Specific Question
I parsed C-CDA with BlueButton.js. Following is from the Medication JSON output. What is the RXNorm (with code system "2.16.840.1.113883.6.88") in this example? It has 577961 and 577962. Which is the correct RxNorm for the patient's medication?
"product": {
"name": "Amphetamine aspartate 5 MG / Amphetamine Sulfate 5 MG / Dextroamphetamine saccharate 5 MG / Dextroamphetamine Sulfate 5 MG Oral Tablet",
"text": "Adderall 20 mg tablet",
"code": "577961",
"code_system": "2.16.840.1.113883.6.88",
"translation": {
"name": "Amphetamine aspartate 5 MG / Amphetamine Sulfate 5 MG / Dextroamphetamine saccharate 5 MG / Dextroamphetamine Sulfate 5 MG Oral Tablet [Adderall]",
"code": "577962",
"code_system": "2.16.840.1.113883.6.88",
"code_system_name": "RxNorm"
}
}
General Question
Where can I get explnanation of these C-CDA elements - that is, the difference between code element in product and translation elements?
References:
HL7-Referenced External Code Systems
So RxNorm is a terminology that used in the United States for recording and transmitting medication information. It's a complex terminology/ontology since it allows for ingredients, coordinated dose forms, brand names, generic names and a bunch more. You can browse RxNorm here online without any login:
https://mor.nlm.nih.gov/RxNav/
(they also have an API that you use, but that should get you started)
Specifically on the drugs you mentioned: 577961 is the generic format and 577962 is the brand of the same drug. According to the standard, either of those codes are technically correct since they are SCD and SBD term types respectively (Semantic Clinical/Brand Drug) I don't know if it's 100% clear whether the patient is on the brand or generic given that both codes are transmitted. There may be other information in the document regarding (such as what drug was dispensed).
In terms of learning about the standard, which is HL7 C-CDA, you could download the standard here, although this requires a free HL7 login: http://www.hl7.org/implement/standards/product_brief.cfm?product_id=492
HL7 is the standards development organization (SDO) for medical data standards. They also offer a lot of educational content on their standards. I hope this helps!
Related
I'm trying to load a dataset into R Studio, where the dataset itself is space-delimited, but it also contains spaces in quoted text like in csv files. Here is the head of the data:
DOC_ID LABEL RATING VERIFIED_PURCHASE PRODUCT_CATEGORY PRODUCT_ID PRODUCT_TITLE REVIEW_TITLE REVIEW_TEXT
1 __label1__ 4 N PC B00008NG7N "Targus PAUK10U Ultra Mini USB Keypad, Black" useful "When least you think so, this product will save the day. Just keep it around just in case you need it for something."
2 __label1__ 4 Y Wireless B00LH0Y3NM Note 3 Battery : Stalion Strength Replacement 3200mAh Li-Ion Battery for Samsung Galaxy Note 3 [24-Month Warranty] with NFC Chip + Google Wallet Capable New era for batteries Lithium batteries are something new introduced in the market there average developing cost is relatively high but Stallion doesn't compromise on quality and provides us with the best at a low cost.<br />There are so many in built technical assistants that act like a sensor in their particular forté. The battery keeps my phone charged up and it works at every voltage and a high voltage is never risked.
3 __label1__ 3 N Baby B000I5UZ1Q "Fisher-Price Papasan Cradle Swing, Starlight" doesn't swing very well. "I purchased this swing for my baby. She is 6 months now and has pretty much out grown it. It is very loud and doesn't swing very well. It is beautiful though. I love the colors and it has a lot of settings, but I don't think it was worth the money."
4 __label1__ 4 N Office Products B003822IRA Casio MS-80B Standard Function Desktop Calculator Great computing! I was looking for an inexpensive desk calcolatur and here it is. It works and does everything I need. Only issue is that it tilts slightly to one side so when I hit any keys it rocks a little bit. Not a big deal.
5 __label1__ 4 N Beauty B00PWSAXAM Shine Whitening - Zero Peroxide Teeth Whitening System - No Sensitivity Only use twice a week "I only use it twice a week and the results are great. I have used other teeth whitening solutions and most of them, for the same results I would have to use it at least three times a week. Will keep using this because of the potency of the solution and also the technique of the trays, it keeps everything in my teeth, in my mouth."
