Initial commit from biomedical workshop

bioasq_task_b.py

@@ -0,0 +1,596 @@
+# coding=utf-8
+# Copyright 2022 The HuggingFace Datasets Authors and the current dataset script contributor.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+BioASQ Task B On Biomedical Semantic QA (Involves IR, QA, Summarization qnd
+More). This task uses benchmark datasets containing development and test
+questions, in English, along with gold standard (reference) answers constructed
+by a team of biomedical experts. The participants have to respond with relevant
+concepts, articles, snippets and RDF triples, from designated resources, as well
+as exact and 'ideal' answers.
+
+Fore more information about the challenge, the organisers and the relevant
+publications please visit: http://bioasq.org/
+"""
+import glob
+import json
+import os
+import re
+
+import datasets
+from utils import schemas
+from utils.configs import BigBioConfig
+from utils.constants import Tasks
+
+_CITATION = """\
+@article{tsatsaronis2015overview,
+	title        = {
+		An overview of the BIOASQ large-scale biomedical semantic indexing and
+		question answering competition
+	},
+	author       = {
+		Tsatsaronis, George and Balikas, Georgios and Malakasiotis, Prodromos
+        and Partalas, Ioannis and Zschunke, Matthias and Alvers, Michael R and
+		Weissenborn, Dirk and Krithara, Anastasia and Petridis, Sergios and
+		Polychronopoulos, Dimitris and others
+	},
+	year         = 2015,
+	journal      = {BMC bioinformatics},
+	publisher    = {BioMed Central Ltd},
+	volume       = 16,
+	number       = 1,
+	pages        = 138
+}
+"""
+
+_DATASETNAME = "bioasq"
+
+_BIOASQ_10B_DESCRIPTION = """\
+The data are intended to be used as training and development data for BioASQ
+10, which will take place during 2022. There is one file containing the data:
+ - training10b.json
+
+The file contains the data of the first nine editions of the challenge: 4234
+questions [1] with their relevant documents, snippets, concepts and RDF
+triples, exact and ideal answers.
+
+Differences with BioASQ-training9b.json
+- 492 new questions added from BioASQ9
+    - The question with id 56c1f01eef6e394741000046 had identical body with
+    602498cb1cb411341a00009e. All relevant elements from both questions
+    are available in the merged question with id 602498cb1cb411341a00009e.
+    - The question with id 5c7039207c78d69471000065 had identical body with
+    601c317a1cb411341a000014. All relevant elements from both questions
+    are available in the merged question with id 601c317a1cb411341a000014.
+	- The question with id 5e4b540b6d0a27794100001c had identical body with
+    602828b11cb411341a0000fc. All relevant elements from both questions
+    are available in the merged question with id 602828b11cb411341a0000fc.
+    - The question with id 5fdb42fba43ad31278000027 had identical body with
+    5d35eb01b3a638076300000f. All relevant elements from both questions
+    are available in the merged question with id 5d35eb01b3a638076300000f.
+    - The question with id 601d76311cb411341a000045 had identical body with
+    6060732b94d57fd87900003d. All relevant elements from both questions
+    are available in the merged question with id 6060732b94d57fd87900003d.
+
+[1] 4234 questions : 1252 factoid, 1148 yesno, 1018 summary, 816 list
+"""
+
+_BIOASQ_9B_DESCRIPTION = """\
+The data are intended to be used as training and development data for BioASQ 9,
+which will take place during 2021. There is one file containing the data:
+ - training9b.json
+
+The file contains the data of the first seven editions of the challenge: 3742
+questions [1] with their relevant documents, snippets, concepts and RDF triples,
+exact and ideal answers.
+
+Differences with BioASQ-training8b.json
+- 499 new questions added from BioASQ8
+    - The question with id 5e30e689fbd6abf43b00003a had identical body with
+    5880e417713cbdfd3d000001. All relevant elements from both questions
+    are available in the merged question with id 5880e417713cbdfd3d000001.
+
+[1] 3742 questions : 1091 factoid, 1033 yesno, 899 summary, 719 list
+"""
+
+_BIOASQ_8B_DESCRIPTION = """\
+The data are intended to be used as training and development data for BioASQ 8,
+which will take place during 2020. There is one file containing the data:
+ - training8b.json
+
+The file contains the data of the first seven editions of the challenge: 3243
+questions [1] with their relevant documents, snippets, concepts and RDF triples,
+exact and ideal answers.
