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xtuition

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xtuition supports RESTful (REpresentational State Transfer) Web Services for accessing crystallization data. You can view this documentation here

Core Resources

Screen

High-Throughput Crystallization Screen

Screen
GET/screen/{screen_id}

Example URI

GET http://xtuition.org/api//screen/1
URI Parameters
HideShow
screen_id
number (required) Example: 1

integer ID of the Screen

Request
HideShow
Headers
Content-Type: application/json
Authorization: Bearer xtuition_access_token
Response  200
HideShow
Headers
Content-Type: application/json
Body
{
  "screen_id": 1,
  "cocktails": 1536,
  "samples": 498,
  "name": "HWI Generation 4",
  "owner": "HWI"
}
Schema
{
  "$schema": "http://json-schema.org/draft-04/schema#",
  "type": "object",
  "properties": {
    "screen_id": {
      "type": "number",
      "description": "ID of the screen"
    },
    "cocktails": {
      "type": "number",
      "description": "number of cocktails in the screen"
    },
    "samples": {
      "type": "number",
      "description": "number of samples using the screen"
    },
    "name": {
      "type": "string",
      "description": "name of the screen"
    },
    "owner": {
      "type": "string",
      "description": "name of entity that owns the screen"
    }
  }
}
Response  404

Screen Cocktails

Fetch all cocktails in the screen

Screen Cocktails
GET/screen/{screen_id}/cocktails

Example URI

GET http://xtuition.org/api//screen/1/cocktails
URI Parameters
HideShow
screen_id
number (required) Example: 1

integer ID of the Screen

Request
HideShow
Headers
Content-Type: application/json
Authorization: Bearer xtuition_access_token
Response  200
HideShow
Headers
Content-Type: application/json
Body
[
  {
    "cocktail_id": 1,
    "screen_id": 1,
    "name": "2_C0193",
    "well_pos": 1432,
    "ph": 7,
    "compounds": "Tris, PEG 2000",
    "components": [
      {
        "concentration": 0.1,
        "unit": "M",
        "ph": 7,
        "component": {
          "compound_id": 1,
          "name": "Tris",
          "chemspider_id": 6257,
          "pubchem_id": 24845612,
          "iupac": "2-amino-2-(hydroxymethyl)propane-1,3-diol",
          "cas": "77-86-1",
          "formula": "C_{4}H_{11}NO_{3}",
          "smiles": "OCC(N)(CO)CO",
          "inchi": "InChI=1/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2",
          "inchi_key": "LENZDBCJOHFCAS-UHFFFAOYAN",
          "common_name": "Tris(hydroxymethyl)aminomethane",
          "average_mass": 121.13500213623047,
          "molecular_weight": 121.13500213623047,
          "monoisotopic_mass": 121.07389068603516,
          "nominal_mass": 121,
          "density": 1.3339999914169312
        }
      }
    ]
  }
]
Schema
{
  "$schema": "http://json-schema.org/draft-04/schema#",
  "type": "array"
}
Response  404

Cocktail

Crystallization Cocktail

Cocktail
GET/cocktail/{cocktail_id}

Example URI

GET http://xtuition.org/api//cocktail/1
URI Parameters
HideShow
cocktail_id
number (required) Example: 1

