omim 1.0.3

OMIM - Online Mendelian Inheritance in Man

OMIM - Online Mendelian Inheritance in Man

Installation

python3 -m pip install -U omim

Basic Usage

main

omim -h

Usage: omim [OPTIONS] COMMAND [ARGS]...

  OMIM - Online Mendelian Inheritance in Man

Options:
  -d, --dbfile TEXT  the path of database file  [default:/usr/local/lib/python3.8/site-packages/omim/data/omim.sqlite3]
  -u, --url TEXT     the url of omim  [default: https://mirror.omim.org]
  --version          Show the version and exit.
  -?, -h, --help     Show this message and exit.

Commands:
  faq     explains of some faq
  query   query something from the database
  stats   statistics of the database
  update  update the database

stats

OMIM Entry Statistics

omim stats

***** updated time: 2024-06-04 *****
+--------------------------+-------+
| MIM_TYPE                 | COUNT |
+--------------------------+-------+
| gene                     | 17290 |
| gene/phenotype           | 18    |
| phenotype                | 8362  |
| predominantly phenotypes | 1736  |
| moved/removed            | 1364  |
| TOTAL COUNT              | 28770 |
+--------------------------+-------+

update

update the database according to the file mim2gene.txt

The method uses web scraping technology, which may lead to IP blocking. Please use it with caution or consider using proxy IPs.

omim update

faq

explains of some FAQ

omim faq

***** Explains of MIM PREFIX *****
+--------+---------------------------------------------------------+
| PREFIX | EXPLAIN                                                 |
+--------+---------------------------------------------------------+
|   *    | Gene description                                        |
|   +    | Gene and phenotype, combined                            |
|   #    | Phenotype description, molecular basis known            |
|   %    | Phenotype description or locus, molecular basis unknown |
|        | Other, mainly phenotypes with suspected mendelian basis |
|   ^    | Moved/Removed                                           |
+--------+---------------------------------------------------------+
***** Explains of PHENOTYPE SYMBOL *****
+--------+------------------------------------------------------------------------------------------------------------------------------+
| SYMBOL | EXPLAIN                                                                                                                      |
+--------+------------------------------------------------------------------------------------------------------------------------------+
|  [ ]   | indicate "nondiseases," mainly genetic variations that lead to apparently abnormal laboratory test values                    |
|  { }   | indicate mutations that contribute to susceptibility to multifactorial disorders                                             |
|        | (e.g., diabetes, asthma) or to susceptibility to infection                                                                   |
|   ?    | before the phenotype name indicates that the relationship between the phenotype and gene is provisional.                     |
|        | More details about this relationship are provided in the comment field of the map and in the gene and phenotype OMIM entries |
|  (1)   | the disorder was positioned by mapping of the wildtype gene                                                                  |
|  (2)   | the disease phenotype itself was mapped                                                                                      |
|  (3)   | the molecular basis of the disorder is known                                                                                 |
|  (4)   | the disorder is a chromosome deletion or duplication syndrome                                                                |
+--------+------------------------------------------------------------------------------------------------------------------------------+

query

omim query -h

Usage: omim query [OPTIONS]

  query something from database

Options:
  -K, --keys               list the available keys
  -s, --search TEXT...     the search string
  -l, --limit INTEGER      limit for output
  -F, --format [json|tsv]  the format for output
  -o, --outfile TEXT       the output filename [stdout]
  -?, -h, --help           Show this message and exit.

