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 *.jpeg filter=lfs diff=lfs merge=lfs -text
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+BioCreative-V-CDR-Corpus/CDR_Data/CDR_Data/BC5CDR.presentation.pdf filter=lfs diff=lfs merge=lfs -text
+chemdner_corpus/development.bioc.xml filter=lfs diff=lfs merge=lfs -text
+chemdner_corpus/evaluation.bioc.xml filter=lfs diff=lfs merge=lfs -text
+chemdner_corpus/evaluation.predictions.bioc.xml filter=lfs diff=lfs merge=lfs -text
+chemdner_corpus/evaluation.predictions.txt filter=lfs diff=lfs merge=lfs -text
+chemdner_corpus/silver.abstracts.txt filter=lfs diff=lfs merge=lfs -text
+chemdner_corpus/silver.predictions.txt filter=lfs diff=lfs merge=lfs -text
+chemdner_corpus/training.bioc.xml filter=lfs diff=lfs merge=lfs -text
+drugprot-gs-training-development/test-background/test_background_abstracts.tsv filter=lfs diff=lfs merge=lfs -text
+drugprot-gs-training-development/test-background/test_background_entities.tsv filter=lfs diff=lfs merge=lfs -text

BioCreative-V-CDR-Corpus/BC5CDR_Evaluation-0.0.3.zip

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BioCreative-V-CDR-Corpus/CDR_Data.zip

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BioCreative-V-CDR-Corpus/CDR_Data/CDR_Data/BC5CDR.presentation.pdf

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BioCreative-V-CDR-Corpus/CDR_Data/CDR_Data/README.txt

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+===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any 
+*  particular purpose.
+*
+*  Please cite the authors in any work or product based on this material:
+*
+*  1. Wei CH, Peng Y, Leaman R, Davis AP, Mattingly CJ, Li J, Wiegers TC, 
+*     Lu Z. Overview of the BioCreative V Chemical Disease Relation (CDR) 
+*     Task, Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 
+*     p154-166, 2015 
+*
+*  2. Li J, Sun Y, Johnson RJ, Sciaky D, Wei CH, Leaman R, Davis AP, Mattingly CJ,
+*     Wiegers TC, Lu Z. Anotating chemicals, diseases and their interactions in 
+*     biomedical literature, Proceedings of the Fifth BioCreative Challenge 
+*     Evaluation Workshop, p173-182, 2015 
+*
+*  3. Leaman R, Dogan RI, Lu Z. DNorm: disease name normalization with pairwise 
+*     learning to rank, Bioinformatics 29(22):2909-17, 2013
+* 
+*  4. Leaman R, Wei CH, Lu Z. tmChem: a high performance approach for chemical 
+*     named entity recognition and normalization. J Cheminform, 7:S3, 2015
+*
+*
+==========================================================================
+
+This directory contains the annotated corpus created and used in the BioCreative 
+V Chemical Disease Relation (CDR) Challenge Task [1]. In addition, it contains 
+text-mined results of two computational tools for disease & chemcial NER. All data
+are made available in both BioC XML and PubTator text formats. 
+
+./CDR.Corpus: The annotated CDR corpus of 1500 PubMed articles of chemicals, 
+diseases, and chemical-induced disease relationships [2]. 
+
+./DNorm.TestSet: The text-mined results of diseases on the test set using DNorm [3].
+		 The normalization performance is 0.81 (P), 0.80 (R), and 0.81 (F). 
+
+./tmChem.TestSet: The text-mined results of chemicals on the test set using tmChem [4].
+		  The normalization performance is 0.92 (P), 0.90 (R), and 0.91 (F). 
+