+
+Differences with BioASQ-training7b.json
+- 500 new questions added from BioASQ7
+- 4 questions were removed
+    - The question with id 5717fb557de986d80d000009 had identical body with
+    571e06447de986d80d000016. All relevant elements from both questions
+    are available in the merged question with id 571e06447de986d80d000016.
+    - The question with id 5c589ddb86df2b917400000b had identical body with
+    5c6b7a9e7c78d69471000029. All relevant elements from both questions
+    are available in the merged question with id 5c6b7a9e7c78d69471000029.
+    - The question with id 52ffb5d12059c6d71c00007c had identical body with
+    52e7870a98d023950500001a. All relevant elements from both questions
+    are available in the merged question with id 52e7870a98d023950500001a.
+    - The question with id 53359338d6d3ac6a3400004f had identical body with
+    589a246878275d0c4a000030. All relevant elements from both questions
+    are available in the merged question with id 589a246878275d0c4a000030.
+
+**** UPDATE 25/02/2020 *****
+The previous version of the dataset contained an inconsistency on question with
+id "5c9904eaecadf2e73f00002e", where the "ideal_answer" field was missing.
+This has been fixed.
+"""
+
+_BIOASQ_7B_DESCRIPTION = """\
+The data are intended to be used as training and development data for BioASQ 7,
+which will take place during 2019. There is one file containing the data:
+ - BioASQ-trainingDataset7b.json
+
+The file contains the data of the first six editions of the challenge: 2747
+questions [1] with their relevant documents, snippets, concepts and RDF triples,
+exact and ideal answers.
+
+Differences with BioASQ-trainingDataset6b.json
+- 500 new questions added from BioASQ6
+    - 4 questions were removed
+        - The question with id 569ed752ceceede94d000004 had identical body with
+        a new question from BioASQ6. All relevant elements from both questions
+        are available in the merged question with id 5abd31e0fcf456587200002c
+        - 3 questions were removed as incomplete: 54d643023706e89528000007,
+        532819afd6d3ac6a3400000f, 517545168ed59a060a00002b
+    - 4 questions were revised for various confusions that have been identified
+        - In 2 questions the ideal answer has been revised :
+        51406e6223fec90375000009, 5172f8118ed59a060a000019
+        - In 4 questions the snippets and documents list has been revised :
+        51406e6223fec90375000009, 5172f8118ed59a060a000019,
+        51593dc8d24251bc05000099, 5158a5b8d24251bc05000097
+        - In 198 questions the documents list has updated with missing
+        documents from the relevant snippets list. [2]
+
+[1] 2747 questions : 779 factoid, 745 yesno, 667 summary, 556 list
+[2] 55031181e9bde69634000014, 51406e6223fec90375000009, 54d643023706e89528000007,
+    52bf1b0a03868f1b06000009, 52bf19c503868f1b06000001, 51593dc8d24251bc05000099,
+    530a5117970c65fa6b000007, 553a8d78f321868558000003, 531a3fe3b166e2b806000038,
+    532819afd6d3ac6a3400000f, 5158a5b8d24251bc05000097, 553653a5bc4f83e828000007,
+    535d2cf09a4572de6f000004, 53386282d6d3ac6a3400005a, 517a8ce98ed59a060a000045,
+    55391ce8bc4f83e828000018, 5547d700f35db75526000007, 5713bf261174fb1755000011,
+    6f15c5a2ac5ed1459000012, 52b2e498f828ad283c000010, 570a7594cf1c325851000026,
+    530cefaaad0bf1360c000012, 530f685c329f5fcf1e000002, 550c4011a103b78016000009,
+    552faababc4f83e828000005, 54cf48acf693c3b16b00000b, 550313aae9bde6963400001f,