omim query -K

+------------------+-----------------------+--------------+
| Key              | Comment               | Type         |
+------------------+-----------------------+--------------+
| mim_number       | MIM Number            | VARCHAR(10)  |
| prefix           | The prefix symbol     | VARCHAR(1)   |
| title            | The title             | VARCHAR(50)  |
| references       | The references        | VARCHAR(300) |
| geneMap          | The geneMap data      | VARCHAR(300) |
| phenotypeMap     | The phenotypeMap data | VARCHAR(300) |
| mim_type         | The mim_type          | VARCHAR(20)  |
| entrez_gene_id   | The entrez_gene_id    | VARCHAR(20)  |
| ensembl_gene_id  | The ensembl_gene_id   | VARCHAR(20)  |
| hgnc_gene_symbol | The hgnc_gene_symbol  | VARCHAR(20)  |
| generated        | The generated time    | DATETIME     |
+------------------+-----------------------+--------------+

omim query -s hgnc_gene_symbol BMPR2

phenotypeMap	references	prefix	mim_number	generated	ensembl_gene_id	mim_type	geneMap	title	hgnc_gene_symbol	entrez_gene_id
None	16429403, 10051328, 17425602, 18548003, 10903931, 21920918, 12571257, 3291115, 12358323, 10973254, 16429395, 11115378, 14583445, 18626305, 18321866, 11484688, 18496036, 18792970, 7644468, 12045205, 12446270, 15965979, 24446489, 11015450, 19620182	*	600799	2021-04-14	ENSG00000204217	gene	[{"Location": "2q33.1-q33.2", "Phenotype": "Pulmonary hypertension, familial primary, 1, with or without HHT", "Phenotype MIM number": "178600", "Inheritance": "AD", "Phenotype mapping key": "3"}, {"Location": "2q33.1-q33.2", "Phenotype": "Pulmonary hypertension, primary, fenfluramine or dexfenfluramine-associated", "Phenotype MIM number": "178600", "Inheritance": "AD", "Phenotype mapping key": "3"}, {"Location": "2q33.1-q33.2", "Phenotype": "Pulmonary venoocclusive disease 1", "Phenotype MIM number": "265450", "Inheritance": "AD", "Phenotype mapping key": "3"}]	BONE MORPHOGENETIC PROTEIN RECEPTOR, TYPE II; BMPR2	BMPR2	659

omim query -s hgnc_gene_symbol BMPR2 -F json

[
  {
    "phenotypeMap": null,
    "references": "16429403, 10051328, 17425602, 18548003, 10903931, 21920918, 12571257, 3291115, 12358323, 10973254, 16429395, 11115378, 14583445, 18626305, 18321866, 11484688, 18496036, 18792970, 7644468, 12045205, 12446270, 15965979, 24446489, 11015450, 19620182",
    "prefix": "*",
    "mim_number": "600799",
    "generated": "2021-04-14",
    "ensembl_gene_id": "ENSG00000204217",
    "mim_type": "gene",
    "geneMap": [
      {
        "Location": "2q33.1-q33.2",
        "Phenotype": "Pulmonary hypertension, familial primary, 1, with or without HHT",
        "Phenotype MIM number": "178600",
        "Inheritance": "AD",
        "Phenotype mapping key": "3"
      },
      {
        "Location": "2q33.1-q33.2",
        "Phenotype": "Pulmonary hypertension, primary, fenfluramine or dexfenfluramine-associated",
        "Phenotype MIM number": "178600",
        "Inheritance": "AD",
        "Phenotype mapping key": "3"
      },
      {
        "Location": "2q33.1-q33.2",
        "Phenotype": "Pulmonary venoocclusive disease 1",
        "Phenotype MIM number": "265450",
        "Inheritance": "AD",
        "Phenotype mapping key": "3"
      }
    ],
    "title": "BONE MORPHOGENETIC PROTEIN RECEPTOR, TYPE II; BMPR2",
    "hgnc_gene_symbol": "BMPR2",
    "entrez_gene_id": "659"
  }
]

