| A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | AA | AB | AC | AD | AE | AF | AG | AH | AI | AJ | AK | ||
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1 | GitHub Issue | Name | DOI | Format | Meta Dataset | Annotations | HF Datasets | Citations (2-22-22) | Year | Official Splits | Paper | Dataset Download URL | Task Types | Domain | License | Dead Souce Dataset Link | Languages | Multilingual | Sources | Description | Annotators | |||||||||||||||||
2 | https://github.com/bigscience-workshop/biomedical/issues/13 | BioCreative V: BC5CDR | 10.1093/database/baw068 | BioC | BLUE | Manual | No | 332 | 2015 | train,dev,test | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860626/ | https://biocreative.bioinformatics.udel.edu/resources/corpora/biocreative-v-cdr-corpus/ | NER/NED, RE | Biomedical | Public Domain | English | No | PubMed Abstracts | ||||||||||||||||||||
3 | https://github.com/bigscience-workshop/biomedical/issues/114 | ChEBI | BRAT | Manual | No | 7 | 2018 | NONE | https://aclanthology.org/L18-1042/ | http://www.nactem.ac.uk/chebi/ | NER, RE | Biomedical | CC BY 4.0 | English | No | Abstracts + Full Papers | ||||||||||||||||||||||
4 | https://github.com/bigscience-workshop/biomedical/issues/14 | AnatEM | 10.1093/bioinformatics/btt580 | CoNLL, Standoff | Manual | No | 53 | 2013 | train,dev,test | https://academic.oup.com/bioinformatics/article/30/6/868/285282 | http://nactem.ac.uk/anatomytagger/#AnatEM | NER | Biomedical | CC BY-SA 3.0 | English | No | PubMed abstracts, PMC OA full texts | Anatomical entity mention recognition | ||||||||||||||||||||
5 | https://github.com/bigscience-workshop/biomedical/issues/206 | AnEM | - | CoNLL | AnatEM | Manual | No | 82 | 2012 | train,dev,test | https://aclanthology.org/W12-4304/ | http://www.nactem.ac.uk/anatomy/ | NER | Biomedical | CC BY-SA 3.0 | English | No | |||||||||||||||||||||
6 | https://github.com/bigscience-workshop/biomedical/issues/15 | JNLPBA | - | CoNLL | GENIA | Manual | https://huggingface.co/datasets/jnlpba | 41 | 2004 | train,test | https://aclanthology.org/W04-1213/ | http://www.geniaproject.org/shared-tasks/bionlp-jnlpba-shared-task-2004 | NER | Biomedical | CC BY NC 3.0 | English | No | PubMed abstracts | Biomedical NER | |||||||||||||||||||
7 | https://github.com/bigscience-workshop/biomedical/issues/16 | MuchMore | - | XML | - | Model | No | -1 | 2001 | NONE | ? | https://muchmore.dfki.de/resources1.htm | NER/NED, POS | Biomedical | ? | English, German | Yes | |||||||||||||||||||||
8 | https://github.com/bigscience-workshop/biomedical/issues/261 | BioASQ Task A | 10.1186/s12859-015-0564-6 | JSON | - | Manual | No | 364 | 2013-2021 | train,test | https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0564-6 | http://participants-area.bioasq.org/general_information/Task9b/ | Topic Classification | Biomedical | DUA | English | No | PubMed abstracts | ||||||||||||||||||||
9 | https://github.com/bigscience-workshop/biomedical/issues/17 | BioASQ Task B | 10.1186/s12859-015-0564-6 | JSON | - | Manual | No | 364 | 2014-2020 | train,test | https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0564-6 | http://participants-area.bioasq.org/general_information/Task9b/ | QA | Biomedical | DUA | English | No | PubMed abstracts | ||||||||||||||||||||
10 | https://github.com/bigscience-workshop/biomedical/issues/208 | BioASQ Task MESINESP / MESINESP2 | 10.5281/zenodo.5602914 | JSON | - | Manual | No | 0 | 2020-2021 | train,dev,test | http://ceur-ws.org/Vol-2936/paper-11.pdf | https://zenodo.org/record/5602914#.YhSXJ5PMKWt | Topic Classification | Biomedical | CC BY 4.0 | Spanish | No | |||||||||||||||||||||
11 | https://github.com/bigscience-workshop/biomedical/issues/209 | BioASQ Task C 2017 | 10.18653/v1/W17-2306 | JSON | - | Manual | No | 52 | 2017 | train,test | https://aclanthology.org/W17-2306.pdf | http://participants-area.bioasq.org/general_information/Task5c/ | NER | Biomedical | NLM License Code: 8283NLM123 | English | No | PubMed abstracts, PMC | ||||||||||||||||||||
12 | https://github.com/bigscience-workshop/biomedical/issues/210 | BioASQ Task Synergy | JSON | - | Manual | No | 0 | 2022 | train,test | http://ceur-ws.org/Vol-2936/paper-10.pdf | http://participants-area.bioasq.org/general_information/Task9b/ | QA | Biomedical | NLM License Code: 8283NLM123 | English | No | ||||||||||||||||||||||
13 | https://github.com/bigscience-workshop/biomedical/issues/18 | BioCreative II: Gene Mention (GM) | 10.1186/gb-2008-9-s2-s2 | CoNLL | Manual | https://huggingface.co/datasets/bc2gm_corpus | 388 | 2008 | train,dev,test | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559986/ | https://github.com/spyysalo/bc2gm-corpus/raw/master/conll/ | NER | Biomedical | MIT License | English | No | MEDLINE articles | |||||||||||||||||||||
