OMIM - Online Mendelian Inheritance in Man

Installation

bash 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

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

manager = Manager(dbfile=omim.DEFAULT_DB)

show columns

print(util.getcolumnstable())

show stats

generated, table = util.getstatstable(manager) print(generated) print(table)

count the database

manager.query(OMIM_DATA).count()

query with key-value

res = manager.query(OMIMDATA, 'prefix', '*') res = manager.query(OMIMDATA, 'mimnumber', '600799') res = manager.query(OMIMDATA, 'hgncgenesymbol', '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.mimnumber, item.title) print(item.asdict) ```

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