+    551177626a8cde6b72000005, 54eded8c94afd6150400000c, 550c3754a103b78016000007,
+    56f555b609dd18d46b000007, 54c26e29f693c3b16b000003, 54da0c524b1fd0d33c00000b,
+    52bf1d3c03868f1b0600000d, 5343bdd6aeec6fbd07000001, 52cb9b9b03868f1b0600002d,
+    55423875ec76f5e50c000002, 571366ba1174fb1755000005, 56c4d14ab04e159d0e000003,
+    550c44d1a103b7801600000a, 5547a01cf35db75526000005, 55422640ccca0ce74b000004,
+    54ecb66d445c3b5a5f000002, 553656c4bc4f83e828000009, 5172f8118ed59a060a000019,
+    513711055274a5fb0700000e, 54d892ee014675820d000005, 52e6c92598d0239505000019,
+    5353aedb288f4dae47000006, 52bf1f1303868f1b06000014, 5519113b622b19434500000f,
+    52b2f1724003448f5500000b, 5525317687ecba3764000007, 554a0cadf35db7552600000f,
+    55152bd246478f2f2c000002, 516c3960298dcd4e51000073, 571e417bbb137a4b0c00000a,
+    551910d3622b194345000008, 54dc8ed6c0bb8dce23000002, 511a4ec01159fa8212000004,
+    54d8ea2c4b1fd0d33c000002, 5148e1d6d24251bc0500003a, 515dbb3b298dcd4e51000018,
+    56f7c15a09dd18d46b000012, 51475d5cd24251bc0500001b, 54db7c4ac0bb8dce23000001,
+    57152ebbcb4ef8864c000002, 57134d511174fb1755000002, 55149f156a8cde6b72000013,
+    56bcd422d36b5da378000005, 54ede5c394afd61504000006, 517545168ed59a060a00002b,
+    5710ed19a5ed216440000003, 53442472aeec6fbd07000008, 55088e412e93f0133a000001,
+    54d762653706e89528000014, 550aef0ec2af5d5b7000000a, 552435602c8b63434a000009,
+    552446612c8b63434a00000c, 54d901ec4b1fd0d33c000006, 54cf45e7f693c3b16b00000a,
+    52fc8b772059c6d71c00006e, 5314d05adae131f84700000d, 5512c91b6a8cde6b7200000b,
+    56c5a7605795f9a73e000002, 55030a6ce9bde6963400000f, 553fac39c6a5098552000001,
+    531a3a58b166e2b806000037, 5509bd6a1180f13250000002, 54f9c40ddd3fc62544000001,
+    553c8fd1f32186855800000a, 56bce51cd36b5da37800000a, 550316a6e9bde69634000029,
+    55031286e9bde6963400001b, 536e46f27d100faa09000012, 5502abd1e9bde69634000008,
+    551af9106b348bb82c000002, 54edeb4394afd6150400000b, 5717cdd2070aa3d072000001,
+    56c5ade15795f9a73e000003, 531464a6e3eabad021000014, 58a0d87a78275d0c4a000053,
+    58a3160d60087bc10a00000a, 58a5d54860087bc10a000025, 58a0da5278275d0c4a000054,
+    58a3264e60087bc10a00000d, 589c8ef878275d0c4a000042, 58a3428d60087bc10a00001b,
+    58a3196360087bc10a00000b, 58a341eb60087bc10a000018, 58a3275960087bc10a00000f,
+    58a342e760087bc10a00001c, 58bd645702b8c60953000010, 58bc8e5002b8c60953000006,
+    58bc8e7a02b8c60953000007, 58a1da4e78275d0c4a000059, 58bcb83d02b8c6095300000f,
+    58bc9a5002b8c60953000008, 589dee3778275d0c4a000050, 58a32efe60087bc10a000013,
+    58a327bf60087bc10a000011, 58bca08702b8c6095300000a, 58bc9dbb02b8c60953000009,
+    58c99fcc02b8c60953000029, 58bca2f302b8c6095300000c, 58cbf1f402b8c60953000036,
+    58cdb41302b8c60953000042, 58cdb80302b8c60953000043, 58cdbaf302b8c60953000044,
+    58cb305c02b8c60953000032, 58caf86f02b8c60953000030, 58c1b2f702b8c6095300001e,
+    58bde18b02b8c60953000014, 58eb7898eda5a57672000006, 58caf88c02b8c60953000031,
+    58e11bf76fddd3e83e00000c, 58cdbbd102b8c60953000045, 58df779d6fddd3e83e000001,
+    58dbb4f08acda3452900001a, 58dbb8968acda3452900001b, 58add7699ef3c34033000009,
+    58dbbbf08acda3452900001d, 58dbba438acda3452900001c, 58dd2cb08acda34529000029,
+    58eb9542eda5a57672000007, 58f3ca5c70f9fc6f0f00000d, 58e9e7aa3e8b6dc87c00000d,
+    58e3d9ab3e8b6dc87c000002, 58eb4ce7eda5a57672000004, 58f3c8f470f9fc6f0f00000c,
+    58f3c62970f9fc6f0f00000b, 58adca6d9ef3c34033000007, 58f4b3ee70f9fc6f0f000013,
