Package: omim
OMIM - Online Mendelian Inheritance in ManInstallationpip3installomimBasic Usagemainomim -hUsage: 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 databasestatsOMIM Entry Statisticsomim 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 |
+--------------------------+-------+updateupdate the database according to the file mim2gene.txtomim updatefaqexplains of some FAQomim 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                                                                |
+--------+------------------------------------------------------------------------------------------------------------------------------+queryomim query -hUsage: 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 BMPR2phenotypeMap	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	659omim 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 Pythonimportomimfromomimimportutilfromomim.dbimportManager,OMIM_DATAmanager=Manager(dbfile=omim.DEFAULT_DB)# show columnsprint(util.get_columns_table())# show statsgenerated,table=util.get_stats_table(manager)print(generated)print(table)# count the databasemanager.query(OMIM_DATA).count()# query with key-valueres=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 resultitem=res.first()items=res.all()# content of resultprint(item.mim_number,item.title)print(item.as_dict)