Datasets:

metaboulie
/

rag-for-ner

Tasks:

Token Classification

Languages:

English

Size:

10M<n<100M

Tags:

medical

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The dataset generation failed

Error code:   DatasetGenerationError
Exception:    DatasetGenerationError
Message:      An error occurred while generating the dataset
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/json/json.py", line 145, in _generate_tables
                  dataset = json.load(f)
                File "/usr/local/lib/python3.9/json/__init__.py", line 293, in load
                  return loads(fp.read(),
                File "/usr/local/lib/python3.9/json/__init__.py", line 346, in loads
                  return _default_decoder.decode(s)
                File "/usr/local/lib/python3.9/json/decoder.py", line 340, in decode
                  raise JSONDecodeError("Extra data", s, end)
              json.decoder.JSONDecodeError: Extra data: line 2 column 1 (char 20988)
              
              During handling of the above exception, another exception occurred:
              
              Traceback (most recent call last):
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1995, in _prepare_split_single
                  for _, table in generator:
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/json/json.py", line 148, in _generate_tables
                  raise e
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/json/json.py", line 122, in _generate_tables
                  pa_table = paj.read_json(
                File "pyarrow/_json.pyx", line 308, in pyarrow._json.read_json
                File "pyarrow/error.pxi", line 154, in pyarrow.lib.pyarrow_internal_check_status
                File "pyarrow/error.pxi", line 91, in pyarrow.lib.check_status
              pyarrow.lib.ArrowInvalid: JSON parse error: Column() changed from object to array in row 0
              
              The above exception was the direct cause of the following exception:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1577, in compute_config_parquet_and_info_response
                  parquet_operations = convert_to_parquet(builder)
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1191, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1027, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1122, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1882, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2038, in _prepare_split_single
                  raise DatasetGenerationError("An error occurred while generating the dataset") from e
              datasets.exceptions.DatasetGenerationError: An error occurred while generating the dataset

