2010 I2b2 / VA Challenge Evaluation

2010 i2b2 / VA Challenge Evaluation

Annotation Guidelines for Relations v8 Ozlem Uzuner and Scott DuVall

These are the guidelines for identifying the relations that exist between: 1. medical problems and treatments 2. medical problems and tests 3. medical problems and other medical problems

For the purposes of this challenge, we assume that the concepts corresponding to medical problems, treatments, and tests have already been marked. In addition, the medical problems have been classified with their assertions, so that problems that have been asserted to be associated with someone other than the patient are left outside the scope of relations. Our task is to identify how problems relate to treatments, tests, and other medical problems in the text.

Relationships are bounded by sentences. To determine the type of relationship that exists between two concepts, only the text within the same sentence may be used.

In the examples below, the related concepts are marked in BLUE.

1. Possible relations for medical problems and treatments are: a. Treatment improves medical problem (TrIP). This includes mentions where the treatment cures the problem. Examples: . at that time with anasarca and congestive heart failure , responsive to diuretics and ACE inhibitors . . at that time with anasarca and congestive heart failure , responsive to diuretics and ACE inhibitors . . at that time with anasarca and congestive heart failure , responsive to diuretics and ACE inhibitors . . at that time with anasarca and congestive heart failure , responsive to diuretics and ACE inhibitors .

. hypertension was controlled on hydrochlorothiazide . She has an elevated cholesterol controlled with Zocor

b. Treatment worsens medical problem (TrWP). This includes mentions where the treatment does not cure the problem. Examples: . was discharged to home to be followed for her coronary artery disease following two failed bypass graft procedure . the tumor was growing despite the available chemotherapeutic regimen . culture taken from the lumbar drain showed Staphylococcus aureus resistant to Nafcillin

c. Treatment causes medical problem (TrCP). The implied context is that the treatment was not administered for the medical condition that it ended up causing. Examples: . Also the risk of ischemia or infarct from the internal carotid artery coil could lead to thromboembolism. . Also the risk of ischemia or infarct from the internal carotid artery coil could lead to thromboembolism. . Also the risk of ischemia or infarct from the internal carotid artery coil could lead to thromboembolism.

. In terms of his liver abnormalities, it was felt that viral hepatitis was in the differential as well as several opportunistic infections of the liver but also was felt that Bactrim could be a cause of these abnormalities . . In terms of his liver abnormalities, it was felt that viral hepatitis was in the differential as well as several opportunistic infections of the liver but also was felt that Bactrim could be a cause of these abnormalities .

. He had an angiogram which shows a severe stenosis in the right distal area with a thrombosing right limb of an aorto femoral graft . He had an angiogram which shows a severe stenosis in the right distal area with a thrombosing right limb of an aorto femoral graft

. There is a question of an allergy to Tylenol . . The patient has a questionable allergy to penicillin , although denies allergies . . He was transfused with red blood cells and given Lasix periodically to prevent him from going into congestive heart failure has he had on his prior transfusion. . hypothyroidism following near total thyroidectomy . No beta blockers were started because of his history of hypertension with beta blockers and because his blood pressure of only 110/70 . He had hypotension with beta blockers and therefore they were not started. . He did have some peripheral neuropathy related to his chemotherapy for testicular cancer .

d. Treatment is administered for medical problem (TrAP). This includes mentions where a treatment is given for a problem, but the outcome is not mentioned in the sentence. Examples: . He was given Flagyl and had already apparently been on Levofloxacin outside the hospital since his recent discharge for questionable pneumonia . . He was given Flagyl and had already apparently been on Levofloxacin outside the hospital since his recent discharge for questionable pneumonia . . He was transfused with 1/2 units of packed red blood cells and given Lasix periodically to prevent him from going into congestive heart failure he has had on his prior transfusion. . He was transfused with 1/2 units of packed red blood cells and given Lasix periodically to prevent him from going into congestive heart failure he has had on his prior transfusion.

. antibiotic therapy for presumed ( but later found to be inflammation only ) of right forearm phlebitis . heparin was restarted four hours after sheath removal and maintained for two days because of a possible small dissection in the RCA . Dexamphetamine 2.5 mg. p.o. q. A.M. for depression. . Excision of right forearm vein for question of phlebitis . He did have some peripheral neuropathy related to his chemotherapy for testicular cancer .

e. Treatment is not administered because of medical problem (TrNAP). This includes mentions where treatment was discontinued because of a medical problem. Examples: . The patient 's antibiotics were discontinued with the thought that prolonged antibiotics only put her at more risk for infection . . The patient 's antibiotics were discontinued with the thought that prolonged antibiotics only put her at more risk for infection .

. The epidural was subsequently removed for concern of possible infection to avoid infection seeding the epidural space . . The epidural was subsequently removed for concern of possible infection to avoid infection seeding the epidural space .