BioCreative-V-CDR-Corpus/README.md

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+# BioCreative-V-CDR-Corpus
+Since the official website of the BioCreative cannot be open any more, we upload the BioCreative-V Chemial-Disease Relation (CDR) Corpus for public research.
+
+
+BioCreative V - Chemical-disease relation (CDR) task corpus release
+
+Task information:
+	Automatic detection of chemical/drugs and diseases, and their relations in PubMed abstracts. In particular, the CDR task focuses on extracting the relationship of drug-induced diseases. 
+
+Organizers:
+	Zhiyong Lu, NCBI (zhiyong.lu@nih.gov)
+	Thomas Wiegers, North Carolina State University (tcwieger@ncsu.edu )
+	
+Files:
+	CDR_sample.txt : Sample Set (50 articles) in PubTator format
+	CDR_sample.xml : Sample Set (50 articles) in BioC format
+	BioC.dtd : The DTD file describes the structure of an XML file, additional information, such as the data semantics, must be known before the data in the XML file can be effectively used.
+	BC5CDR.key: BioC XML file. The key file allows the creator to specify details of how the data in the XML file should be interpreted.
+	
+Format:
+	BioC : It's a sample format to share text data and annotations. You can find sample code (e.g., C++, Java, Perl and Python) in http://bioc.sourceforge.net/ to parse information of BioC file.
+	
+	PubTator : PubTator (http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/) is a web-based tool for accelerating manual literature curation through the use of advanced text-mining techniques.
+		The first row is title, and second row is abstract. The rows below abstract are bioconcept mentions. Between any two articles, a blank line is required. We use six attributes to describe an 
+		annotation, separated by Tab keys. The six attributes are: 
+			
+			PMID<tab>START OFFSET<tab>END OFFSET<tab>text MENTION<tab>mention TYPE (e.g. Disease)<tab>database IDENTIFIER<tab>Individual mentions
+	
+		Note that the last attribute "Individual mentions" is optional. It is only annotated once the MENTION is a composite mention. The START OFFSET is the first character offset of the mention while 
+		END OFFSET is the last. 
+		
+		Example:
+		
+			3403780|t|Paracetamol-associated coma, metabolic acidosis, renal and hepatic failure.
+			3403780|a|A case of metabolic acidosis, acute renal failure and hepatic failure following paracetamol ingestion is presented. The diagnostic difficulty at presentation is highlighted .....
+			3403780	0	11	Paracetamol	Chemical	D000082	
+			3403780	23	27	coma	Disease	D003128	
+			3403780	29	47	metabolic acidosis	Disease	D000138	
+			3403780	39	47	acidosis	Disease	D000138	
+			3403780	49	74	renal and hepatic failure	Disease	D058186|D017093	renal failure|hepatic failure
+			3403780	86	104	metabolic acidosis	Disease	D000138	
+			3403780	96	104	acidosis	Disease	D000138	
+			3403780	106	145	acute renal failure and hepatic failure	Disease	D058186|D017114	acute renal failure|acute hepatic failure
+			3403780	156	167	paracetamol	Chemical	D000082	
+			3403780	CID	D000082	D000138
+			3403780	CID	D000082	D017114
+			3403780	CID	D000082	D058186

BioNLP-ST_2013_PC/BioNLP-ST_2013_PC_development_data/LICENSE

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+1. Copyright of abstracts
+
+The abstracts contained in this corpus are from PubMed(R), a database
+of the U.S. National Library of Medicine (NLM).
+
+NLM data are produced by a U.S. Government agency and include works of
+the United States Government that are not protected by U.S. copyright
+law but may be protected by non-US copyright law, as well as abstracts
+originating from publications that may be protected by U.S. copyright
+law.
+
+NLM assumes no responsibility or liability associated with use of
+copyrighted material, including transmitting, reproducing,
+redistributing, or making commercial use of the data. NLM does not
+provide legal advice regarding copyright, fair use, or other aspects
+of intellectual property rights. Persons contemplating any type of
+transmission or reproduction of copyrighted material such as abstracts
+are advised to consult legal counsel.
+
+2. Copyright of annotations
+
+The copyrights of annotations jointly created by the National Centre
+for Text Mining (NaCTeM) and the Korea Institute of Science and
+Technology Information (KISTI) belong in their entirety to NaCTeM and
+KISTI.
+
+3. Licence terms
+
+Use and distribution of abstracts drawn from PubMed is subject to the
+PubMed(R) license terms as stated in Clause 1.
+
+Annotations are licensed under the Creative Commons
+Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0) license. To view a
+copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/ 
+or send a letter to Creative Commons, 444 Castro Street, Suite 900,
+Mountain View, California, 94041, USA.
+
+4. References
+
+- NaCTeM : http://www.nactem.ac.uk/
+- KISTI  : http://en.kisti.re.kr/
+- PubMed : http://www.pubmed.gov/
+- NLM (United States National Library of Medicine) : http://www.nlm.nih.gov/

