ELM 2016--data update and new functionality of the eukaryotic linear motif resource

Abstract

The Eukaryotic Linear Motif (ELM) resource (http://elm.eu.org) is a manually curated database of short linear motifs (SLiMs). In this update, we present the latest additions to this resource, along with more improvements to the web interface. ELM 2016 contains more than 240 different motif classes with over 2700 experimentally validated instances, manually curated from more than 2400 scientific publications. In addition, more data have been made available as individually searchable pages and are downloadable in various formats.

Figure 1.

ELM history showing the creation date (red line) and date of latest modification (orange line) of each ELM motif class (light blue line) and motif instance (dark blue line) annotated in the ELM database. Note that for each entry only the very latest modification time is recorded, not every modification timestamp.

Figure 2.

Screenshot of the ELM home page showing autocompletion of keyword search and expanded menu bar. The dropdown menu lists individual pages of ELM database content; the top right shows a dropdown of the autocompletion search for the keyword ‘pp2’, different content type is highlighted in different colors (ELM classes: orange, ELM instances: green, ELM class candidates: blue); a click on a link directs to the details page of the entry.

Figure 3.

Percentages of ELM classes (outer ring) and instances (inner ring) by type.

Figure 4.

Taxons annotated in the ELM database ordered by number of instances (in percentages).

Figure 5.

Methods used for ELM annotation, ordered by number of motif instances for which the method has been annotated (in percentages). A full list can be found at http://elm.eu.org/infos/browse_elm_methods.html, which includes links to instances and PSI-MI vocabulary (22).

Figure 6.

‘Wnt Signaling pathway’ from KEGG (29) (ID hsa04310). The color scheme has been modified for the cases having more than one ELM class in order to provide additional clarity. The original figure can be reproduced on the ELM web server (http://elm.eu.org/pathways/index.html?q=wnt)