Parsing dose instructions
Follow the Installation instructions, then get started using the command line:
Note
Run parse_dose_instructions -h on the command line to get help on parsing dose instructions
In the following examples we assume the model en_edris9 is installed. You can provide your own path to an alternative model with the same nine entities.
A single instruction
A single dose instruction can be supplied using the -di argument.
(di-dev)$ parse_dose_instructions -di "take one tablet daily" -mod en_edris9
Logging to command line. Use the --logfile argument to set a log file instead.
2024-05-28 07:45:49,803 Checking input and output files
2024-05-28 07:45:49,803 Setting up parser
2024-05-28 07:46:34,205 Parsing single dose instruction
StructuredDI(inputID=None, text='take one tablet daily', form='tablet', dosageMin=1.0, dosageMax=1.0, frequencyMin=1.0, frequencyMax=1.0, frequencyType='Day', durationMin=None, durationMax=None, durationType=None, asRequired=False, asDirected=False)
Multiple dose instructions
Multiple dose instructions can be supplied from file using the -f argument, where each line in the text file supplied is a dose instruction.
For example, if the file multiple_dis.txt contains the following:
daily 2 tabs
once daily when required
then you will get the corresponding output:
Logging to command line. Use the --logfile argument to set a log file instead.
2024-05-28 07:47:56,270 Checking input and output files
2024-05-28 07:47:56,282 Setting up parser
2024-05-28 07:48:18,003 Parsing multiple dose instructions
Parsing dose instructions
Parsed 100%|██████████████████████████████████████| 2/2 [00:00<00:00, 79.78 instructions/s]
StructuredDI(inputID=0, text='daily 2 tabs', form='tablet', dosageMin=2.0, dosageMax=2.0, frequencyMin=1.0, frequencyMax=1.0, frequencyType='Day', durationMin=None, durationMax=None, durationType=None, asRequired=False, asDirected=False)
StructuredDI(inputID=1, text='once daily when required', form=None, dosageMin=None, dosageMax=None, frequencyMin=1.0, frequencyMax=1.0, frequencyType='Day', durationMin=None, durationMax=None, durationType=None, asRequired=True, asDirected=False)
Where you have a lot of examples to parse you may want to send the output to a file rather than
the command line. To do this, specify the output file location with the -o argument.
If this has .txt extension the results will be presented line by line like they
would on the command line. If this has .csv extension the results will be cast to a
data frame with one entry per row.
(di-dev)$ parse_dose_instructions -f "multiple_dis.txt" -mod en_edris9 -o "out_dis.csv"
The contents of out_dis.csv is as follows:
inputID |
text |
form |
dosageMin |
dosageMax |
frequencyMin |
frequencyMax |
frequencyType |
durationMin |
durationMax |
durationType |
asRequired |
asDirected |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 |
daily 2 tabs |
tablet |
2.0 |
2.0 |
1.0 |
1.0 |
Day |
False |
False |
|||
1 |
once daily when required |
1.0 |
1.0 |
Day |
True |
False |
Note
Sometimes a dose instruction really contains more than one instruction within it. In this case the output will be split into multiple outputs, one corresponding to each part of the instruction. For example, “Take two tablets twice daily for one week then one tablet once daily for two weeks”
$ parse_dose_instructions -di "Take two tablets twice daily for one week then one tablet once daily for two weeks"
Logging to command line. Use the --logfile argument to set a log file instead.
