Import PTM features and metadata from Uniprot proteomics-ptm API

Detailed PTM metadata is available from the JSON endpoint:
https://www.ebi.ac.uk/proteins/api/proteomics-ptm/A0A0P0XJ24

In principle we could use the GFF3 content-type (curl -X GET --header 'Accept:text/x-gff' ') and import directly, but the JSON is much richer:

{
  "accession": "A0A0P0XJ24",
  "entryName": "A0A0P0XJ24_ORYSJ",
  "sequence": "GKSGAKKKKPAAAASASAAATKSSPAATEPKAPTQSQPPAANGAAPHLVDPAVLLRRAHELKEEGNRLFQSRDYGGALRQYELALRLAPRGHPDRAVFHSNRAACLLQLRPVDHKAVAEECSLALQAEPLFPRALLRRARALEALGRHELALTDALALLALDPDHQDAVDLVHRLRSRILSPSSSASGSATSTPEPTSRPSPAALGASAVVAGLGPSLPARPFPKKPSPPPPPAQQQQSVPPMSKFNPSPPSPKLVPFSNSPPSSANASAAESSQKVTPTPLVPSSLSLKDKALMDKKVVTRSRPLKLVYDHDIRLAQMPEKCSFRTLREVVASRFPSSKAVLIKYKDADGDLVTITCSAELRLAESCVDIAGSEVIEDGARHGQKLPMLRLHIVEVSPDQEPPMPTEEEKLEQDNELLVKGEDNSPHASAAVVTDAEVTKQDVENVVAEAEQNTLTGKKDCGHAECKEAEIDDWLLQFADLFRNQVGVDADAHLDLHELGMELCSEALEETVTSEEAQALFEMAAAKFQEVAALALFNWGNVHMCAARKRIPLDESAPKKVMSAQLCTAYDWVRDRYALAGSKYEEALKIKPDFYEGLLALGQQHFETAKLHWSFALADKVDLSAWDSSQTFKLFDSAEHKMRAATEMWEKVEEQRMAELKEPSSEALKKRKKQHNADGQGELTPEEAAEQAAVMRQQIHLFWGNMLFERSQVEFKLDIADWKKNLDASIERFKLAGASESDISAVLKNHFSNTVSECEDKKIMTLDTGISQISNNIEDKCILES",
  "sequenceChecksum": "5941F741151D242B",
  "taxid": 39947,
  "features": [
    {
      "type": "PROTEOMICS_PTM",
      "begin": "246",
      "end": "254",
      "xrefs": [
        {
          "name": "Proteomes",
          "id": "UP000059680",
          "url": "https://www.uniprot.org/proteomes/UP000059680"
        }
      ],
      "evidences": [
        {
          "code": "ECO:0007829",
          "source": {
            "id": "FNPSPPSPK",
            "url": "https://www.ebi.ac.uk/pride/peptidome/peptidedetails?keyword=FNPSPPSPK&proteinAccession=A0A0P0XJ24"
          }
        }
      ],
      "peptide": "FNPSPPSPK",
      "unique": true,
      "ptms": [
        {
          "name": "Phosphorylation",
          "position": 7,
          "sources": [
            "PTMeXchange"
          ],
          "dbReferences": [
            {
              "id": "PXD004939",
              "properties": {
                "Pubmed ID": "28054942",
                "Confidence score": "Gold",
                "PSM Score": "0.9994",
                "Site q value": "0.0",
                "Dataset ID": "PXD004939",
                "Organism part": "Leaf",
                "Universal Spectrum Id": "mzspec:PXD004939:Rice_phos_ABA_12h_20per_F1_R2:scan:12866:FNPSPPS[Phospho]PK/2",
                "Final site probability": "0.9784126",
                "PSM Count (0.05 gFLR)": "30",
                "Proforma": "FNPSPPS[Phospho]PK"
              }
            },
            {
              "id": "PXD005241",
              "properties": {
                "Pubmed ID": "28382632",
                "Confidence score": "Gold",
                "PSM Score": "0.9853",
                "Site q value": "0.0170407241382277",
                "Dataset ID": "PXD005241",
                "Organism part": "Leaf",
                "Universal Spectrum Id": "mzspec:PXD005241:Rice_phos_mature_panicles__TiO2_25per_F2_R1_raw:scan:12925:FNPSPPS[Phospho]PK/2",
                "Final site probability": "0.95002626",
                "PSM Count (0.05 gFLR)": "5",
                "Proforma": "FNPSPPS[Phospho]PK"
              }
            },
            {
              "id": "PXD004705",
              "properties": {
                "Pubmed ID": "28439285",
                "Confidence score": "Gold",
                "PSM Score": "0.9999",
                "Site q value": "0.0024898044423765",
                "Dataset ID": "PXD004705",
                "Organism part": "Leaf",
                "Universal Spectrum Id": "mzspec:PXD004705:Rice_phos_BR_3h_20per_F1_R2:scan:12659:FNPSPPS[Phospho]PK/2",
                "Final site probability": "0.95550444",
                "PSM Count (0.05 gFLR)": "34",
                "Proforma": "FNPSPPS[Phospho]PK"
              }
            },
            {
              "id": "PXD000923",
              "properties": {
                "Pubmed ID": "25074045",
                "Confidence score": "Gold",
                "PSM Score": "0.999",
