protvista-uniprot 3.0.0 → 3.0.7

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (83) hide show
  1. package/dist/protvista-uniprot.mjs +368 -0
  2. package/dist/{protvista-uniprot.js.map → protvista-uniprot.mjs.map} +1 -1
  3. package/dist/types/index.d.ts +7 -0
  4. package/package.json +19 -11
  5. package/src/index.ts +6 -17
  6. package/dist/es/__spec__/filter-config.spec.js +0 -123
  7. package/dist/es/__spec__/filter-config.spec.js.map +0 -1
  8. package/dist/es/adapters/__tests__/__mocks__/uniprotkb-entry-data.js +0 -75
  9. package/dist/es/adapters/__tests__/__mocks__/uniprotkb-entry-data.js.map +0 -1
  10. package/dist/es/adapters/__tests__/structure-adapter.spec.js +0 -14
  11. package/dist/es/adapters/__tests__/structure-adapter.spec.js.map +0 -1
  12. package/dist/es/adapters/alphafold-confidence-adapter.js +0 -26
  13. package/dist/es/adapters/alphafold-confidence-adapter.js.map +0 -1
  14. package/dist/es/adapters/alphamissense-heatmap-adapter.js +0 -36
  15. package/dist/es/adapters/alphamissense-heatmap-adapter.js.map +0 -1
  16. package/dist/es/adapters/alphamissense-pathogenicity-adapter.js +0 -68
  17. package/dist/es/adapters/alphamissense-pathogenicity-adapter.js.map +0 -1
  18. package/dist/es/adapters/config/evidence.js +0 -101
  19. package/dist/es/adapters/config/evidence.js.map +0 -1
  20. package/dist/es/adapters/feature-adapter.js +0 -18
  21. package/dist/es/adapters/feature-adapter.js.map +0 -1
  22. package/dist/es/adapters/interpro-adapter.js +0 -60
  23. package/dist/es/adapters/interpro-adapter.js.map +0 -1
  24. package/dist/es/adapters/proteomics-adapter.js +0 -66
  25. package/dist/es/adapters/proteomics-adapter.js.map +0 -1
  26. package/dist/es/adapters/ptm-exchange-adapter.js +0 -101
  27. package/dist/es/adapters/ptm-exchange-adapter.js.map +0 -1
  28. package/dist/es/adapters/structure-adapter.js +0 -89
  29. package/dist/es/adapters/structure-adapter.js.map +0 -1
  30. package/dist/es/adapters/types/alphafold.js +0 -2
  31. package/dist/es/adapters/types/alphafold.js.map +0 -1
  32. package/dist/es/adapters/variation-adapter.js +0 -31
  33. package/dist/es/adapters/variation-adapter.js.map +0 -1
  34. package/dist/es/adapters/variation-graph-adapter.js +0 -53
  35. package/dist/es/adapters/variation-graph-adapter.js.map +0 -1
  36. package/dist/es/config.json +0 -811
  37. package/dist/es/filter-config.js +0 -157
  38. package/dist/es/filter-config.js.map +0 -1
  39. package/dist/es/index.d.ts +0 -7
  40. package/dist/es/index.js +0 -8
  41. package/dist/es/index.js.map +0 -1
  42. package/dist/es/protvista-uniprot-structure.js +0 -379
  43. package/dist/es/protvista-uniprot-structure.js.map +0 -1
  44. package/dist/es/protvista-uniprot.js +0 -594
  45. package/dist/es/protvista-uniprot.js.map +0 -1
  46. package/dist/es/styles/loader-styles.js +0 -20
  47. package/dist/es/styles/loader-styles.js.map +0 -1
  48. package/dist/es/styles/protvista-styles.js +0 -89
  49. package/dist/es/styles/protvista-styles.js.map +0 -1
  50. package/dist/es/tooltips/featureTooltip.js +0 -160
  51. package/dist/es/tooltips/featureTooltip.js.map +0 -1
  52. package/dist/es/tooltips/structureTooltip.js +0 -15
  53. package/dist/es/tooltips/structureTooltip.js.map +0 -1
  54. package/dist/es/tooltips/variationTooltip.js +0 -82
  55. package/dist/es/tooltips/variationTooltip.js.map +0 -1
  56. package/dist/es/utils.js +0 -28
  57. package/dist/es/utils.js.map +0 -1
  58. package/dist/protvista-uniprot.js +0 -368
  59. /package/dist/{protvista-uniprot.js.LICENSE.txt → protvista-uniprot.mjs.LICENSE.txt} +0 -0
  60. /package/dist/{es → types}/__spec__/filter-config.spec.d.ts +0 -0
  61. /package/dist/{es → types}/adapters/__tests__/__mocks__/uniprotkb-entry-data.d.ts +0 -0
  62. /package/dist/{es → types}/adapters/__tests__/structure-adapter.spec.d.ts +0 -0
  63. /package/dist/{es → types}/adapters/alphafold-confidence-adapter.d.ts +0 -0
  64. /package/dist/{es → types}/adapters/alphamissense-heatmap-adapter.d.ts +0 -0
  65. /package/dist/{es → types}/adapters/alphamissense-pathogenicity-adapter.d.ts +0 -0
  66. /package/dist/{es → types}/adapters/config/evidence.d.ts +0 -0
  67. /package/dist/{es → types}/adapters/feature-adapter.d.ts +0 -0
  68. /package/dist/{es → types}/adapters/interpro-adapter.d.ts +0 -0
  69. /package/dist/{es → types}/adapters/proteomics-adapter.d.ts +0 -0
  70. /package/dist/{es → types}/adapters/ptm-exchange-adapter.d.ts +0 -0
  71. /package/dist/{es → types}/adapters/structure-adapter.d.ts +0 -0
  72. /package/dist/{es → types}/adapters/types/alphafold.d.ts +0 -0
  73. /package/dist/{es → types}/adapters/variation-adapter.d.ts +0 -0
  74. /package/dist/{es → types}/adapters/variation-graph-adapter.d.ts +0 -0
  75. /package/dist/{es → types}/filter-config.d.ts +0 -0
  76. /package/dist/{es → types}/protvista-uniprot-structure.d.ts +0 -0
  77. /package/dist/{es → types}/protvista-uniprot.d.ts +0 -0