omim query -s geneMap '%Pulmonary hypertension%' -F json

[
  {
    "phenotypeMap": null,
    "references": "16429403, 10051328, 17425602, 18548003, 10903931, 21920918, 12571257, 3291115, 12358323, 10973254, 16429395, 11115378, 14583445, 18626305, 18321866, 11484688, 18496036, 18792970, 7644468, 12045205, 12446270, 15965979, 24446489, 11015450, 19620182",
    "prefix": "*",
    "mim_number": "600799",
    "generated": "2021-04-14",
    "ensembl_gene_id": "ENSG00000204217",
    "mim_type": "gene",
    "geneMap": [
      {
        "Location": "2q33.1-q33.2",
        "Phenotype": "Pulmonary hypertension, familial primary, 1, with or without HHT",
        "Phenotype MIM number": "178600",
        "Inheritance": "AD",
        "Phenotype mapping key": "3"
      },
      {
        "Location": "2q33.1-q33.2",
        "Phenotype": "Pulmonary hypertension, primary, fenfluramine or dexfenfluramine-associated",
        "Phenotype MIM number": "178600",
        "Inheritance": "AD",
        "Phenotype mapping key": "3"
      },
      {
        "Location": "2q33.1-q33.2",
        "Phenotype": "Pulmonary venoocclusive disease 1",
        "Phenotype MIM number": "265450",
        "Inheritance": "AD",
        "Phenotype mapping key": "3"
      }
    ],
    "title": "BONE MORPHOGENETIC PROTEIN RECEPTOR, TYPE II; BMPR2",
    "hgnc_gene_symbol": "BMPR2",
    "entrez_gene_id": "659"
  },
  {
    "phenotypeMap": null,
    "references": "22474227, 18237401, 11498544, 9837809, 9662443, 9801158, 16973879, 10079111, 25898808, 29562231, 2541345, 1360410, 15539149, 18211975, 16051704, 1512286, 22328087, 10988071, 15353589, 16001074, 11739396, 11457855, 8552590, 7608210, 26176221, 21610094, 11358800, 21654750, 17178917, 9741627, 16890161, 9717814, 16670769, 12177436, 19487814",
    "prefix": "*",
    "mim_number": "601047",
    "generated": "2021-04-14",
    "ensembl_gene_id": "ENSG00000105974",
    "mim_type": "gene",
    "geneMap": [
      {
        "Location": "7q31.2",
        "Phenotype": "?Lipodystrophy, congenital generalized, type 3",
        "Phenotype MIM number": "612526",
        "Inheritance": "AR",
        "Phenotype mapping key": "3"
      },
      {
        "Location": "7q31.2",
        "Phenotype": "Lipodystrophy, familial partial, type 7",
        "Phenotype MIM number": "606721",
        "Inheritance": "AD",
        "Phenotype mapping key": "3"
      },
      {
        "Location": "7q31.2",
        "Phenotype": "Pulmonary hypertension, primary, 3",
        "Phenotype MIM number": "615343",
        "Inheritance": "AD",
        "Phenotype mapping key": "3"
      }
    ],
    "title": "CAVEOLIN 1; CAV1",
    "hgnc_gene_symbol": "CAV1",
    "entrez_gene_id": "857"
  },
  {
    "phenotypeMap": null,
    "references": "18250325, 9312005, 12198146, 11749039, 9721223, 23883380, 10575216, 16574908, 32499642",
    "prefix": "*",
    "mim_number": "603220",
    "generated": "2021-04-14",
    "ensembl_gene_id": "ENSG00000171303",
    "mim_type": "gene",
    "geneMap": [
      {
        "Location": "2p23.3",
        "Phenotype": "Pulmonary hypertension, primary, 4",
        "Phenotype MIM number": "615344",
        "Inheritance": "AD",
        "Phenotype mapping key": "3"
      }
    ],
    "title": "POTASSIUM CHANNEL, SUBFAMILY K, MEMBER 3; KCNK3",
    "hgnc_gene_symbol": "KCNK3",
    "entrez_gene_id": "3777"
  },
  {
    "phenotypeMap": null,
    "references": "9371779, 18548003, 21920918, 19419974, 21898662, 26122142, 10583507, 24076600, 19211612, 9205116",
    "prefix": "*",
    "mim_number": "603295",
