REST API

OrganiZymeDB exposes a read-only JSON API, with no authentication required. All endpoints return application/json. The base URL is the root of this site (https://organizymedb.org).

Endpoint Overview

Method	Endpoint	Description
`GET`	/api/proteins	List / search all proteins
`GET`	/api/protein/<id>	Full record for one protein + mutations
`GET`	/api/measurements	List / filter all measurements
`GET`	/api/measurements/<id>	Single measurement record
`GET`	/api/solvents	List all solvents
`GET`	/api/solvent/<id>	Single solvent record
`GET`	/api/compounds	List / search all compounds
`GET`	/api/compound/<id>	Single compound record
`GET`	/api/compound/by-name/<name>	Compound lookup by exact name
`GET`	/api/stats	Database statistics

Proteins

/api/proteins

GETReturns a paginated list of all proteins. Supports optional filtering.

Query parameters

Parameter	Type	Description
`q`	string	Free-text search on enzyme name or species (case-insensitive)
`ec`	string	Filter by EC number prefix (e.g. `3.1` matches EC 3.1.x.x)
`species`	string	Filter by species name substring
`page`	integer	Page number (default: 1)
`per_page`	integer	Results per page (default: 50, max: 200)

Example request

GET /api/proteins?q=lipase&page=1&per_page=10

Example response

{
  "data": [
    {
      "protein_id": 17,
      "enzyme_name": "Lipase A (gene lipA) from Bacillus subtilis",
      "enzyme_species": "Bacillus subtilis",
      "ec_number": "3.1.1.3"
    },
    {
      "protein_id": 46,
      "enzyme_name": "Lipase from Pseudomonas cepacia",
      "enzyme_species": "Pseudomonas cepacia",
      "ec_number": "3.1.1.3"
    },
    ...
  ],
  "pagination": {
    "page": 1,
    "per_page": 10,
    "total": 126,
    "total_pages": 13
  }
}

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/api/protein/<protein_id>

GETFull record for a single protein, including its production source, extremophile annotation, and all known mutations.

Example request

GET /api/protein/2

Example response

{
  "protein": {
    "protein_id": 2,
    "enzyme_name": "Ene-reductase DrER from Deinococcus radiodurans",
    "enzyme_species": "Deinococcus radiodurans",
    "ec_number": "1.6.99.1",
    "is_extremophile": true,
    "extremophile_annotation": "polyextremophilic organism",
    "source": "Recombinant, host bacterium Escherichia coli BL21 (DE3)"
  },
  "mutations": []
}

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Measurements

/api/measurements

GETPaginated, filterable list of all experimental measurements. This is the primary endpoint for programmatic data access.

Query parameters

Parameter	Type	Description
`protein_id`	integer	Return only measurements for this protein
`solvent`	string	Filter by exact solvent name (case-insensitive)
`property`	string	Filter by assay/property type substring (e.g. `activity`)
`wt_only`	0 / 1	Set to `1` to return only wild-type measurements
`page`	integer	Page number (default: 1)
`per_page`	integer	Results per page (default: 50, max: 200)

Example request

GET /api/measurements?solvent=dimethyl+sulfoxide&wt_only=1&per_page=20

Example response

{
  "data": [
    {
      "measurement_id": 3410,
      "protein_id": 59,
      "is_extremophile": "No",
      "mutation": "WT",
      "property": "Stability - Incubation",
      "solvent_name": "Dimethyl Sulfoxide",
      "solvent_volume": "10",
      "aqueous_control": "100",
      "wt_control": "NaN",
      "measured_value": "50",
      "units": "%",
      "assay_solution": "Incubation: 50 mM Tris-HCl, 10 mM CaCl2, 450 microM CHAPS, Assay: 50 mM Tris-HCl, 10 mM CaCl2, 450 microM CHAPS",
      "ph": "Incubation: 9, Assay: 9",
      "temperature": "Incubation: 37\u00b0C, Assay: 40\u00b0C",
      "cofactor": "NaN",
      "comments": "Non-incubated control (in %), assay in aqueous phase"
    },
    ...
  ],
  "pagination": {
    "page": 1,
    "per_page": 20,
    "total": 134,
    "total_pages": 7
  }
}

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/api/measurements/<measurement_id>

GETFull record for a single measurement.

