This table compiles the list of biomedically-related corpora available for named entity recognition (and some also suitable for association detection). This has been published as part of the paper:

Dieter Galea, Ivan Laponogov, Kirill Veselkov; Exploiting and assessing multi-source data for supervised biomedical named entity recognition, Bioinformatics, bty152, https://doi.org/10.1093/bioinformatics/bty152

If you know of other relevant corpora, please submit a pull request and I'll happily approve it.

Corpus	Year	Format	Documents	Original Publication	Downloaded From	Other URLs
Ab3P (Abbreviation Plus P-Precision)	2008	BioC	1250 PubMed Abstracts	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2576267/	http://bioc.sourceforge.net/
AIMed	2005	BioC	~ 1000 MEDLINE abstracts (200 abstracts)	http://www.sciencedirect.com/science/article/pii/S0933365704001319	http://corpora.informatik.hu-berlin.de/	http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.101.3218&rep=rep1&type=pdf
AnatEM (Anatomical entity mention recognition)	2013	CONLL, standoff	1212 docs (500 docs from AnEM + 262 from MLEE + 450 others)	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957068/	http://nactem.ac.uk/anatomytagger/#AnatEM
AnEM	2012	BioC	500 docs (PubMed and PMC); abstracts and full text drawn randomly	http://www.nactem.ac.uk/anatomy/docs/ohta2012opendomain.pdf	http://corpora.informatik.hu-berlin.de/
AZDC (Arizona Disease Corpus)	2009	IeXML, .txt	2856 PubMed abstracts (2775 sentences). Other source says 794 PubMed Abstracts	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2352871/	http://www.ebi.ac.uk/Rebholz-srv/CALBC/corpora/IeXML/goldcorpus/azdc-1.xml	http://diego.asu.edu/downloads/AZDC_6-26-2009.txt
BEL (BioCreative V5 BEL Track)	2016	BioC		https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995071/	https://wiki.openbel.org/display/BIOC/Datasets
BioADI	2009	BioC	1201 PubMed abstracts	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788358/	http://bioc.sourceforge.net/
BioCause	2013	standoff	19 full-text documents	http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-2	http://www.nactem.ac.uk/biocause/download.php
BioCreative-PPI		XML			https://www2.informatik.hu-berlin.de/~hakenber/links/benchmarks.html
BioGRID	2017	BioC	120 full text articles	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5225395/	http://bioc.sourceforge.net/BioC-BioGRID.html
BioInfer	2007	BioC	1100 sentences from biomedical literature	http://www.biomedcentral.com/1471-2105/8/50	http://corpora.informatik.hu-berlin.de/	http://mars.cs.utu.fi/BioInfer
BioMedLat	2016	standoff	643 BioASQ questions/factoids	https://www.semanticscholar.org/paper/BioMedLAT-Corpus-Annotation-of-the-Lexical-Answer-Neves-Kraus/b0f09f94015771c31bd2483efdd8f0f86996384e	https://github.com/mariananeves/BioMedLAT
BioText	2004	txt	100 titles and 40 abstracts	http://biotext.berkeley.edu/papers/acl04-relations.pdf	https://www2.informatik.hu-berlin.de/~hakenber/links/benchmarks.html
CDR (BioCreative V)		BioC			http://bioc.sourceforge.net/
CellFinder 1.0	2012	BioC	10 full documents from PMC from (Loser et al. 2009) on "Human Embryonic Stem Cell Lines and Their Use in International Research"	http://www.nactem.ac.uk/biotxtm2012/presentations/Neves-pres.pdf	http://corpora.informatik.hu-berlin.de/	http://cellfinder.de/about/annotation/