14 | https://github.com/bigscience-workshop/biomedical/issues/211 | BioCreative II: Gene Normalization (GN) | Standoff | Manual | No | 377 | 2008 | train,test | https://link.springer.com/article/10.1186/gb-2008-9-s2-s3 | https://biocreative.bioinformatics.udel.edu/resources/corpora/biocreative-ii-corpus/ | NED | Biomedical | English | No | MEDLINE articles | |||||||||||||||||||||||
15 | https://github.com/bigscience-workshop/biomedical/issues/212 | GENETAG | 10.1186/1471-2105-6-S1-S3 | text | Model | No | 298 | 2005 | train,test | https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-S1-S3 | https://github.com/openbiocorpora/genetag | NER | Biomedical | Public Domain | English | No | ||||||||||||||||||||||
16 | https://github.com/bigscience-workshop/biomedical/issues/213 | AIMed | 10.1016/j.artmed.2004.07.016 | text | Manual | No | 486 | 2004 | NONE | https://www.cs.utexas.edu/~ml/papers/bionlp-aimed-04.pdf | https://www.cs.utexas.edu/ftp/mooney/bio-data/ | NER | Biomedical | ? | English | No | PubMed abstracts | genes,proteins | ||||||||||||||||||||
17 | https://github.com/bigscience-workshop/biomedical/issues/214 | BioInfer | 10.1186/1471-2105-8-50 | CSV, XML | Manual | No | 503 | 2007 | train,test | https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-50 | https://github.com/metalrt/ppi-dataset/tree/master/csv_output | RE, NER | Biomedical | ? | Yes | English | No | PubMed abstracts | 6 annotators (2 of them experts) | |||||||||||||||||||
18 | https://github.com/bigscience-workshop/biomedical/issues/215 | HPRD50 | 10.1093/bioinformatics/btl616 | CSV, XML | Model-assisted Manual | No | 716 | 2007 | train,test | https://academic.oup.com/bioinformatics/article/23/3/365/236564 | https://github.com/metalrt/ppi-dataset/tree/master/csv_output | RE | Biomedical | ? | English | No | 2 annotators (with biochemical background) | |||||||||||||||||||||
19 | https://github.com/bigscience-workshop/biomedical/issues/216 | IEPA | CSV, XML | Model-assisted Manual | No | 348 | 2002 | train,test | http://psb.stanford.edu/psb-online/proceedings/psb02/abstracts/p326.html | https://github.com/metalrt/ppi-dataset/tree/master/csv_output | Topic Classification | Biomedical | ? | Yes | English | No | PubMed abstracts | |||||||||||||||||||||
20 | https://github.com/bigscience-workshop/biomedical/issues/217 | LLL | CSV, XML | Manual | No | 287 | 2005 | train,test | http://citeseerx.ist.psu.edu/viewdoc/download;jsessionid=4B3F165F09189F5487A59C6E0C19C855?doi=10.1.1.96.5066&rep=rep1&type=pdf | http://genome.jouy.inra.fr/texte/LLLchallenge/ | RE, NER | Biomedical | ? | English | No | PubMed abstracts | experts (biologists) | |||||||||||||||||||||
21 | https://github.com/bigscience-workshop/biomedical/issues/175 | EBM PICO | 10.18653/v1/P18-1019 | text | - | Manual, Crowdsoured | No | 120 | 2018 | train,test | https://aclanthology.org/P18-1019/ | https://github.com/bepnye/EBM-NLP | NER | Biomedical | ? | English | No | PubMed abstracts | experts for test, AMT for train | |||||||||||||||||||
22 | https://github.com/bigscience-workshop/biomedical/issues/19 | ChemProt | 10.1093/nar/gkq906 | Standoff | BLUE | Rules | No | 91 | 2017 | train,dev,test | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013776/ | https://biocreative.bioinformatics.udel.edu/resources/corpora/chemprot-corpus-biocreative-vi/ | RE, NER/NED | Biomedical | Public / Unknown | English | No | |||||||||||||||||||||
23 | https://github.com/bigscience-workshop/biomedical/issues/20 | NCBI Disease Corpus | 10.1016/j.jbi.2013.12.006 | PubTator | BLUE | Manual | https://huggingface.co/datasets/ncbi_disease | 422 | 2013 | train,dev,test | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951655/ | https://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/ | NER/NED | Biomedical | CC0 1.0 | English | No | |||||||||||||||||||||
24 | https://github.com/bigscience-workshop/biomedical/issues/21 | BIOSSES | 10.1093/bioinformatics/btx238 | Word | BLUE, BLURB | Manual | https://huggingface.co/datasets/biosses | 95 | 2017 | NONE | https://academic.oup.com/bioinformatics/article/33/14/i49/3953954 | https://tabilab.cmpe.boun.edu.tr/BIOSSES/ | Semantic Similarity | Biomedical | GNU Common Public License v.3.0 | English | No | Biomedical articles | 5 experts | |||||||||||||||||||
25 | https://github.com/bigscience-workshop/biomedical/issues/22 | GENIA Term Corpus | 10.1093/bioinformatics/btg1023 | XML | GENIA | Manual | No | 1282 | 2003 | NONE | https://academic.oup.com/bioinformatics/article/19/suppl_1/i180/227927 | http://www.geniaproject.org/genia-corpus/term-corpus | NER | Biomedical | CC BY 3.0 | English | No | |||||||||||||||||||||
26 | https://github.com/bigscience-workshop/biomedical/issues/23 | GENIA Relation Corpus | 10.1093/bioinformatics/btg1023 | Standoff | GENIA | Manual | No | 1282 | 2011 | train,dev,test | https://academic.oup.com/bioinformatics/article/19/suppl_1/i180/227927 | http://www.geniaproject.org/genia-corpus/relation-corpus | RE | Biomedical | CC BY 3.0 | English | No | |||||||||||||||||||||
