OMIM - Online Mendelian Inheritance in Man
Project description
OMIM - Online Mendelian Inheritance in Man
Installation
pip3 install 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: 2021-04-20 *****
+--------------------------+-------+
| MIM_TYPE | COUNT |
+--------------------------+-------+
| gene | 16458 |
| gene/phenotype | 27 |
| phenotype | 7578 |
| predominantly phenotypes | 1762 |
| moved/removed | 1317 |
| TOTAL COUNT | 27142 |
+--------------------------+-------+
update
update the database according to the file mim2gene.txt
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)
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