omim

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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

1. 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 |
+--------------------------+-------+

2. update

update the database according to the file mim2gene.txt

omim update

3. 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                                                                |
+--------+------------------------------------------------------------------------------------------------------------------------------+

4. 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]
  -C, --color              colorful print for json
  -f, --fuzzy              fuzzy search
  --count                  count the number of results
  -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 -C

```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%' --fuzzy -F json -C

```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=True)  # fuzzy query

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

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

This project is designed to support academic research, education, and personal interest. It is not intended for commercial use.