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text string	tags sequence
She has also had decreased level of consciousness since yesterday .	[ "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "O", "O", "O" ]
She was much more congested and her appetite had decreased significantly today .	[ "O", "O", "B-problem", "I-problem", "I-problem", "O", "O", "O", "O", "O", "O", "O", "O" ]
He states that this began approximately one week ago when he was lifting stacks of cardboard .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
He did have a protective clothing including use of gloves at the time of the incident .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
The patient does state that she is somewhat painful throughout the bones of her pelvis as well .	[ "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
The mass increased in size .	[ "O", "B-problem", "O", "O", "O", "O" ]
HISTORY OF PRESENT ILLNESS : The patient presented to Dr .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
No vomiting or diarrhea .	[ "O", "B-problem", "O", "B-problem", "O" ]
She did not do this previously .	[ "O", "O", "O", "O", "O", "O", "O" ]
6 .	[ "O", "O" ]
She underwent TAH with BSO in December of 2003 .	[ "O", "O", "B-treatment", "O", "B-treatment", "O", "O", "O", "O", "O" ]
The parents noticed no improvement with albuterol treatments given in the ER .	[ "O", "O", "O", "O", "O", "O", "B-treatment", "I-treatment", "O", "O", "O", "O", "O" ]
Otherwise , this patient has been active , breast - feeding well , although she falls asleep at the breast .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
She is requesting a colonoscopy for screening as well .	[ "O", "O", "O", "B-test", "I-test", "O", "B-test", "O", "O", "O" ]
She has had this off and on for four months .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
Her hemoglobin was 13 .	[ "B-test", "I-test", "O", "O", "O" ]
The patient stated that the abdominal pain was only associated with coughing .	[ "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "O", "O", "O", "O", "B-problem", "O" ]
It is a dull achy pain .	[ "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "O" ]
She denies any hot flashes or night sweats .	[ "O", "O", "B-problem", "I-problem", "I-problem", "O", "B-problem", "I-problem", "O" ]
He sleeps well , but has been more tired and has been fussy over the past 2 days .	[ "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "O", "O", "O", "B-problem", "O", "O", "O", "O", "O", "O" ]
Mild nausea .	[ "B-problem", "I-problem", "O" ]
She began treatment with CIVI - CAD in December 2007 .	[ "O", "O", "O", "O", "B-treatment", "I-treatment", "I-treatment", "O", "O", "O", "O" ]
MRI showed inflammation and was thought to be secondary to rheumatoid arthritis .	[ "B-test", "O", "B-problem", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "O" ]
HISTORY OF PRESENT ILLNESS : A 50 - year - old female comes to the clinic with complaint of mood swings and tearfulness .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "O", "B-problem", "O" ]
He had his finger of the left hand over the pulse and was inserting a needle using the right hand .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-treatment", "I-treatment", "O", "O", "O", "O", "O" ]
HISTORY OF PRESENT ILLNESS : This is the initial clinic visit for a 29 - year - old man who is seen for new onset of right shoulder pain .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "I-problem", "I-problem", "O" ]
She was having difficulty breathing .	[ "O", "O", "O", "B-problem", "I-problem", "O" ]
She became acutely unresponsive .	[ "O", "O", "B-problem", "I-problem", "O" ]
She is also unable to describe the vomitus .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
At this time , she is being treated aggressively with mechanical ventilation and other supportive measures and has developed disseminated intravascular coagulation with prolonged partial thromboplastin time , prothrombin time , low fibrinogen , and elevated D - dimer .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-treatment", "I-treatment", "O", "B-treatment", "I-treatment", "I-treatment", "O", "O", "O", "B-problem", "I-problem", "I-problem", "O", "B-problem", "I-problem", "I-problem", "I-problem", "O", "B-problem", "I-problem", "O", "B-problem", "I-problem", "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "O" ]
The child was continued on IV fluid and narcotics for pain as well as Unasyn until the time of discharge .	[ "O", "O", "O", "O", "O", "B-treatment", "I-treatment", "O", "B-treatment", "O", "B-problem", "O", "O", "O", "B-treatment", "O", "O", "O", "O", "O", "O" ]
She has had aphasia which is baseline but her aphasia has gotten significantly worse .	[ "O", "O", "O", "B-problem", "O", "O", "O", "O", "B-problem", "I-problem", "O", "O", "B-problem", "I-problem", "O" ]
She does recall having palpitations because of the pain after the fall , but she states she is not having them since and has not had them prior .	[ "O", "O", "O", "O", "B-problem", "O", "O", "B-problem", "I-problem", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
Of note , there are no other enhancing solid masses seen on this MRI .	[ "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "O", "O", "O", "B-test", "O" ]
X from the ENT while in house .	[ "O", "O", "O", "O", "O", "O", "O", "O" ]