6 __label1__ 3 N Health & Personal Care B00686HNUK Tobacco Pipe Stand - Fold-away Portable - Light Weight - For Single Pipe not sure I'm not sure what this is supposed to be but I would recommend that you do a little more research into the culture of using pipes if you plan on giving this as a gift or using it yourself.
7 __label1__ 4 N Toys B00NUG865W ESPN 2-Piece Table Tennis PING PONG TABLE GREAT FOR YOUTHS AND FAMILY "Pleased with ping pong table. 11 year old and 13 year old having a blast, plus lots of family entertainment too. Plus better than kids sitting on video games all day. A friend put it together. I do believe that was a challenge, but nothing they could not handle"
8 __label1__ 4 Y Beauty B00QUL8VX6 "Abundant Health 25% Vitamin C Serum with Vitamin E and Hyaluronic Acid for Youthful Looking Skin, 1 fl. oz." Great vitamin C serum "Great vitamin C serum... I really like the oil feeling, not too sticky. I used it last week on some of my recent bug bites and it helps heal the skin faster than normal."
9 __label1__ 4 N Health & Personal Care B004YHKVCM PODS Spring Meadow HE Turbo Laundry Detergent Pacs 77-load Tub wonderful detergent. "I've used tide pods laundry detergent for many years,its such a great detergent to use having a nice scent and leaver the cloths smelling fresh."
Problem is that it looks tab-delimited but it is not, example would be DOC_ID = 1, where there are only two spaces between useful and "When least...", this way passing sep = "/t" to read.table throws an error saying that line 1 did not have 10 elements, which for some reason is incorrect, because the number of elements should be 9. Here are the parameters that I'm passing(without the original path):
read.table(file = "path", sep ="\t", header = TRUE, strip.white = TRUE)
Also relying on quotes is not a good strategy, because some lines do not have their text quoted, so the delimiter should be something like a double space, which combined with strip.white should work properly, but read.table only accepts single byte delimiters.
So the question is how would you parse such corpus in R or with any other third party software that could convert it adequately to a csv or atleast a tab-delimited file?
Parsing the data using python pandas.read_csv(filename, sep='\t', header = 0, ...) seems to have parsed the data successfully and from this point anything could be done with it. Closing this out.
I need to count the frequency of unique words found in a column that contains descriptions in each row.
So far, I have eliminated a list of stopwords from the original column and I have extracted the unique words from the column and put them into a list called unique_description.
> description[1:5]
[1] "Come stay Vinh & Stuart (Awarded one Australia's top hosts Airbnb CEO Brian Chesky & key shareholder Ashton Kutcher. We're Sydney's #1 reviewed hosts ). Find out 've positively reviewed 500+ times. Message talk first BEFORE make reservation request - And please read listing end (hint hint). Everything need know . We're pretty relaxed hosts, fully appreciate staying someone , home home, -one. This business, hotel. We're casual Airbnb hosts, hoteliers. If 're looking alternative expensive hotel, 're . Here 'll treated same way treat family & friends stay. So... fluffy bathrobes... Please hello message *BEFORE* make reservation request... It'll help speed things up, smooth things out... Please read listing way end. It make getting confirmed reserv"
[2] "Beautifully renovated, spacious quiet, 3 Bedroom, 3 Bathroom home 10 minute walk beaches Fairlight Forty Baskets, 30 minute walk Manly via coastal promenade, Express bus runs 20 mins door. Our home thirty minute walk along seashore promenade Manly, one Sydney's beautiful beaches, village restaurants, cafes, shopping. If prefer more variety, Manly ferry take Sydney CBD 15 minutes. The residence sited sought- family-friendly street short stroll nearby North Harbour reserve Forty Baskets cafe beach. It's short walk further express CBD buses, ferries, Manly entertainment. Or bus (#131 #132) around corner drops Manly 8 minutes. Our home features stainless steel galley kitchen, including Ilve oven gas cooktop. We two separate living areas ground floor. The front lounge enjoys P&O"
[3] "Welcome sanctuary - bright, comfortable one bedroom apartment North Sydney. Free Wifi, heated pool/jacuzzi everything need make stay Sydney very comfortable. Enjoy fabulous Home away home, fantastic stay Sydney! The apartment within walking distance restaurants shops, Luna Park North Sydney business district. Access Sydney CBD easy bus, train, taxi ferry. It short bus ride famous Balmoral Beach Taronga Zoo. My apartment situated North Sydney 3 kms Sydney CBD. Here details apartment: You'll enjoy being centrally located couple blocks away train station go anywhere quickly Sydney. The apartment features several windows tons natural light. It comfortable fully stocked. Here's I here: LIVING ROOM: 50\" LCD TV DVD / blu ray player CD/Radio/Blue tooth syncing w"
[4] "Fully self-contained sunny studio apartment. 10mn walk Bondi beach. Bus city door. Private 13m swimming pool. Sunny, studio apartment . Private terrace. bus door Bondi Junction City Ground floor 1 bedroom double bed plus kitchenette & study desk. shower & toilet, share laundry, kitchen facilities Swimming pool 13m. Separate security private entrance Private entrance. Ground floor. Happy indicate best spots walking, dining, entertaining best sightseeing location Sydney. Upmarket area. Very nice quiet neighbourhood . Very safe place. Bus door city."