+    593ff22b70f9fc6f0f000023, 5a679875b750ff4455000004, 5a774585faa1ab7d2e000005,
+    5a6f7245b750ff4455000050, 5a787544faa1ab7d2e00000b, 5a74d9980384be9551000008,
+    5a6a02a3b750ff4455000021, 5a6e47b1b750ff4455000049, 5a87124561bb38fb24000001,
+    5a6e42f1b750ff4455000046, 5a8b1264fcd1d6a10c00001d, 5a981e66fcd1d6a10c00002f,
+    5a8718c861bb38fb24000008, 5a7615af83b0d9ea6600001f, 5a87140a61bb38fb24000003,
+    5a77072c9e632bc06600000a, 5a897601fcd1d6a10c000008, 5a871a6861bb38fb24000009,
+    5a74e9ad0384be955100000a, 5a79d25dfaa1ab7d2e00000f, 5a6900ebb750ff445500001d,
+    5a87145861bb38fb24000004, 5a871b8d61bb38fb2400000a, 5a897a06fcd1d6a10c00000b,
+    5a8dc6b4fcd1d6a10c000026, 5a8712af61bb38fb24000002, 5a8714e261bb38fb24000005,
+    5aa304f1d6d6b54f79000004, 5a981bcffcd1d6a10c00002d, 5aa3fa73d6d6b54f79000008,
+    5aa55b45d6d6b54f7900000d, 5a981dd0fcd1d6a10c00002e, 5a9700adfcd1d6a10c00002c,
+    5a9d8ffe1d1251d03b000022, 5a96c74cfcd1d6a10c000029, 5aa50086d6d6b54f7900000c,
+    5a95765bfcd1d6a10c000028, 5a96f40cfcd1d6a10c00002b, 5ab144fefcf4565872000012,
+    5aa67b4fd6d6b54f7900000f, 5abd5a62fcf4565872000031, 5abbe429fcf456587200001c,
+    5aaef38dfcf456587200000f, 5abce6acfcf4565872000022, 5aae6499fcf456587200000c
+"""
+
+_BIOASQ_6B_DESCRIPTION = """\
+The data are intended to be used as training and development data for BioASQ 6,
+which will take place during 2018. There is one file containing the data:
+ - BioASQ-trainingDataset6b.json
+
+Differences with BioASQ-trainingDataset5b.json
+- 500 new questions added from BioASQ5
+    - 48 pairs of questions with identical bodies have been merged into one
+    question having only one question-id, but all the documents, snippets,
+    concepts, RDF triples and answers of both questions of the pair.
+        - This normalization lead to the removal of 48 deprecated question
+        ids [2] from the dataset and to the update of the 48 remaining
+        questions [3].
+        - In cases where a pair of questions with identical bodies had some
+        inconsistency (e.g. different question type), the inconsistency has
+        been solved merging the pair manually consulting the BioASQ expert team.
+    - 12 questions were revised for various confusions that have been
+    identified
+        - In 8 questions the question type has been changed to better suit to
+        the question body. The change of type lead to corresponding changes
+        in exact answers existence and format : 54fc4e2e6ea36a810c000003,
+        530b01a6970c65fa6b000008, 530cf54dab4de4de0c000009,
+        531b2fc3b166e2b80600003c, 532819afd6d3ac6a3400000f,
+        532aad53d6d3ac6a34000010, 5710ade4cf1c32585100002c,
+        52f65f372059c6d71c000027
+		- In 6 questions the ideal answer has been revised :
+        532aad53d6d3ac6a34000010, 5710ade4cf1c32585100002c,
+        53147b52e3eabad021000015, 5147c8a6d24251bc05000027,
+        5509bd6a1180f13250000002, 58bbb71f22d3005309000016
+		- In 5 questions the exact answer has been revised :
+        5314bd7ddae131f847000006, 53130a77e3eabad02100000f,
+        53148a07dae131f847000002, 53147b52e3eabad021000015,
+        5147c8a6d24251bc05000027
+		- In 2 questions the question body has been revised :
+        52f65f372059c6d71c000027, 5503145ee9bde69634000022
+    - In lists of ideal answers, documents, snippets, concepts and RDF triples
+    any duplicate identical elements have been removed.