                "Site q value": "0.0055560314053066",
                "Dataset ID": "PXD000923",
                "Organism part": "Flower",
                "Universal Spectrum Id": "mzspec:PXD000923:LHY_T5:scan:02407:FNPSPPS[Phospho]PK/2",
                "Final site probability": "0.91025148767299",
                "PSM Count (0.05 gFLR)": "3",
                "Proforma": "FNPSPPS[Phospho]PK"
              }
            },
            {
              "id": "PXD002222",
              "properties": {
                "Pubmed ID": "26112675",
                "Confidence score": "Gold",
                "PSM Score": "0.9998",
                "Site q value": "0.0",
                "Dataset ID": "PXD002222",
                "Organism part": "Leaf",
                "Universal Spectrum Id": "mzspec:PXD002222:Rice_leaf_0h_phospho_test2:scan:09105:FNPSPPS[Phospho]PK/2",
                "Final site probability": "0.9803039",
                "PSM Count (0.05 gFLR)": "24",
                "Proforma": "FNPSPPS[Phospho]PK"
              }
            }
          ]
        }
      ]
    },
    {
      "type": "PROTEOMICS_PTM",
      "begin": "246",
      "end": "254",
      "xrefs": [
        {
          "name": "Proteomes",
          "id": "UP000059680",
          "url": "https://www.uniprot.org/proteomes/UP000059680"
        }
      ],
      "evidences": [
        {
          "code": "ECO:0007829",
          "source": {
            "id": "FNPSPPSPK",
            "url": "https://www.ebi.ac.uk/pride/peptidome/peptidedetails?keyword=FNPSPPSPK&proteinAccession=A0A0P0XJ24"
          }
        }
      ],
      "peptide": "FNPSPPSPK",
      "unique": true,
      "ptms": [
        {
          "name": "Phosphorylation",
          "position": 7,
          "sources": [
            "PTMeXchange"
          ],
          "dbReferences": [
            {
              "id": "PXD019291",
              "properties": {
                "Pubmed ID": "33658224",
                "Confidence score": "Gold",
                "PSM Score": "1.0",
                "Site q value": "0.0184438306538822",
                "Dataset ID": "PXD019291",
                "Organism part": "Anther",
                "Universal Spectrum Id": "mzspec:PXD019291:S9588TPST_Fr1:scan:20749:[TMT6plex]FNPSPPS[Phospho]PK[TMT6plex]/2",
                "Final site probability": "0.8460922634265026",
                "PSM Count (0.05 gFLR)": "3",
                "Proforma": "[TMT6plex]FNPSPPS[Phospho]PK[TMT6plex]"
              }
            }
          ]
        }
      ]
    },
    {
      "type": "PROTEOMICS_PTM",
      "begin": "422",
      "end": "441",
      "xrefs": [
        {
          "name": "Proteomes",
          "id": "UP000059680",
          "url": "https://www.uniprot.org/proteomes/UP000059680"
        }
      ],
      "evidences": [
        {
          "code": "ECO:0007829",
          "source": {
            "id": "GEDNSPHASAAVVTDAEVTK",
            "url": "https://www.ebi.ac.uk/pride/peptidome/peptidedetails?keyword=GEDNSPHASAAVVTDAEVTK&proteinAccession=A0A0P0XJ24"
          }
        }
      ],
      "peptide": "GEDNSPHASAAVVTDAEVTK",
      "unique": true,
      "ptms": [
        {
          "name": "Phosphorylation",
          "position": 5,
          "sources": [
            "PTMeXchange"
          ],
          "dbReferences": [
            {
              "id": "PXD004939",
              "properties": {
                "Pubmed ID": "28054942",
                "Confidence score": "Gold",
                "PSM Score": "1.0",
                "Site q value": "0.0",
                "Dataset ID": "PXD004939",
                "Organism part": "Leaf",
                "Universal Spectrum Id": "mzspec:PXD004939:Rice_phos_Nip_0h_20per_F1_R1:scan:17365:GEDNS[Phospho]PHASAAVVTDAEVTK/2",
                "Final site probability": "0.977196147205192",
                "PSM Count (0.05 gFLR)": "3",
                "Proforma": "GEDNS[Phospho]PHASAAVVTDAEVTK"
              }
            },
            {
              "id": "PXD005241",
              "properties": {
                "Pubmed ID": "28382632",
                "Confidence score": "Gold",
