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.

• show all available keys

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     |
+------------------+-----------------------+--------------+

• search with a key

omim query -s hgnc_gene_symbol BMPR2

• search with a key and output as json

omim query -s hgnc_gene_symbol BMPR2 -F json -C

• fuzzy search

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

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.