27 | https://github.com/bigscience-workshop/biomedical/issues/24 | GENIA Coreference Corpus | XML | GENIA | Manual | No | 18 | 2011 | NONE | https://aclanthology.org/W11-1811/ | http://www.geniaproject.org/genia-corpus/coreference | Coreference | Biomedical | CC BY 3.0 | English | No | ||||||||||||||||||||||
28 | https://github.com/bigscience-workshop/biomedical/issues/25 | PubMedQA (PQA-L, PQA-U, PQA-A) | JSON | Manual | https://huggingface.co/datasets/pubmed_qa | 73 | 2019 | train,test | https://arxiv.org/abs/1909.06146 | https://github.com/pubmedqa/pubmedqa | QA | Biomedical | MIT License | English | No | |||||||||||||||||||||||
29 | https://github.com/bigscience-workshop/biomedical/issues/26 | MedMentions | - | PubTator | Manual | No | 45 | 2019 | train,dev,test | https://arxiv.org/abs/1902.09476 | https://github.com/chanzuckerberg/MedMentions | NER/NED | Biomedical | CC0 1.0 | English | No | ||||||||||||||||||||||
30 | https://github.com/bigscience-workshop/biomedical/issues/27 | S800 Corpus | 10.1371/journal.pone.0065390 | Standoff | Manual | https://huggingface.co/datasets/species_800 | 115 | 2013 | NONE | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065390 | https://species.jensenlab.org | NER | Biomedical | Public Domain | English | No | ||||||||||||||||||||||
31 | https://github.com/bigscience-workshop/biomedical/issues/28 | CHEMDNER | 10.1186/1758-2946-7-S1-S2 | BioC, Standoff | Manual | No | 197 | 2015 | train,dev,test | https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-7-S1-S2 | http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus/ | NER | Biomedical | Public / Registration | English | No | ||||||||||||||||||||||
32 | https://github.com/bigscience-workshop/biomedical/issues/218 | PUBHEALTH | 10.18653/v1/2020.emnlp-main.623 | text | Manual | https://huggingface.co/datasets/health_fact | 28 | 2020 | train,dev,test | https://aclanthology.org/2020.emnlp-main.623/ | https://github.com/neemakot/Health-Fact-Checking/blob/master/data/DATASHEET.md | Fact-Verification | Health News | MIT License | English | No | Health news articles | |||||||||||||||||||||
33 | https://github.com/bigscience-workshop/biomedical/issues/120 | ProGene | 10.5281/zenodo.3698568 | CoNLL | Manual | No | 2 | 2020 | train,dev,test | https://aclanthology.org/2020.lrec-1.564.pdf | https://zenodo.org/record/3698568#.YhTFu5PMKWs | NER | Biomedical | CC BY 4.0 | English | No | ||||||||||||||||||||||
34 | https://github.com/bigscience-workshop/biomedical/issues/115 | CellFinder | - | BRAT | Manual | No | 39 | 2012 | NONE | https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.385.9703&rep=rep1&type=pdf | https://github.com/openbiocorpora/cellfinder | NER | Biomedical | CC BY-SA 3.0 | English | No | 2 experts | |||||||||||||||||||||
35 | https://github.com/bigscience-workshop/biomedical/issues/30 | SciTail | - | JSONL, DGEM, text | - | Crowdsourced | https://huggingface.co/datasets/scitail | 268 | 2018 | train,dev,test | http://ai2-website.s3.amazonaws.com/team/ashishs/scitail-aaai2018.pdf | https://allenai.org/data/scitail | NLI | Biomedical | Apache License 2.0 | English | No | |||||||||||||||||||||
36 | https://github.com/bigscience-workshop/biomedical/issues/31 | n2c2 2006 - Smoking Status | 10.1197/jamia.M2408 | XML | - | Manual | No | 380 | 2006 | train,test | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2274873/ | https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/ | Topic Classification | Clinical | DUA | English | No | Clinical notes | ||||||||||||||||||||
37 | https://github.com/bigscience-workshop/biomedical/issues/219 | n2c2 2006 - Deidentification | 10.1197/jamia.M2444 | XML | - | Manual | No | 491 | 2006 | train,test | https://academic.oup.com/jamia/article/14/5/550/720189 | https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/ | NER | Clinical | DUA | English | No | Clinical notes | ||||||||||||||||||||
38 | https://github.com/bigscience-workshop/biomedical/issues/32 | n2c2 2008 - Obesity | 10.1197/jamia.M3115 | XML | Manual | No | 261 | 2008 | train,test | https://academic.oup.com/jamia/article/16/4/561/766997 | https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/ | Topic Classification | Clinical | DUA | English | No | Clinical notes | 2 obesity experts | ||||||||||||||||||||
39 | https://github.com/bigscience-workshop/biomedical/issues/33 | n2c2 2009 - Medication | 10.1136/jamia.2010.003947 | text | - | Manual | No | 465 | 2009 | train,test | https://academic.oup.com/jamia/article/17/5/514/2909108 | https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/ | NER | Clinical | DUA | English | No | |||||||||||||||||||||
40 | https://github.com/bigscience-workshop/biomedical/issues/38 | n2c2 2010 - Relations | 10.1136/amiajnl-2011-000203 | text | BLUE | Manual | No | 1001 | 2011 | train,test | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3168320/ | https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/ | RE, NER | Clinical | DUA | English | No | |||||||||||||||||||||