    "generated": "2021-04-14",
    "ensembl_gene_id": "ENSG00000120693",
    "mim_type": "gene",
    "geneMap": [
      {
        "Location": "13q13.3",
        "Phenotype": "Pulmonary hypertension, primary, 2",
        "Phenotype MIM number": "615342",
        "Inheritance": "AD",
        "Phenotype mapping key": "3"
      }
    ],
    "title": "SMAD FAMILY MEMBER 9; SMAD9",
    "hgnc_gene_symbol": "SMAD9",
    "entrez_gene_id": "4093"
  },
  {
    "phenotypeMap": null,
    "references": "6208196, 11474210, 18063578, 2991113, 9711878, 12655559, 21120950, 1840546, 9107685, 8486760, 7590739, 25410056, 3545062, 29801986, 28538732, 19793055, 17310273, 20154341, 16708072, 30842655, 206435, 2991241, 11407344, 6249820, 15465784, 8382576, 21767969, 7587391, 14718356, 12853138, 4944634",
    "prefix": "*",
    "mim_number": "608307",
    "generated": "2021-04-14",
    "ensembl_gene_id": "ENSG00000021826",
    "mim_type": "gene",
    "geneMap": [
      {
        "Location": "2q34",
        "Phenotype": "{Pulmonary hypertension, neonatal, susceptibility to}",
        "Phenotype MIM number": "615371",
        "Inheritance": "",
        "Phenotype mapping key": "3"
      },
      {
        "Location": "2q34",
        "Phenotype": "Carbamoylphosphate synthetase I deficiency",
        "Phenotype MIM number": "237300",
        "Inheritance": "AR",
        "Phenotype mapping key": "3"
      }
    ],
    "title": "CARBAMOYL PHOSPHATE SYNTHETASE I; CPS1",
    "hgnc_gene_symbol": "CPS1",
    "entrez_gene_id": "1373"
  },
  {
    "phenotypeMap": null,
    "references": "21255763, 15779907, 16163389, 24034276",
    "prefix": "*",
    "mim_number": "612804",
    "generated": "2021-04-14",
    "ensembl_gene_id": "ENSG00000104835",
    "mim_type": "gene",
    "geneMap": [
      {
        "Location": "19q13.2",
        "Phenotype": "Hyperuricemia, pulmonary hypertension, renal failure, and alkalosis",
        "Phenotype MIM number": "613845",
        "Inheritance": "AR",
        "Phenotype mapping key": "3"
      }
    ],
    "title": "SERYL-tRNA SYNTHETASE 2; SARS2",
    "hgnc_gene_symbol": "SARS2",
    "entrez_gene_id": "54938"
  },
  {
    "phenotypeMap": null,
    "references": "19165231",
    "prefix": "%",
    "mim_number": "612862",
    "generated": "2021-04-15",
    "ensembl_gene_id": "",
    "mim_type": "phenotype",
    "geneMap": [
      {
        "Location": "6p21.3",
        "Phenotype": "{Pulmonary hypertension, chronic thromboembolic, without deep vein thrombosis, susceptibility to}",
        "Phenotype MIM number": "612862",
        "Inheritance": "",
        "Phenotype mapping key": "2"
      }
    ],
    "title": "PULMONARY HYPERTENSION, CHRONIC THROMBOEMBOLIC, WITHOUT DEEP VEIN THROMBOSIS, SUSCEPTIBILITY TO",
    "hgnc_gene_symbol": "",
    "entrez_gene_id": "100302516"
  }
]

Use omim in Python

import omim
from omim import util
from omim.db import Manager, OMIM_DATA


manager = Manager(dbfile=omim.DEFAULT_DB)

# show columns
print(util.get_columns_table())


# show stats
generated, table = util.get_stats_table(manager)
print(generated)
print(table)

# count the database
manager.query(OMIM_DATA).count()

# query with key-value
res = manager.query(OMIM_DATA, 'prefix', '*')
res = manager.query(OMIM_DATA, 'mim_number', '600799')
res = manager.query(OMIM_DATA, 'hgnc_gene_symbol', 'BMPR2')
res = manager.query(OMIM_DATA, 'geneMap', '%Pulmonary hypertension%')  # fuzzy query

# fetch query result
item = res.first()
items = res.all()

# content of result
print(item.mim_number, item.title)
print(item.as_dict)