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1STITCH 2: an interaction network database for small molecules and proteins
M. Kuhn1, D. Szklarczyk, A. Franceschini, M. Campillos, C. von Mering, L. Jensen, A. Beyer1, and P. Bork. Nucleic Acids Research, (November 2009)
14 years ago by @huiyangsfsu
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CAT
CAT-DBS-protien-chemical
CAT-NETWORK
CAT-ONLINE-SW
CAT-REL-COOR
CAT-REL-NLP
CAT-REL-RULE
CAT-VIZ
STITCH2
bk-ngx
CATCAT-DBS-protien-chemicalCAT-NETWORKCAT-ONLINE-SWCAT-REL-COORCAT-REL-NLPCAT-REL-RULECAT-VIZSTITCH2bk-ngx
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1BioContrasts: Extracting and Exploiting Protein-Protein Contrastive Relations from Biomedical Literature
J. jae Kim, Z. Zhang, J. Park, and S. Ng. Bioinformatics, 22 (5): 597-605 (2006)
14 years ago by @huiyangsfsu
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CAT
CAT-DBS
CAT-ONLINE-SW
CAT-REL-RULE
PPContrast
PPI
bk-ngx
CATCAT-DBSCAT-ONLINE-SWCAT-REL-RULEPPContrastPPIbk-ngx
(0)
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2Mining biomedical literature using information extraction.
R. Feldman, Y. Regev, M. Finkelstein-Landau, E. Hurvitz, and B. Kogan. Current Drug Discovery, (October 2002)
14 years ago by @huiyangsfsu
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CAT
CAT-REL-RULE
biomedical
bk-ngx
clear
extraction
forest
information
CATCAT-REL-RULEbiomedicalbk-ngxclearextractionforestinformation
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3RelEx - Relation extraction using dependency parse trees.
K. Fundel, R. Küffner, and R. Zimmer. Bioinformatics, 23 (3): 365-371 (2007)
14 years ago by @huiyangsfsu
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CAT
CAT-REL-NLP
CAT-REL-RULE
CAT-REL-dependency
bk-ngx
CATCAT-REL-NLPCAT-REL-RULECAT-REL-dependencybk-ngx
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3Textpresso: an ontology-based information retrieval and extraction system for biological literature
H. Müller, E. Kenny, and P. Sternberg. PLoS Biol., 2 (11): e309- (November 2004)
14 years ago by @huiyangsfsu
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CAT
CAT-FULL
CAT-IE
CAT-IE-ONTOLOGY
CAT-IR-ONTOLOGY
CAT-IR-SEMANTIC-QUERY
CAT-ONLINE-SW
CAT-ONTOLOGY
CAT-REL-COOR
CAT-REL-NLP
CAT-REL-RULE
bk-ngx
co-occurence
ontology-based
textpresso
CATCAT-FULLCAT-IECAT-IE-ONTOLOGYCAT-IR-ONTOLOGYCAT-IR-SEMANTIC-QUERYCAT-ONLINE-SWCAT-ONTOLOGYCAT-REL-COORCAT-REL-NLPCAT-REL-RULEbk-ngxco-occurenceontology-basedtextpresso
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5BioRAT: extracting biological information from full-length papers.
D. Corney, B. Buxton, W. Langdon, and D. Jones. Bioinformatics, 20 (17): 3206--3213 (November 2004)
14 years ago by @huiyangsfsu
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CAT
CAT-FULL
CAT-IE
CAT-NER
CAT-ONLINE-SW
CAT-REL-RULE
bk-ngx
CATCAT-FULLCAT-IECAT-NERCAT-ONLINE-SWCAT-REL-RULEbk-ngx
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1protein corral:a web application that combines Information Retrieval and Extraction from Medline.
E. EBI. (2010)
14 years ago by @huiyangsfsu
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CAT
CAT-IE
CAT-IR
CAT-ONLINE-SW
CAT-REL-COOR
CAT-REL-MULT
CAT-REL-NLP
CAT-REL-RULE
CAT-REL-VERB
protein
CATCAT-IECAT-IRCAT-ONLINE-SWCAT-REL-COORCAT-REL-MULTCAT-REL-NLPCAT-REL-RULECAT-REL-VERBprotein
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2Literature mining and database annotation of protein phosphorylation using a rule-based system
Z. Hu, M. Narayanaswamy, K. Ravikumar, K. Vijay-Shanker, and C. Wu. Bioinformatics, (2005)
14 years ago by @huiyangsfsu
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CAT
CAT-DBS-phophorylation
CAT-REL-NLP
CAT-REL-RULE
RLIMS-P
proteins
rule-based
CATCAT-DBS-phophorylationCAT-REL-NLPCAT-REL-RULERLIMS-Pproteinsrule-based