She took several of her MDIs and then was placed on her CPAP .	[ "O", "O", "O", "O", "B-treatment", "I-treatment", "O", "O", "O", "O", "O", "B-treatment", "I-treatment", "O" ]
She was started on Amoxil and Aldex and we told to recheck in 2 weeks to recheck her ear .	[ "O", "O", "O", "O", "B-problem", "O", "B-problem", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
The patient presented to our emergency room for worsening abdominal pain as well as swelling of the right lower leg .	[ "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "O", "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "I-problem", "I-problem", "O" ]
I am unable to get any further history from the patient because , again , she is an extremely poor historian and very hard of hearing .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "O" ]
As he advanced the needle , the patient jerked away , this caused him to pull out of the arm and inadvertently pricked the tip of his index finger .	[ "O", "O", "O", "B-treatment", "I-treatment", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
For full details on the history of present illness , please see the previous history and physical .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
X ' s office on 06/14/07 complaining of a painful left foot .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "O" ]
The patient did not walk after this accident .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
He denies any visual problems .	[ "O", "O", "B-problem", "I-problem", "I-problem", "O" ]
The patient was driving a minivan .	[ "O", "O", "O", "O", "O", "O", "O" ]
His urine output has also decreased ; normally he has 8 to 10 wet and 5 dirty diapers per 24 hours , now he has down to 4 wet diapers per 24 hours .	[ "B-test", "I-test", "I-test", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
She has not been on any other antidepressants in the past .	[ "O", "O", "O", "O", "O", "B-treatment", "I-treatment", "I-treatment", "O", "O", "O", "O" ]
Patient does have a past history compatible with allergic rhinitis and he has been taking Zyrtec serum .	[ "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "O", "O", "O", "O", "O", "B-treatment", "O", "O" ]
5 mg per week .	[ "O", "O", "O", "O", "O" ]
It is currently been gone on for the last week .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
3 with white count of 11 .	[ "O", "O", "B-test", "I-test", "O", "O", "O" ]
HISTORY OF PRESENT ILLNESS : Mrs .	[ "O", "O", "O", "O", "O", "O", "O" ]
4 .	[ "O", "O" ]
If she gets up , it goes away within 15 minutes .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
She has had no problems with methotrexate as far as she knows .	[ "O", "O", "O", "O", "O", "O", "B-treatment", "O", "O", "O", "O", "O", "O" ]
At the time of admission , the patient has a normal prothrombin time and INR of 13 .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-test", "I-test", "I-test", "I-test", "O", "B-test", "O", "O", "O" ]
Mom denies any diarrhea .	[ "O", "O", "B-problem", "I-problem", "O" ]
The patient states that she was driving her vehicle at approximately 40 miles per hour .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
The patient had been treated conservatively in office for approximately 5 days , but symptoms progressed with the need of incision and drainage being decided .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-treatment", "O", "B-treatment", "O", "O", "O" ]
Y and a decision was made to proceed with preoperative chemotherapy .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-treatment", "I-treatment", "O" ]
Sometimes he has to throw the stacks a little bit as well .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
The patient was seen and evaluated at the emergency department at the time of incident and had baseline studies drawn , and has been followed by employee health for his injury .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
HISTORY OF PRESENT ILLNESS : This is a 52 - year - old native American - Indian man with hypertension , chronic intermittent bipedal edema , and recurrent leg venous ulcers , who was admitted on 01/27/09 for scheduled vascular surgery per Dr .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "O", "B-problem", "I-problem", "I-problem", "I-problem", "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "O", "O", "O", "O", "O", "O", "O", "B-treatment", "I-treatment", "I-treatment", "O", "O", "O" ]
HISTORY OF PRESENT ILLNESS : This is a 20 - year - old female who presented with symptoms of pneumonia and developed rapid sepsis and respiratory failure requiring intubation .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "O", "B-problem", "I-problem", "I-problem", "O", "B-problem", "I-problem", "O", "B-treatment", "O" ]
He went to notify EMS and when he returned , she was found to not be breathing .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
HISTORY OF PRESENT ILLNESS : The patient started the last 3 - 4 days to do poorly .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
1 .	[ "O", "O" ]
The patient has been doing well , seen in my office at the end of December for complete physical examination .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
She was able to express her husband ' s name and also recognize some family members , but she continued to be more somnolent when she was in the emergency department .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "O", "O", "O", "O", "O", "O", "O", "O" ]
