Automatic extraction of protein-protein interactions using grammatical relationship graph (Q90681860)

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scientific article published on 23 July 2018

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English	Automatic extraction of protein-protein interactions using grammatical relationship graph	scientific article published on 23 July 2018

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Europe PubMed Central

PMC publication ID

6069288

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30066644%20AND%20SRC:MED&resulttype=core&format=json

retrieved

15 April 2020

title

Automatic extraction of protein-protein interactions using grammatical relationship graph (English)

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Europe PubMed Central

PMC publication ID

6069288

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30066644%20AND%20SRC:MED&resulttype=core&format=json

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15 April 2020

main subject

protein-protein interaction

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Kaixian Yu

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1

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Europe PubMed Central

PMC publication ID

6069288

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15 April 2020

Pei-Yau Lung

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2

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PMC publication ID

6069288

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15 April 2020

Tingting Zhao

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3

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PMC publication ID

6069288

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15 April 2020

Peixiang Zhao

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4

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PMC publication ID

6069288

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15 April 2020

Yan-Yuan Tseng

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5

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PMC publication ID

6069288

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15 April 2020

Jinfeng Zhang

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6

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PMC publication ID

6069288

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publication date

23 July 2018

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Europe PubMed Central

PMC publication ID

6069288

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15 April 2020

published in

BMC Medical Informatics and Decision Making

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Europe PubMed Central

PMC publication ID

6069288

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30066644%20AND%20SRC:MED&resulttype=core&format=json

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15 April 2020

volume

18

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Europe PubMed Central

PMC publication ID

6069288

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15 April 2020

issue

Suppl 2

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Europe PubMed Central

PMC publication ID

6069288

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15 April 2020

page(s)

42

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Europe PubMed Central

PMC publication ID

6069288

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30066644%20AND%20SRC:MED&resulttype=core&format=json

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15 April 2020

copyright license

Creative Commons Attribution 4.0 International

start time

1 July 2018

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April 2022 Public Data File from Crossref

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copyrighted

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cites work

Automatic extraction of biological information from scientific text: protein-protein interactions

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Automatic extraction of protein interactions from scientific abstracts

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Toward Routine Automatic Pathway Discovery from On-line Scientific Text Abstracts

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Automated extraction of information on protein-protein interactions from the biological literature

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

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Event extraction from biomedical papers using a full parser.

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PIES, a protein interaction extraction system.

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A literature network of human genes for high-throughput analysis of gene expression

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

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based on heuristic

inferred from PubMed ID database lookup

Filling preposition-based templates to capture information from medical abstracts.

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Robust relational parsing over biomedical literature: extracting inhibit relations

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

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Learning anchor verbs for biological interaction patterns from published text articles.

1 reference

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

TRANSFAC: transcriptional regulation, from patterns to profiles

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

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The Database of Interacting Proteins: 2004 update

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

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HPID: the Human Protein Interaction Database

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Discovering patterns to extract protein-protein interactions from full texts

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Automatic extraction of gene/protein biological functions from biomedical text

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PDZBase: a protein-protein interaction database for PDZ-domains

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The MIPS mammalian protein-protein interaction database

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Biomolecular Interaction Network Database and related tools 2005 update

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

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Systematic association of genes to phenotypes by genome and literature mining

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Beyond the clause: extraction of phosphorylation information from medline abstracts

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extraction of regulatory gene/protein networks from Medline

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extraction of biological interaction networks from scientific literature

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Argonaute--a database for gene regulation by mammalian microRNAs

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Human protein reference database--2006 update

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

BioGRID: a general repository for interaction datasets

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DBTGR: a database of tunicate promoters and their regulatory elements

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Literature mining for the biologist: from information retrieval to biological discovery

1 reference

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Combination of text-mining algorithms increases the performance

1 reference

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

MINT: the Molecular INTeraction database

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An evaluation of human protein-protein interaction data in the public domain

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Data mining and predictive modeling of biomolecular network from biomedical literature databases

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein interactions and disease: computational approaches to uncover the etiology of diseases.

1 reference

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mining gene-disease relationships from biomedical literature: weighting protein-protein interactions and connectivity measures.

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Kernel approaches for genic interaction extraction

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ORegAnno: an open-access community-driven resource for regulatory annotation

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

STITCH: interaction networks of chemicals and proteins

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PubMed

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12 December 2020

based on heuristic

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RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

1 reference

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example.

1 reference

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Linking entries in protein interaction database to structured text: the FEBS Letters experiment.

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparative analysis of five protein-protein interaction corpora

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mapping proteins to disease terminologies: from UniProt to MeSH

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PIE: an online prediction system for protein-protein interactions from text

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Seeking a new biology through text mining

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Large-scale directional relationship extraction and resolution

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mining physical protein-protein interactions from the literature

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Overview of the protein-protein interaction annotation extraction task of BioCreative II

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The GOA database in 2009--an integrated Gene Ontology Annotation resource

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Human Protein Reference Database--2009 update

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evaluating contributions of natural language parsers to protein-protein interaction extraction

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Bayesian inference of protein-protein interactions from biological literature

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein-protein interaction extraction by leveraging multiple kernels and parsers.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The IntAct molecular interaction database in 2010

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Looking at cerebellar malformations through text-mined interactomes of mice and humans

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

MINT, the molecular interaction database: 2009 update

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extracting causal relations on HIV drug resistance from literature

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A hybrid approach to extract protein–protein interactions

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The BioGRID Interaction Database: 2011 update

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Integrated Bio-Entity Network: A System for Biological Knowledge Discovery

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The BioGRID interaction database: 2013 update

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PPInterFinder--a mining tool for extracting causal relations on human proteins from literature

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

On the efficacy of per-relation basis performance evaluation for PPI extraction and a high-precision rule-based approach

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PIPE: a protein-protein interaction passage extraction module for BioCreative challenge

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sequence-based prediction of protein protein interaction using a deep-learning algorithm.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Distributed smoothed tree kernel for protein-protein interaction extraction from the biomedical literature.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30066644

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/S12911-018-0628-4

1 reference

stated in

Europe PubMed Central

PMC publication ID

6069288

reference URL

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30066644%20AND%20SRC:MED&resulttype=core&format=json

retrieved

15 April 2020

DBLP publication ID

journals/midm/YuLZZTZ18

1 reference

stated in

DBLP Dataset 2021-01-02

retrieved

28 January 2021

PMC publication ID

6069288

1 reference

stated in

Europe PubMed Central

PMC publication ID

6069288

reference URL

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30066644%20AND%20SRC:MED&resulttype=core&format=json

retrieved

15 April 2020

PubMed publication ID

30066644

1 reference

stated in

Europe PubMed Central

PMC publication ID

6069288

reference URL

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30066644%20AND%20SRC:MED&resulttype=core&format=json

retrieved

15 April 2020

 

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