  78. /package/dist/{es → types}/styles/loader-styles.d.ts +0 -0
  79. /package/dist/{es → types}/styles/protvista-styles.d.ts +0 -0
  80. /package/dist/{es → types}/tooltips/featureTooltip.d.ts +0 -0
  81. /package/dist/{es → types}/tooltips/structureTooltip.d.ts +0 -0
  82. /package/dist/{es → types}/tooltips/variationTooltip.d.ts +0 -0
  83. /package/dist/{es → types}/utils.d.ts +0 -0
package/dist/es/config.json DELETED
@@ -1,811 +0,0 @@
1
- {
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- "categories": [
3
- {
4
- "name": "MOLECULE_PROCESSING",
5
- "label": "Molecule processing",
6
- "trackType": "nightingale-track",
7
- "tracks": [
8
- {
9
- "name": "signal",
10
- "label": "Signal peptide",
11
- "filter": "SIGNAL",
12
- "trackType": "nightingale-track",
13
- "data": [
14
- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
17
- }
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- ],
19
- "tooltip": "N-terminal signal peptide"
20
- },
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- {
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- "name": "chain",
23
- "label": "Chain",
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- "filter": "CHAIN",
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- "trackType": "nightingale-track",
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- "data": [
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- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
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- "tooltip": "(aka mature region). This describes the extent of a polypeptide chain in the mature protein following processing"
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- },
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- {
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- "name": "transit",
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- "label": "Transit peptide",
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- "filter": "TRANSIT",
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- "trackType": "nightingale-track",
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- "data": [
40
- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
45
- "tooltip": "This describes the extent of a transit peptide"
46
- },
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- {
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- "name": "init_met",
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- "label": "Initiator methionine",
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- "filter": "INIT_MET",
51
- "trackType": "nightingale-track",
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- "data": [
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- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
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- "tooltip": "This indicates that the initiator methionine is cleaved from the mature protein"
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- },
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- {
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- "name": "propep",
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- "label": "Propeptide",
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- "filter": "PROPEP",
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- "trackType": "nightingale-track",
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- "data": [
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- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
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- "tooltip": "Part of a protein that is cleaved during maturation or activation"
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- },
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- {
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- "name": "peptide",
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- "label": "Peptide",
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- "filter": "PEPTIDE",
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- "trackType": "nightingale-track",
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- "data": [
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- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
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- "tooltip": "The position and length of an active peptide in the mature protein"
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- }
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- ]
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- },
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- {
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- "name": "SEQUENCE_INFORMATION",
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- "label": "Sequence information",
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- "trackType": "nightingale-track",
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- "tracks": [