+    - Ideal answers in format of one string have been converted to a list with
+    one element for consistency with cases where more than one golden ideal
+    answers are available. (i.e. "ideal_ans1" converted to ["ideal_ans1"])
+    - For yesno questions: All exact answers have been normalized to "yes" or
+    "no" (replacing "Yes", "YES" and "No")
+    - For factoid questions: The format of the exact answer was normalized to a
+    list of strings for each question, representing a set of synonyms
+    answering the question (i.e. [`ans1`, `syn11`, ... ]).
+    - For list questions: The format of the exact answer was normalized to a
+    list of lists. Each internal list represents one element of the answer
+    as a set of synonyms
+    (i.e. [[`ans1`, `syn11`, `syn12`], [`ans2`], [`ans3`, `syn31`] ...]).
+    - Empty elements, e.g. empty lists of documents have been removed.
+
+[1] 2251 questions : 619 factoid, 616 yesno, 531 summary, 485 list
+[2] The 48 deprecated question ids are : 52f8b2902059c6d71c000053,
+    52f11bf22059c6d71c000005, 52f77edb2059c6d71c000028, 52ed795098d0239505000032,
+    56d1a9baab2fed4a47000002, 52f7d3472059c6d71c00002f, 52fbe2bf2059c6d71c00006c,
+    52ec961098d023950500002a, 52e8e98298d0239505000020, 56cae5125795f9a73e000024,
+    530cefaaad0bf1360c000007, 530cefaaad0bf1360c000005, 52d63b2803868f1b0600003a,
+    530cefaaad0bf1360c00000a, 516425ff298dcd4e51000051, 55191149622b194345000010,
+    52fa70142059c6d71c000056, 52f77f4d2059c6d71c00002a, 52efc016c8da89891000001a,
+    52efc001c8da898910000019, 52f896ae2059c6d71c000045, 52eceada98d023950500002d,
+    52efc05cc8da89891000001c, 515e078e298dcd4e51000031, 52fe54252059c6d71c000079,
+    514217a6d24251bc05000005, 52d1389303868f1b06000032, 530cf4d5e2bfff940c000003,
+    52fc946d2059c6d71c000071, 52e8e99e98d0239505000021, 52ef7786c8da898910000015,
+    52d8494698d0239505000007, 530cf51d5610acba0c000001, 52f637972059c6d71c000025,
+    52e9f99798d0239505000025, 515de572298dcd4e51000021, 52fe4ad52059c6d71c000077,
+    52f65bf02059c6d71c000026, 52e8e9d298d0239505000022, 52fa74052059c6d71c00005a,
+    52ffbddf2059c6d71c00007d, 56bc932aac7ad1001900001c, 56c02883ef6e394741000017,
+    52d2b75403868f1b06000035, 52f118aa2059c6d71c000003, 52e929eb98d0239505000023,
+    532c12f2d6d3ac6a3400001d, 52d8466298d0239505000006'
+[3] The 48 questions resulting from merging with their pair have the
+    following ids: 5149aafcd24251bc05000045, 515db020298dcd4e51000011,
+    515db54c298dcd4e51000016, 51680a49298dcd4e51000062, 52b06a68f828ad283c000005,
+    52bf1aa503868f1b06000006, 52bf1af803868f1b06000008, 52bf1d6003868f1b0600000e,
+    52cb9b9b03868f1b0600002d, 52d2818403868f1b06000033, 52df887498d023950500000c,
+    52e0c9a298d0239505000010, 52e203bc98d0239505000011, 52e62bae98d0239505000015,
+    52e6c92598d0239505000019, 52e7bbf698d023950500001d, 52ea605098d0239505000028,
+    52ece29f98d023950500002c, 52ecf2dd98d023950500002e, 52ef7754c8da898910000014,
+    52f112bb2059c6d71c000002, 52f65f372059c6d71c000027, 52f77f752059c6d71c00002b,
+    52f77f892059c6d71c00002c, 52f89ee42059c6d71c00004d, 52f89f4f2059c6d71c00004e,
