Metadata-Version: 2.1
Name: omim
Version: 1.0.0
Summary: OMIM - Online Mendelian Inheritance in Man
Home-page: https://github.com/suqingdong/omim
Author: suqingdong
Author-email: suqingdong1114@gmail.com
License: BSD License
Project-URL: Documentation, https://omim.readthedocs.io
Project-URL: Tracker, https://github.com/suqingdong/omim/issues
Description: # OMIM - Online Mendelian Inheritance in Man
        
        
        ## Installation
        ```bash
        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`
        ```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`
        ```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"
          }
        ]
        ```
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Software Development :: Libraries
Description-Content-Type: text/markdown