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- {
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- "name": "compbias",
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- "label": "Compositional bias",
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- "filter": "COMPBIAS",
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- "trackType": "nightingale-track",
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- "data": [
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- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
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- "tooltip": "Position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions"
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- },
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- {
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- "name": "conflict",
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- "label": "Sequence conflict",
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- "filter": "CONFLICT",
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- "trackType": "nightingale-track",
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- "data": [
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- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
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- "tooltip": "Sequence discrepancies of unknown origin"
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- },
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- {
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- "name": "non_cons",
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- "filter": "NON_CONS",
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- "trackType": "nightingale-track",
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- "label": "Non-adjacent residues",
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- "data": [
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- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
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- "tooltip": "Indicates that two residues in a sequence are not consecutive and that there is an undetermined number of unsequenced residues between them"
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- },
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- {
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- "name": "non_ter",
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- "filter": "NON_TER",
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- "trackType": "nightingale-track",
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- "label": "Non-terminal residue",
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- "data": [
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- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
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- "tooltip": "The sequence is incomplete. The residue is not the terminal residue of the complete protein"
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- },
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- {
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- "name": "unsure",
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- "filter": "UNSURE",
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- "trackType": "nightingale-track",
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- "label": "Sequence uncertainty",
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- "data": [
151
- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
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- "tooltip": "Regions of a sequence for which the authors are unsure about the sequence assignment"
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- },
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- {
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- "name": "non_std",
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- "filter": "NON_STD",
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- "trackType": "nightingale-track",
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- "label": "Non-standard residue",
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- "data": [
164
- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
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- "tooltip": "Non-standard amino acids (selenocysteine and pyrrolysine)"
170
- }
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- ]
172
- },
173
- {
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- "name": "TOPOLOGY",
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- "label": "Topology",
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- "trackType": "nightingale-track",
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- "tracks": [
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- {
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- "name": "topo_dom",