+    52f89fba2059c6d71c00004f, 52f89fc62059c6d71c000050, 52f89fd32059c6d71c000051,
+    52fa6ac72059c6d71c000055, 52fa73c62059c6d71c000058, 52fa73e82059c6d71c000059,
+    52fa74252059c6d71c00005b, 52fc8b772059c6d71c00006e, 52fc94572059c6d71c000070,
+    52fc94ae2059c6d71c000073, 52fc94db2059c6d71c000074, 52fe52702059c6d71c000078,
+    52fe58f82059c6d71c00007a, 530cefaaad0bf1360c000008, 530cefaaad0bf1360c000010,
+    533ba218fd9a95ea0d000007, 534bb147aeec6fbd07000014, 55167dec46478f2f2c00000a,
+    56c04412ef6e39474100001b, 56c1f01eef6e394741000046, 56c81fd15795f9a73e00000c,
+    587d016ed673c3eb14000002
+"""
+
+_BIOASQ_5B_DESCRIPTION = """\
+The data are intended to be used as training and development data for BioASQ 5,
+which will take place during 2017. There is one file containing the data:
+ - BioASQ-trainingDataset5b.json
+
+The file contains the data of the first four editions of the challenge: 1799
+questions with their relevant documents, snippets, concepts and rdf triples,
+exact and ideal answers.
+"""
+
+_BIOASQ_4B_DESCRIPTION = """\
+The data are intended to be used as training and development data for BioASQ 4,
+which will take place during 2016. There is one file containing the data:
+ - BioASQ-trainingDataset4b.json
+
+The file contains the data of the first three editions of the challenge: 1307
+questions with their relevant documents, snippets, concepts and rdf triples,
+exact and ideal answers from the first two editions and 497 questions with
+similar annotations from the third editions of the challenge.
+"""
+
+_BIOASQ_3B_DESCRIPTION = """No README provided."""
+
+_BIOASQ_2B_DESCRIPTION = """No README provided."""
+
+_DESCRIPTION = {
+    "bioasq_10b": _BIOASQ_10B_DESCRIPTION,
+    "bioasq_9b": _BIOASQ_9B_DESCRIPTION,
+    "bioasq_8b": _BIOASQ_8B_DESCRIPTION,
+    "bioasq_7b": _BIOASQ_7B_DESCRIPTION,
+    "bioasq_6b": _BIOASQ_6B_DESCRIPTION,
+    "bioasq_5b": _BIOASQ_5B_DESCRIPTION,
+    "bioasq_4b": _BIOASQ_4B_DESCRIPTION,
+    "bioasq_3b": _BIOASQ_3B_DESCRIPTION,
+    "bioasq_2b": _BIOASQ_2B_DESCRIPTION,
+}
+
+_HOMEPAGE = "http://participants-area.bioasq.org/datasets/"
+
+# Data access reqires registering with BioASQ.
+# See http://participants-area.bioasq.org/accounts/register/
+_LICENSE = "https://www.nlm.nih.gov/databases/download/terms_and_conditions.html"
+
+_URLs = {
+    "bioasq_10b": ["BioASQ-training10b.zip", None],
+    "bioasq_9b": ["BioASQ-training9b.zip", "Task9BGoldenEnriched.zip"],
+    "bioasq_8b": ["BioASQ-training8b.zip", "Task8BGoldenEnriched.zip"],
+    "bioasq_7b": ["BioASQ-training7b.zip", "Task7BGoldenEnriched.zip"],
+    "bioasq_6b": ["BioASQ-training6b.zip", "Task6BGoldenEnriched.zip"],
+    "bioasq_5b": ["BioASQ-training5b.zip", "Task5BGoldenEnriched.zip"],
+    "bioasq_4b": ["BioASQ-training4b.zip", "Task4BGoldenEnriched.zip"],
+    "bioasq_3b": ["BioASQ-trainingDataset3b.zip", "Task3BGoldenEnriched.zip"],
+    "bioasq_2b": ["BioASQ-trainingDataset2b.zip", "Task2BGoldenEnriched.zip"],
+}
+
+_SUPPORTED_TASKS = [Tasks.QUESTION_ANSWERING]
+_SOURCE_VERSION = "1.0.0"
+_BIGBIO_VERSION = "1.0.0"
+
+
+class BioasqTaskBDataset(datasets.GeneratorBasedBuilder):
+    """
+    BioASQ Task B On Biomedical Semantic QA.