2024-06-21 08:35:41,765 Checking input and output files
2024-06-21 08:35:41,765 Setting up parser
2024-06-21 08:35:59,572 Parsing single dose instruction
StructuredDI(inputID=None, text='Take two tablets twice daily for one week then one tablet once daily for two weeks', form='tablet', dosageMin=2.0, dosageMax=2.0, frequencyMin=2.0, frequencyMax=2.0, frequencyType='Day', durationMin=1.0, durationMax=1.0, durationType='Week', asRequired=False, asDirected=False)
StructuredDI(inputID=None, text='Take two tablets twice daily for one week then one tablet once daily for two weeks', form='tablet', dosageMin=1.0, dosageMax=1.0, frequencyMin=1.0, frequencyMax=1.0, frequencyType='Day', durationMin=2.0, durationMax=2.0, durationType='Week', asRequired=False, asDirected=False)
Providing input IDs
The inputID value helps to keep track of which outputs correspond to which inputs. The default behaviour is:
For a single dose instruction, set inputID=None
For multiple dose instructions, number each instruction starting from 0 by the order they appear in the input file
You may want to provide your own values for inputID. To do this, provide input dose instructions as a .csv file with columns
inputID specifying the input ID
di specifying the dose instruction
For example, using test.csv with the following contents:
inputID |
di |
|---|---|
eDRIS/XXXX-XXXX/example/001 |
daily 2 caps |
eDRIS/XXXX-XXXX/example/002 |
daily 0.2ml |
eDRIS/XXXX-XXXX/example/003 |
two mane + two nocte |
eDRIS/XXXX-XXXX/example/004 |
2 tabs twice daily increased to 2 tabs three times daily during exacerbation chest symptoms |
eDRIS/XXXX-XXXX/example/005 |
take one in the morning and take two at night as directed |
eDRIS/XXXX-XXXX/example/006 |
1 tablet(s) three times daily for pain/inflammation |
eDRIS/XXXX-XXXX/example/007 |
two puffs at night |
eDRIS/XXXX-XXXX/example/008 |
0.6mls daily |
eDRIS/XXXX-XXXX/example/009 |
to be applied tds-qds |
eDRIS/XXXX-XXXX/example/010 |
take 1 tablet for 3 weeks then take 3 tablets for 4 weeks |
eDRIS/XXXX-XXXX/example/011 |
one to be taken twice a day if sleepy do not drive/use machines. avoid alcohol. swallow whole. |
eDRIS/XXXX-XXXX/example/012 |
1 tab take as required |
eDRIS/XXXX-XXXX/example/013 |
take one daily for allergy |
eDRIS/XXXX-XXXX/example/014 |
2x5ml spoonfuls with meals |
eDRIS/XXXX-XXXX/example/015 |
one per month |
eDRIS/XXXX-XXXX/example/016 |
1 cappful every four weeks |
eDRIS/XXXX-XXXX/example/017 |
take two every 4-6hrs for pain |
eDRIS/XXXX-XXXX/example/018 |
up to qid prn |
eDRIS/XXXX-XXXX/example/019 |
one or two tabs dissolved in a glass of water at night |
eDRIS/XXXX-XXXX/example/020 |
bid-tid |
eDRIS/XXXX-XXXX/example/021 |
change every 2 weeks |
eDRIS/XXXX-XXXX/example/022 |
take every fortnight |
yields the corresponding output
inputID |
text |
form |
dosageMin |
dosageMax |
frequencyMin |
frequencyMax |
frequencyType |
durationMin |
durationMax |
durationType |
asRequired |
asDirected |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
eDRIS/XXXX-XXXX/example/001 |
daily 2 caps |
capsule |
2.0 |
2.0 |
1.0 |
1.0 |
Day |
False |
False |
|||
eDRIS/XXXX-XXXX/example/002 |
daily 0.2ml |
ml |
0.2 |
0.2 |
1.0 |
1.0 |
Day |
False |
False |
|||
eDRIS/XXXX-XXXX/example/003 |
two mane + two nocte |
2.0 |
2.0 |
2.0 |
2.0 |
Day |
False |
False |
||||
eDRIS/XXXX-XXXX/example/004 |
2 tabs twice daily increased to 2 tabs three times daily during exacerbation chest symptoms |
tablet |
2.0 |
2.0 |
5.0 |
5.0 |
Day |
False |
False |
|||
eDRIS/XXXX-XXXX/example/005 |
take one in the morning and take two at night as directed |
3.0 |
3.0 |
1.0 |
1.0 |
Day |
False |
False |
||||
eDRIS/XXXX-XXXX/example/006 |
1 tablet(s) three times daily for pain/inflammation |
tablet |
1.0 |
1.0 |
3.0 |
3.0 |
Day |
False |
False |
|||
eDRIS/XXXX-XXXX/example/007 |
two puffs at night |
puff |
2.0 |
2.0 |
1.0 |
1.0 |
Day |
False |
False |
|||
eDRIS/XXXX-XXXX/example/008 |
0.6mls daily |
ml |
0.6 |
0.6 |
1.0 |
1.0 |
Day |
False |
False |
|||
eDRIS/XXXX-XXXX/example/009 |
to be applied tds-qds |
3.0 |
3.0 |
Day |
False |
False |
||||||
eDRIS/XXXX-XXXX/example/010 |
