2017-03-29 : 4653 EMDB map entries, 1514 PDB coordinate entries PDBe | RCSB    

One-stop shop for 3DEM deposition and retrieval


EM Community Outreach History

In order to develop a community data resource, it is necessary to solicit input from representative members of the scientific community. Below is a summary of past workshops devoted to exchange of cryoEM data that have been organized by members of our project group and other leaders in cryoEM.

Nov 2002, IIMS Workshop, organized by Kim Henrick, Jose-Maria Carazo (Madrid), and Stephen Fuller (Oxford), held at Hinxton, Cambridge, UK

The purpose of this workshop was to promote software development in the field of electron microscopy molecular structure determination. The participants were asked to focus their presentations and discussion on working together in order to foster collaboration on data exchange and harvesting. The workshop discussed many of the issues that arise from deposition, as well as presentation of data in a form useful to non-specialists. Guidelines and release policies were set for the first version of the EMDB. The workshop established the database as a resource for the international community, and an announcement was published in Structure (Fuller, S.D., Depositing electron microscopy maps. Structure (Camb) (2003). 11: 11-12.), followed by an editorial in Nature Structural Biology (Editorial, A database for 'em. Nat Struct Biol (2003). 10: 313). The participants also discussed possible software developments to ease documentation and deposition of such datasets and concluded with a strong endorsement of map deposition and linkage with the family of archival databases in biomedical research. Announcement of the EMDB map archive (Tagari, M. et al Trends in Biochem Sci (2002) 27: 589) and publication describing the initial EMDB deposition system followed soon after (Henrick, K. et al, EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information. J Struct Biol (2003). 144: 228-237).

May 2004, 3D-EM Developers Workshop, Organized by Kim Henrick and held at the EBI (UK).

This workshop aimed to bring together software developers from the 3DEM NoE partners to review the tools and software practices used throughout Europe in the field of cryoEM. The workshop examined the items and data model(s) required to fully describe EM and to allocate tasks to different groups to develop the required standards. The workshop recognized the success of the EMDB in terms of number of entries available (85), and the requirement made by premier research journals for an EMDB ID code prior to publication has established the database worldwide. It was announced at the workshop that the search system was further enhanced with atlas pages for each entry. In addition, this workshop recognized that EMDB had to cope with the following four issues: (i) providing archiving capabilities for the growing field of cryo-electron tomography; (ii) need for suitable cross-referencing between both PDB (atomic coordinates) and EMDB (maps) databases; (iii) problems in converting all map formats in a lossless manner and (iv) review of current standards and conventions to describe a map and its x-y-z coordinate origin and axes.

Oct 2004, CryoEM Structure Deposition Workshop, organized by Helen M. Berman, Wah Chiu, Michael Rossmann (Purdue), held at the RCSB PDB (Rutgers, USA) workshop web site

The goal of the CryoEM Structure Deposition Workshop was to develop a global community consensus on the data items needed for deposition of 3D density maps and atomic models derived from cryoEM studies. The workshop was attended by ~30 scientists including cryoEM, image processing, crystallography, database, funding agency and journal representatives. The version of cryoEM dictionary available at that time (v. 005) was reviewed in two focus groups led by Tim Baker and Bridget Carragher respectively and recommendations for revisions were obtained. Desired improvements in the areas of visualization, data mining and data integration were discussed. A unanimous recommendation of workshop attendees was the need to develop a "one-stop shop" for deposition of map and model data. Since this workshop, the cryoEM dictionary was revised and expanded extensively with a broad community input through an email list and a poster/oral presentation in the 3DEM Gordon Conference. The extended dictionary forms the foundation for a new cryoEM data archive.

Oct 2005, 3D-EM Developers Workshop, organized by Kim Henrick, held at the EBI (UK)

The aim of this meeting was to introduce the latest version of the 3DEM data dictionary to software developers and to facilitate the integration of the data dictionary into the main 3DEM packages and electronic notebook systems. An important outcome of this workshop was the agreement to adopt a common set of conventions for maps (Heymann, J.B., M. Chagoyen, and D.M. Belnap, Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology. J Struct Biol (2005). 151: 196-207). The proposed set of common conventions provides a standardized approach to image interpretation and presentation. In this regard, the conventions serve as the first step on which to build data-exchange solutions among existing software packages and as a vehicle for homogeneous data representation in both the PDB and EMDB data archives. The combined data dictionary that was the outcome of the October 2004 workshop (see above) was unanimously accepted by the developers present. A supplementary dictionary covering 2D images was produced during the workshop itself. The acceptance of the need for software to prepare archive material using the agreed data exchange dictionary, and the production of deposition maps that conform to the map conventions will greatly facilitate the automated harvesting of data from cryoEM structure determination applications.

2006, CryoEM Standards Task Force coordinated by Wah Chiu, David Belnap (Provo, Utah) and Jose-Maria Carazo (Madrid)

Following the recommendations in the previous workshop, a task force committee consisting of cryoEM software developers and representative staff members from EBI PDB and RCSB PDB was set up to gather the necessary information on the different cryoEM map conventions and formats with associated metadata used by different developers so that a conversion table can be made to the 3DEM Image Conventions. This committee has met twice in 2006 in Houston and Provo respectively, and also holds frequent teleconferences. A website has been generated to collect key map convention information from each software developer. This work is being carried out in collaboration with the European 3DEM NoE.