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- "label": "Topological domain",
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- "filter": "TOPO_DOM",
182
- "trackType": "nightingale-track",
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- "data": [
184
- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
187
- }
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- ],
189
- "tooltip": "Location of non-membrane regions of membrane-spanning proteins"
190
- },
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- {
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- "name": "transmem",
193
- "label": "Transmembrane",
194
- "filter": "TRANSMEM",
195
- "trackType": "nightingale-track",
196
- "data": [
197
- {
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- "adapter": "feature-adapter",
199
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
200
- }
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- ],
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- "tooltip": "Extent of a membrane-spanning region"
203
- },
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- {
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- "name": "intramem",
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- "label": "Intramembrane",
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- "filter": "INTRAMEM",
208
- "trackType": "nightingale-track",
209
- "data": [
210
- {
211
- "adapter": "feature-adapter",
212
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
213
- }
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- ],
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- "tooltip": "Extent of a region located in a membrane without crossing it"
216
- }
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- ]
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- },
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- {
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- "name": "DOMAINS",
221
- "label": "Domains",
222
- "trackType": "nightingale-track",
223
- "tracks": [
224
- {
225
- "name": "domain",
226
- "label": "Domain",
227
- "filter": "DOMAIN",
228
- "trackType": "nightingale-track",
229
- "data": [
230
- {
231
- "adapter": "feature-adapter",
232
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
233
- }
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- ],
235
- "tooltip": "Specific combination of secondary structures organized into a characteristic three-dimensional structure or fold"
236
- },
237
- {
238
- "name": "InterPro representative domain",
239
- "label": "InterPro Representative Domain",
240
- "trackType": "nightingale-track",
241
- "data": [
242
- {
243
- "adapter": "interpro-adapter",
244
- "url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/{accession}?type=domain&page_size=100"
245
- }
246
- ],
247
- "tooltip": "InterPro representative domains"
248
- },
249
- {
250
- "name": "region",
251
- "label": "Region",
252
- "filter": "REGION",
253
- "trackType": "nightingale-track",
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- "data": [
255
- {
256
- "adapter": "feature-adapter",
257
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
258
- }
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- ],
260
- "tooltip": "Regions in multifunctional enzymes or fusion proteins, or characteristics of a region, e.g., protein-protein interactions mediation"
261
- },
262
- {
263
- "name": "repeat",
264
- "label": "Repeat",
265
- "filter": "REPEAT",
266
- "trackType": "nightingale-track",
267
- "data": [
268
- {
269
- "adapter": "feature-adapter",
270
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
271
- }
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- ],
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- "tooltip": "Repeated sequence motifs or repeated domains within the protein"
274
- },
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- {
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- "name": "motif",
277
- "label": "Motif",
278
- "filter": "MOTIF",
279
- "trackType": "nightingale-track",
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- "data": [
281
- {
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- "adapter": "feature-adapter",
283
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
284
- }
285
- ],
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- "tooltip": "Short conserved sequence motif of biological significance"
287
- },
288
- {
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- "name": "zn_fing",
290
- "label": "Zinc finger",
291
- "filter": "ZN_FING",
292
- "trackType": "nightingale-track",
293
- "data": [
294
- {
295
- "adapter": "feature-adapter",
296
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
297
- }
298
- ],
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- "tooltip": "Small, functional, independently folded domain that coordinates one or more zinc ions"
300
- }
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- ]
302
- },
303
