H/ICH/MedDRA/FMQs by FDA
The Medical Dictionary for Regulatory Activities (MedDRA) is a set of standardized terminologies commonly used in clinical safety recording, communicating, and reporting activities. MedDRA is developed and maintained by the International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH)[1],[2].
The FDA Medical Queries (FMQs) are groups of MedDRA terms used to describe conditions of interest published by FDA for the goal of improving transparency. FMQ is available in public domain [3],[4],[5]. A consolidated list of FMQ is shipped with this module. The FMQ list shipped with this module is for demonstrating purpose. The author(s) can not provide warranty or promises for the correctness, completeness, or usability of the list.
The module emt includes basic functions for working with FMQs.
Assign FMQ File Path
To find FMQ list file:
from mtbp3.health.emt import Emt
emt = Emt(folder_name='')
print(emt.find_files())
print(emt.find_fmq_file(file_path=""))
([], 'All files found. Version: 26.1; Year: 2023; Month: September; Language: English. N_SOC: 17.')
Default FMQ table found. Table size: (11712, 4)
To get a list of FMQ terms:
fmq_list = emt.find_fmq(fmq=[])
To check if a list of queries are included in the FMQ list file found above:
print( emt.find_fmq(fmq_list[:3]+['This is not a standard query!']) )
[True, True, True, False]
Find Terms Given a FMQ
There are currently 104 FMQs. There are 8,839 PTs utilized to define either broad or narrow scope of FMQs. Note that 4 of 104 FMQs are algorithm based. Algorithm based FMQs may utilize additional data sources, including labs, concomitant medication records, patient histories, etc.
To find a list of PT related to the first FMQ on the list:
pt_list = emt.find_terms_given_fmq(fmq=[fmq_list[0]], narrow_only=False)
print(pt_list['classification'].value_counts())
classification
Narrow 23
Broad 20
Name: count, dtype: int64
FMQ Tree
To list PT under selected FMQs by classification:
print('\n'.join(emt.show_fmq_tree(fmq_list[:2])))
FMQ:
├── Abdominal Pain:
│ ├── [Classification] Broad:
│ │ ├── [PT01] Carnett's sign positive
│ │ ├── [PT02] Complicated appendicitis
│ │ ├── [PT03] Gastric irritation
│ │ ├── [PT04] Gastritis erosive
│ │ ├── [PT05] Gastroenteritis escherichia coli
│ │ ├── [PT06] Gastroenteritis Escherichia coli
│ │ ├── [PT07] Gastroenterostomy
│ │ ├── [PT08] Gastro-enterostomy
│ │ ├── [PT09] Haemorrhagic erosive gastritis
│ │ ├── [PT10] Helicobacter duodenal ulcer
│ │ ├── [PT11] Infantile colic
│ │ ├── [PT12] Large intestine infection
│ │ ├── [PT13] Peptic ulcer
│ │ ├── [PT14] Ulcerative duodenitis
│ │ ├── [PT15] Visceral pain
│ │ ├── [PT16] CRIA syndrome
│ │ ├── [PT17] Bauhin's valve syndrome
│ │ ├── [PT18] Yao syndrome
│ │ ├── [PT19] Peritoneoplasty
│ │ └── [PT20] Segmental arterial mediolysis
│ └── [Classification] Narrow:
│ ├── [PT21] Abdominal discomfort
│ ├── [PT22] Abdominal migraine
│ ├── [PT23] Abdominal pain
│ ├── [PT24] Abdominal pain aggravated
│ ├── [PT25] Abdominal pain lower
│ ├── [PT26] Abdominal pain NOS
│ ├── [PT27] Abdominal pain upper