BioNLP-ST_2013_PC/BioNLP-ST_2013_PC_development_data/PMID-10072383.a1

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+T1	Cellular_component 39 51	kinetochores
+T2	Gene_or_gene_product 59 77	type 1 phosphatase
+T3	Gene_or_gene_product 78 83	Glc7p
+T4	Cellular_component 185 197	kinetochores
+T5	Gene_or_gene_product 238 264	type 1 protein phosphatase
+T6	Gene_or_gene_product 273 280	glc7-10
+T7	Cellular_component 300 311	microtubule
+T8	Cellular_component 342 353	centromeric
+T9	Cellular_component 383 394	kinetochore
+T10	Gene_or_gene_product 462 488	type 1 protein phosphatase
+T11	Gene_or_gene_product 490 493	PP1
+T12	Gene_or_gene_product 521 528	glc7-10
+T13	Cellular_component 554 565	kinetochore
+T14	Cellular_component 566 577	microtubule
+T15	Cellular_component 628 638	chromosome
+T16	Gene_or_gene_product 671 677	Ndc10p
+T17	Complex 718 722	CBF3
+T18	Gene_or_gene_product 749 756	glc7-10
+T19	Gene_or_gene_product 767 773	Ndc10p
+T20	Gene_or_gene_product 800 807	glc7-10
+T21	Gene_or_gene_product 855 861	Ndc10p
+T22	Cellular_component 880 891	microtubule
+T23	Gene_or_gene_product 914 921	glc7-10
+T24	Gene_or_gene_product 964 971	glc7-10
+T25	Cellular_component 1011 1018	spindle
+T26	Cellular_component 1066 1077	kinetochore
+T27	Cellular_component 1078 1089	microtubule
+T28	Cellular_component 1137 1148	kinetochore
+T29	Cellular_component 1171 1178	spindle

BioNLP-ST_2013_PC/BioNLP-ST_2013_PC_development_data/PMID-10072383.a2

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+*	Equiv T10 T11
+T30	Regulation 0 10	Regulation
+E1	Regulation:T30 Theme:T1 Cause:T3
+T31	Regulation 146 156	regulation
+E2	Regulation:T31 Theme:T4
+T32	Phosphorylation 777 796	hyperphosphorylated
+E3	Phosphorylation:T32 Theme:T19
+T33	Phosphorylation 1113 1133	hyperphosphorylation
+E4	Phosphorylation:T33 Theme:T21

BioNLP-ST_2013_PC/BioNLP-ST_2013_PC_development_data/PMID-10072383.txt

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+Regulation of Saccharomyces cerevisiae kinetochores by the type 1 phosphatase Glc7p. 
+We have investigated the role of protein phosphorylation in regulation of Saccharomyces cerevisiae kinetochores. By use of phosphatase inhibitors and a type 1 protein phosphatase mutant (glc7-10), we show that the microtubule binding activity, but not the centromeric DNA-binding activity, of the kinetochore complex is regulated by a balance between a protein kinase and the type 1 protein phosphatase (PP1) encoded by the GLC7 gene. glc7-10 mutant cells exhibit low kinetochore-microtubule binding activity in vitro and a high frequency of chromosome loss in vivo. Specifically, the Ndc10p component of the centromere DNA-binding CBF3 complex is altered by the glc7-10 mutation; Ndc10p is hyperphosphorylated in glc7-10 extracts. Furthermore, addition of recombinant Ndc10p reconstitutes the microtubule-binding activity of a glc7-10 extract to wild-type levels. Finally, the glc7-10-induced mitotic arrest is abolished in spindle checkpoint mutants, suggesting that defects in kinetochore-microtubule interactions caused by hyperphosphorylation of kinetochore proteins activate the spindle checkpoint.

BioNLP-ST_2013_PC/BioNLP-ST_2013_PC_development_data/PMID-10329687.a1

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+T1	Gene_or_gene_product 16 54	Na+-dependent multivitamin transporter
+T2	Cellular_component 108 119	chromosomal
+T3	Gene_or_gene_product 160 198	Na+-dependent multivitamin transporter
+T4	Gene_or_gene_product 200 204	SMVT
+T5	Simple_chemical 251 263	pantothenate
+T6	Simple_chemical 265 271	biotin
+T7	Simple_chemical 277 284	lipoate
+T8	Cellular_component 392 405	transmembrane
+T9	Gene_or_gene_product 473 477	SMVT
+T10	Simple_chemical 665 668	Na+
+T11	Simple_chemical 681 693	pantothenate
+T12	Simple_chemical 695 701	biotin
+T13	Simple_chemical 707 714	lipoate
+T14	Simple_chemical 788 800	pantothenate
+T15	Simple_chemical 804 810	biotin
+T16	Simple_chemical 815 818	Na+
+T17	Simple_chemical 853 856	Na+
+T18	Gene_or_gene_product 897 901	SMVT
+T19	Simple_chemical 988 1000	pantothenate
+T20	Simple_chemical 1002 1008	biotin
+T21	Simple_chemical 1014 1021	lipoate
+T22	Simple_chemical 1027 1030	Na+
+T23	Cellular_component 1136 1147	chromosomal
+T24	Gene_or_gene_product 1174 1178	SMVT
+T25	Gene_or_gene_product 1189 1193	SMVT
+T26	Gene_or_gene_product 1274 1278	SMVT
+T27	Cellular_component 1298 1313	chromosome 2p23