Example request

GET /api/measurements/3410

Example response

{
  "measurement_id": 3410,
  "protein_id": 59,
  "is_extremophile": "No",
  "mutation": "WT",
  "property": "Stability - Incubation",
  "solvent_name": "Dimethyl Sulfoxide",
  "solvent_volume": "10",
  "aqueous_control": "100",
  "wt_control": "NaN",
  "measured_value": "50",
  "units": "%",
  "assay_solution": "Incubation: 50 mM Tris-HCl, 10 mM CaCl2, 450 microM CHAPS, Assay: 50 mM Tris-HCl, 10 mM CaCl2, 450 microM CHAPS",
  "ph": "Incubation: 9, Assay: 9",
  "temperature": "Incubation: 37\u00b0C, Assay: 40\u00b0C",
  "cofactor": "NaN",
  "comments": "Non-incubated control (in %), assay in aqueous phase"
}

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Solvents

/api/solvents

GETReturns the list of all organic solvents referenced in the database, with CAS number, log P, and CHEM21 greenness scores where available.

Example request

GET /api/solvents

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/api/solvent/<solvent_id>

GETFull record for a single solvent.

Example request

GET /api/solvent/1

Example response

{
  "solvent_id": 1,
  "solvent_name": "Dimethyl Sulfoxide",
  "cas_number": "67-68-5",
  "pubchem_id": "679",
  "smiles": "CS(=O)C",
  "log_p": "-1.3500",
  "chem21_safety": "1",
  "chem21_health": "1",
  "chem21_environment": "5",
  "chem21_ranking_default": "Recommended",
  "chem21_ranking_discussion": "Problematic"
}

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Compounds

/api/compounds

GETReturns a paginated list of all compounds (substrates and products). Supports optional search by name or CAS number.

Query parameters

Parameter	Type	Description
`q`	string	Search by name or CAS number substring (case-insensitive)
`page`	integer	Page number (default: 1)
`per_page`	integer	Results per page (default: 50, max: 200)

Example request

GET /api/compounds?q=p-nitrophenyl&per_page=10

Example response

{
  "data": [
    {
      "substrate_product_id": 233,
      "name": "p-Nitrophenyl alpha-D-galactopyranoside",
      "cas_number": "7493-95-0",
      "pubchem_id": "82000",
      "smiles": "C1=CC(=CC=C1[N+](=O)[O-])O[C@@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O)O"
    },
    {
      "substrate_product_id": 9,
      "name": "p-Nitrophenyl beta-D-glucopyranoside",
      "cas_number": "2492-87-7",
      "pubchem_id": "92930",
      "smiles": "C1=CC(=CC=C1[N+](=O)[O-])O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O"
    },
    ...
  ],
  "pagination": {
    "page": 1,
    "per_page": 10,
    "total": 21,
    "total_pages": 3
  }
}

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/api/compound/<compound_id>

GETReturns a single compound record by its internal ID, including CAS number, PubChem ID, and SMILES string.

Example request

GET /api/compound/1

Example response

{
  "substrate_product_id": 1,
  "name": "Cyclohex-2-enone",
  "cas_number": "930-68-7",
  "pubchem_id": "13594",
  "smiles": "C1CC=CC(=O)C1"
}

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/api/compound/by-name/<name>

GETLooks up a compound by its exact name (URL-encoded). Note that CAS number, PubChem ID, and SMILES may be null for compounds where this information was not available during curation.

Example request

GET /api/compound/by-name/Benzaldehyde

Example response

{
  "substrate_product_id": 57,
  "name": "Benzaldehyde",
  "cas_number": "100-52-7",
  "pubchem_id": "240",
  "smiles": "C1=CC=C(C=C1)C=O"
}

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Statistics

/api/stats

GETHigh-level counts for the whole database.