│ ├── [PT28] Abdominal rebound tenderness
│ ├── [PT29] Abdominal rigidity
│ ├── [PT30] Abdominal tenderness
│ ├── [PT31] Acute abdomen
│ ├── [PT32] Enteric neuropathy
│ ├── [PT33] Epigastric discomfort
│ ├── [PT34] Gastrointestinal discomfort
│ ├── [PT35] Gastrointestinal pain
│ ├── [PT36] Gastrointestinal pain NOS
│ ├── [PT37] Gastrointestinal upset
│ ├── [PT38] Intestinal spasm
│ ├── [PT39] Perihepatic discomfort
│ ├── [PT40] Spleen pain
│ ├── [PT41] Stomach discomfort
│ ├── [PT42] Ulcer type pain
│ └── [PT43] Ilioinguinal neuralgia
└── Abnormal Uterine Bleeding:
├── [Classification] Broad:
│ ├── [PT01] Anovulatory cycle
│ ├── [PT02] Bleeding anovulatory
│ ├── [PT03] Dysmenorrhea
│ ├── [PT04] Dysmenorrhoea
│ ├── [PT05] Follicle-stimulating hormone deficiency
│ ├── [PT06] Follicle stimulating hormone deficiency
│ ├── [PT07] Menstrual disorder
│ ├── [PT08] Uterine dehiscence
│ └── [PT09] Ovarian dysfunction
└── [Classification] Narrow:
├── [PT10] Abnormal uterine bleeding
├── [PT11] Abnormal withdrawal bleeding
├── [PT12] Cervix haemorrhage uterine
├── [PT13] Dysfunctional uterine bleeding
├── [PT14] Heavy menstrual bleeding
├── [PT15] Hypomenorrhoea
├── [PT16] Intermenstrual bleeding
├── [PT17] Menometrorrhagia
├── [PT18] Menorrhagia
├── [PT19] Menstruation delayed
├── [PT20] Menstruation irregular
├── [PT21] Metrorrhagia
├── [PT22] Oligomenorrhoea
├── [PT23] Polymenorrhagia
├── [PT24] Polymenorrhoea
├── [PT25] Postmenopausal haemorrhage
├── [PT26] Uterine haemorrhage
├── [PT27] Uterine rupture
└── [PT28] Vaginal haemorrhage
To list PT under selected FMQs by classification and SOC:
print('\n'.join(emt.show_fmq_tree(fmq_list[:2], with_soc=True)))
FMQ:
├── Abdominal Pain:
│ ├── [Classification] Broad:
│ │ ├── [SOC] soc214dfxgAelhGHfEFFkgrAsFYzZBAFs:
│ │ │ ├── [PT01] Complicated appendicitis
│ │ │ ├── [PT02] Gastric irritation
│ │ │ ├── [PT03] Gastritis erosive
│ │ │ ├── [PT04] Gastroenterostomy
│ │ │ ├── [PT05] Helicobacter duodenal ulcer
│ │ │ ├── [PT06] Large intestine infection
│ │ │ ├── [PT07] Peptic ulcer
│ │ │ ├── [PT08] Ulcerative duodenitis
│ │ │ ├── [PT09] Yao syndrome
│ │ │ └── [PT10] Peritoneoplasty
│ │ ├── [SOC] soc360phgmkaCxrALPg:
│ │ │ ├── [PT11] Gastroenteritis escherichia coli
│ │ │ ├── [PT12] Gastroenteritis Escherichia coli
│ │ │ ├── [PT13] Gastro-enterostomy
│ │ │ ├── [PT14] Haemorrhagic erosive gastritis
│ │ │ ├── [PT15] Infantile colic
│ │ │ ├── [PT16] Visceral pain
│ │ │ └── [PT17] CRIA syndrome
│ │ └── [SOC] soc972ZiuFsAfKKVWFbSZdYcgUoCiSTyEYKu:
│ │ ├── [PT18] Carnett's sign positive
│ │ ├── [PT19] Bauhin's valve syndrome
│ │ └── [PT20] Segmental arterial mediolysis
│ └── [Classification] Narrow:
│ ├── [SOC] soc214dfxgAelhGHfEFFkgrAsFYzZBAFs:
│ │ ├── [PT21] Abdominal pain NOS
│ │ ├── [PT22] Abdominal tenderness
│ │ ├── [PT23] Enteric neuropathy
│ │ ├── [PT24] Gastrointestinal pain
│ │ ├── [PT25] Gastrointestinal pain NOS
│ │ └── [PT26] Perihepatic discomfort
│ ├── [SOC] soc360phgmkaCxrALPg:
│ │ ├── [PT27] Abdominal pain aggravated
│ │ ├── [PT28] Abdominal pain lower
│ │ ├── [PT29] Abdominal rebound tenderness