CG Cancer-Genetics (BioNLP-ST 2013)	2013	BioC, standoff		http://aclweb.org/anthology/W/W13/W13-2008.pdf	http://2013.bionlp-st.org/tasks/cancer-genetics
CHEMDNER (BioCreative IV Track 2)	2013	BioC / standoff		http://www.biocreative.org/media/store/files/2013/bc4_v2_1.pdf	http://www.biocreative.org/tasks/biocreative-iv/chemdner/
Chemical Patent Corpus	2014	standoff	200 patents	http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107477	http://biosemantics.org/index.php/resources/chemical-patent-corpus
CoMAGC	2013	XML	821 sentences on prostate, breast and ovarian cancer	http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-323	http://biopathway.org/CoMAGC/
CRAFT	2012		97 full OA biomedical articles		http://bionlp-corpora.sourceforge.net/CRAFT/
Craven (Wisconsin corpus)	1999	other	1,529,731 sentences (automated)	https://www.biostat.wisc.edu/~craven/ie/ReadMe	https://www.biostat.wisc.edu/~craven/ie/
CTD (BioCreative IV Track 3)		BioC			http://www.biocreative.org/tasks/biocreative-iv/track-3-CTD/
DDICorpus	2011 2013	BioC	792 texts from DrugBank and 233 Medline abstracts	https://www.ncbi.nlm.nih.gov/pubmed/23906817	http://bioc.sourceforge.net/ http://corpora.informatik.hu-berlin.de/	http://labda.inf.uc3m.es/ddicorpus
DIP-PPI (Database of Interaction Proteins)		other	Only proteins from yeast.		https://www2.informatik.hu-berlin.de/~hakenber/corpora/
EBI:diseases	2008	other	856 sentences from 624 abstracts	http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-S3-S3	https://www2.informatik.hu-berlin.de/~hakenber/links/benchmarks.html	ftp://ftp.ebi.ac.uk/pub/software/textmining/corpora/diseases
eFIP	2012 2015	xlsx		https://www.ncbi.nlm.nih.gov/pubmed/23221174 https://www.ncbi.nlm.nih.gov/pubmed/25833953	http://research.bioinformatics.udel.edu/iprolink/corpora.php
EMU (Extractor of Mutations)	2011	other		https://www.ncbi.nlm.nih.gov/pubmed/21138947	http://bioinf.umbc.edu/EMU/ftp/
EU-ADR	2012	other	300 PubMed abstracts (drug-disoder, drug-target, gene-disorder, SNP-disorder)	http://www.sciencedirect.com/science/article/pii/S1532046412000573	http://biosemantics.org/index.php/resources/euadr-corpus
Exhaustive PTM (BioNLP 2011)				http://dl.acm.org/citation.cfm?id=2002902.2002920	https://github.com/dterg/exhaustive-ptm
FlySlip	2007	CONLL	82 abstracts, 5 full papers	https://www.ncbi.nlm.nih.gov/pubmed/17990496	http://compbio.ucdenver.edu/ccp/corpora/obtaining.shtml	http://www.wiki.cl.cam.ac.uk/rowiki/NaturalLanguage/FlySlip/Flyslip-resources
FSU-PRGE	2010	leXML	3236 MEDLINE abstracts (35,519 sentences)	http://aclweb.org/anthology/W/W10/W10-1838.pdf	http://www.ebi.ac.uk/Rebholz-srv/CALBC/corpora/corpora.html
GAD	2015	csv		http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0472-9	http://ibi.imim.es/research-lines/biomedical-text-mining/corpora/
GeneReg	2010	BioC	314 Abstracts	http://www.lrec-conf.org/proceedings/lrec2010/pdf/407_Paper.pdf	http://corpora.informatik.hu-berlin.de/	http://www.julielab.de/Resources/GeneReg.html
GeneTag (BioCreative II Gene Mention)	2005	BioC	20,000 sentences MEDLINE	https://www.ncbi.nlm.nih.gov/pubmed/15960837	https://www2.informatik.hu-berlin.de/~hakenber/links/benchmarks.html http://bioc.sourceforge.net/
GENIA (BioNLP Shared Task 2009)					http://www.nactem.ac.uk/tsujii/GENIA/SharedTask/detail.shtml#downloads
GENIA (BioNLP Shared Task 2011)		BioC, standoff			https://sites.google.com/site/bionlpst/home/epigenetics-and-post-translational-modifications http://2011.bionlp-st.org	http://corpora.informatik.hu-berlin.de/