[5] "Sunny warehouse/loft apartment heart one Sydney's best neighbourhoods. Located corner two iconic Darlinghurst streets famous laneway bars eateries, footsteps equally amazing Surry Hills Potts Point. Walk through beautiful parks city less 10 mins, opera house 20 access Bondi Beach easily 25 via bus stop directly front building. My apartment beautiful, simple, open plan / one bedroom loft soaring high ceilings hardwood floors hint 's previous life printing factory 1940s. It huge windows flood space glorious sunshine throughout day provide refreshing breeze during summer. A few key features: * Wireless harman/kardon aura stereo system stream music wirelessly bluetooth device * Internal laundry washer dryer * The kitchen equipped gas cooking, microwave, dishwasher basics preparing m"
> unique_description[1:10]
[1] "Come" "stay" "Vinh" "&" "Stuart" "(Awarded"
[7] "one" "Australia's" "top" "hosts"
I'm not sure how to count the frequency of the words in unique_description that are found in the column 'description'. I tried using freq_terms in library(qdap), but qdap will not load for me so am trying to find another way.
You could use the stringr package.
library(stringr)
x <- "Come stay Vinh & Stuart (Awarded one Australia's top hosts Airbnb CEO Brian Chesky & key shareholder Ashton Kutcher. We're Sydney's #1 reviewed hosts ). Find out 've positively reviewed 500+ times. Message talk first BEFORE make reservation request - And please read listing end (hint hint). Everything need know . We're pretty relaxed hosts, fully appreciate staying someone , home home, -one. This business, hotel. We're casual Airbnb hosts, hoteliers. If 're looking alternative expensive hotel, 're . Here 'll treated same way treat family & friends stay. So... fluffy bathrobes... Please hello message *BEFORE* make reservation request... It'll help speed things up, smooth things out... Please read listing way end. It make getting confirmed reserv"
y <- "come stay Stuart"
unique_desc <- c("come", "stay", "Stuart")
desc <- c(x,y)
result <- lapply(desc, FUN = str_count, pattern = unique_desc)
#result holds first element is counts in first element of desc
lapply will call the str_count function to each element of desc. In this example the ith entry of result there is a vector of counts corresponding to the ith entry of desc and the vector of counts correspond to the counts of each word in unique_desc.
I am working with XML data in .NET from the Federal Register, which contain many references to Executive Orders & chapters from the U.S. Code.
I'd like to be able to hyperlink to these references, unless they're already inside of an <a> tag (which is determined by the XML, and often links within the document itself).
The pattern I've written is matching and deleting leading and trailing characters and not displaying them, even if I include the boundary character in the replacement string:
[?!]([0-9]{1,2})[ ]{0,1}(U\.S\.C\.|USC)[\s]{0,1}([0-9]{1,5})(\b)[^]
An example of the initial XML:
<p>The Regulatory Flexibility Act of 1980 (RFA), 5 U.S.C. 604(b), as amended, requires Federal agencies to consider the potential impact of regulations on small entities during rulemaking.</p>
<p>Small entities include small businesses, small not-for-profit organizations, and small governmental jurisdictions.</p>
<p>Section 605 of the RFA allows an agency to certify a rule, in lieu of preparing an analysis, if the rulemaking is not expected to have a significant economic impact on a substantial number of small entities. Reference: 13 USC 401</p>
<ul>
<li><em>Related laws from 14USC301-345 do not apply.</em></li>
<li>14 USC 301 does apply.</li>
</ul>
As you can see, some references include ranges of U.S. Code sections (e.g. 14 USC 301-345) or references to specific subsections (e.g. 5 U.S.C. 604(b) ). I'd only want to link to the first reference in the range, so the link should terminate at the - or the (.