Example request

GET /api/stats

Example response

{
  "proteins":     705,
  "measurements": 28173,
  "articles":     646,
  "mutations":    3346,
  "solvents":     137,
  "compounds":    696
}

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Usage Examples

Python — export all lipase measurements in ethanol, with full protein details

import requests, csv

BASE = "https://organizymedb.org"

# 1. Find all lipase proteins
proteins = requests.get(f"{BASE}/api/proteins", params={"q": "lipase"}).json()

results = []
for prot_summary in proteins["data"]:
    pid = prot_summary["protein_id"]

    # 2. Fetch full protein-level details once per protein, not once per
    #    measurement (enzyme_name, enzyme_species, ec_numbers, source)
    protein = requests.get(f"{BASE}/api/protein/{pid}").json()["protein"]

    # 3. Fetch this protein's measurements in ethanol, paginating if needed
    page = 1
    while True:
        r = requests.get(f"{BASE}/api/measurements",
                         params={"protein_id": pid, "solvent": "ethanol",
                                 "page": page, "per_page": 200}).json()
        for m in r["data"]:
            results.append({
                # Protein-level fields
                "enzyme_name": protein["enzyme_name"],
                "enzyme_species": protein["enzyme_species"],
                "ec_number": protein["ec_number"],
                "source": protein["source"],
                # Measurement-level fields
                "measurement_id": m["measurement_id"],
                "is_extremophile": m["is_extremophile"],
                "mutation": m["mutation"],
                "property": m["property"],
                "solvent_name": m["solvent_name"],
                "solvent_volume": m["solvent_volume"],
                "aqueous_control": m["aqueous_control"],
                "wt_control": m["wt_control"],
                "measured_value": m["measured_value"],
                "units": m["units"],
                "assay_solution": m["assay_solution"],
                "ph": m["ph"],
                "temperature": m["temperature"],
                "cofactor": m["cofactor"],
                "comments": m["comments"],
            })
        if page >= r["pagination"]["total_pages"]:
            break
        page += 1

fieldnames = list(results[0].keys()) if results else []
with open("lipase_ethanol_measurements.csv", "w", newline="") as f:
    writer = csv.DictWriter(f, fieldnames=fieldnames)
    writer.writeheader()
    writer.writerows(results)

print(f"Saved {len(results)} measurements ({len(fieldnames)} columns) to lipase_ethanol_measurements.csv")

Python — download everything as a DataFrame

import requests, pandas as pd

BASE  = "https://organizymedb.org"
rows, page = [], 1

while True:
    r = requests.get(f"{BASE}/api/measurements",
                     params={"page": page, "per_page": 200}).json()
    rows.extend(r["data"])
    if page >= r["pagination"]["total_pages"]:
        break
    page += 1

df = pd.DataFrame(rows)
print(df.shape)

curl

# All measurements for protein 2, wild-type only
curl "https://organizymedb.org/api/measurements?protein_id=2&wt_only=1"

# Search compounds by name
curl "https://organizymedb.org/api/compounds?q=nitrophenyl"

# All solvents
curl "https://organizymedb.org/api/solvents"

# Database statistics
curl "https://organizymedb.org/api/stats"

Notes

All endpoints are read-only — no POST, PUT, or DELETE operations are exposed.
Pagination metadata (page, per_page, total, total_pages) is included in every list response.
Some text fields (e.g. ph, assay_solution) may contain the literal value "?". This indicates the corresponding information was not reported in the original publication, and is distinct from null (which is used when the field is not applicable rather than simply unreported).
Data are released under CC BY-NC 4.0. For commercial use, contact Romain.Debruyne@ulb.be and Fabrizio.Pucci@ulb.be.
For bulk downloads, the Download page provides pre-built CSV files that may be more convenient than paginating through the API.