│ │ ├── [PT30] Abdominal rigidity
│ │ ├── [PT31] Epigastric discomfort
│ │ ├── [PT32] Gastrointestinal upset
│ │ ├── [PT33] Intestinal spasm
│ │ ├── [PT34] Stomach discomfort
│ │ ├── [PT35] Ulcer type pain
│ │ └── [PT36] Ilioinguinal neuralgia
│ └── [SOC] soc972ZiuFsAfKKVWFbSZdYcgUoCiSTyEYKu:
│ ├── [PT37] Abdominal discomfort
│ ├── [PT38] Abdominal migraine
│ ├── [PT39] Abdominal pain
│ ├── [PT40] Abdominal pain upper
│ ├── [PT41] Acute abdomen
│ ├── [PT42] Gastrointestinal discomfort
│ └── [PT43] Spleen pain
└── Abnormal Uterine Bleeding:
├── [Classification] Broad:
│ ├── [SOC] soc214dfxgAelhGHfEFFkgrAsFYzZBAFs:
│ │ ├── [PT01] Bleeding anovulatory
│ │ ├── [PT02] Dysmenorrhoea
│ │ ├── [PT03] Follicle-stimulating hormone deficiency
│ │ └── [PT04] Ovarian dysfunction
│ ├── [SOC] soc360phgmkaCxrALPg:
│ │ ├── [PT05] Dysmenorrhea
│ │ ├── [PT06] Follicle stimulating hormone deficiency
│ │ └── [PT07] Menstrual disorder
│ └── [SOC] soc972ZiuFsAfKKVWFbSZdYcgUoCiSTyEYKu:
│ ├── [PT08] Anovulatory cycle
│ └── [PT09] Uterine dehiscence
└── [Classification] Narrow:
├── [SOC] soc214dfxgAelhGHfEFFkgrAsFYzZBAFs:
│ ├── [PT10] Cervix haemorrhage uterine
│ ├── [PT11] Dysfunctional uterine bleeding
│ ├── [PT12] Heavy menstrual bleeding
│ ├── [PT13] Menometrorrhagia
│ ├── [PT14] Menstruation delayed
│ └── [PT15] Menstruation irregular
├── [SOC] soc360phgmkaCxrALPg:
│ ├── [PT16] Abnormal uterine bleeding
│ ├── [PT17] Abnormal withdrawal bleeding
│ ├── [PT18] Hypomenorrhoea
│ ├── [PT19] Intermenstrual bleeding
│ ├── [PT20] Menorrhagia
│ ├── [PT21] Metrorrhagia
│ ├── [PT22] Oligomenorrhoea
│ ├── [PT23] Uterine haemorrhage
│ ├── [PT24] Uterine rupture
│ └── [PT25] Vaginal haemorrhage
└── [SOC] soc972ZiuFsAfKKVWFbSZdYcgUoCiSTyEYKu:
├── [PT26] Polymenorrhagia
├── [PT27] Polymenorrhoea
└── [PT28] Postmenopausal haemorrhage
Please note that the SOCs involved in the output above are synthetic, and groupings may NOT make senses. When the simulated distribution files were used, the function uses synthetic SOCs for the purpose of demonstrating the function usage. The reason of using synthetic SOCs is to simplify data sharing during module development.
When a MedDRA distribution folder is assigned by the user, the function will list real SOCs in the output.
To align the output to the right:
print('\n'.join(emt.show_fmq_tree(fmq_list[:2], with_soc=True, to_right=True)))
FMQ
Abdominal Pain ──┤
Broad [Classification] ──┤ │
soc214dfxgAelhGHfEFFkgrAsFYzZBAFs [SOC] ──┤ │ │
Gastro-enterostomy [PT03] ──┤ │ │ │
Gastroenteritis escherichia coli [PT01] ──┤ │ │ │
Gastroenterostomy [PT02] ──┤ │ │ │
Infantile colic [PT04] ──┤ │ │ │
Large intestine infection [PT05] ──┤ │ │ │
Peritoneoplasty [PT08] ──┤ │ │ │
Visceral pain [PT06] ──┤ │ │ │
Yao syndrome [PT07] ──┘ │ │ │
soc360phgmkaCxrALPg [SOC] ──┤ │ │
Carnett's sign positive [PT09] ──┤ │ │ │
Complicated appendicitis [PT10] ──┤ │ │ │
Gastric irritation [PT11] ──┤ │ │ │
Gastritis erosive [PT12] ──┤ │ │ │
Haemorrhagic erosive gastritis [PT13] ──┤ │ │ │
Helicobacter duodenal ulcer [PT14] ──┤ │ │ │
Segmental arterial mediolysis [PT16] ──┤ │ │ │
