---
# 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`
<details>
```
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
```
</details>
- search with a key and output as json
`omim query -s hgnc_gene_symbol BMPR2 -F json -C`
<details>
```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"
}
]
```
</details>
- fuzzy search
`omim query -s geneMap '%Pulmonary hypertension%' --fuzzy -F json -C`
<details>
```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"
}
]
```
</details>
---
## 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.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.
Raw data
{
"_id": null,
"home_page": "https://github.com/suqingdong/omim",
"name": "omim",
"maintainer": null,
"docs_url": null,
"requires_python": null,
"maintainer_email": null,
"keywords": null,
"author": "suqingdong",
"author_email": "suqingdong1114@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/3a/77/b675f318cb8bc459ca825fee07795cb6b5ad007306dc30f00febde874b11/omim-1.0.4.tar.gz",
"platform": null,
"description": "\n\n\n\n\n---\n\n# OMIM - Online Mendelian Inheritance in Man\n\n## Installation\n```bash\npython3 -m pip install -U omim\n```\n\n---\n\n## Basic Usage\n### main\n`omim -h`\n```\nUsage: omim [OPTIONS] COMMAND [ARGS]...\n\n OMIM - Online Mendelian Inheritance in Man\n\nOptions:\n -d, --dbfile TEXT the path of database file [default:/usr/local/lib/python3.8/site-packages/omim/data/omim.sqlite3]\n -u, --url TEXT the url of omim [default: https://mirror.omim.org]\n --version Show the version and exit.\n -?, -h, --help Show this message and exit.\n\nCommands:\n faq explains of some faq\n query query something from the database\n stats statistics of the database\n update update the database\n```\n\n### 1. stats\n> OMIM Entry Statistics\n\n`omim stats`\n```\n***** updated time: 2024-06-04 *****\n+--------------------------+-------+\n| MIM_TYPE | COUNT |\n+--------------------------+-------+\n| gene | 17290 |\n| gene/phenotype | 18 |\n| phenotype | 8362 |\n| predominantly phenotypes | 1736 |\n| moved/removed | 1364 |\n| TOTAL COUNT | 28770 |\n+--------------------------+-------+\n```\n\n### 2. update\n\n> update the database according to the file mim2gene.txt\n\n```\nomim update\n```\n\n### 3. faq\n> explains of some FAQ\n\n`omim faq`\n```\n***** Explains of MIM PREFIX *****\n+--------+---------------------------------------------------------+\n| PREFIX | EXPLAIN |\n+--------+---------------------------------------------------------+\n| * | Gene description |\n| + | Gene and phenotype, combined |\n| # | Phenotype description, molecular basis known |\n| % | Phenotype description or locus, molecular basis unknown |\n| | Other, mainly phenotypes with suspected mendelian basis |\n| ^ | Moved/Removed |\n+--------+---------------------------------------------------------+\n***** Explains of PHENOTYPE SYMBOL *****\n+--------+------------------------------------------------------------------------------------------------------------------------------+\n| SYMBOL | EXPLAIN |\n+--------+------------------------------------------------------------------------------------------------------------------------------+\n| [ ] | indicate \"nondiseases,\" mainly genetic variations that lead to apparently abnormal laboratory test values |\n| { } | indicate mutations that contribute to susceptibility to multifactorial disorders |\n| | (e.g., diabetes, asthma) or to susceptibility to infection |\n| ? | before the