BioNLP-ST_2013_PC/BioNLP-ST_2013_PC_development_data/PMID-10329687.a2

@@ -0,0 +1,15 @@
+*	Equiv T3 T4
+T28	Transport 213 223	transports
+T29	Positive_regulation 213 223	transports
+E1	Transport:T28 Theme:T5
+E2	Positive_regulation:T29 Cause:T3 Theme:E1
+E3	Transport:T28 Theme:T6
+E4	Transport:T28 Theme:T7
+E5	Positive_regulation:T29 Cause:T3 Theme:E3
+E6	Positive_regulation:T29 Cause:T3 Theme:E4
+T30	Gene_expression 908 917	expressed
+E7	Gene_expression:T30 Theme:T18
+T31	Localization 1148 1160	localization
+E8	Localization:T31 ToLoc:T23 Theme:T24
+T32	Localization 1287 1294	located
+E9	Localization:T32 Theme:T26 ToLoc:T27

BioNLP-ST_2013_PC/BioNLP-ST_2013_PC_development_data/PMID-10329687.txt

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+Human placental Na+-dependent multivitamin transporter. Cloning, functional expression, gene structure, and chromosomal localization. 
+We have cloned the human Na+-dependent multivitamin transporter (SMVT), which transports the water-soluble vitamins pantothenate, biotin, and lipoate, from a placental choriocarcinoma cell line (JAR). The cDNA codes for a protein of 635 amino acids with 12 transmembrane domains and 4 putative sites for N-linked glycosylation. The human SMVT exhibits a high degree of homology (84% identity and 89% similarity) to the rat counterpart. When expressed in HRPE cells, the cDNA-induced transport process is obligatorily dependent on Na+ and accepts pantothenate, biotin, and lipoate as substrates. The relationship between the cDNA-specific uptake rate of pantothenate or biotin and Na+ concentration is sigmoidal with a Na+:vitamin stoichiometry of 2:1. The human SMVT, when expressed in Xenopus laevis oocytes, induces inward currents in the presence of pantothenate, biotin, and lipoate in a Na+-, concentration-, and potential-dependent manner. We also report here on the structural organization and chromosomal localization of the human SMVT gene. The SMVT gene is approximately 14 kilobase pairs in length and consists of 17 exons. The SMVT gene is located on chromosome 2p23 as evidenced by somatic cell hybrid analysis and fluorescence in situ hybridization.