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1Extraction of regulatory gene/protein networks from Medline
J. Saric, L. Jensen, R. Ouzounova, I. Rojas, and P. Bork. Bioinformatics, (2006)
14 years ago by @huiyangsfsu
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CAT
CAT-NER
CAT-REL-NLP
CAT-REL-RULE
CAT-SIMILAR
similar-to-GENIES
CATCAT-NERCAT-REL-NLPCAT-REL-RULECAT-SIMILARsimilar-to-GENIES
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2Bidirectional incremental parsing for automatic pathway identification with combinatory categorial grammar
J. Park, H. Kim, and J. Kim. The Pacific Symposium on Biocomputing, http://psb.stanford.edu/psb-online/proceedings/psb01/jcpark.pdf, (February 2001)
14 years ago by @huiyangsfsu
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CAT
CAT-REL-NLP
CAT-REL-RULE
CAT-REL-VERB
PPI
full-parser
templates
verb-based
CATCAT-REL-NLPCAT-REL-RULECAT-REL-VERBPPIfull-parsertemplatesverb-based
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2Event Extraction from Biomedical Papers Using a Full Parser.
A. Yakushiji, Y. Tateisi, Y. Miyao, and J. ichi Tsujii. Pacific Symposium on Biocomputing, page 408-419. (2001)
14 years ago by @huiyangsfsu
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CAT
CAT-REL-NLP-Predicate-Argument
CAT-REL-RULE
CAT-REL-VERB
biomedical
complex
parser
writing
CATCAT-REL-NLP-Predicate-ArgumentCAT-REL-RULECAT-REL-VERBbiomedicalcomplexparserwriting
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1Extraction of protein interaction information from unstructured text using a context-free grammar
J. Temkin, and M. Gilder. Bioinformatics, (2003)
14 years ago by @huiyangsfsu
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CAT
CAT-REL-RULE
PPI
rule-based
CATCAT-REL-RULEPPIrule-based
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1GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data
A. Rzhetsky, M. Krauthammer, T. Koike, P. Kra1, S. Gomez, H. Yu, P. Duboue, W. Weng, S. Johnson, V. Hatzivassiloglou and 1 other author(s). J. Biomed. Inform., (2004)
14 years ago by @huiyangsfsu
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CAT
CAT-IE
CAT-REL-NLP
CAT-REL-RULE
CAT-SIMILAR
CAT-VIZ
GeneWays
CATCAT-IECAT-REL-NLPCAT-REL-RULECAT-SIMILARCAT-VIZGeneWays
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1Ontology-based interactive information extraction from scientific abstracts: Conference Papers
D. Milward, M. Bjäreland, W. Hayes, M. Maxwell, L. Öberg, N. Tilford, J. Thomas, R. Hale, S. Knight, and J. Barnes. Comp. Funct. Genomics, 6 (1-2): 67--71 (2005)
14 years ago by @huiyangsfsu
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CAT
CAT-IE-ONTOLOGY
CAT-REL-ONTOLOGY
CAT-REL-RULE
CAT-VIZ
IE
OBIIE
interactive
CATCAT-IE-ONTOLOGYCAT-REL-ONTOLOGYCAT-REL-RULECAT-VIZIEOBIIEinteractive
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2Extracting molecular binding relationships from biomedical text
T. Rindflesch, J. Rajan, and L. Hunter. Proceedings of the sixth conference on Applied natural language processing, page 188--195. Morristown, NJ, USA, Association for Computational Linguistics, (2000)
14 years ago by @huiyangsfsu
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CAT
CAT-REL-NLP
CAT-REL-RULE
binding
extraction
relation
CATCAT-REL-NLPCAT-REL-RULEbindingextractionrelation
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1PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction
M. Krallinger, C. Rodriguez-Penagos, A. Tendulkar, and A. Valencia1. Nucleic Acids Res., 37 (web server issue): W160-5 (July 2009)
14 years ago by @huiyangsfsu
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CAT
CAT-IE
CAT-IR
CAT-ONLINE-SW
CAT-REL-COOR
CAT-REL-NLP
CAT-REL-RULE
CAT-SIMILAR
CAT-VIZ
PLAN2L
SVM
co-occurrences
extraction
relationship
rules