Ulcerative duodenitis [PT15] ──┘ │ │ │
soc972ZiuFsAfKKVWFbSZdYcgUoCiSTyEYKu [SOC] ──┘ │ │
Bauhin's valve syndrome [PT20] ──┤ │ │
CRIA syndrome [PT19] ──┤ │ │
Gastroenteritis Escherichia coli [PT17] ──┤ │ │
Peptic ulcer [PT18] ──┘ │ │
Narrow [Classification] ──┘ │
soc214dfxgAelhGHfEFFkgrAsFYzZBAFs [SOC] ──┤ │
Abdominal discomfort [PT21] ──┤ │ │
Abdominal migraine [PT22] ──┤ │ │
Abdominal tenderness [PT23] ──┤ │ │
Acute abdomen [PT24] ──┤ │ │
Enteric neuropathy [PT25] ──┤ │ │
Ulcer type pain [PT26] ──┘ │ │
soc360phgmkaCxrALPg [SOC] ──┤ │
Abdominal pain NOS [PT28] ──┤ │ │
Abdominal pain lower [PT27] ──┤ │ │
Abdominal pain upper [PT29] ──┤ │ │
Abdominal rigidity [PT30] ──┤ │ │
Epigastric discomfort [PT31] ──┤ │ │
Gastrointestinal pain [PT32] ──┤ │ │
Gastrointestinal upset [PT33] ──┤ │ │
Intestinal spasm [PT34] ──┘ │ │
soc972ZiuFsAfKKVWFbSZdYcgUoCiSTyEYKu [SOC] ──┘ │
Abdominal pain [PT35] ──┤ │
Abdominal pain aggravated [PT36] ──┤ │
Abdominal rebound tenderness [PT37] ──┤ │
Gastrointestinal discomfort [PT38] ──┤ │
Gastrointestinal pain NOS [PT39] ──┤ │
Ilioinguinal neuralgia [PT43] ──┤ │
Perihepatic discomfort [PT40] ──┤ │
Spleen pain [PT41] ──┤ │
Stomach discomfort [PT42] ──┘ │
Abnormal Uterine Bleeding ──┘
Broad [Classification] ──┤
soc214dfxgAelhGHfEFFkgrAsFYzZBAFs [SOC] ──┤ │
Anovulatory cycle [PT01] ──┤ │ │
Dysmenorrhoea [PT02] ──┤ │ │
Menstrual disorder [PT03] ──┘ │ │
soc360phgmkaCxrALPg [SOC] ──┤ │
Bleeding anovulatory [PT04] ──┤ │ │
Follicle-stimulating hormone deficiency [PT05] ──┤ │ │
Ovarian dysfunction [PT06] ──┘ │ │
soc972ZiuFsAfKKVWFbSZdYcgUoCiSTyEYKu [SOC] ──┘ │
Dysmenorrhea [PT07] ──┤ │
Follicle stimulating hormone deficiency [PT08] ──┤ │
Uterine dehiscence [PT09] ──┘ │
Narrow [Classification] ──┘
soc214dfxgAelhGHfEFFkgrAsFYzZBAFs [SOC] ──┤
Abnormal uterine bleeding [PT10] ──┤ │
Polymenorrhagia [PT11] ──┤ │
Postmenopausal haemorrhage [PT12] ──┤ │
Uterine rupture [PT13] ──┘ │
soc360phgmkaCxrALPg [SOC] ──┤
Abnormal withdrawal bleeding [PT14] ──┤ │
Cervix haemorrhage uterine [PT15] ──┤ │
Dysfunctional uterine bleeding [PT16] ──┤ │
Oligomenorrhoea [PT17] ──┤ │
Polymenorrhoea [PT18] ──┤ │
Uterine haemorrhage [PT19] ──┘ │
soc972ZiuFsAfKKVWFbSZdYcgUoCiSTyEYKu [SOC] ──┘
Heavy menstrual bleeding [PT20] ──┤
Hypomenorrhoea [PT21] ──┤
Intermenstrual bleeding [PT22] ──┤
Menometrorrhagia [PT23] ──┤
Menorrhagia [PT24] ──┤
Menstruation delayed [PT25] ──┤
Menstruation irregular [PT26] ──┤
Metrorrhagia [PT27] ──┤
Vaginal haemorrhage [PT28] ──┘
Save Demo FMQ List to Local
The FMQ list shipped with this module is for demonstrating purpose. The author(s) can not provide warranty or promises for the correctness, completeness, or usability of the list.
To save the FMQ list shipped with this module to a local folder in CSV format:
# emt.save_fmq_consolidated_list_csv(folder_path="a_valid_folder_path")
Appendix - View PTs Given Any FMQ
This folder does not host interactive contents. A web version notebook is provided for using an interactive drop-down menu, and viewing all related PTs without installation of Python.
Please visit the web page here.