BioNLP-ST_2013_PC/BioNLP-ST_2013_PC_development_data/PMID-10424772.a1

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+T1	Gene_or_gene_product 0 16	Aldose reductase
+T2	Simple_chemical 63 77	norepinephrine
+T3	Simple_chemical 124 138	norepinephrine
+T4	Simple_chemical 140 142	NE
+T5	Simple_chemical 161 188	3,4-dihydroxymandelaldehyde
+T6	Simple_chemical 190 195	DHMAL
+T7	Simple_chemical 234 260	3,4-dihydroxymandelic acid
+T8	Simple_chemical 262 266	DHMA
+T9	Simple_chemical 271 296	3,4-dihydroxyphenylglycol
+T10	Simple_chemical 298 302	DHPG
+T11	Gene_or_gene_product 363 379	aldose reductase
+T12	Gene_or_gene_product 387 405	aldehyde reductase
+T13	Simple_chemical 426 430	DHPG
+T14	Simple_chemical 436 441	DHMAL
+T15	Simple_chemical 470 472	NE
+T16	Gene_or_gene_product 478 494	aldose reductase
+T17	Gene_or_gene_product 514 531	monoamine oxidase
+T18	Gene_or_gene_product 533 536	MAO
+T19	Simple_chemical 567 571	DHPG
+T20	Gene_or_gene_product 624 642	aldehyde reductase
+T21	Simple_chemical 658 662	DHPG
+T22	Gene_or_gene_product 705 721	aldose reductase
+T23	Gene_or_gene_product 770 786	aldose reductase
+T24	Gene_or_gene_product 791 809	aldehyde reductase
+T25	Gene_or_gene_product 894 910	aldose reductase
+T26	Gene_or_gene_product 966 982	aldose reductase
+T27	Simple_chemical 1035 1039	DHMA
+T28	Simple_chemical 1119 1121	NE
+T29	Simple_chemical 1167 1171	DHPG
+T30	Simple_chemical 1272 1279	AL 1576
+T31	Gene_or_gene_product 1314 1330	aldose reductase
+T32	Simple_chemical 1341 1345	DHPG
+T33	Simple_chemical 1351 1353	NE
+T34	Gene_or_gene_product 1373 1376	MAO
+T35	Gene_or_gene_product 1406 1422	aldose reductase
+T36	Gene_or_gene_product 1457 1475	aldehyde reductase
+T37	Simple_chemical 1497 1501	DHPG
+T38	Gene_or_gene_product 1517 1533	aldose reductase
+T39	Gene_or_gene_product 1564 1582	aldehyde reductase
+T40	Simple_chemical 1620 1625	DHMAL
+T41	Simple_chemical 1629 1633	DHPG

BioNLP-ST_2013_PC/BioNLP-ST_2013_PC_development_data/PMID-10424772.a2

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+*	Equiv T3 T4
+*	Equiv T5 T6
+*	Equiv T7 T8
+*	Equiv T9 T10
+*	Equiv T17 T18
+T42	Conversion 48 59	deamination
+T43	Positive_regulation 48 59	deamination
+E1	Conversion:T42 Theme:T2
+E2	Positive_regulation:T43 Cause:T1 Theme:E1
+T44	Conversion 147 157	deaminated
+E3	Conversion:T44 Theme:T3 Product:T5
+T45	Conversion 214 223	converted
+E4	Conversion:T45 Theme:T5 Product:T7
+E5	Conversion:T45 Theme:T5 Product:T9
+T46	Positive_regulation 349 359	importance
+E6	Positive_regulation:T46 Theme:E8 Cause:T11
+E7	Positive_regulation:T46 Theme:E8 Cause:T12
+T47	Conversion 413 422	formation
+E8	Conversion:T47 Product:T13 Theme:T14
+T48	Positive_regulation 538 546	resulted
+E9	Positive_regulation:T48 Theme:E11 Cause:T16
+E10	Positive_regulation:T48 Theme:E11 Cause:T17
+T49	Conversion 554 563	formation
+E11	Conversion:T49 Theme:T15 Product:T19
+T50	Conversion 648 657	generated
+T51	Positive_regulation 648 657	generated
+E12	Conversion:T50 Product:T21
+E13	Positive_regulation:T51 Cause:T20 Theme:E12
+T52	Gene_expression 751 761	expression
+E14	Gene_expression:T52 Theme:T23
+E15	Gene_expression:T52 Theme:T24
+T53	Positive_regulation 1005 1014	increased
+E16	Positive_regulation:T53 Theme:T27
+T54	Regulation 1108 1115	effects
+E17	Regulation:T54 Theme:T28
+T55	Negative_regulation 1155 1163	decrease
+E18	Negative_regulation:T55 Theme:T29 Cause:T30
+T56	Conversion 1331 1340	generates
+T57	Positive_regulation 1331 1340	generates
+E19	Conversion:T56 Product:T32 Theme:T33
+E20	Positive_regulation:T57 Theme:E19 Cause:T31
+E21	Positive_regulation:T57 Theme:E19 Cause:T34
+T58	Positive_regulation 1442 1451	important
+E22	Positive_regulation:T58 Theme:E24 Cause:T36
+E23	Positive_regulation:T58 Theme:E24 Cause:T35
+T59	Conversion 1484 1493	formation
+E24	Conversion:T59 Product:T37
+T60	Negative_regulation 1537 1546	inhibited
+E25	Negative_regulation:T60 Theme:T38
+T61	Positive_regulation 1587 1597	compensate
+E26	Positive_regulation:T61 Cause:T39 Theme:E27
+T62	Conversion 1606 1616	conversion
+E27	Conversion:T62 Theme:T40 Product:T41