integer ID of the Cocktail

Request
HideShow
Headers
Content-Type: application/json
Authorization: Bearer xtuition_access_token
Response  200
HideShow
Headers
Content-Type: application/json
Body
{
  "cocktail_id": 1,
  "screen_id": 1,
  "name": "2_C0193",
  "well_pos": 1432,
  "ph": 7,
  "compounds": "Tris, PEG 2000",
  "components": [
    {
      "concentration": 0.1,
      "unit": "M",
      "ph": 7,
      "component": {
        "compound_id": 1,
        "name": "Tris",
        "chemspider_id": 6257,
        "pubchem_id": 24845612,
        "iupac": "2-amino-2-(hydroxymethyl)propane-1,3-diol",
        "cas": "77-86-1",
        "formula": "C_{4}H_{11}NO_{3}",
        "smiles": "OCC(N)(CO)CO",
        "inchi": "InChI=1/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2",
        "inchi_key": "LENZDBCJOHFCAS-UHFFFAOYAN",
        "common_name": "Tris(hydroxymethyl)aminomethane",
        "average_mass": 121.13500213623047,
        "molecular_weight": 121.13500213623047,
        "monoisotopic_mass": 121.07389068603516,
        "nominal_mass": 121,
        "density": 1.3339999914169312
      }
    }
  ]
}
Schema
{
  "$schema": "http://json-schema.org/draft-04/schema#",
  "type": "object",
  "properties": {
    "cocktail_id": {
      "type": "number",
      "description": "ID of the cocktail"
    },
    "screen_id": {
      "type": "number",
      "description": "ID of the screen"
    },
    "name": {
      "type": "string",
      "description": "name of the cocktail"
    },
    "well_pos": {
      "type": "number",
      "description": "The well position"
    },
    "ph": {
      "type": "number",
      "description": "The overall pH of the cocktail"
    },
    "compounds": {
      "type": "string",
      "description": "list of compound names"
    },
    "components": {
      "type": "array",
      "description": "array of components"
    }
  }
}
Response  404

Compound

Chemical Compound

Compound
GET/compound/{compound_id}

Example URI

GET http://xtuition.org/api//compound/1
URI Parameters
HideShow
compound_id
number (required) Example: 1

integer ID of the Compound

Request
HideShow
Headers
Content-Type: application/json
Authorization: Bearer xtuition_access_token
Response  200
HideShow
Headers
Content-Type: application/json
Body
{
  "compound_id": 1,
  "name": "Tris",
  "chemspider_id": 6257,
  "pubchem_id": 24845612,
  "iupac": "2-amino-2-(hydroxymethyl)propane-1,3-diol",
  "cas": "77-86-1",
  "formula": "C_{4}H_{11}NO_{3}",
  "smiles": "OCC(N)(CO)CO",
  "inchi": "InChI=1/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2",
  "inchi_key": "LENZDBCJOHFCAS-UHFFFAOYAN",
  "common_name": "Tris(hydroxymethyl)aminomethane",
  "average_mass": 121.13500213623047,
  "molecular_weight": 121.13500213623047,
  "monoisotopic_mass": 121.07389068603516,
  "nominal_mass": 121,
  "density": 1.3339999914169312
}
Schema
{
  "$schema": "http://json-schema.org/draft-04/schema#",
  "type": "object",
  "properties": {
    "compound_id": {
      "type": "number",
      "description": "ID of the compound"
    },
    "name": {
      "type": "string",
      "description": "name of the compound"
    },
    "chemspider_id": {
      "type": "number",
      "description": "The chemspider ID"
    },
    "pubchem_id": {
      "type": "number",
      "description": "The PubChem ID"
    },
    "iupac": {
      "type": "string"
    },
    "cas": {
      "type": "string"
    },
    "formula": {
      "type": "string"
    },
    "smiles": {
      "type": "string"
    },
    "inchi": {
      "type": "string"
    },
    "inchi_key": {
      "type": "string"
    },
    "common_name": {
      "type": "string"
    },
    "average_mass": {
      "type": "number"
    },
    "molecular_weight": {
      "type": "number"
    },
    "monoisotopic_mass": {
      "type": "number"
    },
    "nominal_mass": {
      "type": "number"
    },
    "density": {
      "type": "number"
    }
  }
}
Response  404

