Closes #900 (version 2) (#904)

Merged and updated in hub

bigbio/hub/hub_repos/czi_drsm/README.md

@@ -4,7 +4,7 @@ language:
 bigbio_language:
   - English
 license: cc0-1.0
-bigbio_license_shortname: cc0-1.0
+bigbio_license_shortname: CC0_1p0
 multilinguality: monolingual
 pretty_name: CZI DRSM
 homepage: https://github.com/chanzuckerberg/DRSM-corpus
@@ -26,40 +26,49 @@ bigbio_tasks:
 Research Article document classification dataset based on aspects of disease research. Currently, the dataset consists of three subsets: 
 
 (A) classifies title/abstracts of papers into most popular subtypes of clinical, basic, and translational papers (~20k papers); 
-    - Clinical Characteristics, Disease Pathology, and Diagnosis - 
-        Text that describes (A) symptoms, signs, or ‘phenotype’ of a disease; 
-        (B) the effects of the disease on patient organs, tissues, or cells; 
-        (C) the results of clinical tests that reveal pathology (including
-        biomarkers); (D) research that use this information to figure out
+
+    - Clinical Characteristics, Disease Pathology, and Diagnosis:
+        Text that describes (i) symptoms, signs, or ‘phenotype’ of a disease; 
+        (ii) the effects of the disease on patient organs, tissues, or cells; 
+        (iii)) the results of clinical tests that reveal pathology (including
+        biomarkers); (iv) research that use this information to figure out
         a diagnosis.
-    - Therapeutics in the clinic - 
+
+    - Therapeutics in the clinic: 
         Text describing how treatments work in the clinic (but not in a clinical trial).
-    - Disease mechanism - 
-        Text that describes either (A) mechanistic involvement of specific genes in disease 
-        (deletions, gain of function, etc); (B) how molecular signalling or metabolism 
-        binding, activating, phosphorylation, concentration increase, etc.) 
-        are involved in the mechanism of a disease; or (C) the physiological 
-        mechanism of disease at the level of tissues, organs, and body systems.
-    - Patient-Based Therapeutics - 
-        Text describing (A) Clinical trials (studies of therapeutic measures being 
-        used on patients in a clinical trial); (B) Post Marketing Drug Surveillance 
+
+    - Disease mechanism: 
+
+    - Patient-Based Therapeutics: 
+        Text describing (i) Clinical trials (studies of therapeutic measures being 
+        used on patients in a clinical trial); (ii) Post Marketing Drug Surveillance 
         (effects of a drug after approval in the general population or as part of 
-        ‘standard healthcare’); (C) Drug repurposing (how a drug that has been 
+        ‘standard healthcare’); (iii) Drug repurposing (how a drug that has been 
         approved for one use is being applied to a new disease).
 
 (B) identifies whether a title/abstract of a paper describes substantive research into Quality of Life (~10k papers); 
-    - -1 - the paper is not a primary experimental study in rare disease
-    - 0 - the study does not directly investigate quality of life
-    - 1 - the study investigates qol but not as its primary contribution
-    - 2 - the study's primary contribution centers on quality of life measures
+
+    - [-1] - the paper is not a primary experimental study in rare disease
+
+    - [0] - the study does not directly investigate quality of life
+
+    - [1] - the study investigates qol but not as its primary contribution
+
+    - [2] - the study's primary contribution centers on quality of life measures
 
 (C) identifies if a paper is a natural history study (~10k papers). 
-   - -1 - the paper is not a primary experimental study in rare disease
-    - 0 - the study is not directly investigating the natural history of a disease
-    - 1 - the study includes some elements a natural history but not as its primary contribution
-    - 2 - the study's primary contribution centers on observing the time course of a rare disease
+
+   - [-1] - the paper is not a primary experimental study in rare disease
+
+    - [0] - the study is not directly investigating the natural history of a disease
+
+    - [1] - the study includes some elements a natural history but not as its primary contribution
+
+    - [2] - the study's primary contribution centers on observing the time course of a rare disease
 
-These classifications are particularly relevant in rare disease research, a field that is generally understudied.
+These classifications are particularly relevant in rare disease research, a field that is generally understudied. 
+
+This data was compiled through the use of a gamified curation approach based on CentaurLabs' 'diagnos.us' platform.
 
 ## Citation Information
 

bigbio/hub/hub_repos/czi_drsm/czi_drsm.py

@@ -60,12 +60,9 @@
 import pandas as pd
 from pathlib import Path
 
-from .bigbiohub import text_features, BigBioConfig, Tasks
-
-#from .bigbiohub import BigBioConfig
-#from .bigbiohub import Tasks
-
-#from .bigbiohub import
+from .bigbiohub import text_features
+from .bigbiohub import BigBioConfig
+from .bigbiohub import Tasks
 
 _LOCAL = False
 
@@ -89,6 +86,7 @@
 Research Article document classification dataset based on aspects of disease research. Currently, the dataset consists of three subsets: 
 
 (A) classifies title/abstracts of papers into most popular subtypes of clinical, basic, and translational papers (~20k papers); 
+
     - Clinical Characteristics, Disease Pathology, and Diagnosis - 
         Text that describes (A) symptoms, signs, or ‘phenotype’ of a disease; 
         (B) the effects of the disease on patient organs, tissues, or cells; 
@@ -111,13 +109,15 @@
         approved for one use is being applied to a new disease).
 
 (B) identifies whether a title/abstract of a paper describes substantive research into Quality of Life (~10k papers); 
+    
     - -1 - the paper is not a primary experimental study in rare disease
     - 0 - the study does not directly investigate quality of life
     - 1 - the study investigates qol but not as its primary contribution
     - 2 - the study's primary contribution centers on quality of life measures
 
 (C) identifies if a paper is a natural history study (~10k papers). 
-`   - -1 - the paper is not a primary experimental study in rare disease
+`   
+    - -1 - the paper is not a primary experimental study in rare disease
     - 0 - the study is not directly investigating the natural history of a disease
     - 1 - the study includes some elements a natural history but not as its primary contribution
     - 2 - the study's primary contribution centers on observing the time course of a rare disease
@@ -126,7 +126,7 @@
 """
 
 _HOMEPAGE = "https://github.com/chanzuckerberg/DRSM-corpus/"
-_LICENSE = "CC0_1p0"
+_LICENSE = 'CC0_1p0'
 
 _LANGUAGES = ['English']
 _PUBMED = False
@@ -143,7 +143,7 @@
     'nhs': "https://raw.githubusercontent.com/chanzuckerberg/DRSM-corpus/main/v2/nhs_all_2023_03_31.tsv"
 }
 
-_SUPPORTED_TASKS = [Tasks.TEXT_CLASSIFICATION]
+_SUPPORTED_TASKS = [Tasks.TEXT_CLASSIFICATION]  
 
 _SOURCE_VERSION = "1.0.0"
 _BIGBIO_VERSION = "1.0.0"