41 | https://github.com/bigscience-workshop/biomedical/issues/34 | n2c2 2011 - Coreference | 10.1136/amiajnl-2011-000784 | text | Manual | No | 172 | 2011 | train,test | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422835/ | https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/ | Coreference | Clinical | DUA | English | No | Clinical notes | 2 annotators | ||||||||||||||||||||
42 | https://github.com/bigscience-workshop/biomedical/issues/36 | n2c2 2012 - Temporal Relations | 10.1136/amiajnl-2013-001628 | XML | Manual | No | 407 | 2012 | train,test | https://academic.oup.com/jamia/article/20/5/806/726374 | https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/ | RE | Clinical | DUA | English | No | Clinical notes | 8 annotators | ||||||||||||||||||||
43 | https://github.com/bigscience-workshop/biomedical/issues/220 | n2c2 2014 - Deidentification & Heart Disease | 10.1016/j.jbi.2015.06.007 | XML | Manual | No | 163 | 2014 | train,test | https://pubmed.ncbi.nlm.nih.gov/26225918/ | https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/ | NER, Topic Classification | Clinical | DUA | English | No | Medical records | 6 annotators | ||||||||||||||||||||
44 | https://github.com/bigscience-workshop/biomedical/issues/37 | n2c2 2018 - Adverse Drug Events and Medication Extraction | 10.1093/jamia/ocz166 | Standoff | Manual | No | 52 | 2018 | train,test | https://academic.oup.com/jamia/article-abstract/27/1/3/5581277?redirectedFrom=fulltext | https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/ | NER, RE | Clinical | DUA | English | No | MIMIC-III | 2 annotators | ||||||||||||||||||||
45 | https://github.com/bigscience-workshop/biomedical/issues/221 | n2c2 2018 - Clinical Trial Cohort Selection | 10.1093/jamia/ocz163 | XML | Manual | No | 19 | 2018 | train,test | https://academic.oup.com/jamia/article-abstract/26/11/1163/5575392?redirectedFrom=fulltext | https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/ | Topic Classification | Clinical | DUA | English | No | Medical records | 2 annotators with medical expertise | ||||||||||||||||||||
46 | https://github.com/bigscience-workshop/biomedical/issues/138 | PharmaCoNER | 10.18653/v1/D19-5701 | text | Manual | No | 49 | 2020 | train,dev,test | https://aclanthology.org/D19-5701/ | https://temu.bsc.es/pharmaconer/index.php/datasets/ | NER | Clinical | CC BY 4.0 | Spanish | No | Spanish Clinical Case Corpus | Physicians and medicinal chemistry experts | ||||||||||||||||||||
47 | https://github.com/bigscience-workshop/biomedical/issues/39 | emrQA | 10.18653/v1/D18-1258 | JSON | Rules | No | 79 | 2018 | train,test | https://www.aclweb.org/anthology/D18-1258 | https://github.com/panushri25/emrQA | QA | Clinical | DUA | English | No | i2b2 | |||||||||||||||||||||
48 | https://github.com/bigscience-workshop/biomedical/issues/40 | MEDIQA 2019 NLI | 10.18653/v1/W19-5039 | JSONL | MEDIQA 2019 | Manual | No | 56 | 2019 | train,test | https://www.aclweb.org/anthology/W19-5039/ | https://physionet.org/content/mednli-bionlp19/1.0.1/ | NLI | Clinical | DUA | English | No | MIMIC-III | experts (clinicians) | |||||||||||||||||||
49 | https://github.com/bigscience-workshop/biomedical/issues/41 | ShAReCLEF 2014 Task 2 | 10.13026/0zgk-9j94 | text | Manual | No | 144 | 2014 | train,test | http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.717.6237&rep=rep1&type=pdf | https://physionet.org/content/shareclefehealth2014task2/1.0/ | NER | Clinical | DUA | English | No | MIMIC-II | |||||||||||||||||||||
50 | https://github.com/bigscience-workshop/biomedical/issues/42 | RadGraph | 10.13026/hm87-5p47 | JSON | Manual | No | 1 | 2021 | train,dev,test | https://arxiv.org/pdf/2106.14463.pdf | https://physionet.org/content/radgraph/1.0.0/ | NER, RE | Clinical | DUA | English | No | ||||||||||||||||||||||
51 | https://github.com/bigscience-workshop/biomedical/issues/43 | MeDAL | 10.18653/v1/2020.clinicalnlp-1.15 | text | Rules | https://huggingface.co/datasets/medal | 5 | 2020 | train,dev,test | https://arxiv.org/abs/2012.13978 | https://github.com/BruceWen120/medal | Abbreviation Disambiguation | Clinical | Apache 2.0 | English | No | PubMed abstracts | Abbreviation disambiguation | reverse substitution (see https://arxiv.org/pdf/1912.06174.pdf) | |||||||||||||||||||
52 | https://github.com/bigscience-workshop/biomedical/issues/44 | MQP - Medical Question Pairs Dataset | 10.1145/3394486.3412861 | CSV | Manual | https://huggingface.co/datasets/medical_questions_pairs | 5 | 2020 | NONE | https://drive.google.com/file/d/1CHPGBXkvZuZc8hpr46HeHU6U6jnVze-s/view | https://github.com/curai/medical-question-pair-dataset | Paraphrasing | Clinical | ? | English | No | experts (clinicians) | |||||||||||||||||||||
