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)
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with P-site tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with A- and P-site tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with A/P- and P/E-site tRNA
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with A- and P/E-site tRNA
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, without tRNA
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with P/E-site tRNA
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with P-site tRNA
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, without tRNA
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with A- and P/E-site tRNA
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with P/E-site tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with A- and P/E-site tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, without tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with A- and P/E-site tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with P-site tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, without tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with P/E-site tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with P-site tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with P/E-site tRNA
Cryo-EM structure of alpha-synuclein filaments from Parkinson's disease with G51D mutaion in SNCA
Cryo-EM structure of alpha-synuclein filaments from Parkinson's disease with H50Q variant in SNCA
N. brasiliensis GlfT2 in a styrene maleic acid liponanoparticle (C1 Unmasked Map)
Structure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(C1)'
Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB
Cryo-EM structure of the Class 3 PI3K alpha/KRas complex on POPC/POPS nanodiscs
Cryo-EM structure of the PI3K alpha/KRas complex on POPC/POPS/PIP2 nanodiscs low-pass filtered to 5 angstroms
Cryo-EM structure of active mutant human green cone opsin (E129Q) in complex with chimeric G protein (miniGist)
Structure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(C2)
Structure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(C1)
Local refinement of active human green opsin mutant E129Q in complex with chimeric G protein
Structure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(2_1)
Single particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 2
Single particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 4
Single particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 3
Single particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 1
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II
Structure of Geobacillus stearothermophilus RNase P ribozyme sub-conformation 3
Structure of Geobacillus stearothermophilus RNase P ribozyme in 5 mM Mg2+
Structure of Geobacillus stearothermophilus RNase P ribozyme sub-conformation 1
Structure of Geobacillus stearothermophilus RNase P ribozyme in complex with precursor tRNA in 5 mM Ca2+
Structure of Geobacillus stearothermophilus RNase P ribozyme in complex with mature tRNA in 5 mM Ca2+
Structure of Geobacillus stearothermophilus RNase P ribozyme tetraloop mutant (sub-conformation 2)
Structure of Geobacillus stearothermophilus RNase P ribozyme in 10 mM Mg2+
Structure of Geobacillus stearothermophilus RNase P ribozyme tetraloop mutant (sub-conformation 1)
Structure of Geobacillus stearothermophilus RNase P ribozyme in complex with mature tRNA in 10 mM Ca2+
Structure of Geobacillus stearothermophilus RNase P ribozyme sub-conformation 2
Cryo-EM structure of the PGD2-bound prostaglandin D2 receptor (DP1)-Gs complex (G protein-focused map)
Cryo-EM structure of the BW245C-bound prostaglandin D2 receptor (DP1)-Gs complex (Receptor-focused map)
Cryo-EM structure of the PGD2-bound prostaglandin D2 receptor (DP1)-Gs complex (Consensus map)
Cryo-EM structure of the BW245C-bound prostaglandin D2 receptor (DP1)-Gs complex (Consensus map)
Structure of Geobacillus stearothermophilus RNase P ribozyme tetraloop mutant (sub-conformation 3)
Cryo-EM structure of the PGD2-bound prostaglandin D2 receptor (DP1)-Gs complex (Receptor-focused map)
Cryo-EM structure of Pseudomonas aeruginosa outer-membrane lipoprotein PA3214 in the open conformation
Two Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Single Particle CryoEM Map with Icosahedral Symmetry Applied
Cryo-EM structure of the BW245C-bound prostaglandin D2 receptor (DP1)-Gs complex (G protein-focused map)
Cryo-EM structure of Pseudomonas aeruginosa soluble lipoprotein PA3214
Cryo-EM structure of Pseudomonas aeruginosa outer-membrane lipoprotein PA3214 bound to MCE protein PA3213 C-terminal peptide (CASP target)
Locally refined DeepEMhanced map of the meizothrombinDESF1-factor Xa complex
Composite map of the meizothrombinDESF1, factor Xa and factor Va complex
Locally refined DeepEMhanced map of the factor Xa-factor Va complex
RNA Vault Shoulder with ADPR bound, compact conformation, focused refinement (MVP/PARP4/TEP1 NADP sample)
Composite map of hypomethylated 80S ribosome treated with hygromycin B
RNA Vault bound to PARP4 MINT, focused refinement (MVP/PARP4/TEP1 NADP sample)
Human Brain RNA Vault Shoulder bound to ADPR, focused refinement (EMPIAR-10766)
Consensus map of the meizothrombinDESF1, factor Xa, factor Va complex
RNA Vault shoulder region with BAD bound, focused refinement (MVP/TEP1 sample)
RNA Vault Shoulder with ADPR bound, extended conformation, focused refinement (MVP/PARP4/TEP1 NADP sample)
Structure of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Asaia platycodi.
Map of the 70S ribosome with E-site tRNA and HPF from the alphaproteobacteria Rhodospirillum rubrum.
Map of the 70S ribosome with E- and P-site tRNA from the gammaproteobacteria Escherichia coli.
Map of the 70S ribosome with E-site tRNA and HPF from the gammaproteobacteria Escherichia coli.
Map of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Rhodospirillum rubrum.