. Of note , shortly after starting on her TPN her phosphate level dropped to 1.8 and TPN was temporarily held due to concerns she may be suffering from receding syndrome . . Of note , shortly after starting on her TPN her phosphate level dropped to 1.8 and TPN was temporarily held due to concerns she may be suffering from receding syndrome .

. She also developed a mild urinary tract infection which responded to Bactrim, but which was subsequently stopped because of diarrhea . . Paroxysmal atrial fibrillation without anticoagulation given a history of gastrointestinal bleed . . Relafen which is contra-indicated because of ulcers. . There was a question of aspiration pneumonia so he was switched from Ampicillin pen-g . . No beta blockers were started because of his history of hypertension with beta blockers and because his blood pressure of only 110/70 . Colace 100 milligrams po q day , hold for loose stools .

f. None of the above defined treatment-problem relationships (NoneTrP). This includes treatments and problems that are in the same sentence, but do not fit into one of the above defined relationships. Examples: . In terms of his liver abnormalities, it was felt that viral hepatitis was in the differential as well as several opportunistic infections of the liver but also was felt that Bactrim could be a cause of these abnormalities . . In terms of his liver abnormalities, it was felt that viral hepatitis was in the differential as well as several opportunistic infections of the liver but also was felt that Bactrim could be a cause of these abnormalities . . In terms of his liver abnormalities, it was felt that viral hepatitis was in the differential as well as several opportunistic infections of the liver but also was felt that Bactrim could be a cause of these abnormalities .

. She was admitted to the Retelk County Medical Center on 04/12 for coronary artery bypass grafting but was discharged because of fever and a probable upper respiratory infection. . She was admitted to the Retelk County Medical Center on 04/12 for coronary artery bypass grafting but was discharged because of fever and a probable upper respiratory infection.

. We have a low threshold for starting antibiotics; however , chest x-ray reveals no acute changes and the patient remained 96% on room air throughout this admission without any stigmata over recurrent pneumonia.

2. Medical problem relations with other medical problems: a. Medical problem indicates medical problem (PIP). This includes medical problems that describe or reveal aspects of the same medical problem and those that cause other medical problems. Examples: . In 05/99 he had increasing abdominal pain and evaluation revealed extensive progressive retroperitoneal disease as well as left hydronephrosis . In 05/99 he had increasing abdominal pain and evaluation revealed extensive progressive retroperitoneal disease as well as left hydronephrosis

. The patient was admitted for acute and chronic respiratory distress with likely chronic obstructive pulmonary disease and question of a pulmonary embolus. . The patient was admitted for acute and chronic respiratory distress with likely chronic obstructive pulmonary disease and question of a pulmonary embolus. . status post sigmoid resection for Duke 's C2 low sigmoid carcinoma admitted on 7/8/96 with abdominal pain and neutropenia . status post sigmoid resection for Duke 's C2 low sigmoid carcinoma admitted on 7/8/96 with abdominal pain and neutropenia

. Azotemia presumed secondary to sepsis and dehydration . Azotemia presumed secondary to sepsis and dehydration

. Also with a history of noninsulin dependent diabetes mellitus , now presenting with acute blurry vision on the left side , which is homonymous .

b. None of the above defined problem-problem relationship (NonePP). This includes problems that are in the same sentence, but do not fit into the PIP relationships. Examples: . She was initially treated for heart failure and pneumonia . . The patient is a 40 year old male with a history of prior anterior myocardial infarction and insulin dependent diabetes mellitus .

3. Test relations with medical problems: a. Test reveals medical problem (TeRP). This includes mentions where a test is conducted and the outcome is known. Examples: . an echocardiogram revealed a pericardial effusion and possible tamponade clinically . an echocardiogram revealed a pericardial effusion and possible tamponade clinically

. In 05/99 he had increasing abdominal pain and evaluation revealed extensive progressive retroperitoneal disease as well as left hydronephrosis . In 05/99 he had increasing abdominal pain and evaluation revealed extensive progressive retroperitoneal disease as well as left hydronephrosis

. chest x-ray revealed an abnormality in the right upper lobe . . A lung biopsy was performed , revealing chorio carcinoma pathologically . An abdominal ultrasound was performed showing no stones . . patient noted to have acute or chronic Hepatitis by chemistries b. Test conducted to investigate medical problem (TeCP). This includes mentions where a test is conducted and the outcome is not known. Examples: . an VQ scan was performed to investigate pulmonary embolus . suggest echocardiogram to check for vegetation . chest x-ray done to rule out pneumonia

c. None of the above defined test-problem relationship (NoneTeP). This includes tests and problems that are in the same sentence, but do not fit into the any of the above defined relationships. Examples: . The patient has history of asthma and a new diagnosis of heart failure diagnosed by echocardiogram .