53 | https://github.com/bigscience-workshop/biomedical/issues/45 | Why-QA | 10.18653/v1/W19-1913 | JSON, text | Manual | No | 4 | 2019 | NONE | https://www.aclweb.org/anthology/W19-1913/ | https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/ | QA | Clinical | DUA | English | No | 2010 i2b2/VA NLP | |||||||||||||||||||||
54 | https://github.com/bigscience-workshop/biomedical/issues/46 | CLIP | 10.18653/v1/2021.acl-long.109 | CSV, JSON | Manual | No | 1 | 2021 | train,dev,test | https://arxiv.org/abs/2106.02524 | https://physionet.org/content/mimic-iii-clinical-action/1.0.0/ | Span Classification, Sentence Classification | Clinical | DUA | English | No | MIMIC-III | 4 physicians and 1 resident | ||||||||||||||||||||
55 | https://github.com/bigscience-workshop/biomedical/issues/47 | DDI | 10.1016/j.jbi.2013.07.011 | XML | BLUE | Manual | No | 213 | 2013 | train,test | http://dx.doi.org/10.1016/j.jbi.2013.07.011 | https://github.com/isegura/DDICorpus | RE, NER/NED | Biomedical | CC BY-NC 4.0 | English | No | DrugBank database and MEDLINE articles | 2 expert pharmacists | |||||||||||||||||||
56 | https://github.com/bigscience-workshop/biomedical/issues/48 | BioNLP Shared Task 2009 | Standoff | Manual | No | 729 | 2009 | train,dev,test | https://www.aclweb.org/anthology/W09-1401.pdf | http://www.geniaproject.org/shared-tasks/bionlp-shared-task-2009 | RE | Biomedical | CC BY NC 3.0 | English | No | PubMed abstracts | Event extraction shared task | |||||||||||||||||||||
57 | https://github.com/bigscience-workshop/biomedical/issues/49 | Scielo | TMX,JSON | Found/model | https://huggingface.co/datasets/scielo | 11 | 2018 | NONE | https://arxiv.org/abs/1905.01852 | https://sites.google.com/view/felipe-soares/datasets#h.p_92uSCyAjWSRB | Translation | Biomedical | CC BY 4.0 | English, Portuguese, Spanish | Yes | |||||||||||||||||||||||
58 | https://github.com/bigscience-workshop/biomedical/issues/50 | SciCite | 10.18653/v1/N19-1361 | JSONL | Crowdsourcing | https://huggingface.co/datasets/scicite | 61 | 2019 | train,dev,test | https://arxiv.org/pdf/1904.01608.pdf | https://github.com/allenai/scicite | Topic Classification | Biomedical | Apache License | English | No | Semantic Scholar corpus | 850 crowdsource workers | ||||||||||||||||||||
59 | https://github.com/bigscience-workshop/biomedical/issues/51 | SCAI disease | CoNLL | Manual | No | 44 | 2010 | NONE | https://pub.uni-bielefeld.de/record/2603398 | http://www.scai.fraunhofer.de/disease-ae-corpus.html | NER | Biomedical | ? | English | No | MEDLINE abstracts | 2 annotators | |||||||||||||||||||||
60 | https://github.com/bigscience-workshop/biomedical/issues/52 | SCAI chemical | 10.1093/bioinformatics/btn181 | CoNLL | Manual | No | 143 | 2008 | NONE | https://pubmed.ncbi.nlm.nih.gov/18586724/ | http://www.scai.fraunhofer.de/chem-corpora.html | NER | Biomedical | ? | English | No | MEDLINE abstracts | 2 annotators | ||||||||||||||||||||
61 | https://github.com/bigscience-workshop/biomedical/issues/53 | miRNA | 10.5256/f1000research.6352.r5979 | XML | Manual | No | 31 | 2014 | train,test | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602280/ | https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/download-mirna-test-corpus.html | NER | Biomedical | ? | English | No | MEDLINE abstracts | 2 annotators | ||||||||||||||||||||
62 | https://github.com/bigscience-workshop/biomedical/issues/55 | MEDIQA 2019 RQE | 10.18653/v1/W19-5039 | XML | MEDIAQ 2019 | No | 56 | 2019 | train,dev,test | https://www.aclweb.org/anthology/W19-5039/ | https://github.com/abachaa/MEDIQA2019/tree/master/MEDIQA_Task2_RQE | RQE | Clinical | ? | English | No | Consumer Health Questions to NLM, FAQs from NIH | |||||||||||||||||||||
63 | https://github.com/bigscience-workshop/biomedical/issues/56 | MASH-QA | 10.18653/v1/2020.findings-emnlp.342 | JSON | Manual | No | 10 | 2020 | train,dev,test | https://people.cs.vt.edu/mingzhu/papers/conf/emnlp2020.pdf | https://github.com/mingzhu0527/MASHQA | QA | Clinical | Apache License 2.0 | English | No | Consumer healthcare articles from WebMD | Healthcare experts | ||||||||||||||||||||
64 | https://github.com/bigscience-workshop/biomedical/issues/57 | PICO extraction | 10.18653/v1/2020.findings-emnlp.274 | JSON | Manual, Crowdsourcing | No | 1 | 2020 | NONE | https://aclanthology.org/2020.findings-emnlp.274/ | https://github.com/Markus-Zlabinger/pico-annotation | Sentence Classification | Clinical | ? | English | No | Sentences annotated with PICO classes. Majority vote does not seem to be materialized in the dataset; needs to be inferred with script. | Experts and crowdsourcing (goal was to compare assisted crowd annotation with expert annotation) | ||||||||||||||||||||