+    Creates configs for BioASQ2 through BioASQ10.
+    """
+
+    DEFAULT_CONFIG_NAME = "bioasq_9b_source"
+    SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
+    BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)
+
+    # BioASQ2 through BioASQ10
+    BUILDER_CONFIGS = []
+    for version in range(2, 11):
+        BUILDER_CONFIGS.append(
+            BigBioConfig(
+                name=f"bioasq_{version}b_source",
+                version=SOURCE_VERSION,
+                description=f"bioasq{version} Task B source schema",
+                schema="source",
+                subset_id=f"bioasq_{version}b",
+            )
+        )
+
+        BUILDER_CONFIGS.append(
+            BigBioConfig(
+                name=f"bioasq_{version}b_bigbio_qa",
+                version=BIGBIO_VERSION,
+                description=f"bioasq{version} Task B in simplified BigBio schema",
+                schema="bigbio_qa",
+                subset_id=f"bioasq_{version}b",
+            )
+        )
+
+    def _info(self):
+
+        # BioASQ Task B source schema
+        if self.config.schema == "source":
+            features = datasets.Features(
+                {
+                    "id": datasets.Value("string"),
+                    "type": datasets.Value("string"),
+                    "body": datasets.Value("string"),
+                    "documents": datasets.Sequence(datasets.Value("string")),
+                    "concepts": datasets.Sequence(datasets.Value("string")),
+                    "ideal_answer": datasets.Sequence(datasets.Value("string")),
+                    "exact_answer": datasets.Sequence(datasets.Value("string")),
+                    "triples": [
+                        {
+                            "p": datasets.Value("string"),
+                            "s": datasets.Value("string"),
+                            "o": datasets.Value("string"),
+                        }
+                    ],
+                    "snippets": [
+                        {
+                            "offsetInBeginSection": datasets.Value("int32"),
+                            "offsetInEndSection": datasets.Value("int32"),
+                            "text": datasets.Value("string"),
+                            "beginSection": datasets.Value("string"),
+                            "endSection": datasets.Value("string"),
+                            "document": datasets.Value("string"),
+                        }
+                    ],
+                }
+            )
+        # simplified schema for QA tasks
+        elif self.config.schema == "bigbio_qa":
+            features = schemas.qa_features
+
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION[self.config.subset_id],
+            features=features,
+            supervised_keys=None,
+            homepage=_HOMEPAGE,
+            license=_LICENSE,
+            citation=_CITATION,
+        )
+
+    def _dump_gold_json(self, data_dir):
+        """
+        BioASQ test data is split into multiple records {9B1_golden.json,...,9B5_golden.json}
+        We combine these files into a single test set file 9Bx_golden.json
+        """
+        version = re.search(r"bioasq_([0-9]+)b", self.config.subset_id).group(1)
+        gold_fpath = os.path.join(
+            data_dir, f"Task{version}BGoldenEnriched/bx_golden.json"
+        )
+
+        if not os.path.exists(gold_fpath):
+            # combine all gold json files
+            filelist = glob.glob(os.path.join(data_dir, "*/*.json"))
+            data = {"questions": []}
+            for fname in sorted(filelist):
+                with open(fname, "rt", encoding="utf-8") as file:
+                    data["questions"].extend(json.load(file)["questions"])
+            # dump gold to json
+            with open(gold_fpath, "wt", encoding="utf-8") as file:
+                json.dump(data, file, indent=2)
+
+        return f"Task{version}BGoldenEnriched/bx_golden.json"
+
+    def _split_generators(self, dl_manager):
+        """Returns SplitGenerators."""