GENIA (term annotation)	2003	BioC, XML			http://corpora.informatik.hu-berlin.de/	http://www.nactem.ac.uk/aNT/genia.html
GETM	2010	BioC, standoff		http://dl.acm.org/citation.cfm?id=1869970	http://corpora.informatik.hu-berlin.de/	http://getm-project.sourceforge.net/
GREC (Gene Regulation Event Corpus)	2009	BioC, standoff, XML	240 MEDLINE (167 on E.coli and 73 on Human)	http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-349	http://corpora.informatik.hu-berlin.de/	http://www.nactem.ac.uk/GREC/
HIMERA	2016	standoff		http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144717	http://www.nactem.ac.uk/himera/
HPRD50 (Human Protein Reference Database)	2004	BioC	50 abstracts	https://www.ncbi.nlm.nih.gov/pubmed/14681466	http://corpora.informatik.hu-berlin.de/	http://www2.bio.ifi.lmu.de/publications/RelEx/
IDP4+	2007	anndoc	860 abstracts/full-texts	https://academic.oup.com/bioinformatics/article/33/12/1852/2991428	https://www.tagtog.net/-corpora/IDP4+
IEPA	2002	BioC	slightly over 300 MEDLINE abstracts	https://www.ncbi.nlm.nih.gov/pubmed/11928487	http://corpora.informatik.hu-berlin.de/	http://orbit.nlm.nih.gov/resource/iepa-corpus
iHOP	2004	other	~ 160 sentences	https://www.ncbi.nlm.nih.gov/pubmed/15226743	http://www.ihop-net.org/UniPub/iHOP/info/gene_index/manual/1.html
iProLINK / RLIMS	2004	other, XML, BioC		https://www.ncbi.nlm.nih.gov/pubmed/15556482	http://research.bioinformatics.udel.edu/iprolink/corpora.php
iSimp	2014	BioC	130 MEDLINE abstracts (1199 sentences)	https://www.ncbi.nlm.nih.gov/pubmed/24850848	http://research.bioinformatics.udel.edu/isimp/corpus.html
Linnaeus	2010	standoff		http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-85	https://www2.informatik.hu-berlin.de/~hakenber/links/benchmarks.html	http://linnaeus.sourceforge.net/
LLL (Learning Language in Logic)	2005	BioC		https://www.cs.york.ac.uk/aig/lll/lll05/lll05-nedellec.pdf	http://corpora.informatik.hu-berlin.de/	http://genome.jouy.inra.fr/texte/LLLchallenge/
MEDSTRACT		BioC	199 PubMed citations	https://www.ncbi.nlm.nih.gov/pubmed/11604766	http://bioc.sourceforge.net/
MedTag	2005	other		https://www.researchgate.net/publication/234785358_MedTag_a_collection_of_biomedical_annotations	ftp://ftp.ncbi.nlm.nih.gov/pub/lsmith/MedTag/medtag.tar.gz https://sourceforge.net/projects/medtag/
Metabolite and Enzyme	2011	BioC, XML	296 abstracts	http://link.springer.com/article/10.1007%2Fs11306-010-0251-6	http://www.nactem.ac.uk/metabolite-corpus/	http://argo.nactem.ac.uk/bioc/
miRTex	2015	BioC, standoff	350 abstracts (200 development, 150 test)	http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004391	http://research.bioinformatics.udel.edu/iprolink/corpora.php
MLEE	2012	CONLL, standoff	262 PubMed abstracts on molecular mechanisms of cancer (specifically relating to angiogenesis)	https://academic.oup.com/bioinformatics/article/28/18/i575/249872/Event-extraction-across-multiple-levels-of	http://nactem.ac.uk/MLEE/
mTOR pathway event corpus (BioNLP 2011)	2011	standoff		http://dl.acm.org/citation.cfm?id=2002919	https://github.com/dterg/mtor-pathway/tree/master/original-data
MutationFinder	2007	other	305 abstract (development data set), 508 abstract test set	https://www.ncbi.nlm.nih.gov/pubmed/17495998	http://mutationfinder.sourceforge.net/	https://github.com/rockt/SETH
Nagel		XML, standoff			http://sourceforge.net/projects/bionlp-corpora/files/ProteinResidue/