Since discharge , the patient has complained of shortness of breath , mainly at night when lying flat , but otherwise he states he has been well and compliant with his medication .	[ "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
She eventually became unresponsive and paramedics were called .	[ "O", "O", "O", "B-problem", "O", "O", "O", "O", "O" ]
Two days post stereotactic core needle biopsy , however , the patient returned to the breast center with severe swelling and pain and mass in the left breast .	[ "O", "O", "O", "B-test", "I-test", "I-test", "I-test", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "O", "B-problem", "O", "B-problem", "I-problem", "I-problem", "I-problem", "I-problem", "O" ]
The patient states that he was attempting to do a blood gas .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-test", "I-test", "I-test", "O" ]
Multiple wound cultures have repeatedly grown Pseudomonas , Enterococcus , and Stenotrophomonas in the past .	[ "B-test", "I-test", "I-test", "O", "O", "O", "B-problem", "O", "B-problem", "O", "O", "B-problem", "O", "O", "O", "O" ]
At that time , physical exam showed a right TM , which was red .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "O" ]
Bleeding has been a problem ; however , it seems to have been abrogated at this time with factor replacement as well as platelet infusion .	[ "B-problem", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-treatment", "I-treatment", "O", "O", "O", "B-treatment", "I-treatment", "O" ]
This consultation was made for better control of his blood sugars .	[ "O", "O", "O", "O", "O", "O", "O", "O", "B-test", "I-test", "I-test", "O" ]
HISTORY OF PRESENT ILLNESS : The patient is a 29 - year - old female who is here today with the above - noted complaints .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
She does not believe that she could be pregnant .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
This resolved , however , recurred in both legs .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
The patient states that she also has some pain low in her abdomen that she believes is likely due to the steering wheel or deployment on the airbag .	[ "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "I-problem", "I-problem", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
Her boss asks her if she was actually on drugs in which she said no .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
He is cutting an eye tooth that causes him to be drooling and sometimes fussy .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "O", "O", "B-problem", "O" ]
It is mild in nature .	[ "O", "O", "O", "O", "O", "O" ]
She continues to have reflux , has noticed that if she stops taking Aciphex , then she has symptoms .	[ "O", "O", "O", "O", "B-problem", "O", "O", "O", "O", "O", "O", "O", "O", "B-treatment", "O", "O", "O", "O", "O", "O" ]
4 with a platelet count of 26 , 000 .	[ "O", "O", "B-test", "I-test", "I-test", "O", "O", "O", "O", "O" ]
The patient , subsequently , had a CBC repeated on the 10th at Hospital where her hemoglobin was 12 .	[ "O", "O", "O", "O", "O", "O", "B-test", "I-test", "O", "O", "O", "O", "O", "O", "O", "B-test", "I-test", "O", "O", "O" ]
She brought him to the emergency room this morning after a bad coughing spell .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "O" ]
If she takes her Aciphex , she seems that she has the reflux belching , burping , and heartburn under control .	[ "O", "O", "O", "B-treatment", "I-treatment", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "B-problem", "O", "B-problem", "O", "O", "B-problem", "O", "O", "O" ]
7 .	[ "O", "O" ]
5 .	[ "O", "O" ]
She has had a decreased oral intake and decreased wet diapers .	[ "O", "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "O", "B-problem", "I-problem", "I-problem", "O" ]
The parents also deny any vomiting , apnea .	[ "O", "O", "O", "O", "B-problem", "I-problem", "O", "B-problem", "O" ]
She has received methotrexate on a weekly basis as an outpatient for many years .	[ "O", "O", "O", "B-treatment", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O" ]
The patient denies any pain in her knees , ankles , or feet .	[ "O", "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "I-problem", "I-problem", "I-problem", "I-problem", "I-problem", "I-problem", "O" ]
The patient has not had any headache , nausea or vomiting .	[ "O", "O", "O", "O", "O", "B-problem", "I-problem", "O", "B-problem", "O", "B-problem", "O" ]
The patient was recently admitted to Hospital with lower extremity cellulitis .	[ "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "O" ]
She eventually underwent surgical resection on May 1 , 2008 with small area of residual disease , but otherwise clear margins .	[ "O", "O", "O", "B-treatment", "I-treatment", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "O", "O", "O", "O", "O", "O" ]
The patient states that her last menstrual cycle was at the end of May .	[ "O", "O", "O", "O", "B-test", "I-test", "I-test", "I-test", "O", "O", "O", "O", "O", "O", "O" ]
Upon my questioning of the patient , she can confirm that she has been sick to her stomach and has vomited .	[ "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "B-problem", "I-problem", "I-problem", "I-problem", "O", "O", "O", "O" ]

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