CATCAT-IECAT-IRCAT-ONLINE-SWCAT-REL-COORCAT-REL-NLPCAT-REL-RULECAT-SIMILARCAT-VIZPLAN2LSVMco-occurrencesextractionrelationshiprules
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2Extracting semantic predications from MEDLINE citations for pharmacogenomics
C. Ahlers, M. Fiszman, D. Demner-fushman, F. michel Lang, and T. Rindflesch. In Proc. Pacific Symposium on Biocomputing, page 209--220. (2007)
15 years ago by @huiyangsfsu
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CAT
CAT-REL-NLP
CAT-REL-RULE
pharmacogenomics
predictions
semantic
semrep
CATCAT-REL-NLPCAT-REL-RULEpharmacogenomicspredictionssemanticsemrep
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1Edgar: Extraction of drugs, genes and relations from the biomedical literature
T. Rindflesch, L. Tanabe, J. Weinstein, and L. Hunter. page 517--528. (2000)
15 years ago by @huiyangsfsu
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CAT
CAT-NER-metamap
CAT-REL-RULE
CAT-REL-VERB
drugs
extraction
genes
relations
simple-sentence
CATCAT-NER-metamapCAT-REL-RULECAT-REL-VERBdrugsextractiongenesrelationssimple-sentence
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2GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles
C. Friedman, P. Kra, H. Yu, M. Krauthammer, and A. Rzhetsky. Comput. Appl. Biosci., 17 (suppl\_1): S74--82 (Jun 1, 2001)
15 years ago by @huiyangsfsu
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CAT
CAT-FULL
CAT-REL-NLP
CAT-REL-RULE
CAT-REL-VERB
GENIES
MedLEE
NLP
extraction
molecular
pathways
CATCAT-FULLCAT-REL-NLPCAT-REL-RULECAT-REL-VERBGENIESMedLEENLPextractionmolecularpathways
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2Extracting causal knowledge from a medical database using graphical patterns
C. Khoo, S. Chan, and Y. Niu. ACL '00: Proceedings of the 38th Annual Meeting on Association for Computational Linguistics, page 336--343. Morristown, NJ, USA, Association for Computational Linguistics, (2000)
15 years ago by @huiyangsfsu
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CAT
CAT-CLINICAL
CAT-REL-RULE
causal
database
knowledge
medical
CATCAT-CLINICALCAT-REL-RULEcausaldatabaseknowledgemedical
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1STITCH 2: an interaction network database for small molecules and proteins

1BioContrasts: Extracting and Exploiting Protein-Protein Contrastive Relations from Biomedical Literature

2Mining biomedical literature using information extraction.

3RelEx - Relation extraction using dependency parse trees.

3Textpresso: an ontology-based information retrieval and extraction system for biological literature

5BioRAT: extracting biological information from full-length papers.

1protein corral:a web application that combines Information Retrieval and Extraction from Medline.

2Literature mining and database annotation of protein phosphorylation using a rule-based system

1Extraction of regulatory gene/protein networks from Medline

2Bidirectional incremental parsing for automatic pathway identification with combinatory categorial grammar

2Event Extraction from Biomedical Papers Using a Full Parser.

1Extraction of protein interaction information from unstructured text using a context-free grammar

1GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data

1Ontology-based interactive information extraction from scientific abstracts: Conference Papers

2Extracting molecular binding relationships from biomedical text

1PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction

2Extracting semantic predications from MEDLINE citations for pharmacogenomics

1Edgar: Extraction of drugs, genes and relations from the biomedical literature

2GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles

2Extracting causal knowledge from a medical database using graphical patterns

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