phenotype name indicates that the relationship between the phenotype and gene is provisional. |\n| | More details about this relationship are provided in the comment field of the map and in the gene and phenotype OMIM entries |\n| (1) | the disorder was positioned by mapping of the wildtype gene |\n| (2) | the disease phenotype itself was mapped |\n| (3) | the molecular basis of the disorder is known |\n| (4) | the disorder is a chromosome deletion or duplication syndrome |\n+--------+------------------------------------------------------------------------------------------------------------------------------+\n```\n\n### 4. **query**\n`omim query -h`\n```\nUsage: omim query [OPTIONS]\n\n query something from database\n\nOptions:\n -K, --keys list the available keys\n -s, --search TEXT... the search string\n -l, --limit INTEGER limit for output\n -F, --format [json|tsv] the format for output\n -o, --outfile TEXT the output filename [stdout]\n -C, --color colorful print for json\n -f, --fuzzy fuzzy search\n --count count the number of results\n -h, -?, --help Show this message and exit.\n```\n\n- show all available keys\n\n`omim query -K` \n```\n+------------------+-----------------------+--------------+\n| Key | Comment | Type |\n+------------------+-----------------------+--------------+\n| mim_number | MIM Number | VARCHAR(10) |\n| prefix | The prefix symbol | VARCHAR(1) |\n| title | The title | VARCHAR(50) |\n| references | The references | VARCHAR(300) |\n| geneMap | The geneMap data | VARCHAR(300) |\n| phenotypeMap | The phenotypeMap data | VARCHAR(300) |\n| mim_type | The mim_type | VARCHAR(20) |\n| entrez_gene_id | The entrez_gene_id | VARCHAR(20) |\n| ensembl_gene_id | The ensembl_gene_id | VARCHAR(20) |\n| hgnc_gene_symbol | The hgnc_gene_symbol | VARCHAR(20) |\n| generated | The generated time | DATETIME |\n+------------------+-----------------------+--------------+\n```\n\n- search with a key\n\n`omim query -s hgnc_gene_symbol BMPR2`\n\n<details>\n\n\n```\nphenotypeMap\treferences\tprefix\tmim_number\tgenerated\tensembl_gene_id\tmim_type\tgeneMap\ttitle\thgnc_gene_symbol\tentrez_gene_id\nNone\t16429403, 10051328, 17425602, 18548003, 10903931, 21920918, 12571257, 3291115, 12358323, 10973254, 16429395, 11115378, 14583445, 18626305, 18321866, 11484688, 18496036, 18792970, 7644468, 12045205, 12446270, 15965979, 24446489, 11015450, 19620182\t*\t600799\t2021-04-14\tENSG00000204217\tgene\t[{\"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\"}]\tBONE MORPHOGENETIC PROTEIN RECEPTOR, TYPE II; BMPR2\tBMPR2\t659\n```\n\n</details>\n\n\n- search with a key and output as json\n\n`omim query -s hgnc_gene_symbol BMPR2 -F json -C`\n\n<details>\n\n```json\n[\n {\n \"phenotypeMap\": null,\n \"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\",\n \"prefix\": \"*\",\n \"mim_number\": \"600799\",\n \"generated\": \"2021-04-14\",\n \"ensembl_gene_id\": \"ENSG00000204217\",\n \"mim_type\": \"gene\",\n \"geneMap\": [\n {\n \"Location\": \"2q33.1-q33.2\",\n \"Phenotype\": \"Pulmonary hypertension, familial primary, 1, with or without HHT\",\n \"Phenotype MIM number\": \"178600\",\n \"Inheritance\": \"AD\",\n \"Phenotype mapping key\": \"3\"\n },\n {\n \"Location\": \"2q33.1-q33.2\",\n \"Phenotype\": \"Pulmonary hypertension, primary, fenfluramine or dexfenfluramine-associated\",\n \"Phenotype MIM number\": \"178600\",\n \"Inheritance\": \"AD\",\n \"Phenotype mapping key\": \"3\"\n },\n {\n \"Location\": \"2q33.1-q33.2\",\n \"Phenotype\": \"Pulmonary venoocclusive disease 1\",\n \"Phenotype MIM number\": \"265450\",\n \"Inheritance\": \"AD\",\n \"Phenotype mapping key\": \"3\"\n }\n ],\n \"title\": \"BONE MORPHOGENETIC PROTEIN RECEPTOR, TYPE II; BMPR2\",\n \"hgnc_gene_symbol\": \"BMPR2\",\n \"entrez_gene_id\": \"659\"\n }\n]\n```\n\n</details>\n\n- fuzzy search\n\n`omim query -s geneMap '%Pulmonary hypertension%' --fuzzy -F json -C`\n\n<details>\n\n```json\n[\n {\n \"phenotypeMap\": null,\n \"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\",\n \"prefix\": \"*\",\n \"mim_number\": \"600799\",\n \"generated\": \"2021-04-14\",\n \"ensembl_gene_id\": \"ENSG00000204217\",\n \"mim_type\": \"gene\",\n \"geneMap\": [\n {\n \"Location\": \"2q33.1-q33.2\",\n \"Phenotype\": \"Pulmonary hypertension, familial primary, 1, with or without HHT\",\n \"Phenotype MIM number\": \"178600\",\n \"Inheritance\": \"AD\",\n \"Phenotype mapping key\": \"3\"\n },\n {\n \"Location\": \"2q33.1-q33.2\",\n \"Phenotype\": \"Pulmonary hypertension, primary, fenfluramine or dexfenfluramine-associated\",\n \"Phenotype MIM number\": \"178600\",\n \"Inheritance\": \"AD\",\n \"Phenotype mapping key\": \"3\"\n },\n {\n \"Location\": \"2q33.1-q33.2\",\n \"Phenotype\": \"Pulmonary venoocclusive disease 1\",\n \"Phenotype MIM number\": \"265450\",\n \"Inheritance\": \"AD\",\n \"Phenotype mapping key\": \"3\"\n }\n ],\n \"title\": \"BONE MORPHOGENETIC PROTEIN RECEPTOR, TYPE II; BMPR2\",\n \"hgnc_gene_symbol\": \"BMPR2\",\n \"entrez_gene_id\": \"659\"\n },\n {\n \"phenotypeMap\": null,\n \"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\",\n \"prefix\": \"*\",\n \"mim_number\": \"601047\",\n \"generated\": \"2021-04-14\",\n \"ensembl_gene_id\": \"ENSG00000105974\",\n \"mim_type\": \"gene\",\n \"geneMap\": [\n {\n \"Location\": \"7q31.2\",\n \"Phenotype\": \"?Lipodystrophy, congenital generalized, type 3\",\n \"Phenotype MIM number\": \"612526\",\n \"Inheritance\": \"AR\",\n \"Phenotype mapping key\": \"3\"\n },\n {\n \"Location\": \"7q31.2\",\n \"Phenotype\": \"Lipodystrophy, familial partial, type 7\",\n \"Phenotype MIM number\": \"606721\",\n \"Inheritance\": \"AD\",\n \"Phenotype mapping key\": \"3\"\n },\n {\n \"Location\": \"7q31.2\",\n \"Phenotype\": \"Pulmonary hypertension, primary, 3\",\n \"Phenotype MIM number\": \"615343\",\n \"Inheritance\": \"AD\",\n \"Phenotype mapping key\": \"3\"\n }\n ],\n \"title\": \"CAVEOLIN 1; CAV1\",\n \"hgnc_gene_symbol\": \"CAV1\",\n \"entrez_gene_id\": \"857\"\n },\n {\n \"phenotypeMap\": null,\n \"references\": \"18250325, 9312005, 12198146, 11749039, 9721223, 23883380, 10575216, 16574908, 32499642\",\n \"prefix\": \"*\",\n \"mim_number\": \"603220\",\n \"generated\": \"2021-04-14\",\n \"ensembl_gene_id\": \"ENSG00000171303\",\n \"mim_type\": \"gene\",\n \"geneMap\": [\n {\n \"Location\": \"2p23.3\",\n \"Phenotype\": \"Pulmonary hypertension, primary, 4\",\n \"Phenotype MIM number\": \"615344\",\n \"Inheritance\": \"AD\",\n \"Phenotype mapping key\": \"3\"\n }\n ],\n \"title\": \"POTASSIUM CHANNEL, SUBFAMILY K, MEMBER 3; KCNK3\",\n \"hgnc_gene_symbol\": \"KCNK3\",\n \"entrez_gene_id\": \"3777\"\n },\n {\n \"phenotypeMap\": null,\n \"references\": \"9371779, 18548003, 21920918, 19419974, 21898662, 26122142, 10583507, 24076600, 19211612, 9205116\",\n \"prefix\": \"*\",\n \"mim_number\": \"603295\",\n \"generated\": \"2021-04-14\",\n \"ensembl_gene_id\": \"ENSG00000120693\",\n \"mim_type\": \"gene\",\n \"geneMap\": [\n {\n \"Location\": \"13q13.3\",\n \"Phenotype\": \"Pulmonary hypertension, primary, 2\",\n \"Phenotype MIM number\": \"615342\",\n \"Inheritance\": \"AD\",\n \"Phenotype mapping key\": \"3\"\n }\n ],\n \"title\": \"SMAD FAMILY MEMBER 9; SMAD9\",\n \"hgnc_gene_symbol\": \"SMAD9\",\n \"entrez_gene_id\": \"4093\"\n },\n {\n \"phenotypeMap\": null,\n \"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\",\n \"prefix\": \"*\",\n \"mim_number\": \"608307\",\n \"generated\": \"2021-04-14\",\n \"ensembl_gene_id\": \"ENSG00000021826\",\n \"mim_type\": \"gene\",\n \"geneMap\": [\n {\n \"Location\": \"2q34\",\n \"Phenotype\": \"{Pulmonary hypertension, neonatal, susceptibility to}\",\n \"Phenotype MIM number\": \"615371\",\n \"Inheritance\": \"\",\n \"Phenotype mapping key\": \"3\"\n },\n {\n \"Location\": \"2q34\",\n \"Phenotype\": \"Carbamoylphosphate synthetase I deficiency\",\n \"Phenotype MIM number\": \"237300\",\n \"Inheritance\": \"AR\",\n \"Phenotype mapping key\": \"3\"\n }\n ],\n \"title\": \"CARBAMOYL PHOSPHATE SYNTHETASE I; CPS1\",\n \"hgnc_gene_symbol\": \"CPS1\",\n \"entrez_gene_id\": \"1373\"\n },\n {\n \"phenotypeMap\": null,\n \"references\": \"21255763, 15779907, 16163389, 24034276\",\n \"prefix\": \"*\",\n \"mim_number\": \"612804\",\n \"generated\": \"2021-04-14\",\n \"ensembl_gene_id\": \"ENSG00000104835\",\n \"mim_type\": \"gene\",\n \"geneMap\": [\n {\n \"Location\": \"19q13.2\",\n \"Phenotype\": \"Hyperuricemia, pulmonary hypertension, renal failure, and alkalosis\",\n \"Phenotype MIM number\": \"613845\",\n \"Inheritance\": \"AR\",\n \"Phenotype mapping key\": \"3\"\n }\n ],\n \"title\": \"SERYL-tRNA SYNTHETASE 2; SARS2\",\n \"hgnc_gene_symbol\": \"SARS2\",\n \"entrez_gene_id\": \"54938\"\n },\n {\n \"phenotypeMap\": null,\n \"references\": \"19165231\",\n \"prefix\": \"%\",\n \"mim_number\": \"612862\",\n \"generated\": \"2021-04-15\",\n \"ensembl_gene_id\": \"\",\n \"mim_type\": \"phenotype\",\n \"geneMap\": [\n {\n \"Location\": \"6p21.3\",\n \"Phenotype\": \"{Pulmonary hypertension, chronic thromboembolic, without deep vein thrombosis, susceptibility to}\",\n \"Phenotype MIM number\": \"612862\",\n \"Inheritance\": \"\",\n \"Phenotype mapping key\": \"2\"\n }\n ],\n \"title\": \"PULMONARY HYPERTENSION, CHRONIC THROMBOEMBOLIC, WITHOUT DEEP VEIN THROMBOSIS, SUSCEPTIBILITY TO\",\n \"hgnc_gene_symbol\": \"\",\n \"entrez_gene_id\": \"100302516\"\n }\n]\n```\n\n</details>\n\n---\n\n## Use omim in Python\n```python\nimport omim\nfrom omim import util\nfrom omim.db import Manager, OMIM_DATA\n\nmanager = Manager(dbfile=omim.DEFAULT_DB)\n\n# show columns\nprint(util.get_columns_table())\n\n# show stats\ngenerated, table = util.get_stats_table(manager)\nprint(generated)\nprint(table)\n\n# count the database\nmanager.query(OMIM_DATA).count()\n\n# query with key-value\nres = manager.query(OMIM_DATA, 'prefix', '*')\nres = manager.query(OMIM_DATA, 'mim_number', '600799')\nres = manager.query(OMIM_DATA, 'hgnc_gene_symbol', 'BMPR2')\nres = manager.query(OMIM_DATA, 'geneMap', '%Pulmonary hypertension%', fuzzy=True) # fuzzy query\n\n# fetch query result\nitem = res.first()\nitems = res.all()\n\n# content of result\nprint(item.mim_number, item.title)\nprint(item.as_dict)\n```\n\n---\n\n> This project is designed to support academic research, education, and personal interest. It is not intended for commercial use.\n\n\n",
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