Sample

Sample

Sample
GET/sample/{sample_id}

Example URI

GET http://xtuition.org/api//sample/1
URI Parameters
HideShow
sample_id
number (required) Example: 1

integer ID of the Sample

Request
HideShow
Headers
Content-Type: application/json
Authorization: Bearer xtuition_access_token
Response  200
HideShow
Headers
Content-Type: application/json
Body
{
  "sample_id": 1,
  "screen_id": 1,
  "xnumber": "X000001071",
  "pnumber": "P000001033",
  "molar_concentration": 0.0004400000034365803,
  "difference_from_purification": 2,
  "date_purified": "2002-08-07T00:00:00Z",
  "setup_date": "2002-08-09T00:00:00Z",
  "instructions": "instructions",
  "setup_notes_before": "clear and colorless",
  "post_translational_modification": "``",
  "sample_additional_notes": "Ni-NTA, gel filtration purified",
  "setup_notes_after_delivery": "mostly clear and some drops show light precipitate",
  "volume_units": "\\u00b5L",
  "volume_sent": 450,
  "experimental_molecular_weight": 22500,
  "sample_ph": 7.5,
  "concentration": 10,
  "concentration_units": "mg/mL",
  "name": "Hypothetical protein",
  "spine_target_id": "QR83",
  "spine_status": "HSQC collected",
  "pfam": "PF03079",
  "pi": "5.29",
  "ext": 31400,
  "length": "183 aa",
  "mass": "21.48 kD",
  "organism": "Aquifex aeolicus",
  "sequence": "MSRLRIYTESGELIKDITDPKE..",
  "gene": "geneName",
  "genus": "Aquifex",
  "species": "aeolicus",
  "strain": "strain",
  "wells": 320,
  "verified_crystals": 123,
  "classified": 1536,
  "screen_name": "HWI Generation 3",
  "structures": [
    {
      "structure_id": "2HJI",
      "exp_method": "X-Ray"
    }
  ],
  "dbrefs": [
    {
      "link": "http://",
      "db": "UniProt"
    }
  ]
}
Schema
{
  "$schema": "http://json-schema.org/draft-04/schema#",
  "type": "object",
  "properties": {
    "sample_id": {
      "type": "number",
      "description": "ID of the sample"
    },
    "screen_id": {
      "type": "number",
      "description": "ID of the screen"
    },
    "xnumber": {
      "type": "string",
      "description": "Unique string ID of sample"
    },
    "pnumber": {
      "type": "string",
      "description": "Unique protien ID of the sample"
    },
    "molar_concentration": {
      "type": "number"
    },
    "difference_from_purification": {
      "type": "number"
    },
    "date_purified": {
      "type": "string"
    },
    "setup_date": {
      "type": "string"
    },
    "instructions": {
      "type": "string"
    },
    "setup_notes_before": {
      "type": "string"
    },
    "post_translational_modification": {
      "type": "string"
    },
    "sample_additional_notes": {
      "type": "string"
    },
    "setup_notes_after_delivery": {
      "type": "string"
    },
    "volume_units": {
      "type": "string"
    },
    "volume_sent": {
      "type": "number"
    },
    "experimental_molecular_weight": {
      "type": "number"
    },
    "sample_ph": {
      "type": "number"
    },
    "concentration": {
      "type": "number"
    },
    "concentration_units": {
      "type": "string"
    },
    "name": {
      "type": "string"
    },
    "spine_target_id": {
      "type": "string"
    },
    "spine_status": {
      "type": "string"
    },
    "pfam": {
      "type": "string"
    },
    "pi": {
      "type": "string"
    },
    "ext": {
      "type": "number"
    },
    "length": {
      "type": "string"
    },
    "mass": {
      "type": "string"
    },
    "organism": {
      "type": "string"
    },
    "sequence": {
      "type": "string"
    },
    "gene": {
      "type": "string"
    },
    "genus": {
      "type": "string"
    },
    "species": {
      "type": "string"
    },
    "strain": {
      "type": "string"
    },
    "wells": {
      "type": "number",
      "description": "total number of wells"
    },
    "verified_crystals": {
      "type": "number",
      "description": "total number of wells with verified crystals"
    },
    "classified": {
      "type": "number",
      "description": "total number of wells that have been auto classified"
    },
    "screen_name": {
      "type": "string",
      "description": "name of screen"
    },
    "structures": {
      "type": "array",
      "description": "array of PDB structures"
    },
    "dbrefs": {
      "type": "array",
      "description": "array of external database references"
    }
  }
}
Response  404

Generated by aglio on 23 Jan 2016