take 1 tablet for 3 weeks then take 3 tablets for 4 weeks |
tablet |
1.0 |
1.0 |
3.0 |
3.0 |
Week |
False |
False |
|||
eDRIS/XXXX-XXXX/example/010 |
take 1 tablet for 3 weeks then take 3 tablets for 4 weeks |
tablet |
3.0 |
3.0 |
4.0 |
4.0 |
Week |
False |
False |
|||
eDRIS/XXXX-XXXX/example/011 |
one to be taken twice a day if sleepy do not drive/use machines. avoid alcohol. swallow whole. |
1.0 |
1.0 |
2.0 |
2.0 |
Day |
False |
False |
||||
eDRIS/XXXX-XXXX/example/012 |
1 tab take as required |
tablet |
1.0 |
1.0 |
True |
False |
||||||
eDRIS/XXXX-XXXX/example/013 |
take one daily for allergy |
1.0 |
1.0 |
1.0 |
1.0 |
Day |
False |
False |
||||
eDRIS/XXXX-XXXX/example/014 |
2x5ml spoonfuls with meals |
ml |
10.0 |
10.0 |
3.0 |
3.0 |
Day |
False |
False |
|||
eDRIS/XXXX-XXXX/example/015 |
one per month |
1.0 |
1.0 |
1.0 |
1.0 |
Month |
False |
False |
||||
eDRIS/XXXX-XXXX/example/016 |
1 cappful every four weeks |
capful |
1.0 |
1.0 |
1.0 |
1.0 |
Month |
False |
False |
|||
eDRIS/XXXX-XXXX/example/017 |
take two every 4-6hrs for pain |
2.0 |
2.0 |
1.0 |
1.0 |
4 Hour |
True |
False |
||||
eDRIS/XXXX-XXXX/example/018 |
up to qid prn |
0.0 |
4.0 |
Day |
True |
False |
||||||
eDRIS/XXXX-XXXX/example/019 |
one or two tabs dissolved in a glass of water at night |
tablet |
1.0 |
2.0 |
1.0 |
1.0 |
Day |
False |
False |
|||
eDRIS/XXXX-XXXX/example/020 |
bid-tid |
2.0 |
3.0 |
Day |
False |
False |
||||||
eDRIS/XXXX-XXXX/example/021 |
change every 2 weeks |
1.0 |
1.0 |
2 Week |
False |
False |
||||||
eDRIS/XXXX-XXXX/example/022 |
take every fortnight |
1.0 |
1.0 |
2 Week |
False |
False |
Note
In this example, eDRIS/XXXX-XXXX/example/010 has been split up into two dose instructions
Usage from Python
For more adaptable usage you can load the package into Python and use it within a script or on the Python prompt. For example, using iPython:
In [1]: import pandas as pd
...: from dose_instruction_parser import parser
In [2]: # Create parser
...: p = parser.DIParser("en_edris9")
In [3]: # Parse one dose instruction
...: p.parse("Take 2 tablets morning and night")
Out[3]: [StructuredDI(inputID=None, text='Take 2 tablets morning and night', form='tablet', dosageMin=2.0, dosageMax=2.0, frequencyMin=2.0, frequencyMax=2.0, frequencyType='Day', durationMin=None, durationMax=None, durationType=None, asRequired=False, asDirected=False)]
In [4]: # Parse many dose instructions
...: parsed_dis = p.parse_many([
...: "take one tablet daily",
...: "two puffs prn",
...: "one cap after meals for three weeks",
...: "4 caplets tid"
...: ])
In [5]: print(parsed_dis)
[StructuredDI(inputID=0, text='take one tablet daily', form='tablet', dosageMin=1.0, dosageMax=1.0, frequencyMin=1.0, frequencyMax=1.0, frequencyType='Day', durationMin=None, durationMax=None, durationType=None, asRequired=False, asDirected=False), StructuredDI(inputID=1, text='two puffs prn', form='puff', dosageMin=2.0, dosageMax=2.0, frequencyMin=None, frequencyMax=None, frequencyType=None, durationMin=None, durationMax=None, durationType=None, asRequired=True, asDirected=False), StructuredDI(inputID=2, text='one cap after meals for three weeks', form='capsule', dosageMin=1.0, dosageMax=1.0, frequencyMin=3.0, frequencyMax=3.0, frequencyType='Day', durationMin=3.0, durationMax=3.0, durationType='Week', asRequired=False, asDirected=False), StructuredDI(inputID=3, text='4 caplets tid', form='carpet', dosageMin=4.0, dosageMax=4.0, frequencyMin=3.0, frequencyMax=3.0, frequencyType='Day', durationMin=None, durationMax=None, durationType=None, asRequired=False, asDirected=False)]
In [6]: # Convert output to pandas dataframe
...: di_df = pd.DataFrame(parsed_dis)
In [7]: print(di_df)
inputID text form dosageMin dosageMax frequencyMin frequencyMax frequencyType durationMin durationMax durationType asRequired asDirected
0 take one tablet daily tablet 1.0 1.0 1.0 1.0 Day NaN NaN None False False
1 two puffs prn puff 2.0 2.0 NaN NaN None NaN NaN None True False
2 one cap after meals for three weeks capsule 1.0 1.0 3.0 3.0 Day 3.0 3.0 Week False False
3 4 caplets tid carpet 4.0 4.0 3.0 3.0 Day NaN NaN None False False