65 | https://github.com/bigscience-workshop/biomedical/issues/58 | Hallmarks of Cancer (HoC) | 10.1093/bioinformatics/btv585 | text | Manual | No | 49 | 2016 | NONE | https://academic.oup.com/bioinformatics/article/32/3/432/1743783 | https://github.com/sb895/Hallmarks-of-Cancer | Topic Classification | Biomedical | GNU General Public License v3.0 | English | No | PubMed abstracts | Hallmarks of Cancers corpus | 1 expert | |||||||||||||||||||
66 | https://github.com/bigscience-workshop/biomedical/issues/59 | CEI | 10.1371/journal.pone.0173132 | text, CoNLL | Model-assisted Manual | No | 13 | 2017 | NONE | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0173132 | https://s-baker.net/resource/cei/ | Topic Classification | Biomedical | CC BY 4.0 | English | No | PubMed abstracts | Chemical Exposure Information (CEI) Corpus | ||||||||||||||||||||
67 | https://github.com/bigscience-workshop/biomedical/issues/60 | Colorado Richly Annotated Full-Text (CRAFT) Corpus | - | CoNLL | Manual | No | 37 | 2015 | train,dev,test | https://hal.inria.fr/hal-01159065/document | https://github.com/UCDenver-ccp/CRAFT | NER/NED, Coreference | Biomedical | CC BY 3.0 | English | No | Full-text journal articles | |||||||||||||||||||||
68 | https://github.com/bigscience-workshop/biomedical/issues/61 | SPL-ADR-200db - Adverse Drug Reactions | 10.1038/sdata.2018.1 | XML | Manual | No | 29 | 2017 | train,test | https://www.nature.com/articles/sdata20181 | https://bionlp.nlm.nih.gov/tac2017adversereactions/ | NER, Negation | Biomedical | ? | English | No | Structured Product Labels | |||||||||||||||||||||
69 | https://github.com/bigscience-workshop/biomedical/issues/62 | Nagel | - | Standoff | Manual | No | 6 | 2009 | NONE | https://www.ebi.ac.uk/sites/ebi.ac.uk/files/shared/documents/phdtheses/kevin_nagel.pdf | http://sourceforge.net/projects/bionlp-corpora/files/ProteinResidue/ | NER | Biomedical | MIT License | English | No | ||||||||||||||||||||||
70 | https://github.com/bigscience-workshop/biomedical/issues/63 | DIANN IberEval 2018 | text | Manual | No | 11 | 2018 | train,test | http://ceur-ws.org/Vol-2150/overview-diann-task.pdf | https://github.com/gildofabregat/DIANN-IBEREVAL-2018 | NER | Biomedical | Unknown/Emailed | Spanish, English | Yes | Elseiver abstracts | parallel annotations | 3 people | ||||||||||||||||||||
71 | https://github.com/bigscience-workshop/biomedical/issues/64 | CodiEsp | - | text | - | Manual | No | 40 | 2020 | train,dev,test | http://ceur-ws.org/Vol-2696/paper_263.pdf | https://zenodo.org/record/3837305#.YL46cfdfjMU | Document Classification | Clinical | CC BY 4.0 | Spanish | No | |||||||||||||||||||||
72 | https://github.com/bigscience-workshop/biomedical/issues/65 | eHealth-KD 2020 | Standoff,JSON | Model-assisted Manual | https://huggingface.co/datasets/ehealth_kd | 22 | 2020 | train,dev,test | http://ceur-ws.org/Vol-2664/eHealth-KD_overview.pdf | https://github.com/knowledge-learning/ehealthkd-2020 | RE, NER/NED | Biomedical | CC BY-NC-SA 4.0 | Spanish | No | Medline | ||||||||||||||||||||||
73 | https://github.com/bigscience-workshop/biomedical/issues/137 | Mantra GSC | 10.1093/jamia/ocv037 | XML | - | Model-assisted Manual | No | 42 | 2015 | NONE | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986661/ | https://files.ifi.uzh.ch/cl/mantra/gsc/GSC-v1.1.zip | NER/NED | Biomedical | CC BY 4.0 | French, Spanish, Dutch, German, English | Yes | European Medicines Agency, Medline, European Patent Office | Parallel datasets | |||||||||||||||||||
74 | https://github.com/bigscience-workshop/biomedical/issues/139 | eHealth-KD 2019 | - | Standoff | - | Manual | No | 19 | 2019 | train,dev,test | http://ceur-ws.org/Vol-2421/eHealth-KD_overview.pdf | https://github.com/knowledge-learning/ehealthkd-2019/tree/master/data | RE, NER/NED | Biomedical | CC BY-NC-SA 4.0 | Spanish | No | Medline | ||||||||||||||||||||
75 | https://github.com/bigscience-workshop/biomedical/issues/66 | DrugSemantics Gold Standard | 10.1016/j.jbi.2017.06.013 | XML | Manual | No | 18 | 2017 | NONE | https://www.sciencedirect.com/science/article/pii/S1532046417301363?via%3Dihub | https://data.mendeley.com/datasets/fwc7jrc5jr/1 | NER | Biomedical | CC BY NC 3.0 | Spanish | No | Medicines Online Information Center - CIMA - that belongs to the Spanish Agency for Medicines and Health Products - AEMPS | |||||||||||||||||||||
76 | https://github.com/bigscience-workshop/biomedical/issues/67 | MoNERo | 10.18653/v1/W19-5008 | CoNLL | Model-assisted Manual | No | 5 | 2019 | train,dev,test | https://www.aclweb.org/anthology/W19-5008.pdf | https://www.racai.ro/en/tools/text/ | NER | Biomedical | CC BY-SA 4.0 | Romanian | No | BioRo corpus | |||||||||||||||||||||
77 | https://github.com/bigscience-workshop/biomedical/issues/68 | CLEF eHealth 2019, Task 1 | text | Manual | No | 16 | 2019 | train,dev | https://journals.plos.org/plosbiology/article/comments?id=10.1371/journal.pbio.2003217 | https://www.openagrar.de/receive/openagrar_mods_00046540?lang=en | Topic Classification | Biomedical | DUA | German | No | AnimalTestInfo database (http://animaltestinfo.de) | classifying text on animal experiments with ICD codes | |||||||||||||||||||||