                "PSM Score": "0.9967",
                "Site q value": "0.0",
                "Dataset ID": "PXD005241",
                "Organism part": "Leaf",
                "Universal Spectrum Id": "mzspec:PXD005241:Rice_phos_young_panicles__TiO2_25per_F3_R1_raw:scan:28028:GEDNS[Phospho]PHASAAVVTDAEVTK/2",
                "Final site probability": "0.9807527998278694",
                "PSM Count (0.05 gFLR)": "10",
                "Proforma": "GEDNS[Phospho]PHASAAVVTDAEVTK"
              }
            },
            {
              "id": "PXD004705",
              "properties": {
                "Pubmed ID": "28439285",
                "Confidence score": "Gold",
                "PSM Score": "1.0",
                "Site q value": "0.0",
                "Dataset ID": "PXD004705",
                "Organism part": "Leaf",
                "Universal Spectrum Id": "mzspec:PXD004705:Rice_phos_BR_3h_20per_F1_R3:scan:17196:GEDNS[Phospho]PHASAAVVTDAEVTK/2",
                "Final site probability": "0.9877999822702022",
                "PSM Count (0.05 gFLR)": "8",
                "Proforma": "GEDNS[Phospho]PHASAAVVTDAEVTK"
              }
            }
          ]
        }
      ]
    },
    {
      "type": "PROTEOMICS_PTM",
      "begin": "255",
      "end": "276",
      "xrefs": [
        {
          "name": "Proteomes",
          "id": "UP000059680",
          "url": "https://www.uniprot.org/proteomes/UP000059680"
        }
      ],
      "evidences": [
        {
          "code": "ECO:0007829",
          "source": {
            "id": "LVPFSNSPPSSANASAAESSQK",
            "url": "https://www.ebi.ac.uk/pride/peptidome/peptidedetails?keyword=LVPFSNSPPSSANASAAESSQK&proteinAccession=A0A0P0XJ24"
          }
        }
      ],
      "peptide": "LVPFSNSPPSSANASAAESSQK",
      "unique": true,
      "ptms": [
        {
          "name": "Phosphorylation",
          "position": 7,
          "sources": [
            "PTMeXchange"
          ],
          "dbReferences": [
            {
              "id": "PXD000923",
              "properties": {
                "Pubmed ID": "25074045",
                "Confidence score": "Bronze",
                "PSM Score": "0.998",
                "Site q value": "0.0202587687670536",
                "Dataset ID": "PXD000923",
                "Organism part": "Flower",
                "Universal Spectrum Id": "mzspec:PXD000923:LHY_T6:scan:12749:LVPFSNS[Phospho]PPSSANASAAESSQK/3",
                "Final site probability": "0.7172018572236077",
                "PSM Count (0.05 gFLR)": "1",
                "Proforma": "LVPFSNS[Phospho]PPSSANASAAESSQK"
              }
            }
          ]
        }
      ]
    },
    {
      "type": "PROTEOMICS_PTM",
      "begin": "277",
      "end": "290",
      "xrefs": [
        {
          "name": "Proteomes",
          "id": "UP000059680",
          "url": "https://www.uniprot.org/proteomes/UP000059680"
        }
      ],
      "evidences": [
        {
          "code": "ECO:0007829",
          "source": {
            "id": "VTPTPLVPSSLSLK",
            "url": "https://www.ebi.ac.uk/pride/peptidome/peptidedetails?keyword=VTPTPLVPSSLSLK&proteinAccession=A0A0P0XJ24"
          }
        }
      ],
      "peptide": "VTPTPLVPSSLSLK",
      "unique": true,
      "ptms": [
        {
          "name": "Phosphorylation",
          "position": 12,
          "sources": [
            "PTMeXchange"
          ],
          "dbReferences": [
            {
              "id": "PXD000923",
              "properties": {
                "Pubmed ID": "25074045",
                "Confidence score": "Bronze",
                "PSM Score": "1.0",
                "Site q value": "0.039115499603902",
                "Dataset ID": "PXD000923",
                "Organism part": "Flower",
                "Universal Spectrum Id": "mzspec:PXD000923:LHY_T4:scan:08926:VTPTPLVPSSLS[Phospho]LK/2",
                "Final site probability": "0.602362602131413",
                "PSM Count (0.05 gFLR)": "1",
                "Proforma": "VTPTPLVPSSLS[Phospho]LK"
              }
            }
          ]
        }
      ]
    }
  ]
}