NCBI Disease	2012	other	6881 sentences in 793 PubMed abstracts	https://www.ncbi.nlm.nih.gov/pubmed/24393765	http://www.ncbi.nlm.nih.gov/CBBresearch/Fellows/Dogan/disease.html
OMM (Open Mutation Miner)	2012	other	40 full texts	https://www.ncbi.nlm.nih.gov/pubmed/22759648	http://www.semanticsoftware.info/open-mutation-miner
OSIRIS	2008	BioC, XML, standoff	105 articles	https://www.ncbi.nlm.nih.gov/pubmed/18251998	http://corpora.informatik.hu-berlin.de/	https://sites.google.com/site/laurafurlongweb/databases-and-tools/corpora
PC (Pathway Curation) (BioNLP-ST 2013)	2013	BioC			http://argo.nactem.ac.uk/bioc/	http://2013.bionlp-st.org/tasks/pathway-curation
PennBioIE-oncology	2004	leXML	1414 PubMed abstracts on cancer	http://www.aclweb.org/anthology/W04-3111	http://www.ebi.ac.uk/Rebholz-srv/CALBC/corpora/corpora.html
pGenN (Plant-GN)	2015	BioC	104 MEDLINE abstracts	http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135305	http://research.bioinformatics.udel.edu/iprolink/corpora.php
PICAD	2011	XML	1037 sentences from PubMed	http://dl.acm.org/citation.cfm?doid=2147805.2147853	http://ani.stat.fsu.edu/~jinfeng/resources/PICAD.txt	http://corpora.informatik.hu-berlin.de/
PolySearch (includes v1. and v2.)		other		https://www.ncbi.nlm.nih.gov/pubmed/25925572	http://polysearch.cs.ualberta.ca/downloads
ProteinResidue		other			http://bionlp-corpora.sourceforge.net/
SCAI_Klinger	2008	CONLL		https://academic.oup.com/bioinformatics/article/24/13/i268/235854/Detection-of-IUPAC-and-IUPAC-like-chemical-names	https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/corpora-for-chemical-entity-recognition.html
SCAI_Kolarik	2008	CONLL		http://www.lrec-conf.org/proceedings/lrec2008/workshops/W4_Proceedings.pdf#page=55	https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/corpora-for-chemical-entity-recognition.html
SETH	2016	standoff	630 publications from The American Journal of Human Genetics and Human Mutation	https://www.ncbi.nlm.nih.gov/pubmed/?term=27256315	https://github.com/rockt/SETH/tree/master/resources/SETH-corpus
SH (Schwartz and Hearst)	2003	BioC	1000 PubMed Abstracts	https://www.ncbi.nlm.nih.gov/pubmed/12603049	http://bioc.sourceforge.net/
SNPCorpus	2011	BioC	296 MEDLINE abstracts	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194196/	http://corpora.informatik.hu-berlin.de/	http://www.scai.fraunhofer.de/snp-normalization-corpus.html
Species	2013	standoff	800 PubMed abstracts	http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065390	http://species.jensenlab.org/	http://species.jensenlab.org/
T4SS (Type 4 Secretion System)	2011	CONLL		http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014780	http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014780
T4SS Event Extraction (BioNLP 2010)	2010	other		http://dl.acm.org/citation.cfm?id=1869961.1869980	https://github.com/dterg/t4ss-event
tmVar	2013	BioC	500 PubMed abstracts	https://www.ncbi.nlm.nih.gov/pubmed/23564842	https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/#tmVar	https://github.com/rockt/SETH
VariomeCorpus (hvp)	2013	BioC		https://www.ncbi.nlm.nih.gov/pubmed/23584833	http://corpora.informatik.hu-berlin.de/	http://www.opennicta.com/home/health/variome
Yapex	2002	other	99 training, 101 test MEDLINE abstracts	https://www.ncbi.nlm.nih.gov/pubmed/12460631	http://www.rostlab.org/~nlprot/yapex.txt	https://www2.informatik.hu-berlin.de/~hakenber/links/benchmarks.html