM id | /ELME000012.html |
InstancesLast modified on: Jan. 30, 2024, 4:28 p.m.
Annotated ELM instances can be queried in a variety of ways. You are encouraged to use the search form to get a feeling for the parameters. Common examples include limiting the query by either instance logic or taxon.
| Name | Example | URL |
|---|---|---|
| all | html | /elms/instances.html?q=* |
| by Uniprot acc | fasta | instances.fasta?q=P12931 |
| by Uniprot name | gff | instances.gff?q=SRC_HUMAN |
| by Uniprot acc | tsv | instances.tsv?q=P12931 |
| by query term | pir | instances.pir?q=PCSK |
| by query term | tsv | instances.tsv?q=src |
| by query term | mitab | instances.mitab?q=src |
| by query term | xml | instances.psimi?q=src |
| by query term using additional parameter "instance logic" | tsv | instances.tsv?q=src&instance_logic=true+positive |
| by Instance id | /ELMI000123.html | |
| All docking motifs annotated in taxon "mouse" | tsv | instances.tsv?q=DOC_&taxon=mus+musculus |
InteractionsLast modified on: Jan. 30, 2024, 4:28 p.m.
Interactions between annotated ELM instances and the corresponding globular interaction partner can be queried as follows. Data is provided either in simple TSV (tab-separated values), PsiMi XML or in MiTAB format.
| Name | Example | URL |
|---|---|---|
| all interactions | tsv | /interactions/as_tsv |
| all interactions | mitab | /interactions/as_mitab |
| all interactions | psimi | /interactions/as_psimi |
| all interactions from certain taxon | mitab | /interactions/as_mitab?taxon=mus%20musculus |
| by Interaction id | mitab | /interactions/ELMINT000120.mitab |
| by Interaction id | xml | /interactions/ELMINT000120.xml |
| by Uniprot acc | mitab | /interactions/P33379.mitab |
| by Uniprot acc | xml | /interactions/P02751.xml |
Interaction DomainsLast modified on: Oct. 21, 2023, 1:03 p.m.
List of all domains annotated as interacting with one or more ELM class.
| Name | Example | URL |
|---|---|---|
| all interaction domains | html | /infos/browse_elm_interactiondomains.html |
| all interaction domains | tsv | /infos/browse_elm_interactiondomains.tsv |
MethodsLast modified on: Sept. 25, 2023, 3:19 p.m.
The following table holds all methods which have been used during the ELM rigourous data curation process.
| Name | Example | URL |
|---|---|---|
| all methods | html | /infos/browse_elm_methods.html |
| all methods | tsv | /infos/browse_elm_methods.tsv |
PDBsLast modified on: Jan. 30, 2024, 4:27 p.m.
The following table holds all PDBs which are annotated in the ELM database.
| Name | Example | URL |
|---|---|---|
| all PDBs | html | /pdbs/ |
| all PDBs | tsv | /pdbs.tsv |
GOTermsLast modified on: Oct. 20, 2023, 5:36 p.m.
The following table shows the GOTerms which are annotated per ELM class.
| Name | Example | URL |
|---|---|---|
| all GOTerms | html | /goterms |
| all GOTerms | tsv | /goterms.tsv |
PathwaysLast modified on: Oct. 20, 2023, 5:36 p.m.
The following tables shows the Pathways which are annotated per ELM instance.
| Name | Example | URL |
|---|---|---|
| all KEGG terms | html | /kegg_terms.html |
| all KEGG terms | tsv | /kegg_terms.tsv |
| all Reactome terms | html | /reactome_terms.html |
| all Reactome terms | tsv | /reactome_terms.tsv |
Renamed ELM classesLast modified on: June 20, 2016, 4:45 p.m.
The following table holds all ELM classes that have been renamed in the past.
| Name | Example | URL |
|---|---|---|
| all renamed ELM classes | tsv | /infos/browse_renamed.tsv |
Templates
These are the annotation templates used to annotate and submit ELM motif classes and instances. Please contact us if you are interested in contributing to ELM.
- elm_template.doc (Template used to annotate novel ELM classes)
- elm_template.xlsx (Template used to collect and annotate ELM instances)
If you're missing a particular format or would like to suggest some changes, please don't hesitate to contact the ELM webmaster.
Media
- switches.elm_ALG2.mp4 A movie about a molecular switch involved in the formation of the ALG2/Alix complex:
ELM data can be downloaded & distributed for non-commercial use according to the ELM Software License Agreement