- {
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- "name": "SITES",
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- "label": "Sites",
306
- "trackType": "nightingale-track",
307
- "tracks": [
308
- {
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- "name": "metal",
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- "label": "Metal binding",
311
- "filter": "METAL",
312
- "trackType": "nightingale-track",
313
- "data": [
314
- {
315
- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
317
- }
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- ],
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- "tooltip": "Binding site for a metal ion"
320
- },
321
- {
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- "name": "site",
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- "label": "Site",
324
- "filter": "SITE",
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- "trackType": "nightingale-track",
326
- "data": [
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- {
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- "adapter": "feature-adapter",
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- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
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- }
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- ],
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- "tooltip": "Any interesting single amino acid site on the sequence"
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- },
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- {
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- "name": "ca_bind",
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- "label": "Calcium binding",
337
- "filter": "CA_BIND",
338
- "trackType": "nightingale-track",
339
- "data": [
340
- {
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- "adapter": "feature-adapter",
342
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
343
- }
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- ],
345
- "tooltip": "Calcium-binding regions, such as the EF-hand motif"
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- },
347
- {
348
- "name": "dna_bind",
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- "label": "DNA binding",
350
- "filter": "DNA_BIND",
351
- "trackType": "nightingale-track",
352
- "data": [
353
- {
354
- "adapter": "feature-adapter",
355
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
356
- }
357
- ],
358
- "tooltip": "DNA-binding domains such as AP2/ERF domain, the ETS domain, the Fork-Head domain, the HMG box and the Myb domain"
359
- },
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- {
361
- "name": "np_bind",
362
- "label": "Nucleotide binding",
363
- "filter": "NP_BIND",
364
- "trackType": "nightingale-track",
365
- "data": [
366
- {
367
- "adapter": "feature-adapter",
368
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
369
- }
370
- ],
371
- "tooltip": "(aka flavin-binding). Region in the protein which binds nucleotide phosphates"
372
- },
373
- {
374
- "name": "binding",
375
- "label": "Binding site",
376
- "filter": "BINDING",
377
- "trackType": "nightingale-track",
378
- "data": [
379
- {
380
- "adapter": "feature-adapter",
381
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
382
- }
383
- ],
384
- "tooltip": "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)"
385
- },
386
- {
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- "name": "act_site",
388
- "label": "Active site",
389
- "filter": "ACT_SITE",
390
- "trackType": "nightingale-track",
391
- "data": [
392
- {
393
- "adapter": "feature-adapter",
394
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
395
- }
396
- ],
397
- "tooltip": "Amino acid(s) directly involved in the activity of an enzyme"
398
- }
399
- ]
400
- },
401
- {
402
- "name": "PTM",
403
- "label": "PTM",
404
- "trackType": "nightingale-track",
405
- "tracks": [
406
- {
407
- "name": "mod_res",
408
- "label": "Modified residue",
409
- "filter": "MOD_RES",
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- "trackType": "nightingale-track",
411
- "data": [
412
- {
413
- "adapter": "feature-adapter",
414
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
415
- }
416
- ],
417
- "tooltip": "Modified residues such as phosphorylation, acetylation, acylation, methylation"
418
- },
419
- {
420
- "name": "mod_res_ls",
421
- "label": "Modified residue (large scale data)",
422
- "filter": "MOD_RES_LS",
423
- "trackType": "nightingale-track",
424
- "data": [
425
- {
426
- "adapter": "proteomics-ptm-adapter",
427
- "url": "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
428
- }
429
- ],
430
- "tooltip": "Modified residues from Large scale studies"
431
- },
432
- {
433
- "name": "carbohyd",
434
- "label": "Glycosylation",
435
- "filter": "CARBOHYD",
436
- "trackType": "nightingale-track",
437
- "data": [
438
- {
439
- "adapter": "feature-adapter",
440
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