78 | https://github.com/bigscience-workshop/biomedical/issues/69 | ESSAI | - | text | Manual | No | 9 | 2020 | NONE | https://www.cambridge.org/core/services/aop-cambridge-core/content/view/5E5DB27872B07185DB58A1507DFA05D8/S1351324920000352a.pdf/div-class-title-supervised-learning-for-the-detection-of-negation-and-of-its-scope-in-french-and-brazilian-portuguese-biomedical-corpora-div.pdf | https://clementdalloux.fr/?page_id=28 | Negation/Speculation Classification | Biomedical | ? | French, Brazilian Portuguese | No | ESSAI, CAS | |||||||||||||||||||||
79 | https://github.com/bigscience-workshop/biomedical/issues/70 | CBLUE (Chinese Biomedical Language Understanding Evaluation Benchmark) | - | JSON | Manual | No | 5 | 2021 | train,dev,test | https://arxiv.org/abs/2106.08087 | https://tianchi.aliyun.com/dataset/dataDetail?dataId=95414&lang=en-us | NER, RE, Topic Classification | Biomedical | CC BY-NC 4.0 | Chinese | No | ||||||||||||||||||||||
80 | https://github.com/bigscience-workshop/biomedical/issues/71 | Hindi Health Dataset | text | Found | No | -1 | 2018 | NONE | https://www.kaggle.com/aijain/hindi-health-dataset/home | NER | Clinical | ? | Hindi | No | tumor morphology | |||||||||||||||||||||||
81 | https://github.com/bigscience-workshop/biomedical/issues/72 | CANTEMIST (CANcer TExt Mining Shared Task) | Standoff | - | Manual | No | 40 | 2020 | train,dev,test | http://ceur-ws.org/Vol-2664/cantemist_overview.pdf | https://temu.bsc.es/cantemist/ | NER/NED, Multi-label Document Classification | Clinical | ? | Spanish | No | ||||||||||||||||||||||
82 | https://github.com/bigscience-workshop/biomedical/issues/73 | Swedish Medical NER | text | Rules,Manual | https://huggingface.co/datasets/swedish_medical_ner | 12 | 2016 | train,dev,test | https://aclanthology.org/W16-5104.pdf | https://github.com/olofmogren/biomedical-ner-data-swedish | NER | Biomedical | CC BY-SA 4.0 | Swedish | No | Swedish Wikipedia, Läkartidningen, and 1177.se. | NER dataset on medical text in Swedish. | |||||||||||||||||||||
83 | https://github.com/bigscience-workshop/biomedical/issues/74 | QUAERO | BRAT | Manual | No | 60 | 2014 | train,test | http://www.lrec-conf.org/proceedings/lrec2014/workshops/LREC2014Workshop-BioTxtM2014%20Proceedings.pdf#page=33 | https://quaerofrenchmed.limsi.fr | NER/NED | Clinical | GNU Free Documentation License | French | No | EMEA/MEDLINE/EPO | ||||||||||||||||||||||
84 | https://github.com/bigscience-workshop/biomedical/issues/222 | PubTator Central | 10.1093/nar/gkz389 | PubTator | - | Model | No | 137 | 2019 | NONE | https://academic.oup.com/nar/article/47/W1/W587/5494727 | https://ftp.ncbi.nlm.nih.gov/pub/lu/PubTatorCentral/ | NER/NED, Coreference | Biomedical | Public Domain | English | No | Pubmed abstracts, full text | ||||||||||||||||||||
85 | https://github.com/bigscience-workshop/biomedical/issues/223 | BioScope | XML | Manual | No | 441 | 2008 | NONE | https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-S11-S9 | https://rgai.inf.u-szeged.hu/node/105 | Negation, Uncertain, Scope | Biomedical | Public for Research | English | No | Clinical texts, biological full papers, biological paper abstracts from Genia | 2 linguists | |||||||||||||||||||||
86 | https://github.com/bigscience-workshop/biomedical/issues/224 | Multi-XScience | 10.18653/v1/2020.emnlp-main.648 | JSON | Rules | https://huggingface.co/datasets/multi_x_science_sum | 16 | 2020 | train,dev,test | https://arxiv.org/abs/2010.14235 | https://github.com/yaolu/Multi-XScience | Multi-doc Summarization | Biomedical | MIT License | English | No | arXiv articles and Microsoft Academic Graph | |||||||||||||||||||||
87 | https://github.com/bigscience-workshop/biomedical/issues/225 | MedHop | JSON | Rules,Manual | https://huggingface.co/datasets/med_hop | 246 | 2017 | train,dev | https://transacl.org/ojs/index.php/tacl/article/viewFile/1325/299 | http://qangaroo.cs.ucl.ac.uk | Reading Comprehension | Biomedical | CC BY-SA 3.0 | English | No | |||||||||||||||||||||||
88 | https://github.com/bigscience-workshop/biomedical/issues/226 | CORD-NER | JSON | Rules | No | 36 | 2020 | NONE | https://arxiv.org/abs/2003.12218 | https://uofi.box.com/s/k8pw7d5kozzpoum2jwfaqdaey1oij93x | NER | Biomedical | ? | English | No | |||||||||||||||||||||||
89 | https://github.com/bigscience-workshop/biomedical/issues/169 | MedQuAD | 10.1186/s12859-019-3119-4 | XML | - | Rules | No | 59 | 2019 | NONE | https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3119-4 | https://github.com/abachaa/MedQuAD | QA | Clinical | CC BY 4.0 | English | No | 12 NIH websites | MedQuAD includes 47,457 medical question-answer pairs created from 12 NIH websites (e.g. cancer.gov, niddk.nih.gov, GARD, MedlinePlus Health Topics). The collection covers 37 question types (e.g. Treatment, Diagnosis, Side Effects) associated with diseases, drugs and other medical entities such as tests. | |||||||||||||||||||