Two Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Subtomogram Averaged CryoEM Map with Icosahedral Symmetry Applied
Structure of a stalled E. coli 70S RNC-NuoK-48 in complex with the SecYEG Translocon.
Structure of a stalled E. coli 70S RNC-NuoK-48 in complex with the SecYEG Translocon (Focused Refinement)
Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with the SecYEG-YidC membrane protein insertase (Focused Refinement)
Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with the SecYEG-YidC membrane protein insertase
Structure of a stalled E. coli 70S RNC-NuoK-86-E36K-E76K-mutant in complex with the SecYEG-YidC membrane protein insertase (Focused Refinement)
Structure of a stalled E. coli 70S RNC-NuoK-86-E36K-E76K-mutant in complex with the SecYEG-YidC membrane protein insertase
Focused map of LRRC58-CDO1 region from LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Focused map of ARIH1-Ub region from LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Focused map of LRRC58-CDO1 region from LRRC58-ELOB/C-CDO1-CUL5-RBX2-NEDD8-ARIH2-UB
Consensus Map of LRRC58-ELOB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub
Structure of the human inner kinetochore CCAN bound to a mono-CENP-A nucleosome
Consensus map of LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Structure of the human inner kinetochore CCAN bound to a 3' CENP-A nucleosome
Structure of the human inner kinetochore CCAN bound to a 5' CENP-A nucleosome
Focused map of CUL2-LRRC58-EloC interface region from LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub
1.80 A cryo-EM structure of Mycobacterium tuberculosis BfrB prepared under isotope-depleted abundance
Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome
1.79 A cryo-EM structure of Mycobacterium tuberculosis BfrB prepared under natural isotope abundance
Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome, consensus map
Structure of the human inner kinetochore CCAN and CENP-C bound to DNA
CryoEM structure of native quinol dependent Nitric Oxide Reductase with HQN at pH 6.5
CryoEM structure of native quinol dependent Nitric Oxide Reductase at pH 8.0.
CryoEM structure of quinol dependent Nitric Oxide Reductase with BRIL
Cryo-EM structure of DddT G101D in substrate-free outward open conformation
Cryo-EM structure of DddT G101D in substrate-free inward open conformation
Cryo-EM structure of human Nav1.6 in complex with Iota-Conotoxin RXIA
Cryo-EM structure of DddT in closed substrate-free conformation in the presence of potassium ions and dimethylsulfoniopropionate
Cryo-EM structure of human Nav1.6 in complex with delta-paraponeritoxin-Pc1a
Electron tomogram of resin-embedded yeast cells expressing Tcb3(1-272)-GFP-chimeraC, deleted for tcb1/2, scs2/22 and ist2
Structure of human MCM2-7 single hexamer without MCM3 CTE, state 2
Structure of human MCM2-7 single hexamer without MCM3 CTE, state 1
CryoEM structure of Arabidopsis thaliana Col-0 Rubisco with D4 symmetry
Structure of human MCM2-7 single hexamer with MCM3-WHD attached to MCM2-CTD
Structure of human MCM2-7 single hexamer with MCM3-WHD attached to MCM2-CTD, state 2
Structure of human MCM2-7 single hexamer with MCM3-WHD attached to MCM2-CTD, state 3
Structure of human MCM2-7 single hexamer with MCM3-WHD attached to MCM2-CTD, containing Meier-Gorlin Syndrome mutation (MCM3-Q761L)
CryoEM structure of Arabidopsis thaliana M309I Rubisco with D4 symmetry
CryoEM structure of Arabidopsis thaliana D397N Rubisco with D4 symmetry
Composite map of LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Asymmetric reconstruction of immature TBEV particle with 2 missing pentamers
Asymmetric reconstruction of immature TBEV particle with 2 irregularities
Cryo-EM structure of Beta-lactamase-like domain from Neomoorella carbonis
Immature TBEV envelope spike with interaction partners underneath - SPA
Asymmetric reconstruction of immature TBEV particle with altered 5-fold
Immature TBEV envelope spike with interaction partners underneath - STA
Phage 812 baseplate in the pre-contraction state - upper arm (segment B)
Phage 812 baseplate in the pre-contraction state - core and wedge module proteins
Phage 812 baseplate in the pre-contraction state - lower arm (segment C)
Phage 812 baseplate in the pre-contraction state - lower arm (lRBP1-uRBP2)
Phage 812 baseplate in the pre-contraction state - lower arm (uRBP1-lRBP2)
Phage 812 baseplate in the pre-contraction state - lower arm (segment DEF)
Phage 812 baseplate in the pre-contraction state - upper arm (segment CDEF)
Phage 812 baseplate in the pre-contraction state - lower arm (segment B)
Phage 812 baseplate in the pre-contraction state - upper arm (segment A)
Phage 812 baseplate in the pre-contraction state - tail sheath initiator and baseplate-proximal tail proteins
Phage 812 baseplate in the pre-contraction state - lower arm (segment A)
Baseplate arm (segment B) of phage 812 in the post-contraction state
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with A/P- and P/E-site tRNA
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with A- and P-site tRNA
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with A- and P-site tRNA
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with A/P- and P/E-site tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with A/P- and P/E-site tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with A- and P-site tRNA