Chart Builder
Introduction
The EMDB Chart Builder (https://emdb-empiar.org/statistics/builder) is a web-based application that provides users with the ability to create customizable, dynamic, and informative charts that help analyse the holdings and trends of the EMDB and EMPIAR archives, powered by the EMDB search engine. The underlying data is based on the metadata of all EMDB entries, enriched by the EMICSS resource (https://emdb-empiar.org/emicss). This tool allows users to define specific search terms, enabling the extraction of data subsets that are directly relevant to their analysis objectives. By organising the extracted data into meaningful categories, users can generate insightful charts to visualise and analyse the results. The Chart Builder can be accessed at https://ebi.ac.uk/emdb/statistics/builder.This page presents a user-friendly interface specifically designed to facilitate the creation of customised charts using both EMDB and EMPIAR data.
Use of the Chart Builder requires some knowledge of the EMDB search engine. Therefore you might find it useful to read the search system documentation and the list of search fields. These resources provide valuable insights into the various search functionalities and parameters that can be employed to refine your data extraction.
The Chart builder now allows you to open and customise most of the charts available at /emdb/statistics. If you see an edit icon, simply click on it to open the corresponding chart in the Chart builder. This feature provides you with the flexibility to modify and personalise the chart according to your specific requirements, enabling you to derive deeper insights from the data visualisation.
Figure 1: Edit button available in EMstats plots.
Fields
Archive
Select if your chart is going to be using data about EMDB or EMPIAR. (Note: the amount of available metadata is currently much greater for EMDB than for EMPIAR.)
Chart type
The Chart Builder currently supports four types of charts:
- Line: This chart type is best suited for visualising trends and changes over time. It can be used to illustrate how properties of one or more subsets of entries evolve over time.
Figure 2: Line chart example
- Bar: The bar chart is ideal for comparing different categories or groups. It provides a visual representation of the distribution and relative magnitudes of specific entries within each category.
Figure 3: Bar chart example
- Pie: The pie chart is a useful tool for illustrating proportions and percentages. It provides a concise visual representation of the distribution of a selected subset of entries among various categories. Pie charts can only have one data series, and the data categories are defined by the Data X parameter.
Figure 4: Pie chart example
- Area: Similar to a line chart, the area chart emphasises the cumulative size of subsets of entries over time.
Figure 5: Area chart example
Global filter
The optional global filter in the Chart Builder allows you to specify a search term that will be applied to the selected entries for the entire chart. This feature ensures that the resulting plot focuses on the specific data subset defined by the search term. For instance, suppose you wish to create a plot showcasing the number of entries related to Sars-Cov-2 per EM method. In that case, you can simply change one of the previous examples and set the following query within the global filter: `natural_source_ncbi_code:"2697049"`. This query narrows down the data to entries associated with the Sars-Cov-2 NCBI code, enabling the creation of a customised plot that visualises the desired information accurately.
Figure 6: Area chart with global filter
Data X
The Data X field determines the data that will be displayed on the X-axis or as categories in a pie chart. Within this field, there are three types of data X definitions:
Year:
The X-axis values in the chart correspond to the release year of the entries. By modifying the Data X settings, you can refine the previously created SARS-CoV-2 chart to display data specifically from the year 2019 and beyond.
Figure 7: Area chart with global filter and zoomed from 2019 to 2023.
Experimental metadata:
When selecting the option of "Experimental metadata" for the Data X field, you have the ability to choose one of the enumeration categories. The chosen category's elements will be displayed on the X-axis of the chart. For instance, you can set the experimental metadata category as an EM method to showcase the number of Sars-Cov-2 entries per each type of experiment.
Figure 8: Column chart with global filter displaying categorical metadata on x-axis
Custom queries:
You can define custom queries to specify a set of criteria that will be displayed on the x-axis of the chart. This allows you to customise the chart further according to your specific requirements. For example, you can modify the previous chart to include only the columns related to single-particle, subtomogram averaging, and tomography by using custom queries.
Figure 9: Column chart with global filter displaying specific metadata on x-axis
Custom queries are particularly important when creating pie charts since they can only have a single data series, and the slices of the pie are defined by the elements in the custom queries. We can modify the previous chart to be displayed as a pie chart. This allows for a concise visual representation of the distribution of the selected subset of entries among each experiment method.
Figure 10: Pie chart with custom metadata on slices
Data Y:
The Data Y field is used to set what information is going to be displayed along the Y-axis of your chart. For example, you can choose to display the number of entries, publications, or resolution on the Y-axis, depending on the nature of your analysis and the insights you seek to derive from the chart.