If I'm understanding you correctly, I think the following should work.
var re = new Regex(#"\d{1,2}\s?U\.?S\.?C\.?\s?\d{1,5}\b(?!</a>)");
var matches = re.Matches(text);
// matches[0].Value = 5 U.S.C. 604
// matches[1].Value = 14USC301
You might even be able to simplify the regex to \d+\s?U\.?S\.?C\.?\s?\d+\b(?!</a>) – I'm not sure if the upper limits of 2 and 5 are significant.
I would like to know if there is a Resource I could use to represent medication alternatives, such as:
If you are taking Drug A , you should use Drug B or Drug C instead
This is not something that FHIR has implemented yet - it's clinical/medical knowledge. The nearest that FHIR currently has is the Clinical Quality Framework: http://hl7-fhir.github.io/cqif/cqif.html
Warning: It's very much a work in progress, and the link above is to the current build, not a stable release
Does anyone know how to replicate the (pg_trgm) postgres trigram similarity score from the similarity(text, text) function in R? I am using the stringdist package and would rather use R to calculate these on a matrix of text strings in a .csv file than run a bunch of postgresql quires.
Running similarity(string1, string2) in postgres give me a number score between 0 and 1.
I tired using the stringdist package to get a score but I think I still need to divide the code below by something.
stringdist(string1, string2, method="qgram",q = 3 )
Is there a way to replicate the pg_trgm score with the stringdist package or another way to do this in R?
An example would be getting the similarity score between the description of a book and the description of a genre like science fiction. For example, if I have two book descriptions and the using the similarity score of
book 1 = "Area X has been cut off from the rest of the continent for decades. Nature has reclaimed the last vestiges of human civilization. The first expedition returned with reports of a pristine, Edenic landscape; the second expedition ended in mass suicide, the third expedition in a hail of gunfire as its members turned on one another. The members of the eleventh expedition returned as shadows of their former selves, and within weeks, all had died of cancer. In Annihilation, the first volume of Jeff VanderMeer's Southern Reach trilogy, we join the twelfth expedition.
The group is made up of four women: an anthropologist; a surveyor; a psychologist, the de facto leader; and our narrator, a biologist. Their mission is to map the terrain, record all observations of their surroundings and of one anotioner, and, above all, avoid being contaminated by Area X itself.
They arrive expecting the unexpected, and Area X delivers—they discover a massive topographic anomaly and life forms that surpass understanding—but it’s the surprises that came across the border with them and the secrets the expedition members are keeping from one another that change everything."
book 2= "From Wall Street to Main Street, John Brooks, longtime contributor to the New Yorker, brings to life in vivid fashion twelve classic and timeless tales of corporate and financial life in America
What do the $350 million Ford Motor Company disaster known as the Edsel, the fast and incredible rise of Xerox, and the unbelievable scandals at GE and Texas Gulf Sulphur have in common? Each is an example of how an iconic company was defined by a particular moment of fame or notoriety; these notable and fascinating accounts are as relevant today to understanding the intricacies of corporate life as they were when the events happened.
Stories about Wall Street are infused with drama and adventure and reveal the machinations and volatile nature of the world of finance. John Brooks’s insightful reportage is so full of personality and critical detail that whether he is looking at the astounding market crash of 1962, the collapse of a well-known brokerage firm, or the bold attempt by American bankers to save the British pound, one gets the sense that history repeats itself.
Five additional stories on equally fascinating subjects round out this wonderful collection that will both entertain and inform readers . . . Business Adventures is truly financial journalism at its liveliest and best."
genre 1 = "Science fiction is a genre of fiction dealing with imaginative content such as futuristic settings, futuristic science and technology, space travel, time travel, faster than light travel, parallel universes, and extraterrestrial life. It often explores the potential consequences of scientific and other innovations, and has been called a "literature of ideas".[1] Authors commonly use science fiction as a framework to explore politics, identity, desire, morality, social structure, and other literary themes."
How can I get a similarity score for the description of each book against the description of the science fiction genre like pg_trgm using an R script?
How about something like this?
library(textcat)
?textcat_xdist
# Compute cross-distances between collections of n-gram profiles.
round(textcat_xdist(
list(
text1="hello there",
text2="why hello there",
text3="totally different"
),
method="cosine"),
3)
# text1 text2 text3
#text1 0.000 0.078 0.731
#text2 0.078 0.000 0.739
#text3 0.731 0.739 0.000