441
- }
442
- ],
443
- "tooltip": "Covalently attached glycan group(s)"
444
- },
445
- {
446
- "name": "disulfid",
447
- "label": "Disulfide bond",
448
- "filter": "DISULFID",
449
- "trackType": "nightingale-track",
450
- "data": [
451
- {
452
- "adapter": "feature-adapter",
453
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
454
- }
455
- ],
456
- "tooltip": "The positions of cysteine residues participating in disulphide bonds"
457
- },
458
- {
459
- "name": "crosslnk",
460
- "label": "Cross-link",
461
- "filter": "CROSSLNK",
462
- "trackType": "nightingale-track",
463
- "data": [
464
- {
465
- "adapter": "feature-adapter",
466
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
467
- }
468
- ],
469
- "tooltip": "Covalent linkages of various types formed between two proteins or between two parts of the same protein"
470
- },
471
- {
472
- "name": "lipid",
473
- "label": "Lipidation",
474
- "filter": "LIPID",
475
- "trackType": "nightingale-track",
476
- "data": [
477
- {
478
- "adapter": "feature-adapter",
479
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
480
- }
481
- ],
482
- "tooltip": "Covalently attached lipid group(s)"
483
- }
484
- ]
485
- },
486
- {
487
- "name": "EPITOPE",
488
- "label": "Epitopes",
489
- "trackType": "nightingale-track",
490
- "tracks": [
491
- {
492
- "name": "epitope",
493
- "label": "Epitope",
494
- "trackType": "nightingale-track",
495
- "data": [
496
- {
497
- "adapter": "feature-adapter",
498
- "url": "https://www.ebi.ac.uk/proteins/api/epitope/{accession}"
499
- }
500
- ],
501
- "tooltip": ""
502
- }
503
- ]
504
- },
505
- {
506
- "name": "ANTIGEN",
507
- "label": "Antigenic sequences",
508
- "trackType": "nightingale-track",
509
- "tracks": [
510
- {
511
- "name": "antigen",
512
- "label": "Antibody binding sequences",
513
- "trackType": "nightingale-track",
514
- "data": [
515
- {
516
- "adapter": "feature-adapter",
517
- "url": "https://www.ebi.ac.uk/proteins/api/antigen/{accession}"
518
- }
519
- ],
520
- "tooltip": ""
521
- }
522
- ]
523
- },
524
- {
525
- "name": "MUTAGENESIS",
526
- "label": "Mutagenesis",
527
- "trackType": "nightingale-track",
528
- "tracks": [
529
- {
530
- "name": "mutagen",
531
- "label": "Mutagenesis",
532
- "filter": "MUTAGEN",
533
- "trackType": "nightingale-track",
534
- "data": [
535
- {
536
- "adapter": "feature-adapter",
537
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
538
- }
539
- ],
540
- "tooltip": "Site which has been experimentally altered by mutagenesis"
541
- },
542
- {
543
- "name": "othermutagen",
544
- "label": "Mutagenesis (large scale data)",
545
- "trackType": "nightingale-track",
546
- "data": [
547
- {
548
- "adapter": "feature-adapter",
549
- "url": "https://www.ebi.ac.uk/proteins/api/mutagenesis/{accession}"
550
- }
551
- ],
552
- "tooltip": "Site which has been experimentally altered by mutagenesis"
553
- }
554
- ]
555
- },
556
- {
557
- "name": "VARIATION",
558
- "label": "Variants",
559
- "trackType": "nightingale-linegraph-track",
560
- "tracks": [
561
- {
562
- "name": "variation_graph",
563
- "label": "Counts",
564
- "trackType": "nightingale-linegraph-track",
565
- "data": [
566
- {
567
- "adapter": "variation-graph-adapter",
568
- "url": "https://www.ebi.ac.uk/proteins/api/variation/{accession}"
569
- }
570
- ],
571
- "tooltip": "Natural variant of the protein, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events"
572
- },
573
- {
574
- "name": "variation",
575
- "filterComponent": "nightingale-filter",
576
- "trackType": "nightingale-variation",
577
- "data": [
578
- {
579
- "adapter": "variation-adapter",
580
- "url": "https://www.ebi.ac.uk/proteins/api/variation/{accession}"
581
- }
582
- ],
583
- "tooltip": "Natural variant of the protein, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events"
584
- }
585
- ]
586
- },
587
- {
588
- "name": "PROTEOMICS",
589
- "label": "Proteomics",
590
- "trackType": "nightingale-track",
591
- "adapter": "proteomics-adapter",
592
- "urls": [
593
- "https://www.ebi.ac.uk/proteins/api/proteomics/{accession}",
594
- "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
595
- ],
596
- "tracks": [
597
- {
598
- "name": "unique",
599
- "label": "Unique peptide",
600
- "filter": "unique",
601
- "trackType": "nightingale-track",
602
- "data": [
603
- {
604
- "adapter": "proteomics-adapter",
605
- "url": "https://www.ebi.ac.uk/proteins/api/proteomics/{accession}"
606
- }
607
- ],
608
- "tooltip": ""
609
- },
610
- {
611
- "name": "non_unique",
612
- "label": "Non-unique peptide",
613
- "filter": "non_unique",
614
- "trackType": "nightingale-track",
615
- "data": [
616
- {
617
- "adapter": "proteomics-adapter",
618
- "url": "https://www.ebi.ac.uk/proteins/api/proteomics/{accession}"
619
- }
620
- ],
621
- "tooltip": ""
622
- },
623
- {
624
- "name": "hpp",
625
- "label": "Human proteome project",
626
- "trackType": "nightingale-track",
627
- "data": [
628
- {
629