Data series:
This field defines the data series that will be displayed in your chart. A data series consists of three pieces of information: operator, query, and label. The available operators depend on the selection made in the Data Y field. If Data Y is a numeric variable, the operator can be average, minimum, maximum, or sum. On the other hand, if Data Y is a categorical variable, the operator can be the count of unique values or cumulative values. Additionally, you can apply an optional filter query for each data series. This is useful when comparing multiple classes of information, as demonstrated in the example below.
Figure 11: Chart composed by multiple data series to illustrate the 10 most common virus families in EMDB
Attributes
There are seven attributes that can be used to print, download, export and change the chart visualisation:
- Change how area and columns are displayed. There are three options: unstacked, stacked and stacked percent.
- Select to display the data series in a logarithmic or linear scale.
- Share the current chart. The resulting URL will be copied into the clipboard.
- Print the current chart.
- Download the chart image or data table.
- Full Screen mode.
- Extra options.
Publications:
Quick links
Recent Entries
(Show all)
Cryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to the Mycobacterium tuberculosis C- 50S ribosomal subunit
Cryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to the Mycobacterium tuberculosis C- 70S ribosome carrying fMet-tRNA(fMet) and deacylated tRNA at ribosome P and E sites.
Cryo-EM structure of the MPY and ribosome-tunnel occluding hibernation factors bound to the Mycobacterium tuberculosis C- 70S ribosome
Focused refinement map of distal right end DNA region within IF3A transposase complex with synapsed ends
Focused refinement of core region of 1F3A transposase complex with synapsed ends
E. coli RNA polymerase elongation complex containing the unnatural dZ:PTP base pair in a trigger-loop-closed conformation
Symmetry relaxed reconstruction of Rhodospirillum rubrum encapsulin:encapsulated ferritin nanocompartment
Single particle reconstruction of Rhodospirillum rubrum encapsulated ferritin in encapsulin nano compartment
Drebrin actin binding domain 1 conformation A (ABD1a) bound to F-actin
Drebrin actin binding domain 1 conformation B (ABD1b) bound to F-actin
Cryo-EM structure of a chemically treated Cyanobacterial Photosystem I core with bound platinum nanoparticles
Cryo-EM structure of the UnCas12m4a-crRNA-tgDNA ternary complex in the NTS-cleaving state
Structure of fimbriae-like lipoprotein by Cryo Electron Microscopy
Cryo-EM structure of the UnCas12m4a-crRNA-tgDNA ternary complex in the TS-cleaving state
Structure of heteromeric mouse LRRC8A/D Volume-Regulated Anion Channel in complex with synthetic nanobody Sb4
Structure of heteromeric mouse LRRC8A/D Volume-Regulated Anion Channel in complex with synthetic nanobody Sb1, Conformation 1
Structure of heteromeric mouse LRRC8A/D Volume-Regulated Anion Channel in complex with synthetic nanobody Sb1, Conformation 2
Xenopus KCNQ1 Intermediate State (E1R/R2E) in complex with UCL2077
Rad55-Rad57-SHU bound to ssDNA with AMP-PNP. Local map focused on 55/57
Native flagellar filament from Leptospira interrogans flaB1- KO mutant strain
amyloid fibril of recombinant transforming growth factor beta induced protein FAS1-4 domain with V624M mutation
amyloid fibril of recombinant transforming growth factor beta induced protein FAS1-4 domain with V624M mutation, refined using helical spacing of peripheral globular domain
Structure of Measles virus fusion protein in pre-fusion in complex with neutralizing Fabs MeV-15 and MeV-104
Rad55-Rad57-SHU homologous recombination complex. Local refinement on Rad55/Rad57
Rad55-Rad57-SHU homologous recombination complex. Local refinement on SHU
Cryo-EM structure of ClassIII Lanthipeptide modification enzyme TherKC with chain A bounded to substrate TherA and ATPrS.
Cryo-EM structure of ClassIII Lanthipeptide modification enzyme TherKC with chain A bounded to substrate TherA and ATPrS.
Cryo-EM structure of the insect sex pheromone receptor ApisOR22-Orco heterocomplex
Cryo-EM structure of the insect sex pheromone receptor ApisOR22-Orco heterocomplex bound with nepetalactone in the open state
Local structure of MERS-CoV S protein bound with receptor DPP4 in the conformation 2 (2 up RBD and 2 DPP4 bound)
Cryo-EM structure of MERS-CoV S protein bound with receptor DPP4 in the conformation 1 (1 up RBD and 1 DPP4 bound).
