Update README.md

README.md

@@ -35,50 +35,41 @@ English (en).
 
 ## Dataset Structure
 
-### PMC-Paitents.json
+The PMC-Patients ReCDS benchmark is presented as retrieval tasks and the data format is the same as [BEIR](https://github.com/beir-cellar/beir) benchmark. 
+To be specific, there are queries, corpus, and qrels (annotations).
 
-This file contains all information about patients summaries in PMC-Patients, which is a list of dict with keys:
+### Queries
 
-- `patient_id`: string. A continuous id of patients, starting from 0.
-- `patient_uid`: string. Unique ID for each patient, with format PMID-x, where PMID is the PubMed Identifier of the source article of the patient and x denotes index of the patient in source article.
-- `PMID`: string. PMID for source article.
-- `file_path`: string. File path of xml file of source article.
-- `title`: string. Source article title.
-- `patient`: string. Patient summary.
-- `age`: list of tuples. Each entry is in format `(value, unit)` where value is a float number and unit is in 'year', 'month', 'week', 'day' and 'hour' indicating age unit. For example, `[[1.0, 'year'], [2.0, 'month']]` indicating the patient is a one-year- and two-month-old infant.
-- `gender`: 'M' or 'F'. Male or Female.
+ReCDS-PAR and ReCDS-PPR tasks share the same query patient set and dataset split.
+For each split (train, dev, and test), queries are stored a `jsonl` file that contains a list of dictionaries, each with two fields: 
+- `_id`: unique query identifier represented by patient_uid.
+- `text`: query text represented by patient summary text.
 
-### PAR & PPR Datasets
+### Corpus
 
-We present data of the two retrieval tasks in exactly the same format as [BEIR](https://github.com/beir-cellar/beir/wiki/Load-your-custom-dataset). we refer the readers to their wiki page for the data format.
+Corpus is shared by different splits. For ReCDS-PAR, the corpus contains 11.7M PubMed articles, and for ReCDS-PPR, the corpus contains 155.2k reference patients from PMC-Patients. The corpus is also presented by a `jsonl` file that contains a list of dictionaries with three fields:
+- `_id`:  unique document identifier represented by PMID of the PubMed article in ReCDS-PAR, and patient_uid of the candidate patient in ReCDS-PPR.
+- `title`: : title of the article in ReCDS-PAR, and empty string in ReCDS-PPR.
+- `text`: abstract of the article in ReCDS-PAR, and patient summary text in ReCDS-PPR.
 
-The PAR and PPR tasks share queries and query splits. The `_id` field for queries and PPR corpus is `patient_uid` in PMC-Patients, and the `_id` for PAR corpus is the PMID of the article.
+### Qrels
+
+Qrels are TREC-style retrieval annotation files in `tsv` format.
+A qrels file contains three tab-separated columns, i.e. the query identifier, corpus identifier, and score in this order. The scores (2 or 1) indicate the relevance level in ReCDS-PAR or similarity level in ReCDS-PPR.
+
+Note that the qrels may not be the same as `relevant_articles` and `similar_patients` in `PMC-Patients.json` due to dataset split (see our manuscript for details).
 
 ### Data Instances
 
-**A sample of patient in PMC-Patients.json**
-{
-  "patient_id": "0",
-  "patient_uid": "7665777-1",
-  "PMID": "33492400",
-  "file_path": "comm/PMC007xxxxxx/PMC7665777.xml",
-  "title": "Early Physical Therapist Interventions for Patients With COVID-19 in the Acute Care Hospital: A Case Report Series",
-  "patient": "This 60-year-old male was hospitalized due to moderate ARDS from COVID-19 with symptoms of fever, dry cough, and dyspnea. We encountered several difficulties during physical therapy on the acute ward. First, any change of position or deep breathing triggered coughing attacks that induced oxygen desaturation and dyspnea. To avoid rapid deterioration and respiratory failure, we instructed and performed position changes very slowly and step-by-step. In this way, a position change to the 135\u00b0 prone position () took around 30 minutes. This approach was well tolerated and increased oxygen saturation, for example, on day 5 with 6 L/min of oxygen from 93% to 97%. Second, we had to adapt the breathing exercises to avoid prolonged coughing and oxygen desaturation. Accordingly, we instructed the patient to stop every deep breath before the need to cough and to hold inspiration for better air distribution. In this manner, the patient performed the breathing exercises well and managed to increase his oxygen saturation. Third, the patient had difficulty maintaining sufficient oxygen saturation during physical activity. However, with close monitoring and frequent breaks, he managed to perform strength and walking exercises at a low level without any significant deoxygenation. Exercise progression was low on days 1 to 5, but then increased daily until hospital discharge to a rehabilitation clinic on day 10.",
-  "age": [
-      [
-          60.0,
-          "year"
-      ]
-  ],
-  "gender": "M"
-}
 
 **A sample of query**
 {"_id": "8699387-1", "text": "A 60-year-old female patient with a medical history of hypertension came to our attention because of several neurological deficits that had developed over the last few years, significantly impairing her daily life. Four years earlier, she developed sudden weakness and hypoesthesia of the right hand. The symptoms resolved in a few days and no specific diagnostic tests were performed. Two months later, she developed hypoesthesia and weakness of the right lower limb. On neurological examination at the time, she had spastic gait, ataxia, slight pronation of the right upper limb and bilateral Babinski sign. Brain MRI showed extensive white matter hyperintensities (WMHs), so leukodystrophy was suspected. However, these WMHs were located bilaterally in the corona radiata, basal ganglia, the anterior part of the temporal lobes and the medium cerebellar peduncle (A–D), and were highly suggestive of CADASIL. Genetic testing was performed, showing heterozygous mutation of the NOTCH3 gene (c.994 C<T; exon 6). The diagnosis of CADASIL was confirmed and antiplatelet prevention therapy was started. Since then, her clinical conditions remained stable, and the lesion load was unchanged at follow-up brain MRIs for 4 years until November 2020, when the patient was diagnosed with COVID-19 after a PCR nasal swab. The patient developed only mild respiratory symptoms, not requiring hospitalization or any specific treatment. Fifteen days after the COVID-19 diagnosis, she suddenly developed aphasia, agraphia and worsened right upper limb motor deficit, but she did not seek medical attention. Some days later, she reported these symptoms to her family medical doctor, and a new brain MRI was performed, showing a subacute ischemic area in the left corona radiata (E,F). Therapy with acetylsalicylic acid was switched to clopidogrel as secondary prevention, while her symptoms improved in the next few weeks. The patient underwent a carotid doppler ultrasound and an echocardiogram, which did not reveal any pathological changes. The review of the blood pressure log, both in-hospital and the personal one the patient had kept, excluded uncontrolled hypertension."}
 
 **A sample of qrels**
 query-id	corpus-id	score
+
 8647806-1	6437752-1	1
+
 8647806-1	6946242-1	1