- "adapter": "proteomics-adapter",
630
- "url": "https://www.ebi.ac.uk/proteins/api/hpp/{accession}"
631
- }
632
- ],
633
- "tooltip": ""
634
- },
635
- {
636
- "name": "proteomics-ptm",
637
- "label": "PTM-containing peptide",
638
- "trackType": "nightingale-track",
639
- "data": [
640
- {
641
- "adapter": "proteomics-adapter",
642
- "url": "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
643
- }
644
- ],
645
- "tooltip": ""
646
- }
647
- ]
648
- },
649
- {
650
- "name": "STRUCTURE_COVERAGE",
651
- "label": "PDBe 3D structure coverage",
652
- "trackType": "nightingale-track",
653
- "tracks": [
654
- {
655
- "name": "pdbe_cover",
656
- "label": "PDBe coverage",
657
- "trackType": "nightingale-track",
658
- "tooltip": "PDBe 3D structure coverage",
659
- "data": [
660
- {
661
- "adapter": "structure-adapter",
662
- "url": "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
663
- }
664
- ]
665
- }
666
- ]
667
- },
668
- {
669
- "name": "ALPHAFOLD_CONFIDENCE",
670
- "label": "AlphaFold",
671
- "trackType": "nightingale-colored-sequence",
672
- "scale": "H:90,M:70,L:50,D:0",
673
- "color-range": "#ff7d45:0,#ffdb13:50,#65cbf3:70,#0053d6:90,#0053d6:100",
674
- "tracks": [
675
- {
676
- "name": "alphafold_confidence",
677
- "label": "AlphaFold Confidence",
678
- "labelUrl": "https://alphafold.ebi.ac.uk/entry/{accession}",
679
- "trackType": "nightingale-colored-sequence",
680
- "data": [
681
- {
682
- "adapter": "alphafold-confidence-adapter",
683
- "url": [
684
- "https://alphafold.ebi.ac.uk/api/prediction/{accession}",
685
- "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
686
- ]
687
- }
688
- ],
689
- "tooltip": "AlphaFold prediction confidence"
690
- }
691
- ]
692
- },
693
- {
694
- "name": "ALPHAMISSENSE_PATHOGENICITY",
695
- "label": "AlphaMissense",
696
- "trackType": "nightingale-colored-sequence",
697
- "scale": "P:100,A:50,B:0",
698
- "color-range": "#9a131a:100,#a8a9ad:50,#3d5493:0",
699
- "tracks": [
700
- {
701
- "name": "alphamissense_pathogenicity",
702
- "label": "Average Pathogenicity Score",
703
- "trackType": "nightingale-colored-sequence",
704
- "data": [
705
- {
706
- "adapter": "alphamissense-pathogenicity-adapter",
707
- "url": [
708
- "https://alphafold.ebi.ac.uk/api/prediction/{accession}",
709
- "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
710
- ]
711
- }
712
- ],
713
- "tooltip": "AlphaMissense pathogenicity"
714
- },
715
- {
716
- "name": "alphamissense_pathogenicity_heatmap",
717
- "label": "AlphaMissense Pathogenicity",
718
- "labelUrl": "https://alphafold.ebi.ac.uk/entry/{accession}",
719
- "trackType": "nightingale-sequence-heatmap",
720
- "data": [
721
- {
722
- "adapter": "alphamissense-heatmap-adapter",
723
- "url": [
724
- "https://alphafold.ebi.ac.uk/api/prediction/{accession}",
725
- "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
726
- ]
727
- }
728
- ],
729
- "tooltip": "AlphaMissense pathogenicity"
730
- }
731
- ]
732
- },
733
- {
734
- "name": "STRUCTURAL",
735
- "label": "Structural features",
736
- "trackType": "nightingale-track",
737
- "tracks": [
738
- {
739
- "name": "helix",
740
- "label": "Helix",
741
- "filter": "HELIX",
742
- "trackType": "nightingale-track",
743
- "data": [
744
- {
745
- "adapter": "feature-adapter",
746
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
747
- }
748
- ],
749
- "tooltip": "The positions of experimentally determined helical regions"
750
- },
751
- {
752
- "name": "strand",
753
- "label": "Beta strand",
754
- "filter": "STRAND",
755
- "trackType": "nightingale-track",
756
- "data": [
757
- {
758
- "adapter": "feature-adapter",
759
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
760
- }
761
- ],
762
- "tooltip": "The positions of experimentally determined beta strands"
763
- },
764
- {
765
- "name": "turn",
766
- "label": "Turn",
767
- "filter": "TURN",
768
- "trackType": "nightingale-track",
769
- "data": [
770
- {
771
- "adapter": "feature-adapter",
772
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
773
- }
774
- ],
775
- "tooltip": "The positions of experimentally determined hydrogen-bonded turns"
776
- },
777
- {
778
- "name": "coiled",
779
- "label": "Coiled coil",
780
- "filter": "COILED",
781
- "trackType": "nightingale-track",
782
- "data": [
783
- {
784
- "adapter": "feature-adapter",
785
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
786
- }
787
- ],
788
- "tooltip": "Coiled coils are built by two or more alpha-helices that wind around each other to form a supercoil"
789
- }
790
- ]
791
- }
792
- ],
793
- "download": [
794
- {
795
- "type": "features",
796
- "url": "https://www.ebi.ac.uk/proteins/api/features/"
797
- },
798
- {
799
- "type": "variants",
800
- "url": "https://www.ebi.ac.uk/proteins/api/variation/"
801
- },
802
- {
803
- "type": "antigens",
804
- "url": "https://www.ebi.ac.uk/proteins/api/antigen/"
805
- },
806
- {
807
- "type": "proteomics",
808
- "url": "https://www.ebi.ac.uk/proteins/api/proteomics/"
809
- }
810
- ]
811
- }