Local structure of MERS-CoV RBD protein bound with receptor DPP4 in the conformation 2 (2 up RBD and 2 DPP4 bound)
Cryo-EM structure of MERS-CoV S protein bound with receptor DPP4 in the conformation 3 (3 up RBD and 3 DPP4 bound).
The focused structure of the C-terminal lobe of the human UBR4-KCMF1-Calmodulin complex
CyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising Fab fragment of RDS045
Local refinement of SARS-CoV-2 KP.3.1.1 RBD with BD57-2704 and AB2-122 Fab
HIV-1 reverse transcriptase in complex with DNA Aptamer and Incorporated dATP
HIV-1 reverse transcriptase in complex with DNAddG Aptamer and unincorporated ISL-triphosphate
HIV-1 reverse transcriptase (F227C) in complex with DNAddG Aptamer and unincorporated ISL-triphosphate
HIV-1 reverse transcriptase (F227C) in complex with DNAddG Aptamer
HIV-1 reverse transcriptase (F227C) in complex with DNA Aptamer and Incorporated dATP
The cryo-EM map of the structure of C. auris ribosome in complex with Cycloheximide and Geneticin G418 focused on the head of the SSU
The cryo-EM map of the structure of C. auris ribosome in complex with Blasticidin S focused on the body of the SSU
CryoEM structure of Candida auris 80S ribosome in complex with Cycloheximide and Geneticin G418
The cryo-EM map of the vacant C. auris ribosome focused on the head of the SSU
The cryo-EM map of the structure of C. auris ribosome in complex with Blasticidin S LSU
The cryo-EM map of the structure of C. auris ribosome in complex with Cycloheximide and Geneticin G418 LSU
The cryo-EM map of the structure of C. auris ribosome in complex with Blasticidin S focused on the head of the SSU
The cryo-EM map of the structure of C. auris ribosome in complex with Cycloheximide and Geneticin G418 focused on the body of the SSU
The cryo-EM map of the vacant C. auris ribosome focused on the body of the SSU
CryoEM structure of Candida auris 80S ribosome in complex with Blasticidin S
mechanosensitive channel MscS from Francisella tularensis, mutant F108A
mechanosensitive channel MscS from Francisella tularensis in nanodiscs
Prefusion-stabilized Hendra virus fusion protein in complex with inhibitory nanobody F130
Cryo-EM structure of the kinetoplastid post-catalytic trans-spliceosome (P complex)
Mouse teneurin-3 A1B1 isoform; microphthalmia-associated R2579W mutant; compact dimer conformation
Mouse teneurin-3 A1B1 isoform; microphthalmia-associated R2579W mutant; non-compact subunit; particle subtracted
Cryo-EM structure of NLRP3 bound to the inhibitor BAL-1516 at 3.06 Ang resolution
Cryo-EM structure of the kinetoplastid trans-spliceosome activated for catalytic step II (C* complex)
Discodermolide stabilised 14-protofilament microtubule C1 reconstruction
Cryo-EM structure of the Arabidopsis thaliana potassium transporter 5 in apo state
Discodermolide stabilised 13-protofilament microtubule C1 reconstruction
Cryo-EM structure of the Arabidopsis thaliana potassium transporter 5 subjected to ATP dialysis
Cryo-EM structure of the Arabidopsis thaliana potassium transporter mutant - H527R, K759H
Cryo-EM structure of the Arabidopsis thaliana potassium transporter mutant - H527R, E565N, K759H
Cryo-EM structure of the Arabidopsis thaliana potassium transporter 5 mutant - H527A
Cryo-EM structure of the Arabidopsis thaliana potassium transporter mutant - H527R, E565N, K759H, K778E, E734K
Cryo-EM structure of the Arabidopsis thaliana potassium transporter 5 purified in the presence of NaCl and ATP
Cryo-EM structure of the Arabidopsis thaliana potassium transporter mutant - K759A
Cryo-EM structure of the Arabidopsis thaliana potassium transporter 5 incubated with AMPPNP
Cryo-EM structure of human UGCG bound to UDP-glucose and a phospholipid
Cryo-EM structure of the Mycobacterium tuberculosis C- 70S ribosome bound to fMet-tRNA(fMet) and deacylated tRNA at ribosome P and E sites
Focused refinement map of IHF region of IF3-a transposase complex with synapsed ends
Cryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to Mycobacterium tuberculosis C- 70S ribosome
Consensus map of the IF-3a transposase complex with synaptic ends
The cryo-EM structure of the periplasmic chaperone Skp from Neisseria meningitidis
Composite map of IF-3a transposase complex with paired transposon ends
Cryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to the Mycobacterium tuberculosis C- 70S ribosome carrying an E-tRNA