90 | this dataset is not available - should we remove it? | MedSTS | 10.1007/s10579-018-9431-1 | ? | BLUE | Manual | No | 43 | 2018 | train,test | https://arxiv.org/abs/1808.09397 | Semantic Similarity | Clinical | PRIVATE | English | No | ||||||||||||||||||||||
91 | https://github.com/bigscience-workshop/biomedical/issues/227 | ShAReCLEF 2013 Task 1 | text | BLUE | Manual | No | 121 | 2013 | https://pubmed.ncbi.nlm.nih.gov/25147248/ | https://physionet.org/content/shareclefehealth2013/1.0/ | NER/NED | Clinical | DUA | English | No | Two professional coders (a healthcare professional who has been trained to analyze clinical records and assign standard codes using a classification system) trained for this task annotated each clinical note in a double-blind manner, followed by adjudication. | ||||||||||||||||||||||
92 | https://github.com/bigscience-workshop/biomedical/issues/228 | MEDIQA 2019 QA | 10.18653/v1/W19-5039 | XML | MEDIQA 2019 | Manual | No | 56 | 2019 | train,dev,test | https://www.aclweb.org/anthology/W19-5039/ | https://github.com/abachaa/MEDIQA2019/tree/master/MEDIQA_Task3_QA | QA | Clinical | ? | English | No | Consumer health QA system CHiQA | Medical experts | |||||||||||||||||||
93 | https://github.com/bigscience-workshop/biomedical/issues/229 | TREC-2017 LiveQA | XML | Found,Manual | No | 20 | 2017 | https://trec.nist.gov/pubs/trec26/papers/Overview-QA.pdf | https://github.com/abachaa/LiveQA_MedicalTask_TREC2017 | QA | Clinical | ? | English | No | Consumer Health Questions to NLM | |||||||||||||||||||||||
94 | https://github.com/bigscience-workshop/biomedical/issues/230 | EPIC-QA | JSON | Model-assisted Manual | No | ? | 2020 | ? | https://bionlp.nlm.nih.gov/epic_qa/#collection | QA | Clinical | https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/ | English | No | CORD-19 | Epidemic Question Answering for ad-hoc questions about the disease COVID-19 | Answer judgments will be provided by librarian indexers at the U.S. National Library of Medicine (NLM). | |||||||||||||||||||||
95 | https://github.com/bigscience-workshop/biomedical/issues/231 | MedDialog | text, JSON | Found | https://huggingface.co/datasets/medical_dialog | 1 | 2020 | train,dev,test | https://arxiv.org/abs/2004.03329 | https://github.com/UCSD-AI4H/Medical-Dialogue-System | Dialog Classification | Clinical | Public for Research | English, Chinese | No | iclinic.com, healthcaremagic.com, haodf.com | The MedDialog dataset contains conversations between doctors and patients. It has 1.1 million dialogues in Chinese and 0.26 million dialogues in English | |||||||||||||||||||||
96 | https://github.com/bigscience-workshop/biomedical/issues/170 | CSIRO: Matching Patients to Clinical Trials | 10.1145/2911451.2914672 | text, XML | - | Manual | No | 14 | 2015 | NONE | https://dl.acm.org/doi/abs/10.1145/2911451.2914672 | https://data.csiro.au/collections/collection/CIcsiro:17152v1 | IR | Clinical | CC BY-SA 4.0 | English | No | ClinicalTrials.gov | A Test Collection for Matching Patient to Clinical Trials | 4 Medical professionals | ||||||||||||||||||
97 | https://github.com/bigscience-workshop/biomedical/issues/232 | ParaMed | text | Found | No | 4 | 2020 | train,dev,test | https://arxiv.org/abs/2005.09133 | https://github.com/boxiangliu/ParaMed | Translation | Biomedical | ? | Mandarin, English | Yes | NEJM | ||||||||||||||||||||||
98 | https://github.com/bigscience-workshop/biomedical/issues/233 | PhoNER | 10.18653/v1/2021.naacl-main.173 | CoNLL | - | Manual | No | 5 | 2021 | train,dev,test | https://aclanthology.org/2021.naacl-main.173/ | https://github.com/VinAIResearch/PhoNER_COVID19 | NER | Biomedical | ? | Vietnamese | No | News sites | ||||||||||||||||||||
99 | https://github.com/bigscience-workshop/biomedical/issues/234 | Evidence-Infer-Treatment | text | Manual | https://huggingface.co/datasets/evidence_infer_treatment | 7 | 2020 | train,dev,test | https://arxiv.org/abs/2005.04177 | https://github.com/jayded/evidence-inference | Reasoning | Clinical | MIT License | English | No | Given both the answers and rationales of the prompt generator and prompt annotator, a third doctor — the verifier — was asked to determine the validity of both of the previous stages | ||||||||||||||||||||||
100 | https://github.com/bigscience-workshop/biomedical/issues/172 | CADEC | 10.1016/j.jbi.2015.03.010 | BRAT | - | Manual | No | 174 | 2015 | NONE | https://www.sciencedirect.com/science/article/pii/S1532046415000532?via%3Dihub | https://data.gov.au/dataset/ds-dap-csiro%3A10948/details?q= | NER/NER, RE | Social Media | CSIRO Data License (Non-commercial) | English | No | AskaPatient | An annotated corpus of consumer reviews in pharmacovigilance. | four medical students |