+
+        if self.config.data_dir is None:
+            raise ValueError(
+                "This is a local dataset. Please pass the data_dir kwarg to load_dataset."
+            )
+
+        train_dir, test_dir = dl_manager.download_and_extract(
+            [
+                os.path.join(self.config.data_dir, _url)
+                for _url in _URLs[self.config.subset_id]
+            ]
+        )
+        gold_fpath = self._dump_gold_json(test_dir)
+
+        # older versions of bioasq have different folder formats
+        train_fpaths = {
+            "bioasq_2b": "BioASQ_2013_TaskB/BioASQ-trainingDataset2b.json",
+            "bioasq_3b": "BioASQ-trainingDataset3b.json",
+            "bioasq_4b": "BioASQ-training4b/BioASQ-trainingDataset4b.json",
+            "bioasq_5b": "BioASQ-training5b/BioASQ-trainingDataset5b.json",
+            "bioasq_6b": "BioASQ-training6b/BioASQ-trainingDataset6b.json",
+            "bioasq_7b": "BioASQ-training7b/trainining7b.json",
+            "bioasq_8b": "training8b.json",  # HACK - this zipfile strips the dirname
+            "bioasq_9b": "BioASQ-training9b/training9b.json",
+            "bioasq_10b": "BioASQ-training10b/training10b.json",
+        }
+
+        return [
+            datasets.SplitGenerator(
+                name=datasets.Split.TRAIN,
+                gen_kwargs={
+                    "filepath": os.path.join(
+                        train_dir, train_fpaths[self.config.subset_id]
+                    ),
+                    "split": "train",
+                },
+            ),
+            datasets.SplitGenerator(
+                name=datasets.Split.TEST,
+                gen_kwargs={
+                    "filepath": os.path.join(test_dir, gold_fpath),
+                    "split": "test",
+                },
+            ),
+        ]
+
+    def _get_exact_answer(self, record):
+        """The value exact_answer can be in different formats based on question type."""
+        if record["type"] == "yesno":
+            exact_answer = [record["exact_answer"]]
+        elif record["type"] == "summary":
+            exact_answer = []
+            # summary question types only have an ideal answer, so use that for bigbio
+            if self.config.schema == "bigbio_qa":
+                exact_answer = (
+                    record["ideal_answer"]
+                    if isinstance(record["ideal_answer"], list)
+                    else [record["ideal_answer"]]
+                )
+
+        elif record["type"] == "list":
+            exact_answer = record["exact_answer"]
+        elif record["type"] == "factoid":
+            # older version of bioasq sometimes represent this as as string
+            exact_answer = (
+                record["exact_answer"]
+                if isinstance(record["exact_answer"], list)
+                else [record["exact_answer"]]
+            )
+        return exact_answer
+
+    def _generate_examples(self, filepath, split):
+        """Yields examples as (key, example) tuples."""
+
+        if self.config.schema == "source":
+            with open(filepath, encoding="utf-8") as file:
+                data = json.load(file)
+                for i, record in enumerate(data["questions"]):
+                    yield i, {
+                        "id": record["id"],
+                        "type": record["type"],
+                        "body": record["body"],
+                        "documents": record["documents"],
+                        "concepts": record["concepts"] if "concepts" in record else [],
+                        "triples": record["triples"] if "triples" in record else [],
+                        "ideal_answer": record["ideal_answer"]
+                        if isinstance(record["ideal_answer"], list)
+                        else [record["ideal_answer"]],
+                        "exact_answer": self._get_exact_answer(record),
+                        "snippets": record["snippets"] if "snippets" in record else [],
+                    }
+
+        elif self.config.schema == "bigbio_qa":
+            with open(filepath, encoding="utf-8") as file:
+                uid = 0
+                data = json.load(file)
+                for record in data["questions"]:
+                    # for questions that do not have snippets, skip
+                    if "snippets" not in record:
+                        continue
+                    for i, snippet in enumerate(record["snippets"]):
+                        yield uid, {
+                            "id": f'{record["id"]}_{i}',
+                            "document_id": snippet["document"],
+                            "question_id": record["id"],
+                            "question": record["body"],
+                            "type": record["type"],
+                            "choices": [],
+                            "context": snippet["text"],
+                            "answer": self._get_exact_answer(record),
+                        }
+                        uid += 1